Source: htslib, python-pysam Control: found -1 htslib/1.9-3 Control: found -1 python-pysam/0.14+ds-2 X-Debbugs-CC: debian-ci@lists.debian.org User: debian-ci@lists.debian.org Usertags: breaks needs-update Dear maintainers, With a recent upload of htslib the autopkgtest of python-pysam fails in testing when that autopkgtest is run with the binary packages of htslib from unstable. It passes when run with only packages from testing. In tabular form: pass fail htslib from testing 1.9-3 python-pysam from testing 0.14+ds-2 all others from testing from testing I copied some of the output at the bottom of this report. Currently this regression is contributing to the delay of the migration of htslib to testing [1]. Due to the nature of this issue, I filed this bug report against both packages. Can you please investigate the situation and reassign the bug to the right package? If needed, please change the bug's severity. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation Paul [1] https://qa.debian.org/excuses.php?package=htslib https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-pysam/1182495/log.gz =================================== FAILURES =================================== ___________________ TestLargeCigar.test_reading_writing_cram ___________________ self = <AlignmentFile_test.TestLargeCigar testMethod=test_reading_writing_cram> def test_reading_writing_cram(self): read = self.build_read() > self.check_read(read, mode="cram") tests/AlignmentFile_test.py:2265: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ tests/AlignmentFile_test.py:2244: in check_read ref_read = next(inf) _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > raise IOError('truncated file') E OSError: truncated file pysam/libcalignmentfile.pyx:1804: OSError =============================== warnings summary =============================== tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 /tmp/autopkgtest-lxc.uirvm7sh/downtmp/build.e1l/src/tests/AlignmentFile_test.py:1395: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) -- Docs: http://doc.pytest.org/en/latest/warnings.html ======== 1 failed, 902 passed, 9 skipped, 1 warnings in 146.53 seconds =========
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