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

[Greg Caporaso]

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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