/Users/milesseidel/nipype/nipype/workflows/dmri/mrtrix/group_connectivity.py:16: UserWarning: cmp not installed warnings.warn('cmp not installed') ......................................................................................................EEEEE.EEEE.EEEE.EE.......EE..EE...E................................................................................................EEEEEE....................................................EEE.E..........................................EE..../Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input scalar_file requires inputs: tract_stat warn(msg) .............................................................................................................................................E...........................................................E............EEEEE.................................................................................................................................................................EEEEEEEEEEEEEEEE........................................................................................................................................................................................EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE./Users/milesseidel/nipype/nipype/interfaces/fsl/preprocess.py:606: UserWarning: This interface has been renamed since 0.12.1, please use nipype.interfaces.fsl.ApplyXFM UserWarning) .EEEEEEEEEE.EE........................................................................................................................E....E........E.......................................................EEEEE................................/Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input slice_order requires inputs: time_interp warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input tr requires inputs: slice_times warn(msg) .....................E................................................................................................................................................................................................................................................................E...........................................................................................................................................................EE.....E.E........E.E.E.E.EEE.......E...................EEEEEEEE...............................................................E.....EException occurred in traits notification handler for object: bar = foo = 1 kung = , trait: bar, old value: , new value: 1 Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 519, in _dispatch_change_event self.dispatch( handler, *args ) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 482, in dispatch handler( *args ) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 417, in _xor_warn raise IOError(msg) OSError: Input "bar" is mutually exclusive with input "foo", which is already set .Exception occurred in traits notification handler for object: foo = 1 , trait: foo, old value: , new value: 1 Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 519, in _dispatch_change_event self.dispatch( handler, *args ) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 482, in dispatch handler( *args ) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 452, in _deprecated_warn raise TraitError(msg) traits.trait_errors.TraitError: Input foo in interface DeprecationSpec1 is deprecated. Will be removed or raise an error as of release 0.1 Exception occurred in traits notification handler for object: foo = 1 , trait: foo, old value: , new value: 1 Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 519, in _dispatch_change_event self.dispatch( handler, *args ) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/traits/trait_notifiers.py", line 482, in dispatch handler( *args ) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 446, in _deprecated_warn trait_spec.new_name) traits.trait_errors.TraitError: Input foo in interface DeprecationSpec2 is deprecated. Replacement trait bar not found .EEEEEE..E....EE..E.EE.E.EE.EE.EEE.FE.EEE......EEE.............EEEEEEEE.EEEEEEEEEEEE.EEEEEEEEEE..EEEEEEE....EEE.E..........E..E.EEEEEEEEEE..E...E..E............/Users/milesseidel/nipype/nipype/interfaces/fsl/preprocess.py:1587: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input icorr requires inputs: shift_in_file warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input encoding_direction requires inputs: readout_times warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input encoding_direction requires inputs: readout_times warn(msg) ..../Users/milesseidel/nipype/nipype/interfaces/fsl/preprocess.py:1587: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input icorr requires inputs: shift_in_file warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input encoding_direction requires inputs: readout_times warn(msg) .../Users/milesseidel/nipype/nipype/interfaces/fsl/preprocess.py:1587: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input icorr requires inputs: shift_in_file warn(msg) ../Users/milesseidel/nipype/nipype/interfaces/fsl/preprocess.py:1587: UserWarning: This has not been fully tested. Please report any failures. warn('This has not been fully tested. Please report any failures.') /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input icorr requires inputs: shift_in_file warn(msg) ../Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input icorr requires inputs: shift_in_file warn(msg) ...../Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input project_data requires inputs: threshold, distance_map, data_file warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input project_data requires inputs: threshold, distance_map, data_file warn(msg) ./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input project_data requires inputs: threshold, distance_map, data_file warn(msg) .EE..............E./Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input curv requires inputs: in_smoothwm warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input curv requires inputs: in_smoothwm warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input intensity_units requires inputs: in_intensity warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input intensity_units requires inputs: in_intensity warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) /Users/milesseidel/nipype/nipype/interfaces/base.py:431: UserWarning: Input th3 requires inputs: cortex_label warn(msg) ..../Users/milesseidel/nipype/nipype/testing/tests/test_utils.py:18: UserWarning: Cannot mount FAT filesystems with FUSE warnings.warn("Cannot mount FAT filesystems with FUSE") .... ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 210, in run self.setUp() File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 293, in setUp self.setupContext(ancestor) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 316, in setupContext try_run(context, names) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/util.py", line 471, in try_run return func() TypeError: setup_class() missing 2 required positional arguments: 'self' and 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_confounds.test_fd ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fd() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_confounds.test_dvars ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_dvars() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_confounds.test_outliers ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_outliers() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_errormap.test_errormap ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_errormap() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_mesh_ops.test_ident_distances ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_ident_distances() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_mesh_ops.test_trans_distances ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_trans_distances() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_mesh_ops.test_warppoints ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_warppoints() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_mesh_ops.test_meshwarpmaths ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_meshwarpmaths() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_misc.test_CreateNifti ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_CreateNifti() missing 1 required positional argument: 'create_analyze_pair_file_in_directory' ====================================================================== ERROR: nipype.algorithms.tests.test_modelgen.test_modelgen1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_modelgen1() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_modelgen.test_modelgen_spm_concat ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_modelgen_spm_concat() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_modelgen.test_modelgen_sparse ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_modelgen_sparse() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_normalize_tpms.test_normalize_tpms ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_normalize_tpms() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_overlap.test_overlap ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_overlap() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.algorithms.tests.test_splitmerge.test_split_and_merge ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_split_and_merge() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 210, in run self.setUp() File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 293, in setUp self.setupContext(ancestor) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 316, in setupContext try_run(context, names) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/util.py", line 471, in try_run return func() TypeError: setup_class() missing 2 required positional arguments: 'self' and 'tmpdir' ====================================================================== ERROR: nipype.caching.tests.test_memory.test_caching ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_caching() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Failure: ValueError (line 16 of the doctest for nipype.interfaces.afni.preprocess.DegreeCentrality has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 16 of the doctest for nipype.interfaces.afni.preprocess.DegreeCentrality has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 14 of the doctest for nipype.interfaces.afni.utils.Autobox has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 14 of the doctest for nipype.interfaces.afni.utils.Autobox has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 14 of the doctest for nipype.interfaces.ants.legacy.buildtemplateparallel has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 14 of the doctest for nipype.interfaces.ants.legacy.buildtemplateparallel has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 31 of the doctest for nipype.interfaces.ants.registration.Registration has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 31 of the doctest for nipype.interfaces.ants.registration.Registration has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.ants.resampling.WarpTimeSeriesImageMultiTransform has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.ants.resampling.WarpTimeSeriesImageMultiTransform has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.ants.segmentation.LaplacianThickness has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.ants.segmentation.LaplacianThickness has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 10 of the doctest for nipype.interfaces.ants.utils.MultiplyImages has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 10 of the doctest for nipype.interfaces.ants.utils.MultiplyImages has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.ants.visualization.ConvertScalarImageToRGB has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.ants.visualization.ConvertScalarImageToRGB has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.ants.tests.test_spec_JointFusion.test_JointFusion_modalities ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_JointFusion_modalities() missing 1 required positional argument: 'm' ====================================================================== ERROR: nipype.interfaces.ants.tests.test_spec_JointFusion.test_JointFusion_method ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_JointFusion_method() missing 2 required positional arguments: 'a' and 'b' ====================================================================== ERROR: nipype.interfaces.ants.tests.test_spec_JointFusion.test_JointFusion_radius ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_JointFusion_radius() missing 2 required positional arguments: 'attr' and 'x' ====================================================================== ERROR: Failure: ValueError (line 19 of the doctest for nipype.interfaces.base.InputMultiPath has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 19 of the doctest for nipype.interfaces.base.InputMultiPath has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 9 of the doctest for nipype.interfaces.bru2nii.Bru2 has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 9 of the doctest for nipype.interfaces.bru2nii.Bru2 has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.c3.C3dAffineTool has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.c3.C3dAffineTool has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 16 of the doctest for nipype.interfaces.dcm2nii.Dcm2niix has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 16 of the doctest for nipype.interfaces.dcm2nii.Dcm2niix has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 12 of the doctest for nipype.interfaces.elastix.registration.Registration has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 12 of the doctest for nipype.interfaces.elastix.registration.Registration has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.freesurfer.longitudinal.FuseSegmentations has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.freesurfer.longitudinal.FuseSegmentations has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.freesurfer.model.Label2Annot has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.freesurfer.model.Label2Annot has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.freesurfer.preprocess.CALabel has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.freesurfer.preprocess.CALabel has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 12 of the doctest for nipype.interfaces.freesurfer.registration.EMRegister has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 12 of the doctest for nipype.interfaces.freesurfer.registration.EMRegister has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 9 of the doctest for nipype.interfaces.freesurfer.utils.Sphere has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 9 of the doctest for nipype.interfaces.freesurfer.utils.Sphere has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_model.test_concatenate ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_concatenate() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_preprocess.test_robustregister ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_robustregister() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_preprocess.test_fitmsparams ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fitmsparams() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_preprocess.test_synthesizeflash ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_synthesizeflash() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_preprocess.test_mandatory_outvol ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mandatory_outvol() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_utils.test_sample2surf ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_sample2surf() missing 1 required positional argument: 'create_files_in_directory_plus_dummy_file' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_utils.test_surfsmooth ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_surfsmooth() missing 1 required positional argument: 'create_surf_file_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_utils.test_surfxfm ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_surfxfm() missing 1 required positional argument: 'create_surf_file_in_directory' ====================================================================== ERROR: nipype.interfaces.freesurfer.tests.test_utils.test_surfshots ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_surfshots() missing 1 required positional argument: 'create_files_in_directory_plus_dummy_file' ====================================================================== ERROR: Failure: ValueError (line 16 of the doctest for nipype.interfaces.fsl.dti.ProbTrackX2 has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 16 of the doctest for nipype.interfaces.fsl.dti.ProbTrackX2 has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 17 of the doctest for nipype.interfaces.fsl.epi.PrepareFieldmap has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 17 of the doctest for nipype.interfaces.fsl.epi.PrepareFieldmap has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.fsl.maths.MultiImageMaths has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.fsl.maths.MultiImageMaths has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.fsl.model.FLAMEO has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.fsl.model.FLAMEO has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 15 of the doctest for nipype.interfaces.fsl.possum.B0Calc has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 15 of the doctest for nipype.interfaces.fsl.possum.B0Calc has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 27 of the doctest for nipype.interfaces.fsl.preprocess.FUGUE has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 27 of the doctest for nipype.interfaces.fsl.preprocess.FUGUE has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.fsl.utils.Smooth has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.fsl.utils.Smooth has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_base.test_gen_fname ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_gen_fname() missing 2 required positional arguments: 'args' and 'desired_name' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_dtifit2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_dtifit2() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_randomise2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/fsl/tests/test_dti.py", line 47, in test_randomise2 rand = fsl.Randomise() AttributeError: module 'nipype.interfaces.fsl.dti' has no attribute 'Randomise' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_Randomise_parallel ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/fsl/tests/test_dti.py", line 123, in test_Randomise_parallel rand = fsl.Randomise_parallel() AttributeError: module 'nipype.interfaces.fsl.dti' has no attribute 'Randomise_parallel' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_Proj_thresh ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/fsl/tests/test_dti.py", line 214, in test_Proj_thresh proj.inputs.volumes = ['vol1', 'vol2', 'vol3'] traits.trait_errors.TraitError: Cannot set the undefined 'volumes' attribute of a 'ProjThreshInputSpec' object. ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_Vec_reg ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/fsl/tests/test_dti.py", line 247, in test_Vec_reg vrg.inputs.infile = 'infile' traits.trait_errors.TraitError: Cannot set the undefined 'infile' attribute of a 'VecRegInputSpec' object. ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_Find_the_biggest ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/fsl/tests/test_dti.py", line 308, in test_Find_the_biggest fbg.inputs.infiles = 'seed*' traits.trait_errors.TraitError: Cannot set the undefined 'infiles' attribute of a 'FindTheBiggestInputSpec' object. ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_tbss_skeleton ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_tbss_skeleton() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_dti.test_distancemap ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_distancemap() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_epi.test_eddy_correct2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_eddy_correct2() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_maths_base ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_maths_base() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_changedt ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_changedt() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_threshold ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_threshold() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_meanimage ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_meanimage() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_stdimage ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_stdimage() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_maximage ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_maximage() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_smooth ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_smooth() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_mask ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mask() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_dilation ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_dilation() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_erosion ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_erosion() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_spatial_filter ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_spatial_filter() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_unarymaths ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_unarymaths() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_binarymaths ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_binarymaths() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_multimaths ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_multimaths() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_maths.test_tempfilt ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_tempfilt() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_model.test_MultipleRegressDesign ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_MultipleRegressDesign() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_bet ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_bet() missing 1 required positional argument: 'setup_infile' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_fast ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fast() missing 1 required positional argument: 'setup_infile' ====================================================================== ERROR: By default (no -o), FSL's fast command outputs files into the same ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fast_list_outputs() missing 1 required positional argument: 'setup_infile' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_flirt ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_flirt() missing 1 required positional argument: 'setup_flirt' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_mcflirt ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mcflirt() missing 1 required positional argument: 'setup_flirt' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_fnirt ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fnirt() missing 1 required positional argument: 'setup_flirt' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_applywarp ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_applywarp() missing 1 required positional argument: 'setup_flirt' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_preprocess.test_fugue ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fugue() missing 3 required positional arguments: 'setup_fugue', 'attr', and 'out_file' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_fslroi ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fslroi() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_fslmerge ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fslmerge() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_fslmaths ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_fslmaths() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_overlay ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_overlay() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_slicer ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_slicer() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_plottimeseries ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_plottimeseries() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_plotmotionparams ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_plotmotionparams() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_convertxfm ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_convertxfm() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: nipype.interfaces.fsl.tests.test_utils.test_swapdims ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_swapdims() missing 1 required positional argument: 'create_files_in_directory_plus_output_type' ====================================================================== ERROR: Failure: ValueError (line 20 of the doctest for nipype.interfaces.io.SelectFiles has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 20 of the doctest for nipype.interfaces.io.SelectFiles has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 27 of the doctest for nipype.interfaces.meshfix.MeshFix has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 27 of the doctest for nipype.interfaces.meshfix.MeshFix has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.minc.base.aggregate_filename has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.minc.base.aggregate_filename has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 10 of the doctest for nipype.interfaces.mne.base.WatershedBEM has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 10 of the doctest for nipype.interfaces.mne.base.WatershedBEM has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.mrtrix.preprocess.DWI2Tensor has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.mrtrix.preprocess.DWI2Tensor has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 16 of the doctest for nipype.interfaces.mrtrix.tracking.StreamlineTrack has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 16 of the doctest for nipype.interfaces.mrtrix.tracking.StreamlineTrack has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 11 of the doctest for nipype.interfaces.mrtrix3.connectivity.LabelConfig has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 11 of the doctest for nipype.interfaces.mrtrix3.connectivity.LabelConfig has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.mrtrix3.preprocess.ReplaceFSwithFIRST has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.mrtrix3.preprocess.ReplaceFSwithFIRST has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 13 of the doctest for nipype.interfaces.mrtrix3.reconst.FitTensor has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 13 of the doctest for nipype.interfaces.mrtrix3.reconst.FitTensor has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 40 of the doctest for nipype.interfaces.mrtrix3.tracking.Tractography has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 40 of the doctest for nipype.interfaces.mrtrix3.tracking.Tractography has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Failure: ValueError (line 49 of the doctest for nipype.interfaces.mrtrix3.utils.ComputeTDI has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 49 of the doctest for nipype.interfaces.mrtrix3.utils.ComputeTDI has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: Test that the coherence analyzer works ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/nitime/tests/test_nitime.py", line 35, in test_coherence_analysis import nitime.analysis as nta ImportError: No module named 'nitime' ====================================================================== ERROR: Failure: ValueError (line 4 of the doctest for nipype.interfaces.slicer.generate_classes.force_to_valid_python_variable_name has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 4 of the doctest for nipype.interfaces.slicer.generate_classes.force_to_valid_python_variable_name has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_base.test_scan_for_fnames ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_scan_for_fnames() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_base.test_spm_path ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/spm/tests/test_base.py", line 38, in test_spm_path spm_path = spm.Info.version()['path'] TypeError: 'NoneType' object is not subscriptable ====================================================================== ERROR: nipype.interfaces.spm.tests.test_base.test_generate_job ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_generate_job() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_base.test_make_matlab_command ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_make_matlab_command() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_slicetiming_list_outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_slicetiming_list_outputs() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_realign_list_outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_realign_list_outputs() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_coregister_list_outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_coregister_list_outputs() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_normalize_list_outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_normalize_list_outputs() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_normalize12_list_outputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_normalize12_list_outputs() missing 1 required positional argument: 'create_files_in_directory' ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_segment ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/spm/tests/test_preprocess.py", line 91, in test_segment if spm.Info.version()['name'] == "SPM12": TypeError: 'NoneType' object is not subscriptable ====================================================================== ERROR: nipype.interfaces.spm.tests.test_preprocess.test_newsegment ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/spm/tests/test_preprocess.py", line 101, in test_newsegment if spm.Info.version()['name'] == "SPM12": TypeError: 'NoneType' object is not subscriptable ====================================================================== ERROR: Failure: ValueError (line 17 of the doctest for nipype.interfaces.utility.base.IdentityInterface has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 17 of the doctest for nipype.interfaces.utility.base.IdentityInterface has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_base.test_rename ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_rename() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_base.test_split ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_split() missing 3 required positional arguments: 'tmpdir', 'args', and 'expected' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_csv.test_csvReader ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_csvReader() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_wrappers.test_function ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_function() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_wrappers.test_should_fail ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_should_fail() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.utility.tests.test_wrappers.test_function_with_imports ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_function_with_imports() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: This tests excution nodes with multiple inputs and auxiliary ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_aux_connect_function() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Failure: ValueError (line 9 of the doctest for nipype.interfaces.vista.vista.VtoMat has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 9 of the doctest for nipype.interfaces.vista.vista.VtoMat has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_bunch ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_bunch() missing 1 required positional argument: 'args' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_TraitedSpec_dynamic ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/tests/test_base.py", line 109, in test_TraitedSpec_dynamic with pytest.raises(Exception): assign_a File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/_pytest/python.py", line 1234, in __exit__ pytest.fail(self.message) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/_pytest/runner.py", line 542, in fail raise Failed(msg=msg, pytrace=pytrace) Failed: DID NOT RAISE ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_namesource ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_namesource() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_chained_namesource ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_chained_namesource() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_cycle_namesource1 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_cycle_namesource1() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_cycle_namesource2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_cycle_namesource2() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_TraitedSpec_withFile ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_TraitedSpec_withFile() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_TraitedSpec_withNoFileHashing ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_TraitedSpec_withNoFileHashing() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_BaseInterface_load_save_inputs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_BaseInterface_load_save_inputs() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_CommandLine_output ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_CommandLine_output() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_base.test_global_CommandLine_output ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_global_CommandLine_output() missing 1 required positional argument: 'setup_file' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_selectfiles ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_selectfiles() missing 3 required positional arguments: 'SF_args', 'inputs_att', and 'expected' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_s3datagrabber_communication ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_s3datagrabber_communication() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_datagrabber_order ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datagrabber_order() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: This function tests to see if the S3 functionality of a DataSink ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datasink_to_s3() missing 2 required positional arguments: 'dummy_input' and 'tmpdir' ====================================================================== ERROR: Function to validate DataSink will make local copy via local_copy ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datasink_localcopy() missing 2 required positional arguments: 'dummy_input' and 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_datasink_substitutions ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datasink_substitutions() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_datafinder_depth ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datafinder_depth() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_datafinder_unpack ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_datafinder_unpack() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_jsonsink_input ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_jsonsink_input() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.interfaces.tests.test_io.test_jsonsink ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_jsonsink() missing 2 required positional arguments: 'tmpdir' and 'inputs_attributes' ====================================================================== ERROR: nipype.interfaces.tests.test_matlab.test_cmdline ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/tests/test_matlab.py", line 33, in test_cmdline matlab_cmd + (' -nodesktop -nosplash -singleCompThread -r "fprintf(1,' TypeError: unsupported operand type(s) for +: 'NoneType' and 'str' ====================================================================== ERROR: nipype.interfaces.tests.test_matlab.test_run_interface ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/tests/test_matlab.py", line 100, in test_run_interface mc.run() File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1085, in run runtime = self._run_wrapper(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1728, in _run_wrapper runtime = self._run_interface(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/matlab.py", line 144, in _run_interface runtime = super(MatlabCommand, self)._run_interface(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1754, in _run_interface (self.cmd.split()[0], runtime.hostname)) OSError: command '/bin//MATLAB' could not be found on host d-i89-201-120.student.eduroam.uq.edu.au Interface MatlabCommand failed to run. ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 210, in run self.setUp() File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 293, in setUp self.setupContext(ancestor) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 316, in setupContext try_run(context, names) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/util.py", line 471, in try_run return func() TypeError: setup_class() missing 1 required positional argument: 'self' ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 210, in run self.setUp() File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 293, in setUp self.setupContext(ancestor) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 316, in setupContext try_run(context, names) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/util.py", line 471, in try_run return func() TypeError: setup_class() missing 1 required positional argument: 'self' ====================================================================== ERROR: Failure: ValueError (line 16 of the doctest for nipype.pipeline.engine.nodes.JoinNode._add_join_item_fields has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1021, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 16 of the doctest for nipype.pipeline.engine.nodes.JoinNode._add_join_item_fields has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_1mod ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_1mod() missing 2 required positional arguments: 'iterables' and 'expected' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_2mods ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_2mods() missing 2 required positional arguments: 'iterables' and 'expected' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_3mods ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_3mods() missing 3 required positional arguments: 'iterables', 'expected', and 'connect' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_mapnode_nested ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mapnode_nested() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_node_hash ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_node_hash() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_old_config ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_old_config() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Tests that mapnodes don't generate excess jsons ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mapnode_json() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_parameterize_dirs_false ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_parameterize_dirs_false() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_serial_input ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_serial_input() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_write_graph_runs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_write_graph_runs() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_engine.test_deep_nested_write_graph_runs ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_deep_nested_write_graph_runs() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_join.test_join_expansion ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_join_expansion() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test setting the joinsource to a Node. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_node_joinsource() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test collecting join inputs to a set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_set_join_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test join with the ``unique`` flag set to True. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_unique_join_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test two join nodes, one downstream of the other. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_multiple_join_nodes() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test an IdentityInterface join. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_identity_join_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test join on several fields. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_multifield_join_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test join on an input node which has the ``synchronize`` flag set to True. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_synchronize_join_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test join on an input node which has an ``itersource``. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_itersource_join_source_node() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test join with a midstream ``itersource`` and an upstream ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_itersource_two_join_nodes() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test collecting join inputs to a set. ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_set_join_node_file_input() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test collecting join inputs within a nested workflow ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_nested_workflow_join() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_clean_working_directory ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_clean_working_directory() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_outputs_removal ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_outputs_removal() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_inputs_removal ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_inputs_removal() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_outputs_removal_wf ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_outputs_removal_wf() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_multi_disconnected_iterable ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_multi_disconnected_iterable() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.engine.tests.test_utils.test_provenance ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_provenance() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test mapnode crash when stop_on_first_crash is True ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mapnode_crash() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test mapnode crash when stop_on_first_crash is False ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mapnode_crash2() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Test mapnode crash when mapnode is embedded in a workflow ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_mapnode_crash3() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Failure: ValueError (line 5 of the doctest for nipype.pipeline.plugins.sge.qsub_sanitize_job_name has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 5 of the doctest for nipype.pipeline.plugins.sge.qsub_sanitize_job_name has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_callback.test_callback_normal ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_callback_normal() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_callback.test_callback_exception ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_callback_exception() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_callback.test_callback_multiproc_normal ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_callback_multiproc_normal() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_callback.test_callback_multiproc_exception ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_callback_multiproc_exception() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_debug.test_debug ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_debug() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_linear.test_run_in_series ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_run_in_series() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_multiproc.test_run_multiproc ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_run_multiproc() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_oar.test_run_oar ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/tests/test_oar.py", line 48, in test_run_oar execgraph = pipe.run(plugin="OAR") File "/Users/milesseidel/nipype/nipype/pipeline/engine/workflows.py", line 583, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/base.py", line 267, in run graph=graph) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/base.py", line 416, in _send_procs_to_workers updatehash=updatehash) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/base.py", line 578, in _submit_job return self._submit_batchtask(batchscriptfile, node) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/oar.py", line 132, in _submit_batchtask str(e)))) RuntimeError: Could not submit OAR task for node mod1 command 'oarsub' could not be found on host d-i89-201-120.student.eduroam.uq.edu.au Interface CommandLine failed to run. -------------------- >> begin captured logging << -------------------- workflow: INFO: Workflow pipe settings: ['check', 'execution', 'logging'] workflow: INFO: Running in parallel. workflow: INFO: Pending[0] Submitting[1] jobs Slots[inf] workflow: INFO: Submitting: mod1 ID: 0 --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_pbs.test_run_pbsgraph ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/tests/test_pbs.py", line 49, in test_run_pbsgraph execgraph = pipe.run(plugin="PBSGraph") File "/Users/milesseidel/nipype/nipype/pipeline/engine/workflows.py", line 583, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/base.py", line 614, in run self._submit_graph(pyfiles, dependencies, nodes) File "/Users/milesseidel/nipype/nipype/pipeline/plugins/pbsgraph.py", line 60, in _submit_graph cmd.run() File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1085, in run runtime = self._run_wrapper(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1728, in _run_wrapper runtime = self._run_interface(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1762, in _run_interface self.raise_exception(runtime) File "/Users/milesseidel/nipype/nipype/interfaces/base.py", line 1686, in raise_exception **runtime.dictcopy())) RuntimeError: Command: sh /private/var/folders/1t/9xvrbc6d2bd5v9f7rgn2yrwr0000gp/T/test_engine_ypaapyxp/pipe/batch/submit_jobs.sh Standard output: Standard error: /private/var/folders/1t/9xvrbc6d2bd5v9f7rgn2yrwr0000gp/T/test_engine_ypaapyxp/pipe/batch/submit_jobs.sh: line 2: qsub: command not found /private/var/folders/1t/9xvrbc6d2bd5v9f7rgn2yrwr0000gp/T/test_engine_ypaapyxp/pipe/batch/submit_jobs.sh: line 3: qsub: command not found Return code: 127 Interface CommandLine failed to run. -------------------- >> begin captured logging << -------------------- workflow: INFO: Workflow pipe settings: ['check', 'execution', 'logging'] --------------------- >> end captured logging << --------------------- ====================================================================== ERROR: nipype.pipeline.plugins.tests.test_somaflow.test_run_somaflow ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_run_somaflow() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: Failure: ValueError (line 21 of the doctest for nipype.utils.filemanip.split_filename has an invalid option: '+ALLOW_UNICODE') ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/manager.py", line 154, in generate for r in result: File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/plugins/doctests.py", line 228, in loadTestsFromModule tests = self.finder.find(module) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 924, in find self._find(tests, obj, name, module, source_lines, globs, {}) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 987, in _find globs, seen) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 974, in _find test = self._get_test(obj, name, module, globs, source_lines) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 1058, in _get_test filename, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 660, in get_doctest return DocTest(self.get_examples(string, name), globs, File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 674, in get_examples return [x for x in self.parse(string, name) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 636, in parse self._parse_example(m, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 717, in _parse_example options = self._find_options(source, name, lineno) File "/Users/milesseidel/anaconda/lib/python3.5/doctest.py", line 748, in _find_options (lineno+1, name, option)) ValueError: line 21 of the doctest for nipype.utils.filemanip.split_filename has an invalid option: '+ALLOW_UNICODE' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_split_filename ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_split_filename() missing 2 required positional arguments: 'filename' and 'split' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_hash_rename ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_hash_rename() missing 2 required positional arguments: 'filename' and 'newname' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_copyfile ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_copyfile() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_copyfile_true ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_copyfile_true() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_copyfiles ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_copyfiles() missing 2 required positional arguments: '_temp_analyze_files' and '_temp_analyze_files_prime' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_linkchain ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_linkchain() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_recopy ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_recopy() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_copyfallback ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_copyfallback() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_get_related_files ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_get_related_files() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_get_related_files_noninclusive ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_get_related_files_noninclusive() missing 1 required positional argument: '_temp_analyze_files' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_filename_to_list ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_filename_to_list() missing 2 required positional arguments: 'filename' and 'expected' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_list_to_filename ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_list_to_filename() missing 2 required positional arguments: 'list' and 'expected' ====================================================================== ERROR: nipype.utils.tests.test_filemanip.test_related_files ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_related_files() missing 3 required positional arguments: 'file', 'length', and 'expected_files' ====================================================================== ERROR: nipype.utils.tests.test_misc.test_str2bool ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_str2bool() missing 2 required positional arguments: 'string' and 'expected' ====================================================================== ERROR: nipype.utils.tests.test_provenance.test_provenance_exists ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) TypeError: test_provenance_exists() missing 1 required positional argument: 'tmpdir' ====================================================================== ERROR: nipype.workflows.dmri.fsl.tests.test_dti.test_create_bedpostx_pipeline ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/workflows/dmri/fsl/tests/test_dti.py", line 21, in test_create_bedpostx_pipeline fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA']) File "/Users/milesseidel/anaconda/lib/python3.5/os.py", line 725, in __getitem__ raise KeyError(key) from None KeyError: 'FSL_COURSE_DATA' ====================================================================== ERROR: nipype.workflows.dmri.fsl.tests.test_epi.test_create_eddy_correct_pipeline ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/workflows/dmri/fsl/tests/test_epi.py", line 20, in test_create_eddy_correct_pipeline fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA']) File "/Users/milesseidel/anaconda/lib/python3.5/os.py", line 725, in __getitem__ raise KeyError(key) from None KeyError: 'FSL_COURSE_DATA' ====================================================================== ERROR: test suite for ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 210, in run self.setUp() File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 293, in setUp self.setupContext(ancestor) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/suite.py", line 316, in setupContext try_run(context, names) File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/util.py", line 471, in try_run return func() TypeError: setup_class() missing 2 required positional arguments: 'self' and 'tmpdir' ====================================================================== FAIL: nipype.interfaces.tests.test_matlab.test_mlab_init ---------------------------------------------------------------------- Traceback (most recent call last): File "/Users/milesseidel/anaconda/lib/python3.5/site-packages/nose/case.py", line 198, in runTest self.test(*self.arg) File "/Users/milesseidel/nipype/nipype/interfaces/tests/test_matlab.py", line 67, in test_mlab_init assert mlab.MatlabCommand().cmd == matlab_cmd AssertionError ---------------------------------------------------------------------- Ran 1973 tests in 37.397s FAILED (errors=219, failures=1) [?1034h