Package: python3-pychopper Version: 2.5.0-1 Severity: normal X-Debbugs-Cc: ple...@debian.org
Hi all, I just tried to routine-update python3-pychopper but it failed. I do not have time to troubleshoot further. I am pasting the error so that you can prepare before picking the ball. Cheers, -- Charles dh_auto_test -- --system=custom --test-args="PYTHONPATH={build_dir} {interpreter} -m pytest -v" pybuild --test --test-pytest -i python{version} -p 3.10 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest -v" I: pybuild base:240: PYTHONPATH=/home/charles-plessy/Debian/python3-pychopper/.pybuild/cpython3_3.10_pychopper/build python3.10 -m pytest -v ============================= test session starts ============================== platform linux -- Python 3.10.7, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.10 cachedir: .pytest_cache hypothesis profile 'default' -> database=DirectoryBasedExampleDatabase('/home/charles-plessy/Debian/python3-pychopper/.hypothesis/examples') rootdir: /home/charles-plessy/Debian/python3-pychopper, configfile: pytest.ini, testpaths: pychopper plugins: openfiles-0.5.0, remotedata-0.3.3, arraydiff-0.5.0, cov-4.0.0, xonsh-0.13.3, hypothesis-6.36.0, timeout-2.1.0, xdist-2.5.0, mock-3.8.2, forked-1.4.0, doctestplus-0.12.1 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: 2 != 0 pychopper/tests/test_regression_simple.py:21: AssertionError ----------------------------- Captured stderr call ----------------------------- /bin/sh: 1: pychopper: not found cmp: /home/charles-plessy/Debian/python3-pychopper/pychopper/tests/data/test_output.fq.gz: No such file or directory _____________________ 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: 2 != 0 pychopper/tests/test_regression_simple.py:35: AssertionError ----------------------------- Captured stderr call ----------------------------- /bin/sh: 1: pychopper: not found cmp: /home/charles-plessy/Debian/python3-pychopper/pychopper/tests/data/test_output_umi.fq.gz: No such file or directory =========================== 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 0.10s ========================== E: pybuild pybuild:379: test: plugin custom failed with: exit code=1: PYTHONPATH=/home/charles-plessy/Debian/python3-pychopper/.pybuild/cpython3_3.10_pychopper/build python3.10 -m pytest -v rm -fr -- /tmp/dh-xdg-rundir-MUPdeGOd dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 --system=custom "--test-args=PYTHONPATH={build_dir} {interpreter} -m pytest -v" returned exit code 13 make[1]: *** [debian/rules:29: override_dh_auto_test] Error 25 make[1]: Leaving directory '/home/charles-plessy/Debian/python3-pychopper' make: *** [debian/rules:7: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 -- System Information: Debian Release: 11.5 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable-security'), (500, 'unstable'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 5.10.0-17-amd64 (SMP w/8 CPU threads) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-pychopper depends on: ii python3 3.10.6-1 ii python3-edlib 1.2.7-3+b1 ii python3-matplotlib 3.5.2-2 ii python3-pandas 1.3.5+dfsg-5 ii python3-parasail 1.2.3-1 ii python3-pytest 7.1.2-3 ii python3-seaborn 0.12.0-1 ii python3-six 1.16.0-2 ii python3-sphinx 4.5.0-4 ii python3-sphinx-rtd-theme 1.0.0+dfsg-1 ii python3-tqdm 4.64.0-2 python3-pychopper recommends no packages. python3-pychopper suggests no packages. -- no debconf information