[Debian-med-packaging] Bug#1094734: FTBFS with NumPy 2
Stefano Rivera
stefanor at debian.org
Thu Jan 30 14:50:34 GMT 2025
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
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