Your message dated Tue, 20 Oct 2026 15:19:31 +0000
with message-id <[email protected]>
and subject line Bug#1114717: fixed in python-pbcore 2.6.0+dfsg-1
has caused the Debian Bug report #1114717,
regarding python-pbcore: FTBFS with NumPy 2.3
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1114717: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1114717
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: python-pbcore
Source-Version: 2.6.0+dfsg-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-pbcore, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated python-pbcore package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 20 Oct 2026 16:41:12 +0200
Source: python-pbcore
Architecture: source
Version: 2.6.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1114717
Changes:
python-pbcore (2.6.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
* d/watch: Use Github template
* Reflow Uploaders field (cme)
* Drop patches applied upstream:
- b24746790c7105212e45dc2f40115d231bd8baae.patch
- numpy_1.24.patch (Closes: #1114717)
- numpy2.patch
* Update exclude_test_missing_data.patch to skip tests that need the
unpackaged PacBioTestData module.
* Add numpy-2.4.patch to fix compatibility with numpy 2.4.
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