[Debian-med-packaging] Testsuite fails when trying to build Debian packages from python-biom-format

[Daniel McDonald]

Hi Andreas,

Can you please confirm the version of pyqi being used?

Thanks,
Daniel


On Wed, May 21, 2014 at 10:38 AM, Greg Caporaso <gregcaporaso at gmail.com>wrote:

> Hi Andreas,
> There is a minor issue with this release which is going to require us to
> build a 2.0.1 release. I'm adding Daniel McDonald to this message as he's
> more closely involved with this release than I am. Daniel, is this the
> issue that you guys are working on addressing?
>
> Thanks!
> Greg
>
>
> On Wed, May 21, 2014 at 8:59 AM, Andreas Tille <andreas at an3as.eu> wrote:
>
>> Hi Greg,
>>
>> I tried to build Debian packages from version 2.0 of biom-format but
>> got this test result when running the test suite:
>>
>>
>> EEE......................
>> ======================================================================
>> ERROR: Failure: NameError (global name '_type_handlers' is not defined)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 414, in
>> loadTestsFromName
>>     addr.filename, addr.module)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in
>> importFromPath
>>     return self.importFromDir(dir_path, fqname)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in
>> importFromDir
>>     mod = load_module(part_fqname, fh, filename, desc)
>>   File
>> "/tmp/buildd/python-biom-format-2.0.0+dfsg/.pybuild/pythonX.Y_2.7/build/biom/interfaces/html/config/convert.py",
>> line 57, in <module>
>>     Help='Process metadata associated with observations when '
>>   File
>> "/usr/lib/python2.7/dist-packages/pyqi/core/interfaces/html/__init__.py",
>> line 67, in __init__
>>     super(HTMLInputOption, self).__init__(Type=Type, **kwargs)
>>   File "/usr/lib/python2.7/dist-packages/pyqi/core/interface.py", line
>> 239, in __init__
>>     self._validate_option()
>>   File
>> "/usr/lib/python2.7/dist-packages/pyqi/core/interfaces/html/__init__.py",
>> line 123, in _validate_option
>>     elif type(self.Choices) not in (_type_handlers.TupleType,
>> types.ListType):
>> NameError: global name '_type_handlers' is not defined
>>
>> ======================================================================
>> ERROR: Failure: ImportError (cannot import name html_list_of_strings)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 414, in
>> loadTestsFromName
>>     addr.filename, addr.module)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in
>> importFromPath
>>     return self.importFromDir(dir_path, fqname)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in
>> importFromDir
>>     mod = load_module(part_fqname, fh, filename, desc)
>>   File
>> "/tmp/buildd/python-biom-format-2.0.0+dfsg/.pybuild/pythonX.Y_2.7/build/biom/interfaces/html/config/show_install_info.py",
>> line 25, in <module>
>>     from pyqi.core.interfaces.html.output_handler import
>> html_list_of_strings
>> ImportError: cannot import name html_list_of_strings
>>
>> ======================================================================
>> ERROR: Failure: ImportError (cannot import name
>> write_or_print_list_of_strings)
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 414, in
>> loadTestsFromName
>>     addr.filename, addr.module)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in
>> importFromPath
>>     return self.importFromDir(dir_path, fqname)
>>   File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in
>> importFromDir
>>     mod = load_module(part_fqname, fh, filename, desc)
>>   File
>> "/tmp/buildd/python-biom-format-2.0.0+dfsg/.pybuild/pythonX.Y_2.7/build/biom/interfaces/optparse/config/summarize_table.py",
>> line 23, in <module>
>>     from pyqi.core.interfaces.optparse.output_handler import (
>> ImportError: cannot import name write_or_print_list_of_strings
>>
>> ----------------------------------------------------------------------
>> Ran 25 tests in 0.245s
>>
>> FAILED (errors=3)
>> E: pybuild pybuild:256: test: plugin distutils failed with: exit code=1:
>> cd /tmp/buildd/python-biom-format-2.0.0+dfsg/.pybuild/pythonX.Y_2.7/build;
>> python2.7 -m nose --with-doctest.
>>
>>
>> Any hint?
>>
>> Kind regards
>>
>>         Andreas.
>>
>>
>> --
>> http://fam-tille.de
>>
>
>
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