Package: src:dcmstack Version: 0.9-3 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202605/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:dcmstack, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3,sphinxdoc --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild pybuild --clean -i python{version} -p "3.14 3.13" --parallel=2 I: pybuild base:385: python3.14 setup.py clean /usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' warnings.warn(msg) /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License [... snipped ...] test/test_cli.py:56: AssertionError ----------------------------- Captured stdout call ----------------------------- No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw __________________________ TestDcmstackCli.test_embed __________________________ self = <test.test_cli.TestDcmstackCli object at 0x7fe50b1b34d0> def test_embed(self): nii_paths = make_niftis(self.out_dir, ['--embed']) > assert len(nii_paths) == 1 E assert 0 == 1 E + where 0 = len([]) test/test_cli.py:60: AssertionError ----------------------------- Captured stdout call ----------------------------- No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw ___________________________ TestNitoolCli.test_basic ___________________________ self = <test.test_cli.TestNitoolCli object at 0x7fe50b1b3610> def test_basic(self): > nii_path = make_niftis(self.out_dir, ['--embed'])[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E IndexError: list index out of range test/test_cli.py:65: IndexError ----------------------------- Captured stdout call ----------------------------- No DICOM files found in /tmp/dcmstack_cli_test_innmxkt4dw _______________________________ test_from_dicom ________________________________ def test_from_dicom(): data_dir = path.join(test_dir, 'data', 'dcmstack', '2D_16Echo_qT2') src_fn = path.join(data_dir, 'TE_40_SlcPos_-33.707626341697.dcm') > src_dcm = pydicom.read_file(src_fn) ^^^^^^^^^^^^^^^^^ E AttributeError: module 'pydicom' has no attribute 'read_file' test/test_dcmmeta.py:1042: AttributeError _____________________________ test_image_collision _____________________________ def test_image_collision(): dcm_path = path.join(test_dir, 'data', 'dcmstack', '2D_16Echo_qT2', 'TE_20_SlcPos_-33.707626341697.dcm') > dcm = pydicom.read_file(dcm_path) ^^^^^^^^^^^^^^^^^ E AttributeError: module 'pydicom' has no attribute 'read_file' test/test_dcmstack.py:212: AttributeError ________________________ TestParseAndGroup.test_default ________________________ self = <test.test_dcmstack.TestParseAndGroup object at 0x7fe50b07a5d0> def test_default(self): > res = dcmstack.parse_and_group(self.in_paths) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/test_dcmstack.py:640: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src_paths = ['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_20_Slc...dcmstack-0.9/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_40_SlcPos_-23.207628249046.dcm'] group_by = ('SeriesInstanceUID', 'SeriesNumber', 'ProtocolName', 'ImageOrientationPatient') extractor = <dcmstack.extract.MetaExtractor object at 0x7fe50b176ba0> force = False, warn_on_except = False close_tests = ('ImageOrientationPatient',) def parse_and_group(src_paths, group_by=default_group_keys, extractor=None, force=False, warn_on_except=False, close_tests=default_close_keys): '''Parse the given dicom files and group them together. Each group is stored as a (list) value in a dict where the key is a tuple of values corresponding to the keys in 'group_by' Parameters ---------- src_paths : sequence A list of paths to the source DICOM files. group_by : tuple Meta data keys to group data sets with. Any data set with the same values for these keys will be grouped together. This tuple of values will also be the key in the result dictionary. extractor : callable Should take a pydicom.dataset.Dataset and return a dictionary of the extracted meta data. force : bool Force reading source files even if they do not appear to be DICOM. warn_on_except : bool Convert exceptions into warnings, possibly allowing some results to be returned. close_tests : sequence Any `group_by` key listed here is tested with `numpy.allclose` instead of straight equality when determining group membership. Returns ------- groups : dict A dict mapping tuples of values (corresponding to 'group_by') to groups of data sets. Each element in the list is a tuple containing the dicom object, the parsed meta data, and the filename. ''' if extractor is None: from .extract import default_extractor extractor = default_extractor results = {} close_elems = {} for dcm_path in src_paths: #Read the DICOM file try: > dcm = pydicom.read_file(dcm_path, force=force) ^^^^^^^^^^^^^^^^^ E AttributeError: module 'pydicom' has no attribute 'read_file' dcmstack/dcmstack.py:1046: AttributeError ________________________ TestParseAndStack.test_default ________________________ self = <test.test_dcmstack.TestParseAndStack object at 0x7fe50b07a710> def test_default(self): > res = dcmstack.parse_and_stack(self.in_paths) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ test/test_dcmstack.py:666: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ dcmstack/dcmstack.py:1156: in parse_and_stack results = parse_and_group(src_paths, _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ src_paths = ['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_20_Slc...dcmstack-0.9/.pybuild/cpython3_3.13_dcmstack/build/test/data/dcmstack/2D_16Echo_qT2/TE_40_SlcPos_-23.207628249046.dcm'] group_by = ('SeriesInstanceUID', 'SeriesNumber', 'ProtocolName', 'ImageOrientationPatient') extractor = <dcmstack.extract.MetaExtractor object at 0x7fe50b176ba0> force = False, warn_on_except = False close_tests = ('ImageOrientationPatient',) def parse_and_group(src_paths, group_by=default_group_keys, extractor=None, force=False, warn_on_except=False, close_tests=default_close_keys): '''Parse the given dicom files and group them together. Each group is stored as a (list) value in a dict where the key is a tuple of values corresponding to the keys in 'group_by' Parameters ---------- src_paths : sequence A list of paths to the source DICOM files. group_by : tuple Meta data keys to group data sets with. Any data set with the same values for these keys will be grouped together. This tuple of values will also be the key in the result dictionary. extractor : callable Should take a pydicom.dataset.Dataset and return a dictionary of the extracted meta data. force : bool Force reading source files even if they do not appear to be DICOM. warn_on_except : bool Convert exceptions into warnings, possibly allowing some results to be returned. close_tests : sequence Any `group_by` key listed here is tested with `numpy.allclose` instead of straight equality when determining group membership. Returns ------- groups : dict A dict mapping tuples of values (corresponding to 'group_by') to groups of data sets. Each element in the list is a tuple containing the dicom object, the parsed meta data, and the filename. ''' if extractor is None: from .extract import default_extractor extractor = default_extractor results = {} close_elems = {} for dcm_path in src_paths: #Read the DICOM file try: > dcm = pydicom.read_file(dcm_path, force=force) ^^^^^^^^^^^^^^^^^ E AttributeError: module 'pydicom' has no attribute 'read_file' dcmstack/dcmstack.py:1046: AttributeError =============================== warnings summary =============================== .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049: UserWarning: Error reading file /tmp/dcmstack_cli_test_innmxkt4dw/TE_20_SlcPos_-23.207628249046.dcm: module 'pydicom' has no attribute 'read_file' warnings.warn('Error reading file %s: %s' % (dcm_path, str(e))) .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049: UserWarning: Error reading file /tmp/dcmstack_cli_test_innmxkt4dw/TE_20_SlcPos_-33.707626341697.dcm: module 'pydicom' has no attribute 'read_file' warnings.warn('Error reading file %s: %s' % (dcm_path, str(e))) .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049: UserWarning: Error reading file /tmp/dcmstack_cli_test_innmxkt4dw/TE_40_SlcPos_-33.707626341697.dcm: module 'pydicom' has no attribute 'read_file' warnings.warn('Error reading file %s: %s' % (dcm_path, str(e))) .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_basic .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestDcmstackCli::test_embed .pybuild/cpython3_3.13_dcmstack/build/test/test_cli.py::TestNitoolCli::test_basic /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build/dcmstack/dcmstack.py:1049: UserWarning: Error reading file /tmp/dcmstack_cli_test_innmxkt4dw/TE_40_SlcPos_-23.207628249046.dcm: module 'pydicom' has no attribute 'read_file' warnings.warn('Error reading file %s: %s' % (dcm_path, str(e))) .pybuild/cpython3_3.13_dcmstack/build/test/test_dcmstack.py::test_fsl_hack .pybuild/cpython3_3.13_dcmstack/build/test/test_dcmstack.py::test_pix_overflow /usr/lib/python3/dist-packages/pydicom/dataset.py:1378: DeprecationWarning: 'Dataset.is_little_endian' will be removed in v4.0, set the Transfer Syntax UID or use the 'little_endian' argument with Dataset.save_as() or dcmwrite() instead warn_and_log( -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED test/test_cli.py::TestDcmstackCli::test_basic - assert 0 == 1 FAILED test/test_cli.py::TestDcmstackCli::test_embed - assert 0 == 1 FAILED test/test_cli.py::TestNitoolCli::test_basic - IndexError: list index o... FAILED test/test_dcmmeta.py::test_from_dicom - AttributeError: module 'pydico... FAILED test/test_dcmstack.py::test_image_collision - AttributeError: module '... FAILED test/test_dcmstack.py::TestParseAndGroup::test_default - AttributeErro... FAILED test/test_dcmstack.py::TestParseAndStack::test_default - AttributeErro... ERROR test/test_dcmstack.py::TestIncongruentImage::test_rows - AttributeError... ERROR test/test_dcmstack.py::TestIncongruentImage::test_columns - AttributeEr... ERROR test/test_dcmstack.py::TestIncongruentImage::test_pix_space - Attribute... ERROR test/test_dcmstack.py::TestIncongruentImage::test_close_pix_space - Att... ERROR test/test_dcmstack.py::TestIncongruentImage::test_orientation - Attribu... ERROR test/test_dcmstack.py::TestIncongruentImage::test_close_orientation - A... ERROR test/test_dcmstack.py::TestInvalidStack::test_empty - AttributeError: m... ERROR test/test_dcmstack.py::TestInvalidStack::test_missing_slice - Attribute... ERROR test/test_dcmstack.py::TestInvalidStack::test_wrong_number_of_files - A... ERROR test/test_dcmstack.py::TestInvalidStack::test_vector_var_over_vol - Att... ERROR test/test_dcmstack.py::TestGetShape::test_single_slice - AttributeError... ERROR test/test_dcmstack.py::TestGetShape::test_three_dim - AttributeError: m... ERROR test/test_dcmstack.py::TestGetShape::test_four_dim - AttributeError: mo... ERROR test/test_dcmstack.py::TestGetShape::test_five_dim - AttributeError: mo... ERROR test/test_dcmstack.py::TestGuessDim::test_single_guess - AttributeError... ERROR test/test_dcmstack.py::TestGuessDim::test_wrong_guess_first - Attribute... ERROR test/test_dcmstack.py::TestGetData::test_single_slice - AttributeError:... ERROR test/test_dcmstack.py::TestGetData::test_three_dim - AttributeError: mo... ERROR test/test_dcmstack.py::TestGetData::test_four_dim - AttributeError: mod... ERROR test/test_dcmstack.py::TestGetData::test_five_dim - AttributeError: mod... ERROR test/test_dcmstack.py::TestGetAffine::test_single_slice - AttributeErro... ERROR test/test_dcmstack.py::TestGetAffine::test_three_dim - AttributeError: ... ERROR test/test_dcmstack.py::TestToNifti::test_single_slice - AttributeError:... ERROR test/test_dcmstack.py::TestToNifti::test_single_vol - AttributeError: m... ERROR test/test_dcmstack.py::TestToNifti::test_slice_dim_reorient - Attribute... ERROR test/test_dcmstack.py::TestToNifti::test_two_time_vol - AttributeError:... ERROR test/test_dcmstack.py::TestToNifti::test_two_vector_vol - AttributeErro... ERROR test/test_extract.py::TestCsa::test_simplify - AttributeError: module '... ERROR test/test_extract.py::TestCsa::test_csa_image_trans - AttributeError: m... ERROR test/test_extract.py::TestCsa::test_parse_phx_line - AttributeError: mo... ERROR test/test_extract.py::TestCsa::test_csa_series_trans - AttributeError: ... ERROR test/test_extract.py::TestMetaExtractor::test_get_elem_key - AttributeE... ERROR test/test_extract.py::TestMetaExtractor::test_get_elem_value - Attribut... ERROR test/test_extract.py::TestMetaExtractor::test_dup_trans - AttributeErro... ERROR test/test_extract.py::TestMetaExtractor::test_reloc_private - Attribute... ERROR test/test_extract.py::TestMetaExtractor::test_non_reloc_private - Attri... ============= 7 failed, 88 passed, 14 warnings, 36 errors in 0.70s ============= E: pybuild pybuild:485: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_dcmstack/build; python3.13 -m pytest test rm -fr -- /tmp/dh-xdg-rundir-iH1DLbmb dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" --parallel=2 returned exit code 13 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
