Source: ont-fast5-api Version: 4.1.1+dfsg-5 Severity: serious Tags: ftbfs Justification: FTBFS
Dear maintainer, During a test rebuild, ont-fast5-api failed to rebuild. ------------------------------------------------------------------------------- [...] test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ... ERROR ====================================================================== ERROR: test_001_put_and_retrieve (test.test_alignment_tools.TestAlignmentTools.test_001_put_and_retrieve) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_alignment_tools.py", line 77, in test_001_put_and_retrieve align.add_alignment_data('template', sam1, sequence1) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/analysis_tools/alignment.py", line 131, in add_alignment_data self.handle.add_analysis_dataset('{}/{}'.format(self.group_name, subgroup), 'SAM', sam_arr) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/fast5_read.py", line 485, in add_analysis_dataset sanitized_data = _sanitize_data_for_writing(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test_001_put_and_retrieve (test.test_basecall_1d_tools.TestBasecall1DTools.test_001_put_and_retrieve) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_basecall_1d_tools.py", line 40, in test_001_put_and_retrieve basecall.add_event_data('template', data1) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/analysis_tools/basecall_1d.py", line 34, in add_event_data self.handle.add_analysis_dataset('{}/{}'.format(self.group_name, event_group), 'Events', data) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/fast5_read.py", line 485, in add_analysis_dataset sanitized_data = _sanitize_data_for_writing(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test_001_put_and_retrieve (test.test_basecall_2d_tools.TestBasecall2DTools.test_001_put_and_retrieve) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_basecall_2d_tools.py", line 33, in test_001_put_and_retrieve basecall.add_prior_alignment(data1) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/analysis_tools/basecall_2d.py", line 42, in add_prior_alignment self.handle.add_analysis_dataset(path, 'Alignment', data) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/fast5_read.py", line 485, in add_analysis_dataset sanitized_data = _sanitize_data_for_writing(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test__sanitize_data (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_data_sanitisation.py", line 44, in test__sanitize_data _sanitize_data_for_writing(test_array)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test__sanitize_data_emptystrings (test.test_data_sanitisation.TestDataSanitisation.test__sanitize_data_emptystrings) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_data_sanitisation.py", line 64, in test__sanitize_data_emptystrings byte_array = _sanitize_data_for_writing(test_ndarray_utf8) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test_sanitise_array_empty_string (test.test_data_sanitisation.TestDataSanitisation.test_sanitise_array_empty_string) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_data_sanitisation.py", line 72, in test_sanitise_array_empty_string output_array = _sanitize_data_for_writing(input_array) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test_002_write_events (test.test_event_detection_tools.TestEventDetectionTools.test_002_write_events) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_event_detection_tools.py", line 38, in test_002_write_events evdet.set_event_data(data, read_attrs) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/analysis_tools/event_detection.py", line 50, in set_event_data self.handle.add_analysis_dataset(read_group, 'Events', data) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/fast5_read.py", line 485, in add_analysis_dataset sanitized_data = _sanitize_data_for_writing(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ====================================================================== ERROR: test_002_events_only (test.test_segmentation_tools.TestSegmentationTools.test_002_events_only) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/test/test_segmentation_tools.py", line 72, in test_002_events_only evdet.set_event_data(data, read_attrs) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/analysis_tools/event_detection.py", line 50, in set_event_data self.handle.add_analysis_dataset(read_group, 'Events', data) File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/fast5_read.py", line 485, in add_analysis_dataset sanitized_data = _sanitize_data_for_writing(data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/build/reproducible-path/ont-fast5-api-4.1.1+dfsg/.pybuild/cpython3_3.12_ont_fast5_api/build/ont_fast5_api/data_sanitisation.py", line 31, in _sanitize_data_for_writing elif isinstance(data, np.ndarray) and data.dtype.kind == np.dtype(np.unicode_): ^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 400, in __getattr__ raise AttributeError( AttributeError: `np.unicode_` was removed in the NumPy 2.0 release. Use `np.str_` instead. ---------------------------------------------------------------------- Ran 76 tests in 1.753s FAILED (errors=8, skipped=5) [...] ------------------------------------------------------------------------------- The above is just how the build ends and not necessarily the most relevant part. If required, the full build log is available here (for the next 30 days): https://debusine.debian.net/artifact/1242083/ About the archive rebuild: The build was made on debusine.debian.net, on arm64 using sbuild. You can find the build task here: https://debusine.debian.net/work-request/72033/ If this is really a bug in one of the build-depends, please use reassign and affects, so that this is still visible in the BTS web page for this package. Thanks, Stefano