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

[Daniel McDonald]

Okay, thank you. BIOM 2.0 requires pyqi 0.3.2, could you try upgrading
please?
-Daniel


On Wed, May 21, 2014 at 11:15 AM, Andreas Tille <andreas at an3as.eu> wrote:

> 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
> > >>
> > >
> > >
>
> --
> http://fam-tille.de
>
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