[Debian-med-packaging] Some remaining test failures (Was: Please help clarifying licensed)

Wed Jul 29 11:27:30 UTC 2015

Hi Jeet,

On Wed, Jul 29, 2015 at 01:09:56AM -0400, Jeet Sukumaran wrote:
> Hi Andreas,
> 
> I just tagged, pushed, and published release 4.0.3.

Thanks a lot for your support.

> Please let me know if there are any issues.

I injected it into Debian packaging Git and tried to build.
Unfortunately there are some remaining errors when running the test
suite.  All four are encoding errors (see attached build log extract).

Are you able to reproduce (and fix this)?

Kind regards

     Andreas.

-- 
http://fam-tille.de
-------------- next part --------------
...
test_multiple_trees1 (dendropy.test.test_dataio_nexus_reader_dataset.NexusDataSetMultiTreesBlockTestCase) ... ok
test_multiple_trees2 (dendropy.test.test_dataio_nexus_reader_dataset.NexusDataSetMultiTreesBlockTestCase) ... ok

======================================================================
ERROR: test_pscores_with_gaps_as_missing (dendropy.test.test_fitch.FitchTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 64, in test_pscores_with_gaps_as_missing
    self.verify_pscores("apternodus.chars.nexus", "apternodus.tre", True, expected_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 70, in verify_pscores
    "nexus")
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/datasetmodel.py", line 131, in _parse_and_create_from_stream
    state_alphabet_factory=charstatemodel.StateAlphabet,
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 253, in read_dataset
    global_annotations_target=dataset)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

======================================================================
ERROR: test_pscores_with_gaps_as_new_state (dendropy.test.test_fitch.FitchTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 51, in test_pscores_with_gaps_as_new_state
    self.verify_pscores("apternodus.chars.nexus", "apternodus.tre", False, expected_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 70, in verify_pscores
    "nexus")
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/datasetmodel.py", line 131, in _parse_and_create_from_stream
    state_alphabet_factory=charstatemodel.StateAlphabet,
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 253, in read_dataset
    global_annotations_target=dataset)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

======================================================================
ERROR: test_pscores_with_standard_data_and_gaps_as_missing (dendropy.test.test_parsimony_scoring.ParsimonyScoringTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 139, in test_pscores_with_standard_data_and_gaps_as_missing
    expected_per_site_scores=expected_per_site_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 465, in verify_pscores
    taxon_namespace=taxon_namespace)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 606, in get
    return cls._get_from(**kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 157, in _get_from
    return cls.get_from_path(src=src, schema=schema, **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 527, in _parse_and_create_from_stream
    global_annotations_target=None)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 375, in read_char_matrices
    global_annotations_target=global_annotations_target)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

======================================================================
ERROR: test_pscores_with_standard_data_and_gaps_as_new_states (dendropy.test.test_parsimony_scoring.ParsimonyScoringTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 83, in test_pscores_with_standard_data_and_gaps_as_new_states
    expected_per_site_scores=expected_per_site_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 465, in verify_pscores
    taxon_namespace=taxon_namespace)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 606, in get
    return cls._get_from(**kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 157, in _get_from
    return cls.get_from_path(src=src, schema=schema, **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_pok

======================================================================
ERROR: test_pscores_with_gaps_as_missing (dendropy.test.test_fitch.FitchTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 64, in test_pscores_with_gaps_as_missing
    self.verify_pscores("apternodus.chars.nexus", "apternodus.tre", True, expected_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 70, in verify_pscores
    "nexus")
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/datasetmodel.py", line 131, in _parse_and_create_from_stream
    state_alphabet_factory=charstatemodel.StateAlphabet,
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 253, in read_dataset
    global_annotations_target=dataset)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546,
----------------------------------------------------------------------
Ran 785 tests in 304.964s

FAILED (errors=4)
E: pybuild pybuild:262: test: plugin distutils failed with: exit code=1: python3.4 setup.py test 
dh_auto_test: pybuild --test -i python{version} -p 3.4 --dir . returned exit code 13
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 25
dpkg-buildpackage: error: debian/rules build gave error exit status 2
E: Failed autobuilding of package
I: user script /var/cache/pbuilder/build/cow.3528/tmp/hooks/C99_failed_build starting
Installing convenience apps: mc less bash-completion 
I: user script /var/cache/pbuilder/build/cow.3528/tmp/hooks/C99_failed_build finished
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
test_fitch.FitchTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 51, in test_pscores_with_gaps_as_new_state
    self.verify_pscores("apternodus.chars.nexus", "apternodus.tre", False, expected_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_fitch.py", line 70, in verify_pscores
    "nexus")
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/datasetmodel.py", line 131, in _parse_and_create_from_stream
    state_alphabet_factory=charstatemodel.StateAlphabet,
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 253, in read_dataset
    global_annotations_target=dataset)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

======================================================================
ERROR: test_pscores_with_standard_data_and_gaps_as_missing (dendropy.test.test_parsimony_scoring.ParsimonyScoringTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 139, in test_pscores_with_standard_data_and_gaps_as_missing
    expected_per_site_scores=expected_per_site_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 465, in verify_pscores
    taxon_namespace=taxon_namespace)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 606, in get
    return cls._get_from(**kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 157, in _get_from
    return cls.get_from_path(src=src, schema=schema, **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 527, in _parse_and_create_from_stream
    global_annotations_target=None)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 375, in read_char_matrices
    global_annotations_target=global_annotations_target)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

======================================================================
ERROR: test_pscores_with_standard_data_and_gaps_as_new_states (dendropy.test.test_parsimony_scoring.ParsimonyScoringTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 83, in test_pscores_with_standard_data_and_gaps_as_new_states
    expected_per_site_scores=expected_per_site_scores)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/test/test_parsimony_scoring.py", line 465, in verify_pscores
    taxon_namespace=taxon_namespace)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 606, in get
    return cls._get_from(**kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 157, in _get_from
    return cls.get_from_path(src=src, schema=schema, **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/basemodel.py", line 220, in get_from_path
    **kwargs)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/datamodel/charmatrixmodel.py", line 527, in _parse_and_create_from_stream
    global_annotations_target=None)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/ioservice.py", line 375, in read_char_matrices
    global_annotations_target=global_annotations_target)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 358, in _read
    self._parse_nexus_stream(stream)
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/nexusreader.py", line 546, in _parse_nexus_stream
    token = self._nexus_tokenizer.next_token()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 127, in next_token
    t = self.__next__()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 177, in __next__
    self._get_next_char()
  File "/tmp/buildd/python-dendropy-4.0.3/dendropy/dataio/tokenizer.py", line 263, in _get_next_char
    self._cur_char = self.src.read(1)
  File "/usr/lib/python3.4/encodings/ascii.py", line 26, in decode
    return codecs.ascii_decode(input, self.errors)[0]
UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 181: ordinal not in range(128)

----------------------------------------------------------------------
Ran 785 tests in 304.964s

FAILED (errors=4)
E: pybuild pybuild:262: test: plugin distutils failed with: exit code=1: python3.4 setup.py test 
dh_auto_test: pybuild --test -i python{version} -p 3.4 --dir . returned exit code 13