Bug#684838: pynn: FTBFS: failed test

Source: pynn
Version: 0.7.2-1
Severity: serious
Tags: wheezy sid
User: debian-qa@lists.debian.org
Usertags: qa-ftbfs-20120814 qa-ftbfs
Justification: FTBFS in wheezy on amd64

Hi,

During a rebuild of all packages in *wheezy*, your package failed to
build on amd64.

Relevant part:

make[1]: Entering directory `/«PKGBUILDDIR»'
for PYVER in `pyversions -d -r -v`; do \
PYTHONPATH=`/bin/ls -d /«PKGBUILDDIR»/build/lib.*-$PYVER` $PYTHON \
/usr/bin/nosetests -s -v --exclude='_(nest|neuron)' test/; done
Failure: SkipTest () ... SKIP
Failure: SkipTest () ... SKIP
system.test_moose.test_recording ... SKIP
system.test_moose.test_synaptic_connections ... SKIP
Failure: SkipTest () ... SKIP
system.test_pcsim.test_PoissonInputNeuron ... SKIP
unittests.test_assembly.test_create_with_zero_populations ... ok
unittests.test_assembly.test_create_with_one_population ... ok
unittests.test_assembly.test_create_with_two_populations ... ok
unittests.test_assembly.test_create_with_non_population_should_raise_Exception ... ok
unittests.test_assembly.test_size_property ... ok
unittests.test_assembly.test_positions_property ... ok
unittests.test_assembly.test__len__ ... ok
unittests.test_assembly.test_iter ... ok
unittests.test_assembly.test__add__population ... ok
unittests.test_assembly.test__add__assembly ... ok
unittests.test_assembly.test_add_inplace_population ... ok
unittests.test_assembly.test_add_inplace_assembly ... ok
unittests.test_assembly.test_add_invalid_object ... ok
unittests.test_assembly.test_initialize ... ok
unittests.test_assembly.test_describe ... ok
unittests.test_assembly.test_get_population ... ok
unittests.test_assembly.test_all_cells ... ok
unittests.test_assembly.test_local_cells ... ok
unittests.test_assembly.test_mask_local ... ok
unittests.test_assembly.test_save_positions ... ok
unittests.test_basepopulation.test__getitem__int ... ok
unittests.test_basepopulation.test__getitem__slice ... ok
unittests.test_basepopulation.test__getitem__list ... ok
unittests.test_basepopulation.test__getitem__tuple ... ok
unittests.test_basepopulation.test__getitem__invalid ... ok
unittests.test_basepopulation.test_len ... ok
unittests.test_basepopulation.test_iter ... ok
unittests.test_basepopulation.test_is_local ... ok
unittests.test_basepopulation.test_all ... ok
unittests.test_basepopulation.test_add ... ok
unittests.test_basepopulation.test_get_cell_position ... ok
unittests.test_basepopulation.test_set_cell_position ... ok
unittests.test_basepopulation.test_get_cell_initial_value ... ok
unittests.test_basepopulation.test_set_cell_initial_value ... ok
unittests.test_basepopulation.test_nearest ... ok
unittests.test_basepopulation.test_sample ... ok
unittests.test_basepopulation.test_get_should_call_get_array_if_it_exists ... ok
unittests.test_basepopulation.test_get_with_no_get_array ... FAIL
unittests.test_basepopulation.test_get_with_gather ... ok
unittests.test_basepopulation.test_set_from_dict ... ok
unittests.test_basepopulation.test_set_from_pair ... ok
unittests.test_basepopulation.test_set_invalid_type ... ok
unittests.test_basepopulation.test_set_inconsistent_type ... ok
unittests.test_basepopulation.test_set_with_no_get_array ... ok
unittests.test_basepopulation.test_set_with_list ... ok
unittests.test_basepopulation.test_tset_with_numeric_values ... ok
unittests.test_basepopulation.test_tset_with_array_values ... ok
Population.tset(): If the size of the valueArray does not match that of the Population, should raise an InvalidDimensionsError. ... ok
unittests.test_basepopulation.test_tset_invalid_dimensions_1D ... ok
Population.rset() ... ok
unittests.test_basepopulation.test_rset_with_native_rng ... ok
unittests.test_basepopulation.test_initialize ... ok
unittests.test_basepopulation.test_initialize_random_distribution ... ok
unittests.test_basepopulation.test_can_record ... ok
unittests.test_basepopulation.test__record ... ok
unittests.test_basepopulation.test__record_invalid_variable ... ok
unittests.test_basepopulation.test_invalid_record_from ... ok
unittests.test_basepopulation.test_spike_recording ... ok
unittests.test_basepopulation.test_record_v ... ok
unittests.test_basepopulation.test_record_gsyn ... ok
unittests.test_basepopulation.test_printSpikes ... ok
unittests.test_basepopulation.test_getSpikes ... ok
unittests.test_basepopulation.test_print_v ... ok
unittests.test_basepopulation.test_get_v ... ok
unittests.test_basepopulation.test_print_gsyn ... ok
unittests.test_basepopulation.test_get_gsyn ... ok
unittests.test_basepopulation.test_get_spike_counts ... ok
unittests.test_basepopulation.test_meanSpikeCount ... ok
unittests.test_basepopulation.test_meanSpikeCount_on_slave_node ... ok
unittests.test_basepopulation.test_inject ... ok
unittests.test_basepopulation.test_inject_into_invalid_celltype ... ok
unittests.test_basepopulation.test_save_positions ... ok
unittests.test_connectors.TestAllToAllConnector.test_connect_with_distance_dependent_weights_parallel_safe ... ok
unittests.test_connectors.TestAllToAllConnector.test_connect_with_random_weights_parallel_safe ... ok
unittests.test_connectors.TestAllToAllConnector.test_connect_with_scalar_weights_and_delays ... ok
unittests.test_connectors.TestAllToAllConnector.test_create_with_delays_None ... ok
unittests.test_connectors.TestAllToAllConnector.test_create_with_delays_too_small ... ok
unittests.test_connectors.TestAllToAllConnector.test_create_with_list_delays_too_small ... ok
unittests.test_connectors.TestDistanceDependentProbabilityConnector.test_connect_with_default_args ... ok
unittests.test_connectors.TestDistanceMatrix.test_really_simple0 ... ok
unittests.test_connectors.TestDistanceMatrix.test_really_simple1 ... ok
unittests.test_connectors.TestFixedNumberPostConnector.test_with_n_smaller_than_population_size ... ok
unittests.test_connectors.TestFixedNumberPreConnector.test_with_n_smaller_than_population_size ... ok
unittests.test_connectors.TestFixedProbabilityConnector.test_connect_with_default_args ... ok
unittests.test_connectors.TestFromFileConnector.test_connect_with_standard_text_file_distributed ... ok
unittests.test_connectors.TestFromFileConnector.test_connect_with_standard_text_file_not_distributed ... ok
unittests.test_connectors.TestFromListConnector.test_connect_with_out_of_range_index ... ok
unittests.test_connectors.TestFromListConnector.test_connect_with_valid_list ... ok
unittests.test_connectors.TestOneToOneConnector.test_connect_with_random_weights ... ok
unittests.test_connectors.TestOneToOneConnector.test_connect_with_scalar_weights_and_delays ... ok
unittests.test_core.test_is_list_like_with_tuple ... ok
unittests.test_core.test_is_list_like_with_list ... ok
unittests.test_core.test_is_list_like_with_iterator ... ok
unittests.test_core.test_is_list_like_with_set ... ok
unittests.test_core.test_is_list_like_with_numpy_array ... ok
unittests.test_core.test_is_list_like_with_string ... ok
unittests.test_core.test_create_with_int ... ok
unittests.test_core.test_create_with_float ... ok
unittests.test_core.test_create_with_list ... ok
unittests.test_core.test_create_with_array ... ok
unittests.test_core.test_create_inconsistent ... ok
unittests.test_core.test_create_with_string ... ok
unittests.test_core.test_setitem_nonexpanded_same_value ... ok
unittests.test_core.test_setitem_invalid_value ... ok
unittests.test_core.test_setitem_nonexpanded_different_value ... ok
unittests.test_core.test_columnwise_iteration_with_flat_array ... ok
unittests.test_core.test_columnwise_iteration_with_structured_array ... ok
unittests.test_core.test_columnwise_iteration_with_random_array_parallel_safe_no_mask ... ok
unittests.test_core.test_columnwise_iteration_with_function ... ok
unittests.test_core.test_columnwise_iteration_with_flat_array_and_mask ... ok
unittests.test_core.test_columnwise_iteration_with_structured_array_and_mask ... ok
unittests.test_core.test_columnwise_iteration_with_random_array_parallel_safe_with_mask ... ok
unittests.test_core.test_as_array_with_flat_array ... ok
unittests.test_core.test_as_array_with_structured_array ... ok
unittests.test_core.test_as_array_with_functional_array ... ok
unittests.test_core.test_iadd_with_flat_array ... ok
unittests.test_core.test_add_with_flat_array ... ok
unittests.test_core.test_lt_with_flat_array ... ok
unittests.test_core.test_lt_with_structured_array ... ok
unittests.test_core.test_structured_array_lt_array ... ok
unittests.test_core.test_multiple_operations_with_structured_array ... ok
unittests.test_core.test_apply_function_to_constant_array ... ok
unittests.test_core.test_apply_function_to_structured_array ... ok
unittests.test_core.test_apply_function_to_functional_array ... ok
unittests.test_core.test_add_two_constant_arrays ... ok
unittests.test_core.test_add_incommensurate_arrays ... ok
unittests.test_core.test_getitem_from_constant_array ... ok
unittests.test_descriptions.test_get_default_template_engine ... ok
unittests.test_descriptions.test_render_with_no_template ... ok
unittests.test_descriptions.test_render_with_template ... ok
unittests.test_descriptions.test_StringTE_get_template ... ok
unittests.test_descriptions.test_StringTE_get_template_from_file ... ok
unittests.test_descriptions.test_StringTE_render ... ok
unittests.test_descriptions.test_Jinja2TE_get_template_from_file ... ok
unittests.test_descriptions.test_Jinja2TE_render ... ok
unittests.test_descriptions.test_CheetahTE_get_template_from_file ... ok
unittests.test_descriptions.test_CheetahTE_render ... ok
unittests.test_files.test__savetxt ... ok
unittests.test_files.test_create_BaseFile ... ok
unittests.test_files.test_del ... ok
unittests.test_files.test_close ... ok
unittests.test_files.test_StandardTextFile_write ... ok
unittests.test_files.test_StandardTextFile_read ... ok
unittests.test_files.test_PickleFile ... ok
unittests.test_files.test_NumpyBinaryFile ... ERROR
unittests.test_files.test_HDF5ArrayFile ... ok
unittests.test_idmixin.Test_IDMixin.test_celltype_property ... ok
unittests.test_idmixin.Test_IDMixin.test_get_initial_value ... ok
unittests.test_idmixin.Test_IDMixin.test_get_parameters ... ok
unittests.test_idmixin.Test_IDMixin.test_getattr_with_nonparameter_attr ... ok
unittests.test_idmixin.Test_IDMixin.test_getattr_with_parameter_attr ... ok
unittests.test_idmixin.Test_IDMixin.test_getattr_with_parent_not_set ... ok
unittests.test_idmixin.Test_IDMixin.test_inject ... ok
unittests.test_idmixin.Test_IDMixin.test_is_standard_cell ... ok
unittests.test_idmixin.Test_IDMixin.test_local_property ... ok
unittests.test_idmixin.Test_IDMixin.test_position_property ... ok
unittests.test_idmixin.Test_IDMixin.test_set_initial_value ... ok
unittests.test_idmixin.Test_IDMixin.test_set_parameters ... ok
unittests.test_idmixin.Test_IDMixin.test_setattr_with_parameter_attr ... ok
unittests.test_lowlevelapi.test_build_create ... ok
unittests.test_lowlevelapi.test_build_connect ... ok
unittests.test_lowlevelapi.test_set ... ok
unittests.test_lowlevelapi.test_build_record ... ok
unittests.test_lowlevelapi.test_build_record_with_assembly ... ok
unittests.test_population.test_create_population_standard_cell_simple ... ok
unittests.test_population.test_create_population_standard_cell_with_params ... ok
unittests.test_population.test_create_population_with_implicit_grid ... ok
unittests.test_population.test_cell_property ... /«PKGBUILDDIR»/build/lib.linux-x86_64-2.7/pyNN/common.py:915: UserWarning: The `Population.cell` attribute is not an official part of the API, and its use is deprecated. It will be removed in a future release. All uses of `cell` may be replaced by `all_cells`
release. All uses of `cell` may be replaced by `all_cells`")
ok
unittests.test_population.test_id_to_index ... ok
unittests.test_population.test_id_to_index_with_array ... ok
unittests.test_population.test_id_to_index_with_populationview ... ok
unittests.test_population.test_id_to_index_with_invalid_id ... ok
unittests.test_population.test_id_to_index_with_invalid_ids ... ok
unittests.test_population.test_id_to_local_index ... ok
unittests.test_population.test_id_to_local_index_with_invalid_id ... ok
unittests.test_population.test_set_structure ... ok
unittests.test_population.test_get_positions ... ok
unittests.test_population.test_set_positions ... ok
unittests.test_population.test_position_generator ... ok
unittests.test_population.test_describe ... ok
unittests.test_populationview.test_create_with_boolean_array_selector ... ok
unittests.test_populationview.test_create_with_index_array_selector ... ok
unittests.test_populationview.test_create_with_slice_selector ... ok
unittests.test_populationview.test_structure_property ... ok
unittests.test_populationview.test_get_positions ... ok
unittests.test_populationview.test_id_to_index ... ok
unittests.test_populationview.test_describe ... ok
unittests.test_projection.test_create_simple ... ok
unittests.test_projection.test_create_with_synapse_dynamics ... ok
unittests.test_projection.test_len ... ok
unittests.test_projection.test_size_no_gather ... ok
unittests.test_projection.test_size_with_gather ... ok
unittests.test_projection.test__getitem ... ok
unittests.test_projection.test_set_weights ... ok
unittests.test_projection.test_randomize_weights ... ok
unittests.test_projection.test_set_delays ... ok
unittests.test_projection.test_randomize_delays ... ok
unittests.test_projection.test_set_synapse_dynamics_param ... ok
unittests.test_projection.test_get_weights ... ok
unittests.test_projection.test_get_delays ... ok
unittests.test_projection.test_save_connections ... ok
unittests.test_projection.test_print_weights_as_list ... ok
unittests.test_projection.test_print_weights_as_array ... ok
unittests.test_projection.test_weight_histogram_with_args ... ok
unittests.test_projection.test_weight_histogram_no_args ... ok
unittests.test_projection.test_describe ... ok
test_create (unittests.test_random.NativeRNGTests) ... ok
test_parallel_safe_with_mask_local (unittests.test_random.ParallelTests) ... ok
test_parallel_safe_with_mask_local_False (unittests.test_random.ParallelTests) ... ok
test_parallel_safe_with_mask_local_None (unittests.test_random.ParallelTests) ... ok
test_parallel_unsafe (unittests.test_random.ParallelTests) ... ok
test_permutation (unittests.test_random.ParallelTests) ... ok
test_boundaries (unittests.test_random.RandomDistributionTests) ... ok
test_gamma (unittests.test_random.RandomDistributionTests) ... ok
test_gaussian (unittests.test_random.RandomDistributionTests) ... ok
test_uniform (unittests.test_random.RandomDistributionTests) ... ok
Calling next(0) should return an empty array. ... ok
Calling next() with no arguments or with n=1 should return a float. ... ok
Calling next(n=m) where m > 1 should return an array. ... ok
Calling next(m) where m < 0 should raise a ValueError. ... ok
test_invalid_seed (unittests.test_random.SimpleTests) ... ok
unittests.test_recording.test_Recorder_create ... ok
unittests.test_recording.test_Recorder_invalid_variable ... ok
unittests.test_recording.test_record ... ok
unittests.test_recording.test_filter_recorded ... ok
unittests.test_recording.test_get__zero_offset ... ok
unittests.test_recording.test_write__with_filename__compatible_output__gather__onroot ... ok
unittests.test_recording.test_metadata_property ... ok
unittests.test_recording.test__make_compatible_spikes ... ok
unittests.test_recording.test__make_compatible_v ... ok
unittests.test_simulation_control.test_setup ... ok
unittests.test_simulation_control.test_end ... ok
unittests.test_simulation_control.test_run ... ok
unittests.test_simulation_control.test_reset ... ok
unittests.test_simulation_control.test_initialize ... ok
unittests.test_simulation_control.test_current_time ... ok
unittests.test_simulation_control.test_time_step ... ok
unittests.test_simulation_control.test_min_delay ... ok
unittests.test_simulation_control.test_max_delay ... ok
unittests.test_simulation_control.test_num_processes ... ok
unittests.test_simulation_control.test_rank ... ok
unittests.test_space.Grid2D_Test.test_calculate_size ... ok
unittests.test_space.Grid2D_Test.test_generate_positions ... ok
unittests.test_space.Grid3D_Test.test_calculate_size ... ok
unittests.test_space.Grid3D_Test.test_generate_positions ... ok
test__eq__ (unittests.test_space.LineTest) ... ok
test_generate_positions (unittests.test_space.LineTest) ... ok
test_generate_positions_default_parameters (unittests.test_space.LineTest) ... ok
test_get_parameters (unittests.test_space.LineTest) ... ok
test_cylindrical_space (unittests.test_space.SpaceTest) ... ok
test_generator_for_infinite_space_with_3D_distances (unittests.test_space.SpaceTest) ... ok
test_infinite_space_with_3D_distances (unittests.test_space.SpaceTest) ... ok
test_infinite_space_with_collapsed_axes (unittests.test_space.SpaceTest) ... ok
test_infinite_space_with_scale_and_offset (unittests.test_space.SpaceTest) ... ok
unittests.test_space.TestCuboid.test_sample ... ok
unittests.test_space.TestRandomStructure.test_generate_positions ... ok
unittests.test_space.TestSphere.test__create ... ok
unittests.test_space.TestSphere.test_sample ... ok
unittests.test_space.test_distance ... ok
unittests.test_standardmodels.test_build_translations ... ok
unittests.test_standardmodels.test_has_parameter ... ok
unittests.test_standardmodels.test_get_parameter_names ... ok
Instantiating a StandardModelType should set self.parameters to the value ... ok
unittests.test_standardmodels.test_checkParameters_without_defaults ... ok
unittests.test_standardmodels.test_checkParameters_with_defaults ... ok
unittests.test_standardmodels.test_checkParameters_with_nonexistent_parameter ... ok
unittests.test_standardmodels.test_checkParameters_with_invalid_value ... ok
unittests.test_standardmodels.test_translate ... ok
unittests.test_standardmodels.test_translate_with_invalid_transformation ... ok
unittests.test_standardmodels.test_translate_with_divide_by_zero_error ... ok
unittests.test_standardmodels.test_reverse_translate ... ok
unittests.test_standardmodels.test_reverse_translate_with_invalid_transformation ... ok
unittests.test_standardmodels.test_simple_parameters ... ok
unittests.test_standardmodels.test_scaled_parameters ... ok
unittests.test_standardmodels.test_computed_parameters ... ok
update_parameters(P) should update self.parameters with the value of ... ok
unittests.test_standardmodels.test_describe ... ok
unittests.test_standardmodels.test_describe_SD ... ok
unittests.test_standardmodels.test_STDPMechanism_create ... ok
unittests.test_standardmodels.test_STDPMechanism_create_invalid_types ... ok
unittests.test_utility_functions.test_is_conductance ... ok
unittests.test_utility_functions.test_is_conductance_with_nonlocal_cell ... ok
unittests.test_utility_functions.test_check_weight_with_scalar ... ok
unittests.test_utility_functions.test_check_weight_with_list ... ok
unittests.test_utility_functions.test_check_weight_with_NaN ... ok
unittests.test_utility_functions.test_check_weight_with_invalid_value ... ok
unittests.test_utility_functions.test_check_weight_is_conductance_is_None ... ok
unittests.test_utility_functions.test_check_delay ... ok

> ERROR: unittests.test_files.test_NumpyBinaryFile
-
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/«PKGBUILDDIR»/test/unittests/test_files.py", line 92, in test_NumpyBinaryFile
assert_equal(nbf.get_metadata(), metadata)
File "/«PKGBUILDDIR»/build/lib.linux-x86_64-2.7/pyNN/recording/files.py", line 216, in get_metadata
self.fileobj.seek(0)
ValueError: I/O operation on closed file

> FAIL: unittests.test_basepopulation.test_get_with_no_get_array
-
Traceback (most recent call last):
File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/«PKGBUILDDIR»/test/unittests/test_basepopulation.py", line 172, in test_get_with_no_get_array
assert_equal(values[0]._name, "i_offset")
AssertionError: <Mock name='mock.i_offset._name' id='32256336'> != 'i_offset'

-
Ran 294 tests in 0.529s

FAILED (SKIP=6, errors=1, failures=1)
make[1]: *** [override_dh_auto_test] Error 1

The full build log is available from:
http://people.debian.org/~lucas/logs/2012/08/14/pynn_0.7.2-1_wheezy.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.


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