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

Andreas Tille andreas at an3as.eu
Wed Jul 29 11:52:41 UTC 2015 

Please note that these error occure only for the Python 3 version
started by 

python3.4 setup.py test.
-setup.py: None
-setup.py: using distutils
-setup.py: using canned package list
-setup.py: packages identified:
                                dendropy : dendropy
                      dendropy.calculate : dendropy/calculate
                         dendropy.dataio : dendropy/dataio
                      dendropy.datamodel : dendropy/datamodel
                        dendropy.interop : dendropy/interop
                         dendropy.legacy : dendropy/legacy
                        dendropy.mathlib : dendropy/mathlib
                          dendropy.model : dendropy/model
                       dendropy.simulate : dendropy/simulate
                           dendropy.test : dendropy/test
                        dendropy.utility : dendropy/utility
                dendropy.utility.libexec : dendropy/utility/libexec

-setup.py: scripts identified: applications/sumtrees/sumtrees.py
-setup.py: setuptools command extensions are available
coverage could not be imported: test coverage analysis not available
DendroPy version      : DendroPy 4.0.3
DendroPy location     : /tmp/buildd/python-dendropy-4.0.3/dendropy
Python version        : 3.4.3+ (default, Jul 28 2015, 13:17:50) [GCC 4.9.3]
Python executable     : /usr/bin/python3.4
Python site packages  : ['/usr/local/lib/python3.4/dist-packages', '/usr/lib/python3/dist-packages', '/usr/lib/python3.4/dist-packages', '/usr/lib/dist-python']
running test
running egg_info
writing dependency_links to DendroPy.egg-info/dependency_links.txt
writing entry points to DendroPy.egg-info/entry_points.txt
writing requirements to DendroPy.egg-info/requires.txt
writing top-level names to DendroPy.egg-info/top_level.txt
writing DendroPy.egg-info/PKG-INFO
reading manifest file 'DendroPy.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
-setup.py: coverage analysis not available
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.gitignore' found anywhere in distribution
warning: no previously-included files matching '.gitattributes' found anywhere in distribution
warning: no previously-included files matching '.idea' found anywhere in distribution
warning: no previously-included files matching '__pycache__' found anywhere in distribution
writing manifest file 'DendroPy.egg-info/SOURCES.txt'
running build_ext
PAUP interoperability not available: skipping PAUP tests
PAUP interoperability not available: skipping split counting tests
test_pscores_with_gaps_as_missing (dendropy.test.test_fitch.FitchTest) ... ERROR
test_pscores_with_gaps_as_new_state (dendropy.test.test_fitch.FitchTest) ... ERROR
test_product_of_credibilities (dendropy.test.test_tree_summarization_and_consensus.TestBasicCredibilityScoring) ... ok
...



Python 2 is OK and ends in

Ran 785 tests in 333.683s


Kind regards

        Andreas.
On Wed, Jul 29, 2015 at 01:27:30PM +0200, Andreas Tille wrote:
> 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

> ...
> 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

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