[From nobody Fri Apr 17 15:45:06 2026 Received: (at submit) by bugs.debian.org; 20 Sep 2024 11:22:40 +0000 X-Spam-Checker-Version: SpamAssassin 3.4.6-bugs.debian.org_2005_01_02 (2021-04-09) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-104.2 required=4.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA, FROMDEVELOPER,FVGT_m_MULTI_ODD,SPF_HELO_NONE,SPF_NONE,SUBJ_LACKS_WORDS, USER_IN_DKIM_WELCOMELIST,USER_IN_DKIM_WHITELIST autolearn=ham autolearn_force=no version=3.4.6-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 150; hammy, 150; neutral, 300; spammy, 0. spammytokens: hammytokens:0.000-+--python3, 0.000-+--pkgbuilddir, 0.000-+--PKGBUILDDIR, 0.000-+--pybuild, 0.000-+--H*UA:NeoMutt Return-path: <stefanor@debian.org> Received: from smtp.tumbleweed.org.za ([212.47.253.1]:54950) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.94.2) (envelope-from <stefanor@debian.org>) id 1srbii-007NfM-GB for submit@bugs.debian.org; 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Fri, 20 Sep 2024 11:22:37 +0000 (UTC) Received: by haydn.kardiogramm.net (Postfix, from userid 1000) id 7C6B5120B17A; Fri, 20 Sep 2024 13:22:34 +0200 (SAST) Date: Fri, 20 Sep 2024 13:22:34 +0200 From: Stefano Rivera <stefanor@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: FTBFS: TestIntegration.testIntegration: AssertionError: 1 != 0 Message-ID: <cdgd4kdweegxvqah43skuid5sqkht6ddm6pessi7ffy2wm4cry@orpwqf7i7sbe> X-Reportbug-Version: 13.0.1 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline User-Agent: NeoMutt/20240425 Delivered-To: submit@bugs.debian.org Source: pychopper Version: 2.7.10-1 Severity: serious Tags: ftbfs Justification: FTBFS Dear maintainer, During a test rebuild, pychopper failed to rebuild. ------------------------------------------------------------------------------- [...] debian/rules override_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_test -- --system=custom --test-args="export PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts:$PATH; \ chmod +x /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper; PYTHONPATH={build_dir} {interpreter} -m pytest -v" pybuild --test --test-pytest -i python{version} -p 3.12 --system=custom "--test-args=export PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games; chmod +x /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper; PYTHONPATH={build_dir} {interpreter} -m pytest -v" I: pybuild pybuild:308: cp -av /<<PKGBUILDDIR>>/pychopper/tests/ /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/ '/<<PKGBUILDDIR>>/pychopper/tests/' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests' '/<<PKGBUILDDIR>>/pychopper/tests/__init__.py' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/__init__.py' '/<<PKGBUILDDIR>>/pychopper/tests/data' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data' '/<<PKGBUILDDIR>>/pychopper/tests/data/.gitignore' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/.gitignore' '/<<PKGBUILDDIR>>/pychopper/tests/data/PCS111_umi_test_reads.fastq.gz' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/PCS111_umi_test_reads.fastq.gz' '/<<PKGBUILDDIR>>/pychopper/tests/data/PCS111_umi_test_reads_expected.fastq' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/PCS111_umi_test_reads_expected.fastq' '/<<PKGBUILDDIR>>/pychopper/tests/data/barcodes.fas' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/barcodes.fas' '/<<PKGBUILDDIR>>/pychopper/tests/data/expected_output.fas' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/expected_output.fas' '/<<PKGBUILDDIR>>/pychopper/tests/data/ref.fas.gz' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/ref.fas.gz' '/<<PKGBUILDDIR>>/pychopper/tests/data/ref.fq.gz' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/data/ref.fq.gz' '/<<PKGBUILDDIR>>/pychopper/tests/test_detector.py' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/test_detector.py' '/<<PKGBUILDDIR>>/pychopper/tests/test_regression_simple.py' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/test_regression_simple.py' '/<<PKGBUILDDIR>>/pychopper/tests/__pycache__' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/__pycache__' '/<<PKGBUILDDIR>>/pychopper/tests/__pycache__/__init__.cpython-312.pyc' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/__pycache__/__init__.cpython-312.pyc' '/<<PKGBUILDDIR>>/pychopper/tests/__pycache__/test_detector.cpython-312.pyc' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/__pycache__/test_detector.cpython-312.pyc' '/<<PKGBUILDDIR>>/pychopper/tests/__pycache__/test_regression_simple.cpython-312.pyc' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/tests/__pycache__/test_regression_simple.cpython-312.pyc' I: pybuild base:311: export PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games; chmod +x /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper; PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build python3.12 -m pytest -v ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 -- /usr/bin/python3.12 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase(PosixPath('/<<PKGBUILDDIR>>/.hypothesis/examples')) rootdir: /<<PKGBUILDDIR>> configfile: pytest.ini testpaths: pychopper plugins: mock-3.14.0, openfiles-0.6.0, hypothesis-6.112.0, forked-1.6.0, remotedata-0.4.1, typeguard-4.3.0, xdist-3.6.1, arraydiff-0.6.1, doctestplus-1.2.1, timeout-2.3.1, xonsh-0.15.1, cov-5.0.0 collecting ... collected 4 items pychopper/tests/test_detector.py::TestDetector::testPairAlign PASSED [ 25%] pychopper/tests/test_detector.py::TestDetector::testScoreCutoff PASSED [ 50%] pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration FAILED [ 75%] pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration_umi FAILED [100%] =================================== FAILURES =================================== _______________________ TestIntegration.testIntegration ________________________ self = <pychopper.tests.test_regression_simple.TestIntegration testMethod=testIntegration> def testIntegration(self): """ Integration test. """ base = path.dirname(__file__) test_base = path.join(base, 'data') barcodes = path.join(test_base, 'barcodes.fas') input_fasta = path.join(test_base, 'ref.fq.gz') output_fasta = path.join(test_base, 'test_output.fq.gz') expected_output = path.join(test_base, 'expected_output.fas') subprocess.call("{} {} {} {} {}".format('pychopper', "-Y 0 -B 3 -q 0.5 -m edlib -b", barcodes, input_fasta, output_fasta), shell=True) retval = subprocess.call(['cmp', output_fasta, expected_output]) > self.assertEqual(retval, 0) E AssertionError: 1 != 0 pychopper/tests/test_regression_simple.py:21: AssertionError ----------------------------- Captured stderr call ----------------------------- Using kit: /<<PKGBUILDDIR>>/pychopper/tests/data/barcodes.fas Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP" Processing the whole dataset using a batch size of 3: 0%| | 0/1665 [00:00<?, ?it/s]concurrent.futures.process._RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.12/concurrent/futures/process.py", line 263, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/process.py", line 212, in _process_chunk return [fn(*args) for args in chunk] ^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/edlib_backend.py", line 94, in _find_locations_single refined_locations = refine_locations(read, all_primers, all_locations) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 54, in refine_locations aln = pair_align(seq[loc.RefStart:loc.RefEnd], all_primers[loc.Query], loc.Query, subs_mat, aln_params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 45, in pair_align return process_alignment(aln, query, query_name, params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 30, in process_alignment fo = first_cigar(aln.cigar.decode.decode()) ^^^^^^^^^ File "/usr/lib/python3/dist-packages/parasail/bindings_v2.py", line 403, in cigar return self.get_cigar() ^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/parasail/bindings_v2.py", line 390, in get_cigar raise AttributeError("'Result' object has no traceback") AttributeError: 'Result' object has no traceback. Did you mean: '_cigar'? """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper", line 572, in <module> main() File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper", line 509, in main for read, (segments, hits, usable_len) in backend(batch, executor, ^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/chopper.py", line 150, in chopper_edlib for i, hits in enumerate(batch_hits): ^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/edlib_backend.py", line 14, in find_locations for res in pool.map(_find_locations_single, zip(batch, [(all_primers, max_ed)] * len(batch))): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/process.py", line 642, in _chain_from_iterable_of_lists for element in iterable: ^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 619, in result_iterator yield _result_or_cancel(fs.pop()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 317, in _result_or_cancel return fut.result(timeout) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 456, in result return self.__get_result() ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result raise self._exception AttributeError: 'Result' object has no traceback 0%| | 0/1665 [00:00<?, ?it/s] cmp: EOF on /<<PKGBUILDDIR>>/pychopper/tests/data/test_output.fq.gz which is empty _____________________ TestIntegration.testIntegration_umi ______________________ self = <pychopper.tests.test_regression_simple.TestIntegration testMethod=testIntegration_umi> def testIntegration_umi(self): """ Integration test. """ base = path.dirname(__file__) test_base = path.join(base, 'data') input_fasta = path.join(test_base, 'PCS111_umi_test_reads.fastq.gz') output_fasta = path.join(test_base, 'test_output_umi.fq.gz') expected_output = path.join(test_base, 'PCS111_umi_test_reads_expected.fastq') subprocess.call("{} {} {} {}".format('pychopper', "-U -m edlib -k PCS111", input_fasta, output_fasta), shell=True) retval = subprocess.call(['cmp', output_fasta, expected_output]) > self.assertEqual(retval, 0) E AssertionError: 1 != 0 pychopper/tests/test_regression_simple.py:35: AssertionError ----------------------------- Captured stderr call ----------------------------- Using kit: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/primer_data/PCS111_primers.fas Configurations to consider: "+:SSP,-VNP|-:VNP,-SSP" Counting fastq records in input file: /<<PKGBUILDDIR>>/pychopper/tests/data/PCS111_umi_test_reads.fastq.gz Total fastq records in input file: 4 Tuning the cutoff parameter (q) on 4 sampled reads (100.0%) passing quality filters (Q >= 7.0). Optimizing over 30 cutoff values. 0%| | 0/30 [00:00<?, ?it/s] 0%| | 0/30 [00:00<?, ?it/s] concurrent.futures.process._RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.12/concurrent/futures/process.py", line 263, in _process_worker r = call_item.fn(*call_item.args, **call_item.kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/process.py", line 212, in _process_chunk return [fn(*args) for args in chunk] ^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/edlib_backend.py", line 94, in _find_locations_single refined_locations = refine_locations(read, all_primers, all_locations) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 54, in refine_locations aln = pair_align(seq[loc.RefStart:loc.RefEnd], all_primers[loc.Query], loc.Query, subs_mat, aln_params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 45, in pair_align return process_alignment(aln, query, query_name, params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/parasail_backend.py", line 30, in process_alignment fo = first_cigar(aln.cigar.decode.decode()) ^^^^^^^^^ File "/usr/lib/python3/dist-packages/parasail/bindings_v2.py", line 403, in cigar return self.get_cigar() ^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/parasail/bindings_v2.py", line 390, in get_cigar raise AttributeError("'Result' object has no traceback") AttributeError: 'Result' object has no traceback. Did you mean: '_cigar'? """ The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper", line 572, in <module> main() File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper", line 468, in main in backend(batch, executor, qv, max(1000, int((len(read_sample)) / args.t))): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/chopper.py", line 150, in chopper_edlib for i, hits in enumerate(batch_hits): ^^^^^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/edlib_backend.py", line 14, in find_locations for res in pool.map(_find_locations_single, zip(batch, [(all_primers, max_ed)] * len(batch))): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/process.py", line 642, in _chain_from_iterable_of_lists for element in iterable: ^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 619, in result_iterator yield _result_or_cancel(fs.pop()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 317, in _result_or_cancel return fut.result(timeout) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 456, in result return self.__get_result() ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result raise self._exception AttributeError: 'Result' object has no traceback cmp: EOF on /<<PKGBUILDDIR>>/pychopper/tests/data/test_output_umi.fq.gz which is empty =========================== short test summary info ============================ FAILED pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration FAILED pychopper/tests/test_regression_simple.py::TestIntegration::testIntegration_umi ========================= 2 failed, 2 passed in 2.58s ========================== E: pybuild pybuild:389: test: plugin custom failed with: exit code=1: export PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games; chmod +x /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper; PYTHONPATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build python3.12 -m pytest -v rm -fr -- /tmp/dh-xdg-rundir-bkd7fhbm dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.12 --system=custom "--test-args=export PATH=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games; chmod +x /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_pychopper/build/pychopper/scripts/pychopper; PYTHONPATH={build_dir} {interpreter} -m pytest -v" returned exit code 13 make[1]: *** [debian/rules:30: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:10: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2024-09-19T22:14:00Z ------------------------------------------------------------------------------- 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/799470/ 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/38973/ 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 ]