Public bug reported: Imported from Debian bug http://bugs.debian.org/1114717:
Source: python-pbcore Version: 2.1.2+dfsg-12 Severity: important User: [email protected] Usertags: numpy2.3 Tags: ftbfs, forky, sid Dear maintainer, During a test rebuild for NumPy 2.3, python-pbcore failed to rebuild. Log Summary: ------------------------------------------------------------------------------- [...] self = BAM alignment: movie1/54130/0_10 @ - 0 11 21 orientation = 'native', style = 'gusfield' def transcript(self, orientation="native", style="gusfield"): """ A text representation of the alignment moves (see Gusfield). This can be useful in pretty-printing an alignment. """ uc = self.unrolledCigar(orientation) # MIDNSHP=X _exoneratePlusTrans = np.frombuffer(b"Z ZZZZ|*", dtype=np.int8) _exonerateTrans = np.frombuffer(b"Z ZZZZ| ", dtype=np.int8) _cigarTrans = np.frombuffer(b"ZIDZZZZMM", dtype=np.int8) _gusfieldTrans = np.frombuffer(b"ZIDZZZZMR", dtype=np.int8) if style == "exonerate+": return _exoneratePlusTrans[uc].tostring().decode("ascii") elif style == "exonerate": return _exonerateTrans[uc].tostring().decode("ascii") elif style == "cigar": return _cigarTrans[uc].tostring().decode("ascii") else: > return _gusfieldTrans[uc].tostring().decode("ascii") ^^^^^^^^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'numpy.ndarray' object has no attribute 'tostring' pbcore/io/align/BamAlignment.py:356: AttributeError ______________________ TestQvConversion.testAsciiFromQvs _______________________ [gw1] linux -- Python 3.13.7 /usr/bin/python3.13 self = <test_pbcore_io_FastqIO.TestQvConversion object at 0x7fb9ef16a990> def testAsciiFromQvs(self): > assert self.ASCII == asciiFromQvs(self.QVS) ^^^^^^^^^^^^^^^^^^^^^^ tests/test_pbcore_io_FastqIO.py:17: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ a = range(0, 94) def asciiFromQvs(a): > return (np.clip(a, 0, 93).astype(np.uint8) + > 33).tostring().decode("ascii") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'numpy.ndarray' object has no attribute 'tostring' pbcore/io/FastqIO.py:239: AttributeError =============================== warnings summary =============================== tests/test_pbcore_io_AlnFileReaders.py: 3 warnings tests/test_pbdataset_split.py: 16 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align/PacBioBamIndex.py:159: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) ntId = int(peek("u4", 1)) tests/test_pbdataset_split.py: 249 warnings tests/test_pbdataset_utils.py: 10 warnings /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset/utils.py:24: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). time = datetime.datetime.utcnow().strftime("%y%m%d_%H%M%S%f")[:-3] tests/test_pbdataset_split.py::TestDataSetSplit::test_split tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/dataset/utils.py:30: DeprecationWarning: datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(datetime.UTC). return datetime.datetime.utcnow().strftime("%Y-%m-%dT%H:%M:%S%f")[:-6] tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsByName /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/pbcore/io/align/_AlignmentMixin.py:70: DeprecationWarning: `in1d` is deprecated. Use `np.isin` instead. rns = np.flatnonzero(np.in1d(self.qId, rgs) & -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html - generated xml file: /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build/nosetests.xml - ---------- coverage: platform linux, python 3.13.7-final-0 ----------- Coverage XML written to file coverage.xml ============================= slowest 20 durations ============================= 0.13s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split_and_maxChunks 0.11s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_by_contigs_with_split 0.09s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws_targetsize 0.07s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testReadsInRange 0.07s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testReadsInRange 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zmws 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigset_split 0.04s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split 0.03s setup tests/test_pbcore_io_AlnFileReaders.py::TestMultipleReadGroups::test_retrieve_read_group_properties 0.02s call tests/test_pbindex.py::TestPbIndex::test_pbindex_bam_consistency 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindows 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreadset_split_metadata_element_name 0.01s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::test_dosLineEndingsFasta 0.01s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBasicOperations 0.01s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasicOperations 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHoleNumbers 0.01s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_dataset_uuid (1 durations < 0.005s hidden. Use -vv to show these durations.) =========================== short test summary info ============================ FAILED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test__str__ - Attrib... FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRead FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRead FAILED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement1 FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedRead FAILED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complement2 FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedReference FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedReference FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testTranscript FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testTranscript FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testClippedAlignments FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlignments FAILED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq1 - A... FAILED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq2 - A... FAILED tests/test_pbcore_io_FastqIO.py::TestFastqWriter::test_writeFastq3 - A... FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testErrorCounts FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_alignment_identity_unindexed FAILED tests/test_pbcore_extract_bam_sequence.py::TestCase::test_reverse_complement FAILED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs - ... =========== 20 failed, 102 passed, 18 skipped, 283 warnings in 1.70s =========== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbcore/build; python3.13 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make[1]: *** [debian/rules:39: override_dh_auto_test] Error 25 make[1]: Leaving directory '/build/reproducible-path/python-pbcore-2.1.2+dfsg' make: *** [debian/rules:14: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2025-09-08T08:11:22Z ------------------------------------------------------------------------------- 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/debian/developers-roehling.numpy/artifact/2455293/ About the archive rebuild: The build was made on debusine.debian.net, using sbuild. You can find the build task here: https://debusine.debian.net/debian/developers-roehling.numpy/work-request/163915/ 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. Cheers Timo ** Affects: hinge (Ubuntu) Importance: Undecided Status: New ** Affects: kineticstools (Ubuntu) Importance: Undecided Status: New ** Affects: numpy (Ubuntu) Importance: Undecided Status: New ** Affects: python-pbcommand (Ubuntu) Importance: Undecided Status: New ** Affects: python-pbcore (Ubuntu) Importance: Undecided Status: New ** Affects: smrtanalysis (Ubuntu) Importance: Undecided Status: New ** Affects: python-pbcore (Debian) Importance: Unknown Status: Confirmed ** Tags: ftbfs update-excuse ** Bug watch added: Debian Bug tracker #1114717 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114717 ** Changed in: python-pbcore (Debian) Remote watch: None => Debian Bug tracker #1114717 ** Also affects: numpy (Ubuntu) Importance: Undecided Status: New ** Tags added: ftbfs update-excuse -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2135242 Title: python-pbcore: FTBFS with NumPy 2.3 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/hinge/+bug/2135242/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
