[Debian-med-packaging] Bug#835213: python-cogent: FTBFS in testing (AssertionError)

[Santiago Vila]

Package: src:python-cogent
Version: 1.5.3-10
Severity: serious

Dear maintainer:

I tried to build this package in stretch with "dpkg-buildpackage -A"
(which is what the "Arch: all" autobuilder would do to build it)
but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-indep
dh build-indep --with python2 --buildsystem=pybuild
   dh_testdir -i -O--buildsystem=pybuild
   dh_update_autotools_config -i -O--buildsystem=pybuild
   dh_auto_configure -i -O--buildsystem=pybuild
I: pybuild base:184: python2.7 setup.py config 
running config
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
I: pybuild base:184: /usr/bin/python setup.py build 
running build
running build_py

[... snipped ...]

  File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got [['cdhit_test_seqs_0'], ['cdhit_test_seqs_1'], ['cdhit_test_seqs_2'], ['cdhit_test_seqs_3'], ['cdhit_test_seqs_4'], ['cdhit_test_seqs_5'], ['cdhit_test_seqs_6'], ['cdhit_test_seqs_7'], ['cdhit_test_seqs_8'], ['cdhit_test_seqs_9']], but expected [['cdhit_test_seqs_0'], ['cdhit_test_seqs_1'], ['cdhit_test_seqs_2'], ['cdhit_test_seqs_3'], ['cdhit_test_seqs_4'], ['cdhit_test_seqs_5'], ['cdhit_test_seqs_6', 'cdhit_test_seqs_8'], ['cdhit_test_seqs_7'], ['cdhit_test_seqs_9']]

======================================================================
FAIL: test_base_command (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT BaseCommand should return the correct BaseCommand
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 25, in test_base_command
    ''.join(['cd "',getcwd(),'/"; ','cdhit']))
  File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 'cd "/<<PKGBUILDDIR>>/tests/"; cd-hit', but expected 'cd "/<<PKGBUILDDIR>>/tests/"; cdhit'

======================================================================
FAIL: test_cdhit_from_seqs (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT should return expected seqs
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 52, in test_cdhit_from_seqs
    self.assertEqual(res.toFasta(), protein_expected)
  File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got '>seq1\nMGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK\n>seq2\nMGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT\n>seq3\nMGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR\n>seq4\nMGKIWSKSSIVGWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ\n>seq6\nMGKIWSKSSLVGWPEIRERIRRQTPEPAVGVGAVSQDLANRGAITTSNTKDNNQTVAWLEAQEEPVRPQVPLRPM\n>seq7\nMGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV\n>seq8\nMGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP\n>seq9\nMGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV', but expected '>seq1\nMGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK\n>seq2\nMGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQVPLRPT\n>seq3\nMGGKWSKSSIVGWPAIRERMRRARPAADRVGTQPAADGVGAVSQDLARHGAVTSSNTSHNNPDCAWLEAQEEEEVGVR\n>seq4\nMGKIWSKSSIVGWPEIRERMRRQRPHEPAVEPAVGVGAASQDLANRGALTTSNTRTNNPTVAWVEAQEEEGEVVRPQ\n>seq5\nMGKIWSKSSLVGWPEIRERMRRQTQEPAVEPAVGAGAASQDLANRGAITIRNTRDNNESIAWLEAQEEEFPVRPQV\n>seq7\nMGNALRKGKFEGWAAVRERMRRTRTFPESEPCAPGVGQISRELAARGGIPSSHTPQNNESHQEEEVGFPVAPQV\n>seq8\nMGNAWSKSKFAGWSEVRDRMRRSSSDPQQPCAPGVGAVSRELATRGGISSSALAFLDSHKDEDVGFPVRPQVP\n>seq9\nMGNVLGKDKFKGWAAVRERMRKTSSDPDPQPCAPGVGPVSRELSYTPQNNAALAFLESHEDEDVGFPVXPQV'

======================================================================
FAIL: test_changing_working_dir (test_app.test_cd_hit.CD_HIT_Tests)
CD_HIT BaseCommand should change according to WorkingDir
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/<<PKGBUILDDIR>>/tests/test_app/test_cd_hit.py", line 38, in test_changing_working_dir
    ''.join(['cd "','/tmp/cdhit_test','/"; ','cdhit']))
  File "/<<PKGBUILDDIR>>/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got 'cd "/tmp/cdhit_test/"; cd-hit', but expected 'cd "/tmp/cdhit_test/"; cdhit'

----------------------------------------------------------------------
Ran 3518 tests in 60.189s

FAILED (failures=6)
debian/rules:71: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules:38: recipe for target 'build-indep' failed
make: *** [build-indep] Error 2
dpkg-buildpackage: error: debian/rules build-indep gave error exit status 2
--------------------------------------------------------------------------------

The failure seems reproducible and it started to happen in stretch
at some point between 2016-08-17 and 2016-08-23.

The way it fails may be related to Bug #730515.

Once you manage to fix this, please consider uploading in source-only form,
so that we get pretty official build logs here:

https://buildd.debian.org/status/package.php?p=python-cogent

Thanks.