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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