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

[Andreas Tille]

Hi,

On Tue, Aug 23, 2016 at 02:45:59PM +0000, Santiago Vila wrote:
> The way it fails may be related to Bug #730515.

I confirm that this was related and this very reason is fixed in SVN.
There is also a new upstream version.

Unfortunately there are 4 remaining failures.  For a test I was just
"hiding the eyes from these" by adding a "|| true" to the actual test
call in debian/rules.  It would be great if somebody could have a look
since I currently have no time to hunt this down and it seems to be a
bit more complex.

Any help would be welcome

         Andreas.


This is the build log output showing the errors:

...
Environment variable TEST_DB=1 not set: skipping db tests
...............................................................................................................................................................................................
  return reshape(newshape, order=order)
...............................................................................................................................................................................................
======================================================================
ERROR: test_tree_threeway_rates (test_seqsim.test_analysis.analysisTests)
tree_threeway_rates should give plausible results on rand trees
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_seqsim/test_analysis.py", line 31, in wrapped
    return test_method(*args)
  File "/build/python-cogent-1.9/tests/test_seqsim/test_analysis.py", line 192, in test_tree_threeway_rates
    result = tree_threeway_rates(t, depths)
  File "/build/python-cogent-1.9/cogent/seqsim/analysis.py", line 204, in tree_threeway_rates
    rates = probs_to_rates(counts_to_probs(counts), fix_f, normalize)
  File "/build/python-cogent-1.9/cogent/seqsim/analysis.py", line 172, in probs_to_rates
    rate = val.toRates(normalize)
  File "/build/python-cogent-1.9/cogent/seqsim/usage.py", line 683, in toRates
    return Rates(logm(self._data), self.Alphabet, self.Name, normalize)
  File "/build/python-cogent-1.9/cogent/maths/matrix_logarithm.py", line 89, in logm
    raise ArithmeticError("eigendecomposition failed")
ArithmeticError: eigendecomposition failed

======================================================================
FAIL: test_cdhit_from_seqs (test_app.test_cd_hit.CD_HIT_EST_Tests)
CD_HIT should return expected seqs
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_cd_hit.py", line 100, in test_cdhit_from_seqs
    self.assertEqual(res.toFasta(), dna_expected)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got '>cdhit_test_seqs_0\nAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT\n>cdhit_test_seqs_2\nCCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAA

======================================================================
FAIL: test_cdhit_from_seqs_synonym (test_app.test_cd_hit.CD_HIT_EST_Tests)
CD_HIT should return expected seqs with -c synonym
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_cd_hit.py", line 105, in test_cdhit_from_seqs_synonym
    self.assertEqual(res.toFasta(), dna_expected)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got '>cdhit_test_seqs_0\nAACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT\n>cdhit_test_seqs_2\nCCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAA

======================================================================
FAIL: test_cdhit_clusters_from_seqs (test_app.test_cd_hit.CD_HIT_SupportMethodTests)
cdhit_clusters_from_seqs returns expected clusters
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/build/python-cogent-1.9/tests/test_app/test_cd_hit.py", line 133, in test_cdhit_clusters_from_seqs
    self.assertEqual(obs, exp)
  File "/build/python-cogent-1.9/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_t

======================================================================
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 "/build/python-cogent-1.9/tests/test_app/test_cd_hit.py", line 64, in test_cdhit_from_seqs
    self.assertEqual(res.toFasta(), protein_expected)
  File "/build/python-cogent-1.9/cogent/util/unit_test.py", line 316, in failUnlessEqual
    (msg or 'Got %s, but expected %s' % (`observed`, `expected`))
AssertionError: Got '>seq1\nMGNKWSKSWPQVRDRMRRAAPAPAADGVGAVSQDLAKHGAITSSNTAATNDDCAWLEAQTEEEVGFPVRPQVPLRPMTYK\n>seq2\nMGGKWSKSSIVGWSTVRERMRKTPPAADGVGAVSQDLDKHGAVTSSNTAFNNPDCAWLEAQEDEDVGFPVRPQV

----------------------------------------------------------------------
Ran 3560 tests in 90.326s

FAILED (failures=4, errors=1)


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