[Debian-med-packaging] Bug#905548: python-pysam: FTBFS - tests fail: AttributeError: 'module' object has no attribute 'HAVE_LIBCURL'

[Andreas Beckmann]

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