Source: python-pysam Version: 0.15.0.1+ds-1 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the past)
Hi, python-pysam FTBFS on all architectures with testsuite errors. I can also reproduce this on amd64 in a clean pbuilder environment. https://buildd.debian.org/status/package.php?p=python-pysam&suite=experimental =================================== FAILURES =================================== ________________ TestEmptyHeader.test_bam_without_seq_in_header ________________ self = <AlignmentFile_test.TestEmptyHeader testMethod=test_bam_without_seq_in_header> def test_bam_without_seq_in_header(self): > s = pysam.AlignmentFile(os.path.join(BAM_DATADIR, > "example_no_seq_in_header.bam")) tests/AlignmentFile_test.py:1406: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ pysam/libcalignmentfile.pyx:734: in pysam.libcalignmentfile.AlignmentFile.__cinit__ ??? _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > ??? E IOError: [Errno 2] could not open alignment file `/<<BUILDDIR>>/python-pysam-0.15.0.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/pysam_data/example_no_seq_in_header.bam`: No such file or directory pysam/libcalignmentfile.pyx:933: IOError _______________________ TestRemoteFileHTTP.testFetchAll ________________________ self = <tabix_test.TestRemoteFileHTTP testMethod=testFetchAll> def setUp(self): > if not pysam.config.HAVE_LIBCURL or not check_url(self.url): E AttributeError: 'module' object has no attribute 'HAVE_LIBCURL' tests/tabix_test.py:1049: AttributeError ________________________ TestRemoteFileHTTP.testHeader _________________________ self = <tabix_test.TestRemoteFileHTTP testMethod=testHeader> def setUp(self): > if not pysam.config.HAVE_LIBCURL or not check_url(self.url): E AttributeError: 'module' object has no attribute 'HAVE_LIBCURL' tests/tabix_test.py:1049: AttributeError __________________ TestRemoteFileHTTPWithHeader.testFetchAll ___________________ self = <tabix_test.TestRemoteFileHTTPWithHeader testMethod=testFetchAll> def setUp(self): > if not pysam.config.HAVE_LIBCURL or not check_url(self.url): E AttributeError: 'module' object has no attribute 'HAVE_LIBCURL' tests/tabix_test.py:1088: AttributeError ___________________ TestRemoteFileHTTPWithHeader.testHeader ____________________ self = <tabix_test.TestRemoteFileHTTPWithHeader testMethod=testHeader> def setUp(self): > if not pysam.config.HAVE_LIBCURL or not check_url(self.url): E AttributeError: 'module' object has no attribute 'HAVE_LIBCURL' tests/tabix_test.py:1088: AttributeError =============================== warnings summary =============================== .pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py::TestTruncatedBAM::testTruncatedBam2 /<<BUILDDIR>>/python-pysam-0.15.0.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/AlignmentFile_test.py:1441: UserWarning: no BGZF EOF marker; file may be truncated ignore_truncation=True) .pybuild/cpython2_2.7_pysam/build/tests/samtools_test.py::SamtoolsTest::testStatements /<<BUILDDIR>>/python-pysam-0.15.0.1+ds/.pybuild/cpython2_2.7_pysam/build/tests/samtools_test.py:140: UserWarning: versions of pysam.samtools and samtools differ: 1.9 != 1.7 samtools_version)) -- Docs: http://doc.pytest.org/en/latest/warnings.html ======== 5 failed, 903 passed, 17 skipped, 2 warnings in 94.95 seconds ========= E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: cd /<<BUILDDIR>>/python-pysam-0.15.0.1+ds/.pybuild/cpython2_2.7_pysam/build; python2.7 -m pytest tests dh_auto_test: pybuild --test --test-pytest -i python{version} -p 2.7 returned exit code 13 make[1]: *** [debian/rules:31: override_dh_auto_test] Error 25 make[1]: Leaving directory '/<<BUILDDIR>>/python-pysam-0.15.0.1+ds' make: *** [debian/rules:24: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 Network access (beyond localhost) is not available during build. Andreas
