clipper-python Build Log

Checking out clipper-python 2019-09-06 13:11:11.431
bzr pull bzr+ssh://ccp4um@fg.oisin.rc-harwell.ac.uk/var/lib/gforge/chroot/scmrepos/bzr/series-70/clipper-python/
 M  clipper.i
All changes applied successfully.
Now on revision 48.
Configuring clipper-python 2019-09-06 13:11:13.285
cmake -DCMAKE_INSTALL_PREFIX='/opt/xtal/ccp4-7.0-linux32' -DLIB_INSTALL_DIR='/opt/xtal/ccp4-7.0-linux32/lib' -Dlibdir='/opt/xtal/ccp4-7.0-linux32/lib'   -DBUILD_SHARED_LIBS=ON -D CMAKE_SKIP_RPATH=1 /home/ccb63/Downloads/devtools/checkout/clipper-python
-- Found SWIG: /usr/local/bin/swig (found version "3.0.6") 
-- Python interpreter: /opt/xtal/ccp4-7.0-linux32/devbin/python
-- Python sys.prefix: /opt/xtal/ccp4-7.0-linux32/devbin/..
-- Python library: /opt/xtal/ccp4-7.0-linux32/lib/libpython2.7.so
-- Python.h is in: /opt/xtal/ccp4-7.0-linux32/include/python2.7
-- Looking for mmdb2/mmdb_defs.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libmmdb2.so  
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for clipper/clipper.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-core.so  
-- FFTW2 libraries - /opt/xtal/ccp4-7.0-linux32/lib/libfftw.so
--                 - /opt/xtal/ccp4-7.0-linux32/lib/librfftw.so
-- FFTW2 header directory - /opt/xtal/ccp4-7.0-linux32/include
-- Performing Test _LINKING_WITH_CLIPPER_CORE
-- Performing Test _LINKING_WITH_CLIPPER_CORE - Success
-- Looking for clipper/clipper-mmdb.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-mmdb.so  
-- Looking for clipper/clipper-ccp4.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-ccp4.so  
-- Looking for clipper/clipper-cif.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-cif.so  
-- Looking for clipper/clipper-minimol.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-minimol.so  
-- Looking for clipper/clipper-contrib.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libclipper-contrib.so  
-- Looking for ccp4/ccp4_general.h - /opt/xtal/ccp4-7.0-linux32/include
-- Found CCP4: /opt/xtal/ccp4-7.0-linux32/lib/libccp4c.so  
-- CCP4 include directory: /opt/xtal/ccp4-7.0-linux32/include
-- Found PythonInterp: /opt/xtal/ccp4-7.0-linux32/devbin/python (found version "2.7.10") 
CMake Warning (dev) at /usr/local/share/cmake-3.1/Modules/UseSWIG.cmake:79 (if):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "PYTHON" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /usr/local/share/cmake-3.1/Modules/UseSWIG.cmake:219 (SWIG_MODULE_INITIALIZE)
  CMakeLists.txt:66 (SWIG_ADD_MODULE)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/local/share/cmake-3.1/Modules/UseSWIG.cmake:81 (elseif):
  Policy CMP0054 is not set: Only interpret if() arguments as variables or
  keywords when unquoted.  Run "cmake --help-policy CMP0054" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  Quoted variables like "PYTHON" will no longer be dereferenced when the
  policy is set to NEW.  Since the policy is not set the OLD behavior will be
  used.
Call Stack (most recent call first):
  /usr/local/share/cmake-3.1/Modules/UseSWIG.cmake:219 (SWIG_MODULE_INITIALIZE)
  CMakeLists.txt:66 (SWIG_ADD_MODULE)
This warning is for project developers.  Use -Wno-dev to suppress it.

-- Python module path: /opt/xtal/ccp4-7.0-linux32/lib/py2
-- Configuring done
-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

    libdir


-- Build files have been written to: /home/ccb63/Downloads/devtools/builddir/clipper-python
Building clipper-python 2019-09-06 13:11:19.352
make -j 2
[ 50%] Swig source
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/clipper_util.h:62: Warning 325: Nested union not currently supported (U32 ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/clipper_util.h:63: Warning 325: Nested union not currently supported (U64 ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_info.h:139: Warning 325: Nested class not currently supported (HKL_reference_base ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_info.h:171: Warning 325: Nested class not currently supported (HKL_reference_index ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_info.h:240: Warning 325: Nested class not currently supported (HKL_reference_coord ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_data.h:69: Warning 325: Nested class not currently supported (Key ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/xmap.h:70: Warning 325: Nested class not currently supported (Key ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/xmap.h:176: Warning 325: Nested class not currently supported (Map_reference_base ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/xmap.h:228: Warning 325: Nested class not currently supported (Map_reference_index ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/xmap.h:298: Warning 325: Nested class not currently supported (Map_reference_coord ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/nxmap.h:116: Warning 325: Nested class not currently supported (Map_reference_base ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/nxmap.h:161: Warning 325: Nested class not currently supported (Map_reference_index ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/nxmap.h:217: Warning 325: Nested class not currently supported (Map_reference_coord ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/ccp4/ccp4_mtz_io.h:240: Warning 325: Nested struct not currently supported (datacolinf ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/ccp4/ccp4_mtz_io.h:241: Warning 325: Nested struct not currently supported (datasetinf ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/ccp4/ccp4_mtz_io.h:242: Warning 325: Nested struct not currently supported (crystalinf ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/ccp4/ccp4_mtz_io.h:243: Warning 325: Nested struct not currently supported (hkldatacol ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/contrib/sfweight.h:91: Warning 325: Nested struct not currently supported (TargetResult ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/resol_fn.h:81: Warning 325: Nested class not currently supported (Fderiv ignored)
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/resol_fn.h:124: Warning 325: Nested class not currently supported (Rderiv ignored)
/home/ccb63/Downloads/devtools/checkout/clipper-python/clipper.i:955: Warning 303: %extend defined for an undeclared class clipper::data64::Flag.
/home/ccb63/Downloads/devtools/checkout/clipper-python/clipper.i:975: Warning 303: %extend defined for an undeclared class clipper::data32::Flag.
/home/ccb63/Downloads/devtools/checkout/clipper-python/clipper.i:946: Warning 303: %extend defined for an undeclared class clipper::data64::Flag_bool.
/home/ccb63/Downloads/devtools/checkout/clipper-python/clipper.i:966: Warning 303: %extend defined for an undeclared class clipper::data32::Flag_bool.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/clipper_types.h:64: Warning 402: Base class 'std::string' is incomplete.
/usr/local/share/swig/3.0.6/typemaps/std_string.swg:16: Warning 402: Only forward declaration 'std::string' was found.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/symop.h:150: Warning 503: Can't wrap 'operator int' unless renamed to a valid identifier.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/spacegroup_data.h:64: Warning 462: Unable to set dimensionless array variable
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/spacegroup_data.h:66: Warning 462: Unable to set dimensionless array variable
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_datatypes.h:324: Warning 503: Can't wrap 'operator std::complex<float>' unless renamed to a valid identifier.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/hkl_datatypes.h:324: Warning 503: Can't wrap 'operator std::complex<double>' unless renamed to a valid identifier.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/resol_fn.h:92: Warning 473: Returning a pointer or reference in a director method is not recommended.
/opt/xtal/ccp4-7.0-linux32/include/clipper/../clipper/core/rotation.h:183: Warning 503: Can't wrap 'operator *' unless renamed to a valid identifier.
Scanning dependencies of target _clipper
[100%] Building CXX object CMakeFiles/_clipper.dir/clipperPYTHON_wrap.cxx.o
Linking CXX shared module _clipper.so
[100%] Built target _clipper
Installing clipper-python 2019-09-06 13:13:26.474
make -j 2 install DESTDIR=/opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python
[100%] Built target _clipper
Install the project...
-- Install configuration: ""
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/_clipper.so
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/__init__.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/xray
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/xray/cut_density.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/xray/structure_factors.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/xray/coordinate_kicks.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/xray/__init__.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/general.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/em
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/em/structure_factors.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/em/__init__.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/io
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/io/structure_factors.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/io/__init__.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/io/maps.py
-- Installing: /opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python/opt/xtal/ccp4-7.0-linux32/lib/py2/clipper_tools/io/molecules.py
Moving temporary DESTDIR u'/opt/xtal/ccp4-7.0-linux32/_jhbuild/root-clipper-python' into build prefix
0 files remaining from previous build
Install complete: 14 files copied
Succeeded 2019-09-06 13:13:29.400