Configuring module compatibility version SVN.r14111
Configuring module base version SVN.r14111 with Boost.FileSystem
Configuring module benchmark version SVN.r14111 with Boost.ProgramOptions
Configuring module RMF version SVN.r14111
Configuring module cgal version SVN.r14111
Configuring module algebra version SVN.r14111 with cgal
Configuring module kernel version SVN.r14111 with Boost.FileSystem
Configuring module display version SVN.r14111 with cgal
Configuring module core version SVN.r14111 with cgal
Configuring module container version SVN.r14111
Configuring module atom version SVN.r14111 with Boost.FileSystem, cgal
Configuring module statistics version SVN.r14111
Configuring module rmf version SVN.r14111
Configuring module domino version SVN.r14111 with RMF
Configuring module em version SVN.r14111
Configuring module saxs version SVN.r14111
Configuring module gsl version SVN.r14111
Configuring module modeller version SVN.r14111
Configuring module restrainer version SVN.r14111
Configuring module multifit version SVN.r14111
Configuring module em2d version SVN.r14111 with OpenCV21
Configuring module misc version SVN.r14111
Configuring module system version SVN.r14111
Configuring module isd version SVN.r14111
Configuring module example version SVN.r14111
Configuring module kmeans version SVN.r14111
Configuring module parallel version SVN.r14111
Configuring module pepdock version SVN.r14111
Configuring module scratch version SVN.r14111
Configuring application EModel2D version SVN.r14111
Configuring application foxs version SVN.r14111
Configuring application integrative_docking version SVN.r14111
Configuring application saxs_tools version SVN.r14111
Configuring application saxs_merge version SVN.r14111
Configuring application em_tools version SVN.r14111
Configuring application ligand_score version SVN.r14111
Configuring application multifit_tools version SVN.r14111
Configuring application rmf_tools version SVN.r14111
Configuring application pdb_tools version SVN.r14111
Configuring application example_app version SVN.r14111
Configuring system Groel version SVN.r14111
Configuring system rnapii version SVN.r14111
Configuring system nup84 version SVN.r14111
Configuring module example_system_local version SVN
Configuring system example_system version SVN.r14111
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/base/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/base/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.base --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/base/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/base/test/test_objects.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/base/test/test_random.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/base_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_base_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/base/test/test.results.out) > /dev/null
Test getting all objects ... ok
Test the random number generator ... ok
Running C++ test basetest_cache ... ok
Running C++ test basetest_pair_memoizer ... ok
Running C++ test basetest_show ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 9 tests in 1.228s

OK
base module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/benchmark/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/benchmark/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.benchmark --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/benchmark/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_benchmark_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/benchmark/test/test.results.out) > /dev/null
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.021s

OK
benchmark module unit tests succeeded
modules/atom/src/MolecularDynamics.cpp: In member function 'virtual void IMP::atom::MolecularDynamics::assign_velocities(IMP::Float)':
modules/atom/src/MolecularDynamics.cpp:190: warning: 'sampler.boost::variate_generator >::_dist.boost::normal_distribution::_cached_rho' may be used uninitialized in this function
modules/atom/src/MolecularDynamics.cpp:190: warning: 'sampler.boost::variate_generator >::_dist.boost::normal_distribution::_r1' may be used uninitialized in this function
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/librmf/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/adding_data.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/alias.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/create.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/rmf_decorator.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/rmf_xml.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/examples/test.results.out) > /dev/null
Run example adding_data.py ... in 1.750s ... ok
Run example alias.py ... ok
Run example create.py ... ok
Run example rmf_decorator.py ... ok
Run example rmf_xml.py ... ok

----------------------------------------------------------------------
Ran 5 tests in 2.541s

OK
RMF examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/librmf/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=RMF --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_aliases.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_associations.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_backwards.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_bad_geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_closing.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_copy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_data_types.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_description.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_errors.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_file_level.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_low_level.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_multikey.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_prmf.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test_sets.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/RMF_cpp_test_programs.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/librmf/test/test.results.out) > /dev/null
Test that aliases can be used and resolve ... ok
Test that associations work from python ... ok
Test opening pre-category change files ... ok
Test example where fill was bad ... ok
Test closing an RMF file ... ok
Test copying an rmf file ... in 3.377s ... ok
Test that the various data types work ... ok
Test the description of an rmf file ... ok
Test that opening a non-existent file causes and exception ... ok
Test that opening a file 2x works ... ok
Test creating a simple hierarchy file with frames ... ok
Test creating a simple hierarchy file ... ok
Test null values ... ok
Test arrays of integers ... ok
Test strings data set ... ok
Test strings data set ... ok
Test low level usage of hdf5 with attributes ... ok
Test low level usage of hdf5 with datasets ... ok
Test writing of blocks with data sets ... ok
Test low level usage of hdf5 with datasets that grow ... ok
Test low level usage of hdf5 ... ok
Test creating a simple hierarchy file ... ok
Test copying a rmf file to a prmf file ... skipped 'No google protobuf support'
Test copying a simple rmf file to prmf ... skipped 'No google protobuf support'
Test node sets ... ok
Test node pairs ... ok
Running C++ test RMFtest_associations ... ok

----------------------------------------------------------------------
Ran 27 tests in 4.898s

OK (skipped=2)
RMF module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/algebra/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/examples/geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/examples/grid_space.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/examples/test.results.out) > /dev/null
Run example geometry.py ... ok
Run example grid_space.py ... ok

----------------------------------------------------------------------
Ran 2 tests in 0.034s

OK
algebra examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/algebra/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.algebra --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_bounding_box.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_cone.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_cylinder.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_dynamic_nn.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_eigen_analysis.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_geom_alignment.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_grid.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_inverse.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_log_grid.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_matrix2d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_matrix3d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_nearest_neighbor.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_random_ball.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_random_chain.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_random_rotations.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_regression_fit.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_rigid_transformation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_rotation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_shortest_segment.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_sphere_cover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_sphere_patch.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_spherical_coords.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_transformation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_triangle3d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_uniform_rotation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_vector3d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_vector4d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_vector_on_box.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_vectorkd.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_vol.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_xyz.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test_zyz.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/algebra_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_algebra_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/algebra/test/test.results.out) > /dev/null
Check that the bounding box is constructed correctly ... ok
Check the union function ... ok
Check that cones on Z are constructed correctly ... ok
Testing sampling a patch ... ok
Check Cylinder3D construction from vectors ... ok
Check grid cover when the direction of the ... ok
Check grid cover when the center of cylinder ... ok
Check grid cover when the direction of the ... ok
Check uniform cover with cylinder not on the Z axis ... ok
Check whether the cylinder volume is uniformly sampled ... in 2.539s ... ok
Check that dynamic nearest neighbor queries work ... ok
Testing eigen analysis ... ok
Testing eigen analysis ... ok
Testing that the eigen values are invariante to rotation ... ok
Testing rigid alignment of point sets, no translation ... ok
Testing rigid alignment of point sets ... ok
Check sparse grid of ints ... ok
Check that the the inverse of a transformation works ... ok
Test mixed log embedding ... ok
Check sparse grid of ints ... ok
Check Matrix2D access ... ok
Check Matrix2D addition ... ok
Check cross_correlation of Matrix2D with itself ... ok
Check cross_correlation matrices with different origins ... ok
Check Matrix2D division ... ok
Check Matrix2D multiplication ... ok
Check Matrix2D scalar addition ... ok
Check Matrix2D scalar division ... ok
Check Matrix2D scalar multiplication ... ok
Check Matrix2D scalar subtraction ... ok
Check proper creation and resizing ... ok
Check Matrix2D subtraction ... ok
Check writing an empty matrix ... ok
Check Matrix3D access ... ok
Check Matrix3D addition ... ok
Check cross_correlation of Matrix3D with itself ... ok
Check cross_correlation of 3D matrices with different origins ... ok
Check Matrix3D division ... ok
Check Matrix3D multiplication ... ok
Check Matrix3D scalar addition ... ok
Check Matrix3D scalar division ... ok
Check Matrix3D scalar multiplication ... ok
Check Matrix3D scalar subtraction ... ok
Check proper creation and resizing ... ok
Check Matrix3D subtraction ... ok
Check that nearest neighbor works ... ok
Check that NN queries work ... ok
Testing the creation of a points on a sphere ... ok
Testing the creation of a points on a sphere ... ok
Testing the creation of a random chain ... ok
Testing the creation of a random chain with obstacles ... in 1.305s ... ok
Test uniform random rotation ... skipped 'IMP.cgal module disabled'
Check Linear Fit ... ok
Check Parabolic Fit ... ok
Check weighted Linear Fit ... ok
Check weighted Linear Fit ... ok
Check that the delta transformation between two transformations is correct ... ok
Check that the rotation function is ok ... ok
Check rotation about axis ... ok
Check the quaternion derivatives ... ok
Check that the function get_axis_and_angle is correct ... ok
Check that rotations can be interpolated ... ok
Check that two rotations are equal ... ok
Check that the rotation inverse is an inverse ... ok
Check that the rotation between two vectors is correct ... ok
Check rotation about axis ... ok
Check degenerate shortest segments of segments ... ok
Check enclosing sphere ... ok
Verify uniform sampling within a sphere ... ok
Check that sphere are constructed correctly ... ok
Check uniform cover on a sphere ... ok
Check uniform cover when the the center is not on (0,0,0) ... ok
Check uniform cover on a patch of a sphere ... ok
Check that a patch of a sphere is constructed correctly ... ok
Check that spherical coords work ... ok
Check difference between two transformations ... ok
Check that Z coordinate stays zero after transformation ... ok
Check calculating a transformation between two reference frames ... ok
Check building a Transformation2D from point sets ... ok
Check building a Transformation3D from Transformation2D ... ok
Check that triangles constructed correctly ... ok
test conversion of euler angles ... ok
test_euler_sampling (_test_26.UniformRotationSmaplingTest) ... ok
Check Vector3D addition ... ok
Test that vectors can't be compared ... ok
Check Vector3D components ... ok
Check Vector3D difference ... ok
Check distance between two vectors ... ok
Check Vector3D from floats ... ok
Check the Vector3D generators ... ok
Check I/O of Vector3Ds ... ok
Check Vector3D length ... ok
Check Vector3D magnitude ... ok
Check that multiplying vectors by scalars works ... ok
Check Vector3D division by a scalar ... ok
Check Vector3D multiplication by a scalar ... ok
Check Vector3D scalar product ... ok
Check vector 3D show ... ok
Check Vector3D vector product ... ok
Check Vector4D addition ... ok
Check Vector4D components ... ok
Check Vector4D difference ... ok
Check Vector4D length ... ok
Check Vector4D magnitude ... ok
Check creation of a rotation from a 4D vector ... ok
Check Vector4D division by a scalar ... ok
Check Vector4D multiplication by a scalar ... ok
Check Vector4D scalar product ... ok
Testing the distribution of vectors on a box ... ok
Check VectorKD addition ... ok
Check VectorKD components ... ok
Check VectorKD difference ... ok
Check VectorKD length ... ok
Check VectorKD magnitude ... ok
Check VectorKD division by a scalar ... ok
Check VectorKD multiplication by a scalar ... ok
Check VectorKD scalar product ... ok
Check volume and surface area of random ... skipped 'IMP.cgal module disabled'
Check Euler XYZ conversions ... ok
Check Euler ZYZ conversions ... ok
Running C++ test algebratest_grid ... ok
Running C++ test algebratest_grid_apply ... ok
Running C++ test algebratest_grid_storage ... ok
Running C++ test algebratest_piecewise_linear ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 1.343s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 128 tests in 9.636s

OK (skipped=2)
algebra module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/kernel/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/basic_optimization.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/chain.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/dependency_graph.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/dock_with_crosslinks.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/graph.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/nup84_cg.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/nup84_rb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/write_a_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/write_an_optimizer_state.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/examples/test.results.out) > /dev/null
Run example basic_optimization.py ... ok
Run example chain.py ... ok
Run example dependency_graph.py ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Run example dock_with_crosslinks.py ... ok
Run example graph.py ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Run example nup84_cg.py ... ok
Run example nup84_rb.py ... in 3.306s ... ok
Run example write_a_restraint.py ... ok
Run example write_an_optimizer_state.py ... ok

----------------------------------------------------------------------
Ran 9 tests in 5.204s

OK
kernel examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/kernel/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_comparisons.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_config_set.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_dependency_graph.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_directories.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_exceptions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_file.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_key.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_log.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_model.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_particle_tuples.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_refcount.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_restraint_sets.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_score_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_scoreing_function.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_temp_scoring.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test_typemaps.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/kernel_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_kernel_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/kernel/test/test.results.out) > /dev/null
Test comparisons in python ... ok
Testing restore a know state with ConfigurationSet ... ok
Testing no-ops with the ConfigurationSet ... ok
Testing restore with ConfigurationSet ... ok
Test dependency graph ... ok
get_data_directory should raise an error if it does not exist ... ok
Test the get_data_directory function ... ok
Test class hierarchy of IMP exceptions ... ok
Test bad paths trigger IO exceptions with overloads ... ok
Test that conversions to input files work properly ... ok
Test that conversions to output files work properly ... ok
Test temporary files ... ok
Test key aliases ... ok
Test function log looks ok ... ok
Test log targets ... ok
Test log targets at MEMORY log level ... ok
Test time log looks ok ... ok
Check dependencies with restraints and score states ... ok
Check that exceptions raised in directors are handled ... ok
Check particle methods ... ok
Test float attribute ranges ... ok
Refcounting should prevent director Restraints from being deleted ... ok
Refcounting should prevent director ScoreStates from being deleted ... ok
Check restraint methods ... ok
Check score state methods ... ok
Check Model.show() method ... ok
Test score state show method ... ok
Check free restraint methods ... ok
Test ParticlePair objects ... ok
Test ParticleQuad objects ... ok
Test ParticleTriplet objects ... ok
Test browsing of particle attributes ... ok
Test comparisons of particles and decorators ... ok
Test get/set of derivatives ... ok
Check particle identity ... ok
Test particle get_ and set_ methods ... ok
Check that particles and decorators hash in python ... ok
Test that we can allocate many particles ... in 3.061s ... ok
Check that operations fail on particles once the model is gone ... ok
Test that particle attributes are available and correct ... ok
Test that attributes can be removed ... ok
Python Particles from vector accessors should survive model deletion ... ok
Python Restraints from vector accessors should survive model deletion ... ok
Python restraints from vector accessors should survive model deletion ... ok
Constructed Python Particles should survive model deletion ... ok
Python Restraints from iterators should survive model deletion ... ok
Check that ref counting works with removing particles ... ok
Test that sequences are refcounted properly ... ok
Check that ref counting of particles works within python ... ok
Check reference counting of restraints ... ok
Check that removed particles are skipped ... ok
Test evaluate() of RestraintSets and their children ... ok
Test restraints added multiple times ... ok
Test that sets can be printed ... ok
Test that restraints are usable after set is destroyed ... ok
Check access to RestraintSet's restraints ... ok
Test ScoreState::show() ... ok
Test scoring function linkage ... ok
Check that scoring functions are cleaned up ... ok
Check float typemaps ... ok
Check int typemaps ... ok
Check ints list typemaps ... ok
Check ints lists typemaps ... ok
Check string typemaps ... ok
Test that casting objects works ... ok
Check floatkey typemaps ... ok
Check decorators ... ok
Checking decorator conversions work ... ok
Checking conversion of decorators to particles ... ok
Checking conversion of decorator to particle ... ok
Check decorators traits ... ok
Test that decorator particle methods can be called ... ok
Test director methods in restraint ... ok
Checking bad list ... ok
Check int pairs typemap ... ok
Test that model objects can get passed from python ... ok
Check particle typemaps ... ok
Checking that overloading works ... ok
Check overloaded functions with decorators ... ok
Checking that conversion to/from pairs is OK ... ok
Checking that conversion from IntRange is OK with overload ... ok
Check pairs ... ok
Test that decorators provide particle methods ... ok
test_particles_temps (_test_17.ParticleTests) ... ok
Checking tuple conversions work ... ok
Running C++ test kerneltest_memory ... ok
Running C++ test kerneltest_pdb ... ok
Running C++ test kerneltest_stream_io ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 1.338s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 92 tests in 5.337s

OK
kernel module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/display/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/basic_geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/display_log.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/displaying_ensembles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/show_particles_as_spheres.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/display/examples/test.results.out) > /dev/null
Run example basic_geometry.py ... ok
Run example display_log.py ... ok
Run example displaying_ensembles.py ... in 10.134s ... ok
Run example show_particles_as_spheres.py ... ok

----------------------------------------------------------------------
Ran 4 tests in 10.949s

OK
display examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/display/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.display --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_chimera.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_cmm.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_colormap.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_create_writer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_isosurface.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_log.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_mesh.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_pivy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_polygon.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_pymol.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_textwriter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test_writers.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_display_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/display/test/test.results.out) > /dev/null
Testing the Chimera writer and frames ... ok
Testing the CMM writer without frames ... ok
Testing the CMM writer with a singlet file but frames ... ok
Testing the CMM writer and frames ... ok
Testing the jet color map ... ok
Testing the writer creater ... ok
Testing isosurface geometry ... skipped 'IMP.cgal module disabled'
Testing the Bild log ... ok
Testing the CMM log ... ok
Testing skin surface ... skipped 'IMP.cgal is disabled'
Testing the pivy writer and frames ... skipped 'pivy Python module unavailable'
Testing polygon decomposition and writing ... skipped 'IMP.cgal module disabled'
Testing trivial polygon decomposition and writing ... skipped 'IMP.cgal module disabled'
Testing the CGO writer and frames ... ok
Testing the text writer ... ok
Testing the CMM writer ... ok
Testing the Bild writer ... ok
Testing the chimera writer ... ok
Testing the CGO writer ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 1.014s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 23 tests in 1.663s

OK (skipped=5)
display module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/core/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/XYZR_Decorator.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/XYZ_Decorator.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/connectivity_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/cover_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/excluded_volume.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/incremental_mc.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/ms_connectivity_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/optimize_balls.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/pair_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/restrain_diameter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/rigid_collisions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/symmetry.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/core/examples/test.results.out) > /dev/null
Run example XYZR_Decorator.py ... ok
Run example XYZ_Decorator.py ... ok
Run example connectivity_restraint.py ... ok
Run example cover_particles.py ... ok
Run example excluded_volume.py ... ok
Run example incremental_mc.py ... ok
Run example ms_connectivity_restraint.py ... ok
Run example optimize_balls.py ... in 7.491s ... ok
Run example pair_restraint.py ... ok
Run example restrain_diameter.py ... ok
Run example rigid_bodies.py ... in 1.268s ... ok
Run example rigid_collisions.py ... ok
Run example symmetry.py ... ok

----------------------------------------------------------------------
Ran 13 tests in 10.724s

OK
core examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/core/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.core --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_angle.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_blame.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_box.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_centroid.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_cg_optimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_children.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_close_pair_finders.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_close_pairs_ps.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_connectivity.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_cosine.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_cover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_cover_refiner.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_destroy_rigid_body.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_diameter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_dihedral.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_display_deriv.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_distance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_ev.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_geom_alignment.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_get_from.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_harmonic.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_hierarchy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_incremenal_mc.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_incremenal_scoring.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_linear.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_mccg.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_ms_connectivity.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_nested_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_refined_pairs_ps.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_restraints_scoring_function.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_rigid_distance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_score_log.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_sd_optimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_splines.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_table.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_to_from_refined.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_transform.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_transform_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_truncated_harmonic.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_typed_pair_score.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test_xyzr.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/core_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_core_standards.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/expensive_test_ev_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/expensive_test_mc.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/expensive_test_mc_rigid.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/expensive_test_volume.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/core/test/test.results.out) > /dev/null
Check derivatives of angle restraints ... ok
Check score of angle restraints ... ok
Check AngleRestraint::show() method ... ok
Check that code to display blame runs ... ok
Test the box score ... ok
Test centroid of refined decorator ... ok
Check that we can optimize the Woods function with CG ... ok
Make sure the Children refiner works ... ok
Testing GridClosePairsFinder ... in 3.402s ... ok
Testing NearestNeighborsClosePairsFinder ... in 3.232s ... ok
Testing QuadraticClosePairsFinder ... in 2.918s ... ok
Testing RigidClosePairsFinder ... in 1.841s ... ok
Testing BoxSweepClosePairsFinder ... in 2.663s ... ok
Checking close pairs pair score ... ok
Checking k-close pairs pair score ... ok
Test connectivity restraint. ... ok
Test that cosine values are correct ... ok
Test cover refined ... ok
Test cover refined decorator ... ok
Testing destroy rigid body ... ok
Test that diameter restraints are reasonable ... ok
Check score of dihedral restraints ... ok
Testing execution of derivative display support ... ok
Test that distance restraints are reasonable ... ok
Test filters on excluded volume ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Testing rigid alignment of xyz sets ... ok
Test get_from cast ... ok
Test get_from with NULL pointer ... ok
Test Harmonic accessors ... ok
Check Harmonic::show() method ... ok
Test that harmonic values are correct ... ok
Check that an alternate hierarchy works fine ... ok
Check that the hierarchy works fine ... ok
Testing incremental scoring with Monte Carlo ... ok
Testing incremental scoring with Monte Carlo and a nbl ... ok
Testing incremental scoring with non-bonded ... ok
Testing incremental scoring with rigid bodies ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Testing incremental scoring ... ok
Test Linear accessors ... ok
Check Linear::show() method ... ok
Test that linear values are correct ... ok
Check that MCCG can make spheres connect not penetrate ... ok
Test for the connectivity restraint. ... ok
Test for the correctness of the graph 1. ... ok
Test for the correctness of the graph 2. ... ok
Test nested rigid bodies and close pairs ... ok
Checking refine pairs pair score ... ok
Test that restraints decompose ok ... ok
Test that sets can be weighted ... ok
Testing create_rigid_body ... ok
Testing create_rigid_bodies ... ok
Testing tearing down rigid bodies ... ok
Checking rigid distance pair score ... ok
Checking rigid distance pair score against one ... ok
Test restraint score log ... ok
Test that steepest descent optimizer brings particles together ... ok
Test that steepest descent optimizer spreads particles apart ... ok
Test that spline-interpolated values are correct ... ok
Test for spline out of range condition ... ok
Check cubic spline show() methods ... ok
Make sure the Table PR works ... ok
Test copying derivatives from refined ... ok
Test copying derivatives to refined ... ok
Test the transform pair score basics ... ok
Test the transform pair score optimization ... ok
Test the TransformationFunction class ... ok
Check TruncatedHarmonicLowerBound ... ok
Check TruncatedHarmonicUpperBound ... ok
Check TruncatedHarmonicBound ... ok
Check TypedPairScore::evaluate() ... ok
Check TypedPairScore behavior with invalid particle types ... ok
Testing XYZR decorators ... ok
Testing XYZR overload decorators ... ok
Running C++ test coretest_generic ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 2.912s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok
Testing excluded volume restraint ... in 1.064s ... ok
Testing excluded volume serial restraint ... ok
Test montecarlo from starting position 1 ... ok
Test montecarlo from starting position 2 ... ok
Test montecarlo from starting position 3 ... ok
test monte carlo with rigid bodies ... ok
Testing that volume restraint can separate balls ... ok

----------------------------------------------------------------------
Ran 85 tests in 22.630s

OK
core module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/container/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/bipartite_nonbonded_interactions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/connectivity.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/filter_close_pairs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/nonbonded_interactions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/restrain_in_sphere.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/container/examples/test.results.out) > /dev/null
Run example bipartite_nonbonded_interactions.py ... ok
Run example connectivity.py ... ok
Run example filter_close_pairs.py ... ok
Run example nonbonded_interactions.py ... ok
Run example restrain_in_sphere.py ... ok

----------------------------------------------------------------------
Ran 5 tests in 0.456s

OK
container examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/container/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.container --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_all_pairs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_close_bipartite_pairs_score_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_close_pairs_score_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_connectivity_container.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_consecutive_pair_container.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_decomp.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_distribute.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_events.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_particle_pair_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_particle_pair_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_particle_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_particle_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test_removes.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/container_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_container_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/container/test/test.results.out) > /dev/null
Check AllPairContainer ... in 2.194s ... ok
Testing that CloseBipartitePairContainer responds to changes in filters ... ok
Test CloseBipartitePairContainer ... ok
Test CloseBipartitePairContainer with rigid body 0 ... ok
test_it_2 (_test_2.Tests) ... ok
Test CloseBipartitePairContainer with rigid body 2 ... ok
Test ClosePairContainer ... ok
Test ClosePairContainer with a restraint ... ok
Test ClosePairContainer over time ... in 1.806s ... ok
Test ClosePairContainer complete list over time ... in 1.900s ... ok
Test ClosePairContainer with rigid finder ... in 5.956s ... ok
Test connectivity zero set ... ok
Test connectivity ... ok
Test consecutive pair container decomposition ... ok
Checking decomposition of plural restraints ... ok
Checking distribute particles ... ok
Check the event optimizer states ... ok
Test the MinimumPairRestraint ... ok
Test the MinimumPairScore ... ok
Test the PairsRestraint ... ok
Testing PairContainerSet ... ok
Test the PairRestraint ... ok
Testing PairsConstraint ... ok
Testing PairConstraint ... ok
Test the MinimumSingletonRestraint ... ok
Test the MinimumSingletonScore ... ok
Test the SingletonsRestraint ... ok
Testing SingletonContainerSet ... ok
Test the SingletonRestraint ... ok
Testing SingletonsConstraint ... ok
Testing SingletonConstraint ... ok
Check that removal from a list container works and removal from model ... ok
Running C++ test containertest_consecutive_pair_container ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 2.033s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 37 tests in 17.507s

OK
container module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/atom/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/assess_dope.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/brownian_statistics.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/cg_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/charmm_forcefield.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/charmm_forcefield_verbose.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/load_protein_restrain_bonds.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/markers.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/molecular_hierarchy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/rigid_brownian_dynamics.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/score_protein_with_ligand.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/structure_from_sequence.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/examples/test.results.out) > /dev/null
Run example assess_dope.py ... in 1.408s ... ok
Run example brownian_statistics.py ... ok
Run example cg_pdb.py ... ok
Run example charmm_forcefield.py ... in 6.138s ... ok
Run example charmm_forcefield_verbose.py ... in 6.046s ... ok
Run example load_protein_restrain_bonds.py ... ok
Run example markers.py ... ok
Run example molecular_hierarchy.py ... in 2.073s ... ok
Run example rigid_brownian_dynamics.py ... ok
Run example score_protein_with_ligand.py ... in 76.660s ... ok
Run example structure_from_sequence.py ... ok

----------------------------------------------------------------------
Ran 11 tests in 93.492s

OK
atom examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/atom/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.atom --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_bd_singleton_score.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_bond_decorator_particle_pair_container.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_bond_refiner.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_bonds.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_charged_decorator.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_charmm_atom.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_charmm_parameters.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_charmm_stereochemistry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_charmm_topology.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_clone.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_coulomb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_cover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_cover_bond.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_create_protein.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_dihedrals.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_distance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_dna_simpl.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_element.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_estimates.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_force_switch.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_fragment.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_free_model.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_get_residue.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_hierarchy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_hierarchy_conversion.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_hierarchy_navigation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_lennard_jones_decorator.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_lennard_jones_pair_score.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_md_optimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_md_states.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_mol2.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_pattern.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_pdb_frames.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_pdb_string.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_protein_ligand_score.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_rb_bd.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_ref_optimizer_states.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_refcount_hierarchy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_residue.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_residue_type.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_rg.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_rigid_alignment_with_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_rmsd_and_no.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_simplify.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_stereo_pair_filter.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_atom_standards.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_bd.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_pdb.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test.results.out) > /dev/null
Test derivatives of the bond SingletonScore ... ok
Test the bond decorator score ... ok
Test bond decorator pair container ... ok
Check that BondRefiner works ... ok
Check bonds ... ok
Check creation of Charged decorators ... ok
Check get/set methods of Charged decorators ... ok
Check show method of Charged decorators ... ok
Check creation of CHARMMAtom decorators ... ok
Check get/set methods of CHARMMAtom decorators ... ok
Check show method of CHARMMAtom decorators ... ok
Check alternate CHARMM keywords ... ok
Check extraction of bond parameters ... ok
Test that new atom types from CHARMM get elements assigned ... ok
Check mapping of CHARMM names to PDB ... ok
Check read and lookup of RNA/DNA ... ok
Check parsing of topology file ... ok
Make sure that splitting works with tabs ... ok
Test CHARMMStereochemistryRestraint pair filter ... ok
Test CHARMMStereochemistryRestraint input particles ... ok
Test CHARMMStereochemistryRestraint::evaluate() ... ok
Check addition of bonds/angles/dihedrals/impropers ... ok
Test adding coordinates to a backbone- or CA-only structure ... ok
Test adding coordinates to a completely empty structure ... ok
Test add_dihedrals() method ... ok
Check add/get atom from CHARMM residues ... ok
Check addition of internal coordinates ... ok
Test adding missing atoms ... ok
Test CHARMMTopology::add_sequence() ... ok
Check creation and methods of CHARMMAtomTopology ... ok
Check CHARMM bond class ... ok
Check CHARMM bond endpoint class ... ok
Check default patches of CHARMM residues ... ok
Check delete atom from CHARMM residues ... ok
Make sure dihedrals can have negative stiffness ... ok
Test application of two-residue patches ... ok
Test construction of hierarchy from empty topology ... ok
Test adding/getting patches and residues to/from forcefields ... ok
Test read of topology from files ... ok
Test CHARMMTopology::get_parameters() ... ok
Test get or removal of untyped atoms ... ok
Test CHARMM topology handling of HEME residues ... ok
Test construction of hierarchy from topology ... ok
Test construction of topology with manual patching ... ok
Test construction of topology ... in 3.859s ... ok
Test manual construction of topology ... ok
Check the CHARMM patch class ... ok
Test CHARMM residue topology objects ... ok
Test CHARMMTopology::setup_hierarchy() method ... ok
Test application of single-residue patches ... ok
Check close and destroy Hierarchy ... ok
Destroy of a child should update the parent ... ok
Check derivatives of CoulombPairScore ... ok
Check CoulombPairScore get/set methods ... ok
Check smoothing of CoulombPairScore ... ok
Check score value of CoulombPairScore ... ok
Check cover from selection ... ok
Check cover from rigid selection ... in 1.608s ... ok
Test cover bond ... ok
Test dihedral functions ... FAIL
Test drms measure taking into account rigid bodies ... ok
Testing that component placement score returns the same transformation if called twice ... in 1.122s ... ok
Test drms measure ... ok
Testing the mass and volume estimates ... ok
Test simplifying DNA ... ok
Test simplifying DNA 2 ... ok
Check element assignment based on atom name ... ok
Check assigning elements and masses to pdb with one protein ... ok
Check writing to pdb unknown elements ... ok
Testing the diffusion coeff estimate ... FAIL
Testing the mass and volume estimates ... ok
Check ForceSwitch creation ... ok
Check derivatives of ForceSwitch ... ok
Check ForceSwitch methods ... ok
Check value of ForceSwitch ... ok
Check Fragment ... ok
Check that deleting the model doesn't make things crash ... skipped 'Only tested in debug mode'
Check getting a residue from a cg protein ... ok
Check getting a residue from an atomic protein ... ok
Check equality of AtomType types ... ok
Check hierarchy get_by_type ... ok
Check hierarchy get_internal_bonds ... ok
Test conversion from atom.hierarchy ... ok
Check reading a pdb with one protein ... ok
Check creation of LennardJones decorators ... ok
Check get/set methods of LennardJones decorators ... ok
Check show method of LennardJones decorators ... ok
Check derivatives of LennardJonesPairScore ... ok
Check LennardJonesPairScore get/set methods ... ok
Check smoothing of LennardJonesPairScore ... ok
Check score value of LennardJonesPairScore ... ok
Test get_optimizer_states() method ... ok
Test that MD generates particle velocities ... ok
Should skip particles without xyz attributes ... ok
Check that non-rigid MD translation is Newtonian ... ok
Test thermostatting by velocity rescaling ... ok
Check temperature ... ok
Check that velocity capping works ... ok
Test Berendsen thermostat ... ok
Test Langevin thermostat ... ok
Ensure that rigid removal works with a 1-particle system ... ok
Ensure that rigid rotation is removed ... ok
Ensure that rigid translation is removed ... ok
Check that written mol2s look right ... ok
Check reading a mol2 file containing small molecules ... ok
Check that a mol2-created hierarchy can be written to a PDB ... ok
Check use of Selection ... ok
Check that read_pdb behaves OK on invalid files ... ok
Check that only the first model is read ... ok
Test PDBSelectors implemented in Python ... ok
Check reading a pdb with one protein ... ok
Check that the Hydrogen selector can identify all hydrogens ... ok
Check that problem lines are read properly ... ok
Check that the default pdb reader skips waters ... ok
Check that only the first model is read ... ok
Reading of successive models from a pdb ... ok
Test that PDB atom names are not mangled ... ok
Make sure that atom names are padded correctly in PDB files ... ok
Test that all fields are read from PDB ATOM records ... ok
Test that we can read PDB ATOM record with coordinates only ... ok
Simple test of writing a PDB ... ok
Test protein ligand restraint 2 ... in 1.303s ... ok
Check brownian dynamics with rigid bodies ... in 3.062s ... ok
OptimizerStates from vector accessors should survive Optimizer del. ... ok
Constructed Python states should survive optimizer deletion ... ok
Check reference counting of OptimizerStates ... ok
Check that pdbs with rigid bodies don't have circular ref counts ... ok
Check Residue get_is_*() methods ... ok
Check equality of ResidueType types ... ok
Check get residue type from one-letter code ... ok
Check radius of gyration of a ball ... ok
Check radius of gyration with two balls ... in 1.684s ... ok
Check radius of gyration ... ok
Rigid aligment with rigid bodies ... in 2.292s ... ok
Rigid aligment without rigid bodies ... ok
Testing proper results for RMSD ... ok
Testing proper results for native overlap ... ok
Testing proper results for RMSD ... ok
Test RMSD for vectors and XYZs ... ok
Test protein simplification by residues ... ok
Test protein simplification by segments ... ok
Check the StereochemistryPairFilter exclusions ... ok
Check StereochemistryPairFilter input particles ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 2.179s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok
Test brownian free diffusion ... in 46.044s ... ok
Test a brownian harmonic ... FAIL
in 69.246s ... Test brownian linear diffusion ... FAIL
in 69.310s ... Check reading a pdb with one protein and a hetatm ... in 12.475s ... ok
Testing that we can read and write various pdbs ... in 17.945s ... ok

======================================================================
FAIL: Test dihedral functions
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_dihedrals.py", line 40, in test_dihedral
    self.assertAlmostEqual(d, -math.pi, delta=1e-4)
AssertionError: 3.1415926535897931 != -3.1415926535897931 within 0.0001 delta

======================================================================
FAIL: Testing the diffusion coeff estimate
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/test_estimates.py", line 40, in test_d
    self.assertAlmostEqual(nd, dd.get_diffusion_coefficient(), delta= .1*nd)
AssertionError: 2.1363104220734943e-05 != 2.3713211431188351e-05 within 2.1363104220734942e-06 delta

======================================================================
FAIL: Test a brownian harmonic
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_bd.py", line 172, in test_harmonic
    self._check((mn, std), ([0*angstrom, 0*angstrom, 0*angstrom], [sigma, sigmaf, sigmaf]), nreps)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_bd.py", line 128, in _check
    self.assertAlmostEqual(std[i], float(calc_std[i]/angstrom), delta=2.0*self._get_sigma_error(std[i], n))
AssertionError: 7.5857557724725311 != 10.0 within 1.3245105329704105 delta

======================================================================
FAIL: Test brownian linear diffusion
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_bd.py", line 156, in test_linear
    self._check((mn, std), ([mean, 0*angstrom, 0*angstrom], [sigma, sigma, sigma]), nreps)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/atom/test/expensive_test_bd.py", line 127, in _check
    self.assertAlmostEqual(mn[i], float(calc_mn[i]/angstrom), delta=2.0*std[i]*2/n**.5)
AssertionError: -16.4908900000001 != -18.0 within 0.54334856732361581 delta

----------------------------------------------------------------------
Ran 152 tests in 247.976s

FAILED (failures=4, skipped=1)
scons: *** Error 1
atom module unit tests FAILED
Running atom module unit tests
scons: *** [modules/atom/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/statistics/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/examples/kmeans.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/examples/write_a_metric.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/examples/test.results.out) > /dev/null
Run example kmeans.py ... ok
Run example write_a_metric.py ... ok

----------------------------------------------------------------------
Ran 2 tests in 0.165s

OK
statistics examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/statistics/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.statistics --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_bin_cluster.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_centrality_cluster.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_connectivity_clustering.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_diameter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_histogram.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_histogram_d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_recursive.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_show_histogram.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test_simple_kmeans.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_statistics_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/statistics/test/test.results.out) > /dev/null
Test bin clustering ... in 6.675s ... ok
Check that the centrality clustering works on trivial sets ... in 1.132s ... ok
Test connectivity clustering ... ok
Test metric connectivity clustering ... ok
Test connectivity clustering distance cutoff ... ok
Diameter clustering ... ok
Test that histogram top works ... ok
Check that the histogram is constructed correctly ... ok
Check that the uniform histogram is constructed correctly ... ok
Check that the histogramD of a gaussian is OK ... ok
Recursive clustering ... skipped 'bad test'
Check showing the histogram1D of a gaussian ... ok
Check showing the histogram2D of a gaussian ... skipped 'No x available for 2d'
Check showing the histogram3D of a gaussian ... skipped 'no DISPLAY variable found'
Kmeans clustering ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 19 tests in 11.692s

OK (skipped=3)
statistics module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/rmf/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/multiresolution.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/simulation.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/examples/test.results.out) > /dev/null
Run example geometry.py ... ok
Run example multiresolution.py ... in 18.113s ... ok
Run example pdb.py ... ok
Run example simulation.py ... in 84.247s ... ok

----------------------------------------------------------------------
Ran 4 tests in 103.142s

OK
rmf examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/rmf/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.rmf --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_hierarchy.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_model_dependencies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_multiframe.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_restraints.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_rigid_bodies_external.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_round_trip.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test_static_geometry.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_rmf_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/rmf/test/test.results.out) > /dev/null
Testing surface geometry ... skipped 'IMP.cgal module disabled'
Test reading and writing geometry ... ok
Test writing a large hierarchy ... ok
Test that navigation of read hierarchies works ... ok
Test writing a simple hierarchy ... ok
Test that writing restraints doesn't reset model dependencies ... ok
Test multi frame files ... ok
Test reading and writing particles ... ok
Test reading and writing particles with frames ... ok
Test writing restraints rmf ... ok
Test writing restraints to rmf with no particles ... ok
Test writing dynamic restraints ... ok
Test loading and saving of rigid bodies ... ok
Test loading and saving of rigid bodies ... ok
Test round trip 1 ... ok
Test round trip ... ok
Test reading and writing geometry ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 21 tests in 3.947s

OK (skipped=1)
rmf module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/domino/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/custom_filter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/domino_approach.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/interactive.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/interactive_with_containers.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/merge_tree.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/multiscale.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/restraint_cache.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/rigid_body_excluded_volume.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/save_assignments.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/six_particles_optimization.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/test_examples.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/examples/test.results.out) > /dev/null
Test example six_particles_optimization.py ... ok
Test example custom_filter.py ... ok
Run example domino_approach.py ... ok
Run example interactive.py ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Run example interactive_with_containers.py ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Run example merge_tree.py ... ok
Run example multiscale.py ... ok
Run example restraint_cache.py ... ok
Run example rigid_body_excluded_volume.py ... ok
Run example save_assignments.py ... ok

----------------------------------------------------------------------
Ran 10 tests in 1.406s

OK
domino examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/domino/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.domino --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_bandb_sampler.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_cache.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_caching_sampling.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_cluster.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_containers.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_default_subset_states.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_default_subset_states_with_filtering.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_filters.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_find_pairs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_interaction_graph.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_ints_list.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_junction_tree.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_merge_tree.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_nested_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_nested_states.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_order.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_permutation_state.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_restraint_cache.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_sampling.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_static_container.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_stray_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test_write_merge_tree.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_domino_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/domino/test/test.results.out) > /dev/null
Testing branch and bound sampler ... ok
Test caching of restraint scores ... ok
Test non-caching of restraint scores ... ok
Test capped caching of restraint scores ... ok
Test sampling with edge scores ... ok
Test clustering of states ... ok
Testing default subset states writing to an binary data set ... ok
Testing the cluster container ... in 8.244s ... ok
Testing default subset states writing to an hdf5 data set ... ok
Testing heap sample container ... ok
Testing default sample container ... ok
Test branch and bound subset states ... in 1.202s ... ok
Test recursive subset states ... in 1.212s ... ok
Test simple subset states ... in 1.210s ... ok
Test filtering with simple and minimal ... in 5.150s ... ok
Test filtering with recursive ... in 6.375s ... ok
Test filtering with simple ... in 6.388s ... ok
Test exclusion filtering pairs ... ok
Test exclusion filtering all ... in 1.511s ... ok
Test equivalence filtering ... ok
Test minimum filtering ... ok
Test close pairs list generation ... ok
Test that simple interaction graphs are fine ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Test that more involved graphs are fine ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
in 5.151s ... ok
Test that showing interaction graphs is fine ... ok
Test proper ints list ... ok
Testing junction tree algorithm ... ok
Testing random junction tree ... in 1.160s ... ok
Testing balanced merge tree algorithm ... ok
Test nested rigid bodies ... ok
Test nested with transformations ... ok
Testing enumeration with ordering ... ok
Testing enumeration with equiv excl ordering ... ok
Test permutation particle states ... ok
Test cache with decomposition with no max is empty ... ok
Test cache with decomposition with with a max is non-empty ... ok
Test cache with decomposition with set exclusion ... ok
Test cache with decomposition with nested sets ... ok
Test cache with simple restraint ... ok
Testing splitting restraints with rigid bodies ... ok
Testing finding minima with rigid bodies ... The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.
ok
Testing splitting restraints with rigid bodies and interestings scores ... ok
Test sampling ... ok
Test sampling with edge scores ... ok
Test handling of unattached particles ... ok
Testing writing and reading a merge tree ... 0 [label=0]
1 [label=1]
10 [label=9 8]
11 [label=7 6]
12 [label=5 4]
13 [label=2 3]
14 [label=0 1]
15 [label=2 0 1 3]
16 [label=5 4 7 6]
17 [label=5 9 4 8 7 6]
18 [label=2 0 5 9 4 8 1 7 6 3]
2 [label=2]
3 [label=3]
4 [label=4]
5 [label=5]
6 [label=6]
7 [label=7]
8 [label=8]
9 [label=9]
10 -> 8 []
10 -> 9 []
11 -> 6 []
11 -> 7 []
12 -> 4 []
12 -> 5 []
13 -> 2 []
13 -> 3 []
14 -> 0 []
14 -> 1 []
15 -> 14 []
15 -> 13 []
16 -> 12 []
16 -> 11 []
17 -> 16 []
17 -> 10 []
18 -> 15 []
18 -> 17 []
ending graph []
ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 1.215s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 50 tests in 41.961s

OK
domino module unit tests succeeded
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/em/DensityMap.h:587: Warning(314): 'from' is a python keyword, renaming to '_from'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/em/DensityMap.h:587: Warning(314): 'from' is a python keyword, renaming to '_from'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/em/DensityMap.h:675: Warning(314): 'in' is a python keyword, renaming to '_in'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/em/DensityMap.h:675: Warning(314): 'in' is a python keyword, renaming to '_in'
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/em/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/analyze_convergence.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/cube.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/fit_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/generate_density_map_of_fixed_dimension.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/local_fitting.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/pdb2density.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/em/examples/test.results.out) > /dev/null
Run example analyze_convergence.py ... in 1.116s ... ok
Run example cube.py ... ok
Run example fit_restraint.py ... in 3.840s ... ok
Run example generate_density_map_of_fixed_dimension.py ... ok
Run example local_fitting.py ... in 79.206s ... ok
Run example pdb2density.py ... in 2.211s ... ok

----------------------------------------------------------------------
Ran 6 tests in 86.946s

OK
em examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/em/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.em --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_add_map2map/test_add_map2map.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_calc_cc/test_calc_cc.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_calc_cc/test_correlation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_correlation_decomposition.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_coverters.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_crop.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_density2particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_densityMapVolumetrics.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_derivs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_em_fit.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_envelope_penetration_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_fitting_grid_search_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_fitting_of_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_get_density.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_kernel_parameters.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_local_fitting.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_map_header.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_module.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_origin_spacing.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_pad_margin.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_protein_fit_at_different_resolutions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_read_write_maps/test_read_write_map.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_refcount.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_resample.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_resample_by_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_rigid_cc_score_by_grid_rotation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_rigid_fitting_by_grid_rotation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_sample_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_sample_particles/test_sample_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_spacing.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_surface/test_geo_score.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_surface/test_pad.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_surface_sample_particles.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_surface_sample_protein.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_transform.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_volumes_and_images.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_em_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test.results.out) > /dev/null
test that adding a map to each other works ... ok
Check the last index is included ... in 55.658s ... ok
test that the create map is reasonable ... ok
test that the correlation at intervals functionality works ... FAIL
in 7.987s ... test that two maps that sample the same particles have cc score of 1 ... in 1.859s ... ok
test that padding option does not affect the CC score ... in 1.442s ... ok
test that translating either the map or the particles does not change the cc score ... in 1.889s ... ok
test that the simple fast ccc function works ... in 1.282s ... ok
Test that correlation and decomposed correlation return the same score ... in 2.864s ... ok
Test that the full and decomposed fit restraint return the same score ... in 6.281s ... ok
Test that the normalization factor is a constant ... in 10.013s ... ok
test_covert_to_particles (_test_5.ConvertersTest) ... ok
test_covert_to_vectors (_test_5.ConvertersTest) ... ok
Test the cropping functionality ... ok
Test the cropping functionality works when the input bb is larger than the density ... ok
Test conversion of a density map into a set of particles ... ok
Test conversion of particles to a density map ... ok
test_get_molecular_mass_at_threshold (_test_8.DensityMapVolumetricsTest) ... ok
Test calculated derivatives for a distorted model's map ... in 1.545s ... ok
Test if the derivatives can pull the particles back into the density ... in 1.502s ... ok
Testing FitRestraint derivative magnitudes ... in 4.784s ... ok
Make sure that we can cast Restraint* to FitRestraint* ... ok
Check that correlation of particles with their own density is 1 ... ok
Check FitRestraint's get methods ... ok
Check that load of nonexistent file is handled cleanly ... ok
Check the restraint is being evaluated ... in 1.949s ... ok
test_penetration (_test_11.EnvelopePenetrationRestraintTest) ... in 2.029s ... ok
Check that the local rigid fitting grid search works ... in 18.302s ... ok
Test that multiple rigid bodies are correctly pulled into the density ... in 8.943s ... ok
Check get_density ... in 30.390s ... ok
test_for_resolution_of_10 (_test_15.KernelParametersTest) ... ok
test_for_resolution_of_10_and_radius_of_1 (_test_15.KernelParametersTest) ... ok
test_get_parameters_by_radius (_test_15.KernelParametersTest) ... ok
Check that fast and slow local fitting converge to the same score ... in 8.095s ... ok
Check memory management of DensityHeader ... in 1.033s ... ok
test_header_values (_test_17.HeaderTest) ... ok
test em format read/write ... in 1.021s ... ok
test mrc format read/write ... ok
Make sure that exceptions work correctly ... ok
test_origin_spacing_data_is_kept_in_mrc_format1 (_test_19.FittingTest) ... ok
test_origin_spacing_data_is_kept_in_mrc_format2 (_test_19.FittingTest) ... ok
test_origin_spacing_data_is_kept_in_mrc_format3 (_test_19.FittingTest) ... ok
test_origin_spacing_data_is_kept_in_mrc_format4 (_test_19.FittingTest) ... ok
Test the pad_margin function ... ok
test_compare_fit_score_to_imp_generated_maps (_test_21.ProteinFittingTest) ... in 14.801s ... ok
test correct I/O of EM header ... ok
Check refcounting of IMP.em.DensityMap objects read from files ... ok
Check resampling of maps ... in 153.734s ... ok
test resampling with and without rigid bodies ... in 24.988s ... ok
test_compute_fitting_scores (_test_26.RigidBodyCorrelationByGridRotation) ... in 10.754s ... ok
Check that CC score does not change after grid and protein rotation ... ok
Check that CC score does not change after grid and protein rotation ... ok
Check that sampling particles works ... in 2.369s ... ok
test that the sampling works ... ok
Check that the correct spacing gets the highest CC ... in 2.738s ... ok
Check bad geometric complementarity score ... ok
Check good geometric complementarity score ... ok
Test map padding ... in 1.515s ... ok
Check that surface sampling works ... ok
Check that protein surface sampling works ... ok
Check transforming a density map ... in 48.811s ... ok
Check functionality of the get_transformed_into function ... ok
Check volume reading and writing ... in 3.195s ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

======================================================================
FAIL: test that the correlation at intervals functionality works
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/em/test/test_calc_cc/test_correlation.py", line 126, in test_corr_at_intervals
    self.assertEqual(result,scores_intervals[i][0],2)
AssertionError: -1.8977158955379991e-08 != -1.8977159399469201e-08 : 2

----------------------------------------------------------------------
Ran 67 tests in 439.046s

FAILED (failures=1)
scons: *** Error 1
em module unit tests FAILED
Running em module unit tests
scons: *** [modules/em/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/saxs/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/examples/profile.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/examples/profile_fit.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/examples/test.results.out) > /dev/null
Run example profile.py ... ok
Run example profile_fit.py ... ok

----------------------------------------------------------------------
Ran 2 tests in 1.549s

OK
saxs examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/saxs/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.saxs --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/test/test_saxs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/test/test_surface.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_saxs_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/saxs/test/test.results.out) > /dev/null
Check protein profile computation ... ok
Check residue level saxs restraint ... ok
Check saxs restraint ... ok
Check the surface area handle points on boundary ... ok
Check protein surface computation ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 9 tests in 2.646s

OK
saxs module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/gsl/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/examples/simplex.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/examples/test.results.out) > /dev/null
Run example simplex.py ... ok

----------------------------------------------------------------------
Ran 1 test in 0.146s

OK
gsl examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/gsl/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.gsl --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test_cg_optimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test_qn_minimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test_simplex_minimizer.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_gsl_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/gsl/test/test.results.out) > /dev/null
Check that we can optimize the Woods function with CG ... ok
Check that we can optimize the Woods function with QN ... ok
Test the simplex optimizer with given starting conditions ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 7 tests in 1.291s

OK
gsl module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/modeller/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/imp_restraints_in_modeller.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/load_modeller_model.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/modeller_restraints_in_imp.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/examples/test.results.out) > /dev/null
Run example imp_restraints_in_modeller.py ... in 1.617s ... ok
Run example load_modeller_model.py ... in 1.298s ... ok
Run example modeller_restraints_in_imp.py ... in 1.208s ... ok

----------------------------------------------------------------------
Ran 3 tests in 4.125s

OK
Exception AttributeError: "'NoneType' object has no attribute 'mod_model_free'" in  ignored
Exception AttributeError: "'NoneType' object has no attribute 'mod_io_data_free'" in > ignored
Exception AttributeError: "'NoneType' object has no attribute 'mod_libraries_free'" in > ignored
modeller examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/modeller/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.modeller --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test_dynamic_restraints.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test_imp_restraints.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test_load_model_atoms.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test_modeller_restraints.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test_rsr_file_read.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_modeller_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/modeller/test/test.results.out) > /dev/null
Check loading of Modeller electrostatic restraints ... in 1.491s ... ok
Check loading of Modeller Lennard-Jones restraints ... in 1.478s ... ok
Check loading of Modeller soft sphere restraints ... in 1.281s ... ok
Check using IMP restraints in Modeller ... in 1.239s ... ok
Check that Modeller bonds and angles are loaded ... in 5.126s ... ok
Check reading a dna with one chain ... in 2.699s ... ok
Check reading a Modeller model with one protein ... in 3.430s ... ok
Check using Modeller restraints in IMP ... in 1.288s ... ok
Check angle restraints against Modeller ... in 1.471s ... ok
Check bond restraints against Modeller ... in 1.477s ... ok
Check dihedral restraints against Modeller ... in 1.468s ... ok
Check improper restraints against Modeller ... in 1.452s ... ok
Check loading of Modeller static restraints ... in 1.486s ... ok
Check reading of arbitrary Modeller restraint files ... in 1.302s ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 18 tests in 27.802s

OK
modeller module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/restrainer/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/nup84_complex_in_bead_representation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/basic_setup.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/rigid_body_and_excluded_volume_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/em_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/saxs_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/basic_display.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/examples/test.results.out) > /dev/null
Run example nup84_complex_in_bead_representation.py ... ok
Run example basic_setup.py ... ok
Run example rigid_body_and_excluded_volume_restraint.py ... ok
Run example em_restraint.py ... ok
Run example saxs_restraint.py ... ok
Run example basic_display.py ... ok

----------------------------------------------------------------------
Ran 6 tests in 1.154s

OK
restrainer examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/restrainer/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.restrainer --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_connectivity_for_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_connectivity_for_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_diameter_for_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_diameter_for_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_display.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_distance_for_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_distance_for_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_em.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_get_rigid_body.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_methods_for_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_methods_for_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_representation_mix.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_representation_pdb.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_representation_sphere.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_saxs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_connectivity_on_molecules.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_connectivity_on_rigid_bodies.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_diameter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_distance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_em_fit.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test_simple_excluded_volume.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_restrainer_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/restrainer/test/test.results.out) > /dev/null
Check get_restraint_by_name, get_weight, and set_weight for connectivity restraint for pdb ... ok
Check connectivity restraint for sphere ... ok
Check diameter restraint for pdb ... ok
Check diameter restraint for sphere ... ok
Check display ... ok
Check distance restraint for pdb ... ok
Check distance restraint for sphere ... ok
Check EM restraint ... ok
Check get_rigid_body_by_id and get_all_rigid_bodies methods ... ok
Check multiple input restraints for pdb ... ok
Check multiple input restraints for sphere ... ok
Check pdb and sphere representations ... ok
Check pdb representation ... ok
Check sphere representation ... ok
Check saxs restraint ... ok
Test simple connectivity restraint on molecules. ... ok
Check SimpleConnectivity's methods for molecules ... ok
Check SimpleConnectivity's methods for rigid bodies ... ok
Check SimpleDiameter's methods ... ok
Test that simple diameter restraints are reasonable ... ok
Check SimpleDistance's methods ... ok
Test simple distance restraint ... ok
Make sure that we can cast Restraint* to FitRestraint* ... ok
Check that correlation of particles with their own density is 1 ... ok
Check SimpleEMFit's methods ... ok
Test excluded volume restraint on molecules ... ok
Test excluded volume restraint on rigid bodies ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 31 tests in 3.222s

OK
restrainer module unit tests succeeded
modules/multifit/src/fft_based_rigid_fitting.cpp: In member function 'void IMP::multifit::FFTFitting::fftw_translational_search(const IMP::multifit::internal::EulerAngles&, int)':
modules/multifit/src/fft_based_rigid_fitting.cpp:417: warning: comparison between signed and unsigned integer expressions
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/multifit/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/examples/patchdock_multifit.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/examples/test.results.out) > /dev/null
Run example patchdock_multifit.py ... --patchdock_binary is required
ok

----------------------------------------------------------------------
Ran 1 test in 0.497s

OK
multifit examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/multifit/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.multifit --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_add_surface_index.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_anchor_graph.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_connected_components.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_geometric_hash.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_mol_coarsening.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_radius_of_gyration_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_read_anchors_data.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_read_fitting_solutions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_read_proteomics_data.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_read_settings.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_rigid_fitting_fft.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_rmsd_clustering.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_settings_data.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_surface_sample_protein.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_weighted_excluded_volume_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_weighted_excluded_volume_restraint_3.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/multifit_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_multifit_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test.results.out) > /dev/null
Check that the surface indexes are added correctly ... ok
test_anchor_graph_formation (_test_2.AnchorGraphTest) ... ok
test_probability_calculation (_test_2.AnchorGraphTest) ... ok
test connected components ... ok
test_neighbors (_test_4.GeometricHashTest) ... in 2.989s ... ok
test_coarsening (_test_5.MolCoarseningTests) ... in 19.152s ... ok
test_density_coarsening (_test_5.MolCoarseningTests) ... in 12.275s ... ok
Test radius of gyration restraint ... ok
Check correct reading of proteomics file ... ok
Check correct parsing of fitting solutions file ... ok
Check the fitting solutions writer ... ok
Check correct reading of proteomics file ... ERROR
Check that the correct answer is returned when reading setting file ... ok
test fft based fitting ... ERROR
test fft based fitting ... ERROR
Testing proper clustering ... ERROR
test correct reading of settings data ... ok
Check that reading a map back in preserves the stdevs ... ok
Check that weighted excluded volume restraint works ... ok
Check that weighted excluded volume restraint 3 works ... FAIL
in 2.266s ... Running C++ test multifittest_geometric_complementarity ... in 6.455s ... ok
Running C++ test multifittest_get_candidate_transformations_match_1st_surface_to_2nd ... in 9.301s ... ok
Test that module class names follow the standards ... FAIL
Test that module function names follow the standards ... FAIL
Test all objects have show ... FAIL
Test that module classes are either values or objects ... FAIL

======================================================================
ERROR: Check correct reading of proteomics file
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_read_proteomics_data.py", line 18, in test_run
    self.prot_data = IMP.multifit.read_proteomics_data(self.data_file)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/multifit/__init__.py", line 2288, in read_proteomics_data
    return _IMP_multifit.read_proteomics_data(*args)
RuntimeError: bad lexical cast: source type value could not be interpreted as target

======================================================================
ERROR: test fft based fitting
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_rigid_fitting_fft.py", line 57, in test_fft_based_rigid_fitting
    IMP.algebra.get_uniform_cover_rotations_3d(10),1,False,False)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/multifit/__init__.py", line 1064, in fft_based_rigid_fitting
    return _IMP_multifit.fft_based_rigid_fitting(*args)
TypeError: fft_based_rigid_fitting() takes exactly 3 arguments (8 given)

======================================================================
ERROR: test fft based fitting
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_rigid_fitting_fft.py", line 96, in test_fft_based_rigid_fitting_translation_with_gmm
    [IMP.algebra.get_identity_rotation_3d()],10,False,True)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/multifit/__init__.py", line 1064, in fft_based_rigid_fitting
    return _IMP_multifit.fft_based_rigid_fitting(*args)
TypeError: fft_based_rigid_fitting() takes exactly 3 arguments (8 given)

======================================================================
ERROR: Testing proper clustering
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_rmsd_clustering.py", line 29, in test_clustering
    IMP.multifit.fitting_clustering(mh,ts,out_ts,3,100,30)
AttributeError: 'module' object has no attribute 'fitting_clustering'

======================================================================
FAIL: Check that weighted excluded volume restraint 3 works
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/multifit/test/test_weighted_excluded_volume_restraint_3.py", line 63, in test_weighted_excluded_volume_restraint
    self.assertEqual(evr.evaluate(False), 0)
AssertionError: 10.364754531023499 != 0

======================================================================
FAIL: Test that module class names follow the standards
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_multifit_standards.py", line 17, in test_classes
    spelling_exceptions)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 359, in assertClassNames
    % (str(bad)))
AssertionError: 3 != 0 : All IMP classes should be properly spelled. The following are not: ['MolCnSymmAxisDetector', 'MolCnSymmAxisDetector', 'ProteomicsData']. Add words to the spelling_exceptions variable of the IMPModuleTest if needed.

======================================================================
FAIL: Test that module function names follow the standards
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_multifit_standards.py", line 22, in test_functions
    spelling_exceptions)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 453, in assertFunctionNames
    message)
AssertionError: 109 != 0 : All IMP methods should have lower case names separated by underscores and beginning with a verb, preferably one of ['add', 'remove', 'get', 'set', 'create', 'destroy']. Each of the words should be a properly spelled english word. The following do not (given our limited list of verbs that we check for):
ComponentHeader.get_cmm_ap_fn
ComponentHeader.set_cmm_ap_fn
DensitySegmentationByCommunities.build_density_graph
DensitySegmentationByCommunities.calculate_communities
DensitySegmentationByCommunities.calculate_connected_components
DoubleVector.append
DoubleVector.assign
DoubleVector.back
DoubleVector.begin
DoubleVector.capacity
DoubleVector.empty
DoubleVector.end
DoubleVector.erase
DoubleVector.front
DoubleVector.insert
DoubleVector.iterator
DoubleVector.rbegin
DoubleVector.rend
DoubleVector.resize
DoubleVector.size
FFTFitting.fit
FFTFitting.fit_local_fitting
FittingSolutionRecord.get_rmsd_to_reference
FittingSolutionRecord.set_rmsd_to_reference
FittingSolutionRecords.append
FittingSolutionRecords.assign
FittingSolutionRecords.back
FittingSolutionRecords.begin
FittingSolutionRecords.capacity
FittingSolutionRecords.empty
FittingSolutionRecords.end
FittingSolutionRecords.erase
FittingSolutionRecords.front
FittingSolutionRecords.insert
FittingSolutionRecords.iterator
FittingSolutionRecords.rbegin
FittingSolutionRecords.rend
FittingSolutionRecords.resize
FittingSolutionRecords.size
GeometricHash2.Map
GeometricHash2.begin
GeometricHash2.bucket
GeometricHash2.end
GeometricHash2.neighbors
GeometricHash2.neighbors_data
GeometricHash2.resolution
GeometricHash3.Map
GeometricHash3.begin
GeometricHash3.bucket
GeometricHash3.end
GeometricHash3.neighbors
GeometricHash3.neighbors_data
GeometricHash3.resolution
GeometricHash4.Map
GeometricHash4.begin
GeometricHash4.bucket
GeometricHash4.end
GeometricHash4.neighbors
GeometricHash4.neighbors_data
GeometricHash4.resolution
GeometricHash5.Map
GeometricHash5.begin
GeometricHash5.bucket
GeometricHash5.end
GeometricHash5.neighbors
GeometricHash5.neighbors_data
GeometricHash5.resolution
IntVector.append
IntVector.assign
IntVector.back
IntVector.begin
IntVector.capacity
IntVector.empty
IntVector.end
IntVector.erase
IntVector.front
IntVector.insert
IntVector.iterator
IntVector.rbegin
IntVector.rend
IntVector.resize
IntVector.size
MolCnSymmAxisDetector.calc_symm_score
MolCnSymmAxisDetector.get_pca
MolCnSymmAxisDetector.init_from_protein
ProbabilisticAnchorGraph.are_probabilities_for_particle_set
ProteomicsData.add_ev_pair
ProteomicsData.add_xlink_interaction
ProteomicsData.get_ev_pair
ProteomicsData.get_interaction_linker_lenght
ProteomicsData.get_num_allowed_violated_ev
ProteomicsData.get_num_allowed_violated_xlinks
ProteomicsData.get_number_of_ev_pairs
ProteomicsData.get_number_of_xlinks
ProteomicsData.get_xlink
ProteomicsData.get_xlink_length
ProteomicsData.get_xlink_part_of_filter
ProteomicsData.set_num_allowed_violated_ev
ProteomicsData.set_num_allowed_violated_xlinks
SettingsData.get_asmb_fn
SettingsData.set_asmb_fn
SymmetricFit.set_patchdock_executable
SymmetricFit.set_patchdock_log_file
SymmetricFit.set_patchdock_log_level
SymmetricFit.set_prot_lib_file
SymmetricFit.set_protein_pdb_file
TransformationClustering.cluster_by_rmsd
TransformationClustering.cluster_by_rotation
TransformationClustering.cluster_by_transformation
If there is a good reason for them not to (eg it does start with a verb, just one with a meaning that is not covered by the normal list), add them to the function_name_exceptions variable in the IMPModuleTest call. Otherwise, please fix. The current verb list is ['add', 'remove', 'get', 'set', 'evaluate', 'show', 'create', 'destroy', 'push', 'pop', 'write', 'read', 'do', 'show', 'load', 'save', 'reset', 'clear', 'handle', 'update', 'apply', 'optimize', 'reserve', 'dump', 'propose', 'setup', 'teardown', 'visit', 'find', 'run', 'swap', 'link']
Misspelled words: cmm, ev, rmsd, lenght, prot, xlink, xlinks, asmb, pdb, pca, patchdock. Add words to the spelling_exceptions variable of the IMPModuleTest if needed.

======================================================================
FAIL: Test all objects have show
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_multifit_standards.py", line 26, in test_show
    return self.assertShow(IMP.multifit, exceptions)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 478, in assertShow
    message)
AssertionError: 15 != 0 : All IMP classes should support show and __str__. The following do not:
DensitySegmentationByCommunities
DoubleVector
FFTFitting
FFTFittingOutput
FFTScore
FittingSolutionRecords
GeometricHash2
GeometricHash3
GeometricHash4
GeometricHash5
IntVector
ProteinRecordData
RotScore
SymmetricFit
TransformationClustering
 If there is a good reason for them not to, add them to the show_exceptions variable in the IMPModuleTest call. Otherwise, please fix.

======================================================================
FAIL: Test that module classes are either values or objects
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_multifit_standards.py", line 12, in test_value_objects
    return self.assertValueObjects(IMP.multifit,exceptions)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 314, in assertValueObjects
    message)
AssertionError: 20 != 0 : All IMP classes should be labeled values or as objects to get memory management correct in python. The following are not:
['AnchorsData', 'DensitySegmentationByCommunities', 'DoubleVector', 'FFTFitting', 'FFTFittingOutput', 'FFTScore', 'FittingSolutionRecord', 'FittingSolutionRecords', 'GeometricHash2', 'GeometricHash3', 'GeometricHash4', 'GeometricHash5', 'IntVector', 'MolCnSymmAxisDetector', 'ProbabilisticAnchorGraph', 'ProteinRecordData', 'ProteomicsData', 'RotScore', 'SymmetricFit', 'TransformationClustering']
Please add an IMP_SWIG_OBJECT or IMP_SWIG_VALUE call to the python wrapper, or if the class has a good reason to be neither, add the name to the value_object_exceptions list in the IMPModuleTest call.

----------------------------------------------------------------------
Ran 26 tests in 55.978s

FAILED (failures=5, errors=4)
scons: *** Error 1
multifit module unit tests FAILED
Running multifit module unit tests
scons: *** [modules/multifit/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/em2d/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/clustering_of_pdb_models.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/collision_cross_section.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/em_images_conversion.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/optimize_em2d_with_montecarlo.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/examples/test.results.out) > /dev/null
Run example clustering_of_pdb_models.py ... in 11.398s ... ok
Run example collision_cross_section.py ... ok
Run example em_images_conversion.py ... ok
Run example optimize_em2d_with_montecarlo.py ... in 1.681s ... ok

----------------------------------------------------------------------
Ran 4 tests in 14.043s

OK
em2d examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/em2d/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.em2d --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_align2d.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_clustering_of_models.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_collision_cross_section.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_domino_filters.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_em2d_restraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_fft_operations.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_images_opencv.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_project.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_projection_registration.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_registration_results.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_relative_mover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_rigid_bodies_image_fit.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_segmentation_routines.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test_selection_files.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_em2d_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/em2d/test/test.results.out) > /dev/null
Test the complete alignment in 2D routine (new) ... ok
Test the rotational alignment in 2D routine (new) ... ok
Test the translational alignment in 2D routine ... ok
Test hierarchical clustering of models ... in 10.195s ... ok
Test the calculation of the collision cross section of a complex ... ok
Test filtering distances with domino ... ok
Test that an a optimization with em2d restraint is properly built ... ok
Test autocorrelation of an image using OpenCV ... ok
Test the correlation between two images using FFT ... ok
Test that extending the borders of an image is done correctly ... ok
Test that the function returns > 0 when there is overlap, and 0 ... ok
Test of polar resampling of images ... ok
Test read/write for the images using OpenCV data storage ... ok
Test of JPGReaderWriter reading ... in 1.078s ... ok
Test of TIFFReaderWriter reading ... ok
Test subtracting images ... ok
Test that the variance filter is working ... ok
Test that writing with JPGReaderWriter fails with bad extension ... ok
Test that writing with TIFFReaderWriter fails with bad extension ... ok
Test of JPGReaderWriter writing ... ok
Test of TIFFReaderWriter writing ... ok
Evenly distributed em2d image projections from a PDB file ... ok
Test the generation of noisy projections ... in 3.235s ... ok
Generation of random projection from a PDB file with em2d images ... ok
Test the registration of 3 subjects from 1gyt.pdb at 0.5 SNR ... in 9.908s ... ok
Test the generation of evenly distributed RegistrationResults ... ok
test back a forth of the Rotation in RegistrationResult class ... ok
Test the rotation error between 2 RegistrationResults classes ... ok
test the shift error between 2 RegistrationResults classes ... ok
Test the RelativePositionMover ... in 24.880s ... ok
Test scoring with RigidBodiesImageFitRestraint ... in 6.376s ... ok
Test the diffusion filtering on Nup84 class average ... in 8.203s ... ok
test the do_fill_holes_routine ... ok
test the labeling function ... ok
test the segmentation of particles from negative stained classes ... ok
Test reading selection files ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... in 1.016s ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 40 tests in 70.822s

OK
em2d module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/misc/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/examples/decay.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/examples/test.results.out) > /dev/null
Run example decay.py ... in 1059.130s ... ok

----------------------------------------------------------------------
Ran 1 test in 1059.131s

OK
misc examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/misc/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.misc --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test_common_endpoint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test_decay.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test_lrps.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test_wlc.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_misc_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/misc/test/test.results.out) > /dev/null
Test common endpoints container ... ok
Test that decay has the right halflife ... ok
Check that LowestRefinedPairScore returns the lowest ... ok
Test that the WormLikeChain values are sane ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 8 tests in 1.369s

OK
misc module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/system/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/system/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.system --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/system/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_system_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/system/test/test.results.out) > /dev/null
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.023s

OK
system module unit tests succeeded
In file included from build/include/IMP/isd/GaussianProcessInterpolation.h:14,
                 from modules/isd/src/GaussianProcessInterpolation.cpp:7:
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Linear1DFunction::get_derivative_matrix(const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:228: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:231: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Linear1DFunction::get_second_derivative_vector(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:254: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:257: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::GeneralizedGuinierPorodFunction::get_derivative_matrix(const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:591: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:594: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::GeneralizedGuinierPorodFunction::get_second_derivative_vector(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:839: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:842: warning: comparison between signed and unsigned integer expressions
In file included from build/include/IMP/isd/GaussianProcessInterpolation.h:15,
                 from modules/isd/src/GaussianProcessInterpolation.cpp:7:
build/include/IMP/isd/bivariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Covariance1DFunction::get_derivative_matrix(unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/bivariate_functions.h:364: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h:367: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Covariance1DFunction::get_second_derivative_matrix(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/bivariate_functions.h:436: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h:439: warning: comparison between signed and unsigned integer expressions
modules/isd/src/GaussianProcessInterpolation.cpp: In member function 'IMP::Floats IMP::isd::GaussianProcessInterpolation::get_posterior_covariance_derivative(IMP::Floats, bool) const':
modules/isd/src/GaussianProcessInterpolation.cpp:253: warning: comparison between signed and unsigned integer expressions
modules/isd/src/GaussianProcessInterpolation.cpp: In member function 'IMP::FloatsList IMP::isd::GaussianProcessInterpolation::get_posterior_covariance_hessian(IMP::Floats, bool) const':
modules/isd/src/GaussianProcessInterpolation.cpp:402: warning: comparison between signed and unsigned integer expressions
modules/isd/src/GaussianProcessInterpolation.cpp:404: warning: comparison between signed and unsigned integer expressions
In file included from build/include/IMP/isd/GaussianProcessInterpolation.h:14,
                 from build/include/IMP/isd/GaussianProcessInterpolationRestraint.h:15,
                 from modules/isd/src/GaussianProcessInterpolationRestraint.cpp:7:
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Linear1DFunction::get_derivative_matrix(const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:228: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:231: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Linear1DFunction::get_second_derivative_vector(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:254: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:257: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::GeneralizedGuinierPorodFunction::get_derivative_matrix(const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:591: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:594: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::GeneralizedGuinierPorodFunction::get_second_derivative_vector(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/univariate_functions.h:839: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/univariate_functions.h:842: warning: comparison between signed and unsigned integer expressions
In file included from build/include/IMP/isd/GaussianProcessInterpolation.h:15,
                 from build/include/IMP/isd/GaussianProcessInterpolationRestraint.h:15,
                 from modules/isd/src/GaussianProcessInterpolationRestraint.cpp:7:
build/include/IMP/isd/bivariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Covariance1DFunction::get_derivative_matrix(unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/bivariate_functions.h:364: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h:367: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h: In member function 'virtual IMP::FloatsList IMP::isd::Covariance1DFunction::get_second_derivative_matrix(unsigned int, unsigned int, const IMP::FloatsList&, bool) const':
build/include/IMP/isd/bivariate_functions.h:436: warning: comparison between signed and unsigned integer expressions
build/include/IMP/isd/bivariate_functions.h:439: warning: comparison between signed and unsigned integer expressions
modules/isd/src/GaussianProcessInterpolationRestraint.cpp: In member function 'IMP::FloatsList IMP::isd::GaussianProcessInterpolationRestraint::get_hessian(bool) const':
modules/isd/src/GaussianProcessInterpolationRestraint.cpp:274: warning: comparison between signed and unsigned integer expressions
modules/isd/src/GaussianProcessInterpolationRestraint.cpp:276: warning: comparison between signed and unsigned integer expressions
modules/isd/src/MolecularDynamics.cpp: In member function 'virtual void IMP::isd::MolecularDynamics::assign_velocities(IMP::Float)':
modules/isd/src/MolecularDynamics.cpp:188: warning: 'sampler.boost::variate_generator >::_dist.boost::normal_distribution::_cached_rho' may be used uninitialized in this function
modules/isd/src/MolecularDynamics.cpp:188: warning: 'sampler.boost::variate_generator >::_dist.boost::normal_distribution::_r1' may be used uninitialized in this function
/scratch/nightly-build-5850/imp-SVN.r14111/build/swig/IMP_isd.i:120: Warning(303): %extend defined for an undeclared class IMP::isd::GaussianProcessInterpolationSparse.
/scratch/nightly-build-5850/imp-SVN.r14111/build/swig/IMP_isd.i:122: Warning(303): %extend defined for an undeclared class IMP::isd::GaussianProcessInterpolationRestraintSparse.
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
/scratch/nightly-build-5850/imp-SVN.r14111/build/include/IMP/isd/bivariate_functions.h:129: Warning(314): 'lambda' is a python keyword, renaming to '_lambda'
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/isd/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/harmonic/demux_trajs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/harmonic/harmonic.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/harmonic/shared_functions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/ubiquitin/demux_trajs.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/ubiquitin/replica_exchange.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/ubiquitin/shared_functions.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/examples/test.results.out) > /dev/null
Run example demux_trajs.py ... ok
Run example harmonic.py ... This example needs the Python Pyro module
ok
Run example shared_functions.py ... ok
Run example demux_trajs.py ... ok
Run example replica_exchange.py ... This example needs the Python Pyro module
ok
Run example shared_functions.py ... ok

----------------------------------------------------------------------
Ran 6 tests in 0.490s

OK
isd examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/isd/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.isd --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_AmbiguousNOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Covariance1DFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_FNormal.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumerically.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumericallyNoMean.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumericallyNoSigma.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumerically.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumericallyNoMean.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumericallyNoSigma.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintSparse.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationSparse.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GeneralizedGuinierPorodFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_HybridMonteCarlo.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_JeffreysRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Linear1DFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_LognormalRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MaintainScaleOrderConstraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MarginalHBondRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MarginalNOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsMover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsNuisance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsXYZ.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_NOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Nuisance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_NuisanceRangeModifier.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Replica.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_RepulsiveDistancePairScore.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Scale.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_SlidingPriorRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Switching.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TALOSRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TBLReader.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TuneRex.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_communication.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_shared_functions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMises.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesKappaConjugateRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesKappaJeffreysRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesSufficient.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/isd_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_isd_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results.out) > /dev/null
test get_input_containers ... ok
test derivative w/r to X ... ok
test derivative w/r to sigma ... ok
test derivative w/r to X ... ok
test get_input_particles ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
test if score is equal to ... ok
test if score is equal to ... ok
test if score is equal to ... ok
test if score is equal to ... ok
test if probability is equal to ... ok
test if probability is equal to ... ok
test if probability is equal to ... ok
test if probability is equal to ... ok
testAddToParticleDerivative (_test_2.TestCovariance1DFunction) ... ok
testDerivNumericLam (_test_2.TestCovariance1DFunction) ... ok
testDerivNumericTau (_test_2.TestCovariance1DFunction) ... ok
testDerivOne (_test_2.TestCovariance1DFunction) ... ok
testDerivOneSame (_test_2.TestCovariance1DFunction) ... ok
testFail (_test_2.TestCovariance1DFunction) ... FAIL
testGetDerivativeMatrix (_test_2.TestCovariance1DFunction) ... ok
testHessianNumericLamLam (_test_2.TestCovariance1DFunction) ... ok
testHessianNumericLamTau (_test_2.TestCovariance1DFunction) ... ok
testHessianNumericTauLam (_test_2.TestCovariance1DFunction) ... ok
testHessianNumericTauTau (_test_2.TestCovariance1DFunction) ... ok
testValue (_test_2.TestCovariance1DFunction) ... in 1.072s ... ok
testValues (_test_2.TestCovariance1DFunction) ... in 1.065s ... ok
test_has_changed (_test_2.TestCovariance1DFunction) ... ok
tests FNormal.density ... ok
tests FNormal.evaluate ... ok
tests FNormal.evaluate_derivative_FA ... ok
tests FNormal.evaluate_derivative_FM ... ok
tests FNormal.evaluate_derivative_JA ... ok
tests FNormal.evaluate_derivative_sigma ... ok
testDOFSigma (_test_4.TestGaussianProcessInterpolation2Points) ... expected failure
testOptimizedParticles (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorCovarianceLambda (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorCovarianceMatrixSigma (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorCovarianceSigma (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorCovarianceTau (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanAlpha (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanBeta (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanLambda (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanSigma (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanTau (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testValuePosteriorMeanTau2 (_test_4.TestGaussianProcessInterpolation2Points) ... ok
testCovDerivNumericG (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovDerivNumericLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovDerivNumericRg (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovDerivNumericSigma (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovDerivNumericTau (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericGG (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericGLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericGRg (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericGSigma (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericGTau (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericLambdaLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericRgLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericRgRg (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericRgSigma (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericRgTau (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericSigmaLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericSigmaSigma (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericSigmaTau (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericTauLambda (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovHessianNumericTauTau (_test_5.TestGaussianProcessInterpolationNumerically) ... ok
testCovDerivNumericLambda (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovDerivNumericSigma (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovDerivNumericTau (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericLambdaLambda (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericSigmaLambda (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericSigmaSigma (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericSigmaTau (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericTauLambda (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovHessianNumericTauTau (_test_6.TestGaussianProcessInterpolationNumericallyNoMean) ... ERROR
testCovDerivNumericG (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovDerivNumericLambda (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovDerivNumericRg (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovDerivNumericTau (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericGG (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericGLambda (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericGRg (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericGTau (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericLambdaLambda (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericRgLambda (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericRgRg (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericRgTau (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericTauLambda (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testCovHessianNumericTauTau (_test_7.TestGaussianProcessInterpolationNumericallyNoSigma) ... ERROR
testDerivNumericAlpha (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivNumericBeta (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivNumericLambda (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivNumericSigma (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivNumericTau (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivativesAll (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
test derivatives by varying alpha ... ok
test derivatives by varying beta ... ok
test derivatives by varying lambda ... ok
test derivatives by varying sigma ... ok
test derivatives by varying tau ... ok
testEnergyTerms (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testGetInputThings (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueDensityAlpha (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueDensityBeta (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueDensityLambda (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueDensitySigma (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueDensityTau (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergyAll (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergyAlpha (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergyBeta (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergyLambda (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergySigma (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testValueEnergyTau (_test_8.TestGaussianProcessInterpolationRestraint2Points) ... ok
testDerivNumericG (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testDerivNumericLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testDerivNumericRg (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testDerivNumericSigma (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testDerivNumericTau (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericGG (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericGLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericGRg (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericGSigma (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericGTau (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericLambdaLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericLambdaRg (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericRgG (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericRgLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericRgRg (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericRgSigma (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericRgTau (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericSigmaLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericSigmaSigma (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericSigmaTau (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericTauLambda (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianNumericTauTau (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ok
testHessianSymmetry (_test_9.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
test if the scorestate works ... ok
testDerivNumericLambda (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testDerivNumericSigma (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testDerivNumericTau (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericLambdaLambda (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericSigmaLambda (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericSigmaSigma (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericSigmaTau (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericTauLambda (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testHessianNumericTauTau (_test_10.TestGaussianProcessInterpolationRestraintNumericallyNM) ... ERROR
testDerivNumericG (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testDerivNumericLambda (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testDerivNumericRg (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testDerivNumericTau (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericGG (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericGLambda (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericGRg (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericGTau (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericLambdaLambda (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericLambdaRg (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericRgG (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericRgLambda (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericRgRg (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericRgTau (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericTauLambda (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
testHessianNumericTauTau (_test_11.TestGaussianProcessInterpolationRestraintNumerically) ... ERROR
test derivatives by varying alpha ... skipped 'IMP not built with CHOLMOD'
test derivatives by varying beta ... skipped 'IMP not built with CHOLMOD'
test derivatives by varying lambda ... skipped 'IMP not built with CHOLMOD'
test derivatives by varying tau ... skipped 'IMP not built with CHOLMOD'
testValueDensityAlpha (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueDensityBeta (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueDensityLambda (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueDensityTau (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueEnergyAll (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueEnergyAlpha (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueEnergyBeta (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueEnergyLambda (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValueEnergyTau (_test_12.TestGaussianProcessInterpolationRestraint2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorCovarianceLambda (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorCovarianceSigma (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorCovarianceTau (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanAlpha (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanBeta (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanLambda (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanSigma (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanTau (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testValuePosteriorMeanTau2 (_test_13.TestGaussianProcessInterpolation2Points) ... skipped 'IMP not built with CHOLMOD'
testE (_test_14.TestGaussianRestraintSimple11) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdsigma (_test_14.TestGaussianRestraintSimple11) ... ok
testE (_test_14.TestGaussianRestraintSimple12) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_14.TestGaussianRestraintSimple12) ... ok
testE (_test_14.TestGaussianRestraintSimple13) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdx (_test_14.TestGaussianRestraintSimple13) ... ok
testE (_test_14.TestGaussianRestraintSimple21) ... ok
test if score is -log(prob) ... FAIL
test if prob is exp(-score) ... ok
testdmu (_test_14.TestGaussianRestraintSimple21) ... ok
testdx (_test_14.TestGaussianRestraintSimple21) ... ok
testE (_test_14.TestGaussianRestraintSimple22) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdsigma (_test_14.TestGaussianRestraintSimple22) ... ok
testdx (_test_14.TestGaussianRestraintSimple22) ... ok
testE (_test_14.TestGaussianRestraintSimple23) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_14.TestGaussianRestraintSimple23) ... ok
testdsigma (_test_14.TestGaussianRestraintSimple23) ... ok
testE (_test_14.TestGaussianRestraintSimple3) ... ok
testFail (_test_14.TestGaussianRestraintSimple3) ... FAIL
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_14.TestGaussianRestraintSimple3) ... ok
testdsigma (_test_14.TestGaussianRestraintSimple3) ... ok
testdx (_test_14.TestGaussianRestraintSimple3) ... ok
testAddToParticleDerivative (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivMult (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivNumericA (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivNumericG (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivNumericRg (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivNumericd (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivNumerics (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testDerivOne (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testGetDerivativeMatrix (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericA (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericGG (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericGRg (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericGd (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericGs (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericRgG (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericRgRg (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericRgd (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericRgs (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericdd (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericds (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testHessianNumericss (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testValue (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
testValues (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
test_has_changed (_test_15.TestGeneralizedGuinierPorodFunction) ... ok
test ensemble averages ... FAIL
test ensemble averages against the standard Monte Carlo ... in 1.375s ... ok
test that the HMC moves the particles ... ok
testContainers (_test_17.TestJeffreysRestraint) ... ok
test the derivative of the restraint ... ok
raise ValueError if negative ... ok
raise ValueError if negative ... ok
raise ValueError if zero ... ok
raise ValueError if zero ... ok
testParticles (_test_17.TestJeffreysRestraint) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
test if score is log(scale) ... ok
test if probability is 1/scale ... ok
testAddToParticleDerivative (_test_18.TestLinear1DFunction) ... ok
testDerivMult (_test_18.TestLinear1DFunction) ... ok
testDerivNumericAlpha (_test_18.TestLinear1DFunction) ... ok
testDerivNumericBeta (_test_18.TestLinear1DFunction) ... ok
testDerivOne (_test_18.TestLinear1DFunction) ... ok
testGetDerivativeMatrix (_test_18.TestLinear1DFunction) ... ok
testValue (_test_18.TestLinear1DFunction) ... ok
testValues (_test_18.TestLinear1DFunction) ... ok
test_has_changed (_test_18.TestLinear1DFunction) ... ok
testE (_test_19.TestLognormalRestraintSimple11) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdsigma (_test_19.TestLognormalRestraintSimple11) ... ok
testE (_test_19.TestLognormalRestraintSimple12) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_19.TestLognormalRestraintSimple12) ... ok
testE (_test_19.TestLognormalRestraintSimple13) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdx (_test_19.TestLognormalRestraintSimple13) ... ok
testE (_test_19.TestLognormalRestraintSimple21) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_19.TestLognormalRestraintSimple21) ... ok
testdx (_test_19.TestLognormalRestraintSimple21) ... ok
testE (_test_19.TestLognormalRestraintSimple22) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdsigma (_test_19.TestLognormalRestraintSimple22) ... ok
testdx (_test_19.TestLognormalRestraintSimple22) ... ok
testE (_test_19.TestLognormalRestraintSimple23) ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_19.TestLognormalRestraintSimple23) ... ok
testdsigma (_test_19.TestLognormalRestraintSimple23) ... ok
testE (_test_19.TestLognormalRestraintSimple3) ... ok
testFail (_test_19.TestLognormalRestraintSimple3) ... FAIL
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
testdmu (_test_19.TestLognormalRestraintSimple3) ... ok
testdsigma (_test_19.TestLognormalRestraintSimple3) ... ok
testdx (_test_19.TestLognormalRestraintSimple3) ... ok
testContainers (_test_20.TestMaintainScaleOrderConstraint) ... ERROR
tests if randomly shuffled scales are nicely sorted after that ... ERROR
tests if randomly shuffled scales are nicely sorted after that. Also ... ERROR
testParticles (_test_20.TestMaintainScaleOrderConstraint) ... ERROR
test get_input_containers ... ok
test derivative wrt x for 3 particles and 2 contributions ... ok
test get_input_particles ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
test energy on three particles ... ok
test energy on n particles ... ok
test logsquares on n particles ... ok
test n on n particles ... ok
test probability on three particles ... ok
test probability on n particles ... ok
test get_input_containers ... ok
test derivative wrt x for 3 particles and 2 contributions ... FAIL
test get_input_particles ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
test energy on three particles ... FAIL
test energy on n particles ... FAIL
test gamma hat on n particles ... ERROR
test n on n particles ... ok
test probability on three particles ... FAIL
test probability on n particles ... ERROR
test sum of squares on n particles ... FAIL
resetting the move without redrawing velocities should lead to the ... ok
resetting the move by redrawing velocities should lead to a different ... ok
test get/set the number of MD steps. ... ok
test that the mover moves the particles ... ok
changing the length of the simulation should lead to a different ... ok
reset should revert to the first set of coordinates ... ok
Test get_optimizer_states() method ... ok
Test that MD generates particle velocities ... ok
Should skip particles without xyz attributes ... ok
Check that non-rigid MD translation is Newtonian ... ok
Check temperature ... ok
Check that velocity capping works ... ok
Test get_optimizer_states() method ... ok
Test that MD generates particle velocities ... ok
Should skip particles without xyz attributes ... ok
Check that non-rigid MD translation is Newtonian ... ok
Check temperature ... ok
Check that velocity capping works ... ok
tests to satisfy a restraint between two points ... ok
test get_input_containers ... ok
test derivative w/r to X ... ok
test derivative w/r to sigma ... ok
test derivative w/r to X ... ok
test get_input_particles ... ok
test if score is -log(prob) ... ok
test if prob is exp(-score) ... ok
test value of chi by changing distance. ... ok
test if score is equal to ... ok
test if score is equal to ... ok
test if score is equal to ... ok
test if probability is equal to ... ok
test if probability is equal to ... ok
test if probability is equal to ... ok
tests get and set (sanity checks) ... ok
tests get and set (border check) ... ok
set returns nothing ... ok
test_Setup1 (_test_27.TestNuisanceParam) ... ok
test_Setup2 (_test_27.TestNuisanceParam) ... ok
a parameter cannot take other things than numbers as input ... ok
test setting/getting derivative ... ok
test_nuisance_down (_test_28.TestNuisanceRangeModifier) ... ok
test_nuisance_up (_test_28.TestNuisanceRangeModifier) ... ok
test_scale_down (_test_28.TestNuisanceRangeModifier) ... ok
test_scale_up (_test_28.TestNuisanceRangeModifier) ... ok
test_switching_down (_test_28.TestNuisanceRangeModifier) ... ok
test_switching_up (_test_28.TestNuisanceRangeModifier) ... ok
test_energies (_test_29.TestReplicaExchange) ... ok
test_gen_pairs_list_gromacs (_test_29.TestReplicaExchange) ... ok
test_gen_pairs_list_gromacs_neighbors (_test_29.TestReplicaExchange) ... ok
test_gen_pairs_list_rand_neighbors (_test_29.TestReplicaExchange) ... ok
test_gen_pairs_list_rand_singletons (_test_29.TestReplicaExchange) ... ok
Test uniformity of randomly generated replica pairs ... in 5.336s ... ok
test_get_metropolis (_test_29.TestReplicaExchange) ... ok
test_perform_exchanges_replicanums (_test_29.TestReplicaExchange) ... ok
test_perform_exchanges_statenums (_test_29.TestReplicaExchange) ... ok
test_perform_exchanges_steps (_test_29.TestReplicaExchange) ... ok
test_perform_exchanges_temps (_test_29.TestReplicaExchange) ... ok
test_sort_errors (_test_29.TestReplicaExchange) ... ok
test_sort_per_replica (_test_29.TestReplicaExchange) ... ok
test_sort_per_state (_test_29.TestReplicaExchange) ... ok
test_sort_sanity (_test_29.TestReplicaExchange) ... ok
tests if derivative is -2*(d-x0)**3 ... ok
tests if energy is a repulsive quadric with zero at van der waals ... ok
tests get and set (sanity checks) ... ok
tests get and set (border check) ... ok
test that a Nuisance can be converted to a Scale ... ok
set returns nothing ... ok
test_Setup1 (_test_31.TestScaleParam) ... sh: line 1: 10429 Segmentation fault      ( /scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.isd --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_AmbiguousNOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Covariance1DFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_FNormal.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolation.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumerically.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumericallyNoMean.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationNumericallyNoSigma.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumerically.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumericallyNoMean.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintNumericallyNoSigma.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationRestraintSparse.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianProcessInterpolationSparse.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GaussianRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_GeneralizedGuinierPorodFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_HybridMonteCarlo.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_JeffreysRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Linear1DFunction.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_LognormalRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MaintainScaleOrderConstraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MarginalHBondRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MarginalNOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsMover.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsNuisance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_MolecularDynamicsXYZ.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_NOERestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Nuisance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_NuisanceRangeModifier.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Replica.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_RepulsiveDistancePairScore.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Scale.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_SlidingPriorRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_Switching.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TALOSRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TBLReader.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_TuneRex.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_communication.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_shared_functions.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMises.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesKappaConjugateRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesKappaJeffreysRestraint.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test_vonMisesSufficient.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/isd_cpp_test_programs.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_isd_standards.py > /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results.out ) > /dev/null
scons: *** Error 139
isd module unit tests FAILED
Running isd module unit tests
scons: *** [modules/isd/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/example/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/example/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/examples/range_restriction.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/example/examples/test.results.out) > /dev/null
Run example range_restriction.py ... ok

----------------------------------------------------------------------
Ran 1 test in 0.354s

OK
example examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/example/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.example --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test_assembly.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test_filter.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test_modifier.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_example_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/example/test/test.results.out) > /dev/null
Test getting complex assembly ... in 5.390s ... ok
Test example filter ... ok
Test example modifier ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 7 tests in 6.563s

OK
example module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/kmeans/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/examples/kmeans_example.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/examples/test.results.out) > /dev/null
Run example kmeans_example.py ... ERROR

======================================================================
ERROR: Run example kmeans_example.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "", line 5, in test_run_example
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 499, in run_example
    exec open(filename) in vars
  File "/scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/examples/kmeans_example.py", line 2, in 
    from IMP.kmeans import KMeans
ImportError: No module named kmeans

----------------------------------------------------------------------
Ran 1 test in 0.003s

FAILED (errors=1)
scons: *** Error 1
kmeans examples FAILED
Running kmeans examples
scons: *** [modules/kmeans/examples/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/kmeans/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.kmeans --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/test/test_kmeans.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_kmeans_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/kmeans/test/test.results.out) > /dev/null
test_simple_kmeans (_test_1.KMeansTest) ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... FAIL
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

======================================================================
FAIL: Test that module function names follow the standards
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_kmeans_standards.py", line 22, in test_functions
    spelling_exceptions)
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 453, in assertFunctionNames
    message)
AssertionError: 2 != 0 : All IMP methods should have lower case names separated by underscores and beginning with a verb, preferably one of ['add', 'remove', 'get', 'set', 'create', 'destroy']. Each of the words should be a properly spelled english word. The following do not (given our limited list of verbs that we check for):
KMeans.execute
KMeans.print_centers
If there is a good reason for them not to (eg it does start with a verb, just one with a meaning that is not covered by the normal list), add them to the function_name_exceptions variable in the IMPModuleTest call. Otherwise, please fix. The current verb list is ['add', 'remove', 'get', 'set', 'evaluate', 'show', 'create', 'destroy', 'push', 'pop', 'write', 'read', 'do', 'show', 'load', 'save', 'reset', 'clear', 'handle', 'update', 'apply', 'optimize', 'reserve', 'dump', 'propose', 'setup', 'teardown', 'visit', 'find', 'run', 'swap', 'link']

----------------------------------------------------------------------
Ran 5 tests in 1.040s

FAILED (failures=1)
scons: *** Error 1
kmeans module unit tests FAILED
Running kmeans module unit tests
scons: *** [modules/kmeans/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/parallel/examples/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-examples.py --excluded= --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/examples/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/examples/local_distance.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/examples/tasks.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/examples/test.results.out) > /dev/null
Run example local_distance.py ... ok
Run example tasks.py ... ok

----------------------------------------------------------------------
Ran 2 tests in 0.526s

OK
parallel examples succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/parallel/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.parallel --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test_sge.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test_startup.py /scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test_tasks.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_parallel_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/parallel/test/test.results.out) > /dev/null
Test _SGEPESlave class ... ok
Test SGEPESlaveArray class ... ok
Test that slave tasks can start up and communicate ... ok
Test context startup callable ... ok
Make sure that startup failures cause a timeout ... ok
Test that startup with no slaves causes a failure ... ok
Check that NaN and Inf floats are pickled correctly ... ok
Test that exceptions can be passed to and from tasks ... ok
Test that exceptions raised by a task are propagated ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 13 tests in 2.481s

OK
parallel module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/pepdock/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/pepdock/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.pepdock --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/pepdock/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_pepdock_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/pepdock/test/test.results.out) > /dev/null
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.018s

OK
pepdock module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/modules/scratch/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp modules/scratch/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.scratch --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/modules/scratch/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_scratch_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/modules/scratch/test/test.results.out) > /dev/null
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 4 tests in 0.017s

OK
scratch module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/EModel2D/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=EModel2D --pycoverage=no --pyexe=em2d_domino_model.py --pyexe=em2d_cluster_solutions.py --pyexe=em2d_score_updated.py --pyexe=em2d_docking.py --pyexe=convert_spider_to_jpg.py --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_argminmax.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_buildxlinks.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_cluster_solutions.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_csv_related.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_database.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_dock_related.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_domino_modeling.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_mc_modeling.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test_sampling.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/EModel2D/test/test.results.out) > /dev/null
EModel2D application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/foxs/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=foxs --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/test_saxs.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/test.results.out) > /dev/null
Simple test of SAXS profile application ... foxs /scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/input/6lyz.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/input/lyzexp.dat 
Computing profile for /scratch/nightly-build-5850/imp-SVN.r14111/applications/foxs/test/input/6lyz.pdb
ok

----------------------------------------------------------------------
Ran 1 test in 0.631s

OK
foxs application unit tests succeeded
applications/integrative_docking/em3d_dock/MapScorer.cpp: In member function 'IMP::em::DensityMap* MapScorer::get_transformed(const IMP::algebra::Transformation3D&) const':
applications/integrative_docking/em3d_dock/MapScorer.cpp:67: warning: comparison between signed and unsigned integer expressions
applications/integrative_docking/em3d_dock/MapScorer.cpp: In member function 'IMP::em::DensityMap* MapScorer::get_transformed(const IMP::algebra::Transformation3D&, const IMP::algebra::Transformation3D&) const':
applications/integrative_docking/em3d_dock/MapScorer.cpp:87: warning: comparison between signed and unsigned integer expressions
build/include/IMP/Key.h: In function 'void get_residue_solvent_accessibility(const IMP::Particles&, const IMP::Particles&, const std::vector >&, std::vector >&)':
build/include/IMP/Key.h:120: warning: dereferencing pointer '' does break strict-aliasing rules
/usr/lib/gcc/i686-redhat-linux/4.4.6/../../../../include/c++/4.4.6/bits/stl_tree.h:175: note: initialized from here
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/integrative_docking/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=integrative_docking --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test_em2d_dock.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test_em3d_dock.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test_foxsdock.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test_nmr_rtc.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test.results.out) > /dev/null
Simple test of EM2D single PDB score application ... em2d_single_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/complex-2d.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_1.pgm /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_2.pgm /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_3.pgm -s 2.2 -n 200 
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
height = 1 all images 3
7824 atoms were read from file /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/complex-2d.pdb
200 projections were created
Image 0 Best projection 171 -135.204 0 0 0.95263 0.310345
Image 1 Best projection 27 198.988 0 0 0.94528 0.342167
Image 2 Best projection 152 75.5035 0 0 0.943201 0.289988
Total score = 2.84111
height = 1 all images 3
in 15.875s ... ok
Simple test of EM2D score application ... em2d_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/2p4e.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/model4.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transforms10 /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_1.pgm /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_2.pgm /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/image_3.pgm -s 2.2 -n 200 
Receptor /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/2p4e.pdb ligand /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/model4.pdb trans file /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transforms10
4400 atoms were read from file /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/2p4e.pdb
3424 atoms were read from file /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/model4.pdb
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Image width = 110 height = 110 max color val = 255
Max distance = 136.684 threshold 129.849
Image 0 Best projection 8 60.7273 0 0 0.956441 0
Image 1 Best projection 176 102.016 0 0 0.942828 0
Image 2 Best projection 34 200.819 0 0 0.94691 0
Transform: 0 | 0.948726 | 0.885369 -0.2878 -0.363943 0.0289545 || (82.62, 59.28, -1.011)
Image 0 Best projection 8 66.3251 0 0 0.954957 0
Image 1 Best projection 176 96.7903 0 0 0.937965 0
Image 2 Best projection 55 214.944 0 0 0.952796 0
Transform: 1 | 0.948573 | 0.936686 -0.156171 -0.297768 0.0977994 || (75.69, 67.15, -0.3048)
Image 0 Best projection 18 -2.63004 0 0 0.954611 0
Image 1 Best projection 177 82.8248 0 0 0.944182 0
Image 2 Best projection 35 215.657 0 0 0.941264 0
Transform: 2 | 0.946686 | 0.919489 -0.209453 -0.331709 -0.0252783 || (84.94, 58.97, 3.343)
Image 0 Best projection 33 -20.2402 0 0 0.947739 0
Image 1 Best projection 176 94.0595 0 0 0.934408 0
Image 2 Best projection 54 202.089 0 0 0.951565 0
Transform: 3 | 0.94457 | 0.939604 -0.18398 -0.24281 0.156011 || (64.77, 67.4, -8.547)
Image 0 Best projection 170 -121.324 0 0 0.952135 0
Image 1 Best projection 13 -141.859 0 0 0.940216 0
Image 2 Best projection 171 72.3652 0 0 0.943596 0
Transform: 4 | 0.945315 | 0.367553 -0.603749 0.672282 0.220064 || (-27.56, 9.718, 17.52)
Image 0 Best projection 185 -114.459 0 0 0.95091 0
Image 1 Best projection 3 197.867 0 0 0.932851 0
Image 2 Best projection 171 78.0449 0 0 0.950104 0
Transform: 5 | 0.944622 | 0.361231 -0.412601 0.797644 0.251069 || (-24.84, 19.74, 24.11)
Image 0 Best projection 170 -122.98 0 0 0.949282 0
Image 1 Best projection 12 199.383 0 0 0.938632 0
Image 2 Best projection 151 83.7775 0 0 0.947222 0
Transform: 6 | 0.945045 | 0.431571 -0.563967 0.683474 0.168969 || (-20.62, 0.9181, 12.18)
Image 0 Best projection 18 -7.59236 0 0 0.95551 0
Image 1 Best projection 177 87.2614 0 0 0.94374 0
Image 2 Best projection 35 210.383 0 0 0.94346 0
Transform: 7 | 0.94757 | 0.880682 -0.269008 -0.370728 -0.120808 || (92.21, 53.57, 1.334)
Image 0 Best projection 34 -15.8019 0 0 0.959015 0
Image 1 Best projection 159 89.7029 0 0 0.942542 0
Image 2 Best projection 55 205.542 0 0 0.945863 0
Transform: 8 | 0.94914 | 0.932902 -0.259141 -0.244257 -0.0536557 || (83.29, 57.29, -2.52)
Image 0 Best projection 137 144.982 0 0 0.947115 0
Image 1 Best projection 53 -76.7277 0 0 0.926034 0
Image 2 Best projection 139 -16.4056 0 0 0.954722 0
Transform: 9 | 0.942624 | 0.0934506 0.37914 0.82229 0.413955 || (37.67, 40.1, 89.39)
in 263.214s ... ok
Simple test of EM3D single PDB score application ... em3d_single_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/complex-3d.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/complex.mrc 
Best score = 3945 best_found 1best_trans 0.143947 -0.328361 0.526557 0.770841 || (102.698, 131.858, 130.324)
FAIL
in 32.467s ... Simple test of EM3D score application ... em3d_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/2p4e.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/fab.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transforms10 /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/complex.mrc 
in 32.017s ... ok
Simple test of SAXS profile application ... saxs_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/static.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transformed.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transforms-foxs10 /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/iq.dat 
Computing profile for /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/static.pdb min = 0.0 max = 0.5 delta=0.0025
Computing profile for /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transformed.pdb min = 0.0 max = 0.5 delta=0.0025
Profile read from file /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/iq.dat min = 0 max = 0.499 delta = 0.001 size = 500
Rg = 16.9558
/scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/iq.dat Rg= 16.9558 range 15.2602-17.634
in 2.298s ... ok
Simple test of nmr_rtc application ... interface_rtc /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/static.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transformed.pdb 
ok
Simple test of nmr_rtc application ... nmr_rtc_score /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/static.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transformed.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/transforms-foxs10 /scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/input/receptor_rare4.txt - 
ok

======================================================================
FAIL: Simple test of EM3D single PDB score application
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/applications/integrative_docking/test/test_em3d_dock.py", line 18, in test_simple
    self.assertAlmostEqual(float(m.group(1)), 3842, delta=100.0)
AssertionError: 3945.0 != 3842 within 100.0 delta

----------------------------------------------------------------------
Ran 7 tests in 346.209s

FAILED (failures=1)
scons: *** Error 1
integrative_docking application unit tests FAILED
Running integrative_docking application unit tests
scons: *** [applications/integrative_docking/test/test.results] Error 1
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/saxs_tools/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=saxs_tools --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/test_saxs_tools.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/test.results.out) > /dev/null
Simple test of SAXS profile application ... rg /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/input/6lyz.pdb /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_tools/test/input/lyzexp.dat 
Rg = 15.1949
ok

----------------------------------------------------------------------
Ran 1 test in 0.084s

OK
saxs_tools application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/saxs_merge/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=saxs_merge --pycoverage=no --pyexe=saxs_merge.py --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test_profile.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test_merge.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test_merge2.py /scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test_benchmark.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/saxs_merge/test/test.results.out) > /dev/null
test add_data ... in 1.891s ... ok
test add_data ... ok
test add_data offset=1 ... ok
test add_data ... ok
test add_data ... ok
test_default_gamma (_test_1.SAXSProfileTest) ... ok
test get_data ... ok
test get_data with gamma != 1 ... ok
test get_data with gamma != 1 twice ... ok
test get_data colwise ... ok
get_data should copy the data, not reference it ... ok
get_data should fail with the wrong number of arguments ... ok
test get_data with the filter keyword as a string ... ok
test get_data with the filter keyword as a list ... ok
test get_data with the filter keyword as None ... ok
test get_data with an invalid filter keyword ... ok
test get_data for correct sorting ... ok
test get_data for correct sorting ... ok
test get_data with a specified range ... ok
test get_flag ... ok
get_flag raises an error for invalid arguments ... ok
get_flag returns something for a value outside of known bounds ... ok
test_get_flag_intervals (_test_1.SAXSProfileTest) ... ok
test get_flag_names ... ok
test get_mean defaults ... ok
test get_mean defaults ... ok
test get_mean with the filter keyword as a string ... ok
test get_mean with the filter keyword as a list ... ok
test get_mean with the filter keyword as None ... ok
test get_mean with an invalid filter keyword ... ok
test get_mean defaults ... ok
test num ... ok
test qmin and qmax ... ok
test qvalues ... ok
get_params should return a dict ... ok
test get_raw_data with gamma != 1 ... ok
test get_raw_data colwise ... ok
get_raw_data should copy the data, not reference it ... ok
test get_raw_data for correct sorting ... ok
test get_data for correct sorting ... ok
test new_flag ... ok
test set_flag ... ok
test_set_flag_interval (_test_1.SAXSProfileTest) ... ok
test set_flag_intervals when they overlap ... ok
test set_flag_intervals when they overlap ... ok
test set_flag_intervals when they overlap ... ok
test set_flag_intervals when they overlap ... ok
test_set_gamma (_test_1.SAXSProfileTest) ... ok
test_set_interpolant (_test_1.SAXSProfileTest) ... ok
simple classification test ... ok
test cleanup q_cutoff ... ok
test cleanup good/bad ... ok
simple merge test without the fitting part ... ok
test rescaling of two perfectly agreeing functions ... ok
test rescaling of two perfectly agreeing functions ... ok
simple classification test ... ok
simple merge test without the fitting part ... ok
test rescaling of two perfectly agreeing functions ... ok
test rescaling of two perfectly agreeing functions ... ok
Simple test of SAXS merge benchmark / application for Nup116 ... in 241.340s ... ok
Simple test of SAXS merge benchmark / application for Nup192 ... in 212.601s ... ok

----------------------------------------------------------------------
Ran 61 tests in 456.511s

OK
saxs_merge application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/em_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/em_tools/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=em_tools --pycoverage=no --pyexe=resample_density.py --pyexe=mol2pca.py --pyexe=map2pca.py --pyexe=simulate_density_from_pdb.py --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/em_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/em_tools/test/test_em_tools.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/em_tools/test/test.results.out) > /dev/null
Simple test of map2pca application ... ok
Simple test of mol2pca application ... ok
Simple test of resample_density application ... ok
Simple test of simulate_density_from_pdb application ... ok

----------------------------------------------------------------------
Ran 4 tests in 2.227s

OK
em_tools application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/ligand_score/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/ligand_score/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=ligand_score --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/ligand_score/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/ligand_score/test/test_ligand_score.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/ligand_score/test/test.results.out) > /dev/null
Simple test of ligand score application ... ok

----------------------------------------------------------------------
Ran 1 test in 0.847s

OK
ligand_score application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/multifit_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/multifit_tools/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=multifit_tools --pycoverage=no --pyexe=complex_to_anchor_graph.py --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/multifit_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/multifit_tools/test/test_complex.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/multifit_tools/test/test.results.out) > /dev/null
Simple test of complex_to_anchor_graph application ... ok

----------------------------------------------------------------------
Ran 1 test in 0.886s

OK
multifit_tools application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/pdb_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/pdb_tools/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=pdb_tools --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/pdb_tools/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/pdb_tools/test/test_pdb_check.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/pdb_tools/test/test.results.out) > /dev/null
Simple test of pdb_check application ... ok

----------------------------------------------------------------------
Ran 1 test in 0.192s

OK
pdb_tools application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/applications/example_app/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp applications/example_app/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --application=example_app --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/applications/example_app/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/applications/example_app/test/test_example.py >/scratch/nightly-build-5850/imp-SVN.r14111/applications/example_app/test/test.results.out) > /dev/null
Simple test of example application ... ok

----------------------------------------------------------------------
Ran 1 test in 0.021s

OK
example_app application unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/local/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp biological_systems/example_system/local/test/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-tests.py --module=IMP.example_system_local --pycoverage=no --results=/scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/local/test/test.results /scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/local/test/test_modifier.py /scratch/nightly-build-5850/imp-SVN.r14111/build/test/test_example_system_local_standards.py >/scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/local/test/test.results.out) > /dev/null
Test local modifier ... ok
Test that module class names follow the standards ... ok
Test that module function names follow the standards ... ok
Test all objects have show ... ok
Test that module classes are either values or objects ... ok

----------------------------------------------------------------------
Ran 5 tests in 1.072s

OK
example_system_local module unit tests succeeded
tempfile /scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/test.results /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp biological_systems/example_system/test.results.result
mkdir -p /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; cd /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp; (/scratch/nightly-build-5850/imp-SVN.r14111/tools/imppy.sh python /scratch/nightly-build-5850/imp-SVN.r14111/scons_tools/run-all-system.py /scratch/nightly-build-5850/imp-SVN.r14111/build/tmp /scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/sample_0.py /scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/analyze_0.py >/scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/test.results.out) > /dev/null
Run sample_0.py ... in 1.972s ... ok
Run analyze_0.py ... FAIL
in 1.558s ... 
======================================================================
FAIL: Run analyze_0.py
----------------------------------------------------------------------
Traceback (most recent call last):
  File "", line 9, in test_run_example
  File "/scratch/nightly-build-5850/imp-SVN.r14111/build/lib/IMP/test/__init__.py", line 672, in assertApplicationExitedCleanly
    + error)
AssertionError: 1 != 0 : Application exited uncleanly, with exit code 1
Traceback (most recent call last):
  File "/scratch/nightly-build-5850/imp-SVN.r14111/biological_systems/example_system/analyze_0.py", line 43, in 
    for i in range(0, IMP.rmf.get_number_of_frames(fh, all)):
AttributeError: 'module' object has no attribute 'get_number_of_frames'


----------------------------------------------------------------------
Ran 2 tests in 3.532s

FAILED (failures=1)
scons: *** Error 1
example_system systems FAILED
Running example_system systems
scons: *** [biological_systems/example_system/test.results] Error 1


IMP configuration:
boost               ='yes'
boostlibs           =''
boostversion        ='104100'
boostlibsuffix      ='-mt'
endian              ='little'
boost_filesystem    ='yes'
boost_filesystemlibs='boost_filesystem-mt'
google_perftools_profile='no'
boost_programoptions='yes'
boost_programoptionslibs='boost_program_options-mt'
hdf5                ='yes'
hdf5libs            ='hdf5'
boost_thread        ='yes'
boost_threadlibs    ='boost_thread-mt'
protobuf            ='no'
cgal                ='yes'
cgallibs            ='CGAL:gmp:mpfr:gmpxx:boost_thread-mt:pthread:m'
cgalversion         ='1030611000'
ann                 ='no'
boost_graph         ='yes'
boost_graphlibs     ='boost_graph-mt'
gsl                 ='yes'
gsllibs             ='gsl:gslcblas:m'
fftw3               ='yes'
fftw3libs           ='fftw3:m'
opencv21            ='yes'
opencv21libs        ='cv:cxcore:highgui'
opencv22            ='no'
eigen3              ='yes'
eigen3libs          =''
eigen3includepath   ='/usr/include/eigen3'
cholmod             ='no'
build               ='fast'
modeller            ='/salilab/diva1/home/modeller/9.10'
prefix              ='/usr'
local               ='True'
pythonpath          ='/scratch/nightly-build-5850/imp-SVN.r14111'
libpath             ='/scratch/nightly-build-5850/imp-SVN.r14111'
ldlibpath           ='/scratch/nightly-build-5850/imp-SVN.r14111'
swigpath            ='/scratch/nightly-build-5850/imp-SVN.r14111'
datapath            ='/scratch/nightly-build-5850/imp-SVN.r14111'
cxxcompiler         ='g++'
cxxflags='-isystem /scratch/nightly-build-5850/imp-SVN.r14111 -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wmissing-declarations -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations --param inline-unit-growth=200 -fearly-inlining -fno-signed-zeros -freciprocal-math -fassociative-math'
pythoncxxflags='-isystem /scratch/nightly-build-5850/imp-SVN.r14111 -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -Wno-deprecated -Winit-self -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations --param inline-unit-growth=200 -fearly-inlining -fno-signed-zeros -freciprocal-math -fassociative-math'
bincxxflags='-isystem /scratch/nightly-build-5850/imp-SVN.r14111 -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -D_GNU_SOURCE -fPIC -Wall -Wextra -Wno-deprecated -Winit-self -Wstrict-aliasing=2 -Wcast-align -fno-operator-names -Wundef -Woverloaded-virtual -O3 -fexpensive-optimizations -ffast-math -ftree-vectorize -ffinite-math-only -fstrict-aliasing -fno-trapping-math -fno-signaling-nans -fno-float-store -Wno-unused -funsafe-loop-optimizations --param inline-unit-growth=200 -fearly-inlining -fno-signed-zeros -freciprocal-math -fassociative-math'
shliblinkflags      =' -shared'
arliblinkflags      =''
binlinkflags        =''
pythonlinkflags     =' -shared'
rpath               ='False'
static              ='False'
pythonsosuffix      ='.so'
pkgconfig           ='True'
path                ="/usr/bin:/bin"
python              ="python"


Enabled dependencies:  CGAL, HDF5, OpenCV21, Boost.Thread, Boost.FileSystem, modeller, eigen3, Boost.ProgramOptions, Boost.Graph, FFTW3, Boost, GSL
Disabled dependencies: ProtoBuf, ANN, CHOLMOD, google_perftools_profile, OpenCV22

Enabled modules:  em, kernel, scratch, domino, misc, kmeans, rmf, statistics, container, saxs, system, parallel, RMF, example, benchmark, core, algebra, cgal, restrainer, multifit, example_system_local, base, atom, compatibility, gsl, pepdock, modeller, em2d, display, isd

Enabled applications:  rmf_tools, pdb_tools, saxs_merge, saxs_tools, multifit_tools, example_app, em_tools, integrative_docking, EModel2D, ligand_score, foxs

Enabled systems:  Groel, example_system, nup84, rnapii

no file /scratch/nightly-build-5850/imp-SVN.r14111/modules/isd/test/test.results
Failed tests:
  IMP.atom:
    Test dihedral functions
    Testing the diffusion coeff estimate
    Test a brownian harmonic
    Test brownian linear diffusion
  IMP.em:
    test that the correlation at intervals functionality works
  IMP.multifit:
    Check correct reading of proteomics file
    test fft based fitting
    test fft based fitting
    Testing proper clustering
    Check that weighted excluded volume restraint 3 works
    Test that module class names follow the standards
    Test that module function names follow the standards
    Test all objects have show
    Test that module classes are either values or objects
  IMP.kmeans:
    Test that module function names follow the standards

Skipped tests:
  RMF:
    Test copying a rmf file to a prmf file
    Test copying a simple rmf file to prmf
  IMP.algebra:
    Test uniform random rotation
    Check volume and surface area of random
  IMP.display:
    Testing isosurface geometry
    Testing skin surface
    Testing the pivy writer and frames
    Testing polygon decomposition and writing
    Testing trivial polygon decomposition and writing
  IMP.atom:
    Check that deleting the model doesn't make things crash
  IMP.statistics:
    Recursive clustering
    Check showing the histogram2D of a gaussian
    Check showing the histogram3D of a gaussian
  IMP.rmf:
    Testing surface geometry

Fast build FAILED
BUILD COMPLETED