[Debian-med-packaging] Bug#805687: python-pbcore: FTBFS: AttributeError: 'pysam.csamfile.Samfile' object has no attribute '_hasIndex'

[Chris West (Faux)]

Source: python-pbcore
Version: 1.2.4+dfsg-1
Severity: serious
Justification: fails to build from source
Tags: sid stretch
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs
X-Debbugs-CC: reproducible-builds at lists.alioth.debian.org

Dear Maintainer,

The package fails to build:


======================================================================
ERROR: test_pbcore_io_AlnFileReaders.TestBasicBam.testBasicOperations
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/python-pbcore-1.2.4+dfsg/tests/test_pbcore_io_AlnFileReaders.py", line 42, in testBasicOperations
    EQ(False, self.f.isEmpty)
  File "/python-pbcore-1.2.4+dfsg/pbcore/io/align/BamIO.py", line 282, in isEmpty
    return (len(self) == 0)
  File "/python-pbcore-1.2.4+dfsg/pbcore/io/align/BamIO.py", line 54, in f
    if not bamReader.peer._hasIndex():
AttributeError: 'pysam.csamfile.Samfile' object has no attribute '_hasIndex'

----------------------------------------------------------------------
Ran 252 tests in 24.262s

FAILED (errors=1, skipped=14)
E: pybuild pybuild:274: test: plugin custom failed with: exit code=1: python2.7 setup.py test

Full build log:
https://reproducible.debian.net/rb-pkg/unstable/amd64/python-pbcore.html

-- System Information:
Debian Release: stretch/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)