[From nobody Tue Oct 20 16:21:06 2026 Received: (at maintonly) by bugs.debian.org; 8 Sep 2025 19:44:39 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-100.0 required=4.0 tests=BAYES_00,BODY_E_CIGAR, DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,FOURLA, FROMDEVELOPER,FVGT_m_MULTI_ODD,MSGID_FROM_MTA_HEADER,SPF_HELO_NONE, SPF_NONE,UNPARSEABLE_RELAY,USER_IN_DKIM_WELCOMELIST autolearn=no autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 141; hammy, 150; neutral, 261; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <roehling@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:38166) by buxtehude.debian.org with utf8esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <roehling@debian.org>) id 1uvhn5-00ASoA-0I for maintonly@bugs.debian.org; Mon, 08 Sep 2025 19:44:39 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:To:From:Subject:MIME-Version: Content-Transfer-Encoding:Content-Type:Message-ID:Date:Reply-To:Cc:Content-ID :Content-Description:In-Reply-To:References; bh=EPv/lHAfhuCsz7+8uO6qLMGdtKDFi+2fPsU+FVHyCV8=; b=YPfuMQK7zNyWh82rvfKNvdP6pz tdZ+pz80nbBFqlgR21itRbWkeAU3UG5np4NjOXc8gSyIfLylpx2qRLxEPMh/qFID3MpNAs1C/GrCM zxZ/JqLrGbtbccPR9sYLTl8at5PZplXgk5LTHcRCFZYpVZnzqBYd4c2qMiA8XLqIZ8/e1ezob4WSU 1YHcvYAUVsSJ6Duqa5gEZCG7O7KD2/HGB9/5Msipgf6ffbII/h9AdVEiHxZpbq33JpffmKDAW5mJ2 FzLAqlifxQrMk3FauSINvhEu8dSwdzq7UdckP273LlHeXm/dojkFdi8/0YtCV00xPm44CMOSjfVU1 84APLn5w==; Received: from authenticated user by stravinsky.debian.org with utf8esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <roehling@debian.org>) id 1uvhn2-006iNv-Rn for maintonly@bugs.debian.org; Mon, 08 Sep 2025 19:44:37 +0000 Date: Mon, 08 Sep 2025 21:44:36 +0200 Message-ID: <3e93316d0fd72d6acad244acc8ca49ac@debian.org> Received: from roehling3.cms.fkie.fraunhofer.de (localhost.localdomain [127.0.0.1]) by localhost.localdomain [127.0.0.1] (msmtpd) with ESMTP; Mon, 08 Sep 2025 21:44:35 +0200 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 Subject: python-pbcore: FTBFS with NumPy 2.3 From: roehling@debian.org To: maintonly@bugs.debian.org X-Debian-User: roehling Delivered-To: maintonly@bugs.debian.org Source: python-pbcore Version: 2.1.2+dfsg-12 Severity: important User: debian-python@lists.debian.org 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 =3D BAM alignment: movie1/54130/0_10 @ - 0 11 21 orientation =3D 'native', style =3D 'gusfield' def transcript(self, orientation=3D"native", style=3D"gusfield"): """ A text representation of the alignment moves (see Gusfield). This can be useful in pretty-printing an alignment. """ uc =3D self.unrolledCigar(orientation) # MIDNSHP=3DX _exoneratePlusTrans =3D np.frombuffer(b"Z ZZZZ|*", dtype=3Dnp.int8) _exonerateTrans =3D np.frombuffer(b"Z ZZZZ| ", dtype=3Dnp.int8) _cigarTrans =3D np.frombuffer(b"ZIDZZZZMM", dtype=3Dnp.int8) _gusfieldTrans =3D np.frombuffer(b"ZIDZZZZMR", dtype=3Dnp.int8) =20 if style =3D=3D "exonerate+": return _exoneratePlusTrans[uc].tostring().decode("ascii") elif style =3D=3D "exonerate": return _exonerateTrans[uc].tostring().decode("ascii") elif style =3D=3D "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 =3D <test_pbcore_io_FastqIO.TestQvConversion object at 0x7fb9ef16a990> def testAsciiFromQvs(self): > assert self.ASCII =3D=3D asciiFromQvs(self.QVS) ^^^^^^^^^^^^^^^^^^^^^^ tests/test_pbcore_io_FastqIO.py:17:=20 _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _= _=20 a =3D range(0, 94) def asciiFromQvs(a): > return (np.clip(a, 0, 93).astype(np.uint8) + 33).tostring().decode("a= scii") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ E AttributeError: 'numpy.ndarray' object has no attribute 'tostring' pbcore/io/FastqIO.py:239: AttributeError =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D warnings summary =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 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_pb= core/build/pbcore/io/align/PacBioBamIndex.py:159: DeprecationWarning: Convers= ion of an array with ndim > 0 to a scalar is deprecated, and will error in fu= ture. Ensure you extract a single element from your array before performing t= his operation. (Deprecated NumPy 1.25.) ntId =3D 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_pb= core/build/pbcore/io/dataset/utils.py:24: DeprecationWarning: datetime.dateti= me.utcnow() is deprecated and scheduled for removal in a future version. Use = timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(d= atetime.UTC). time =3D 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_metada= ta_element_name /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pb= core/build/pbcore/io/dataset/utils.py:30: DeprecationWarning: datetime.dateti= me.utcnow() is deprecated and scheduled for removal in a future version. Use = timezone-aware objects to represent datetimes in UTC: datetime.datetime.now(d= atetime.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_pb= core/build/pbcore/io/align/_AlignmentMixin.py:70: DeprecationWarning: `in1d` = is deprecated. Use `np.isin` instead. rns =3D 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/.pybu= ild/cpython3_3.13_pbcore/build/nosetests.xml - ---------- coverage: platform linux, python 3.13.7-final-0 ----------- Coverage XML written to file coverage.xml =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D slowest 20 durations =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 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_zm= ws_targetsize 0.07s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testRe= adsInRange 0.07s call tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testRead= sInRange 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_split_zm= ws 0.05s call tests/test_pbdataset_split.py::TestDataSetSplit::test_contigse= t_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_consisten= cy 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_refWindo= ws 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_a= lignment_identity_unindexed 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::test_a= lignment_identity 0.01s call tests/test_pbdataset_split.py::TestDataSetSplit::test_subreads= et_split_metadata_element_name 0.01s call tests/test_pbcore_io_FastaTable.py::TestIndexedFastaReader::te= st_dosLineEndingsFasta 0.01s setup tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testBa= sicOperations 0.01s setup tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testBasi= cOperations 0.01s call tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testHo= leNumbers 0.01s call tests/test_pbdataset_utils.py::TestDataSetUtils::test_get_data= set_uuid (1 durations < 0.005s hidden. Use -vv to show these durations.) =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D short test summary info =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 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_complem= ent1 FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testUnalignedR= ead FAILED tests/test_pbcore_io_FastqIO.py::TestFastqRecord::test_reverse_complem= ent2 FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testUnalignedRead FAILED tests/test_pbcore_io_AlnFileReaders.py::TestIndexedBam::testAlignedRef= erence FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testAlignedRefer= ence 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::testClippedAli= gnments FAILED tests/test_pbcore_io_AlnFileReaders.py::TestBasicBam::testClippedAlign= ments 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_comp= lement FAILED tests/test_pbcore_io_FastqIO.py::TestQvConversion::testAsciiFromQvs - = ... =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D 20 failed, 102 passed, 18 skipped, 283 warn= ings in 1.70s =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D E: pybuild pybuild:389: test: plugin distutils failed with: exit code=3D1: cd= /build/reproducible-path/python-pbcore-2.1.2+dfsg/.pybuild/cpython3_3.13_pbc= ore/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 pa= rt. 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/163= 915/ 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 ]