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

[Andreas Tille]

Hi Daniel,

On Wed, May 21, 2014 at 10:46:42AM -0600, Daniel McDonald wrote:
> Hi Andreas,
> 
> Can you please confirm the version of pyqi being used?

0.3.1

Thanks for your and Gregs fast response

     Andreas.

> 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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