[Debian-med-packaging] Bug#848410: python-biom-format: FTBFS randomly (failing tests)

[Greg Caporaso]

Hi Andreas, I'm cc'ing Daniel McDonald on this message, who is the primary
maintainer of the biom-format package these days. Daniel, could you follow
up with Andreas?

On Sat, Dec 17, 2016 at 3:53 PM, Andreas Tille <andreas at an3as.eu> wrote:

> Hi Greg,
>
> the Debian packaged biom-format received a bug report which leaves me
> clueless how to track it down.  Is there possibly some way to make the
> test suite more verbose to find out what part might cause the random
> failure which you can see in the buil logs linked from the bug page
>
>    https://bugs.debian.org/848410
>
> Thanks for any idea to track this down
>
>       Andreas.
>
> On Sat, Dec 17, 2016 at 01:34:49PM +0100, Santiago Vila wrote:
> > Package: src:python-biom-format
> > Version: 2.1.5+dfsg-5
> > Severity: serious
> >
> > Dear maintainer:
> >
> > I tried to build this package in stretch with "dpkg-buildpackage -A"
> > (which is what the "Arch: all" autobuilder would do to build it)
> > but it failed:
> >
> > ------------------------------------------------------------
> --------------------
> > [...]
> >  debian/rules build-indep
> > dh build-indep --with python2,python3,bash-completion,sphinxdoc
> --buildsystem=pybuild
> >    dh_testdir -i -O--buildsystem=pybuild
> >    dh_update_autotools_config -i -O--buildsystem=pybuild
> >    dh_auto_configure -i -O--buildsystem=pybuild
> >       pybuild --configure --test-nose -i python{version} -p 2.7
> > I: pybuild base:184: python2.7 setup.py config
> > running config
> >       pybuild --configure --test-nose -i python{version} -p 3.5
> > I: pybuild base:184: python3.5 setup.py config
> > running config
> >    debian/rules override_dh_auto_build
> > make[1]: Entering directory '/<<BUILDDIR>>/python-biom-
> format-2.1.5+dfsg'
> >
> > [... snipped ...]
> >
> > ImportError: No module named _filter
> > /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/doc/
> documentation/table_objects.rst:1: WARNING: autodoc: failed to import
> module u'biom.table'; the following exception was raised:
> > Traceback (most recent call last):
> >   File "/usr/lib/python2.7/dist-packages/sphinx/ext/autodoc.py", line
> 526, in import_object
> >     __import__(self.modname)
> >   File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/biom/__init__.py",
> line 53, in <module>
> >     from .table import Table
> >   File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/biom/table.py",
> line 195, in <module>
> >     from ._filter import _filter
> > ImportError: No module named _filter
> > looking for now-outdated files... none found
> > pickling environment... done
> > checking consistency... done
> > writing... biom.1 { documentation/index documentation/biom_format
> documentation/format_versions/biom-1.0 documentation/format_versions/biom-2.0
> documentation/format_versions/biom-2.1 documentation/quick_usage_examples
> documentation/table_objects documentation/biom_conversion
> documentation/adding_metadata documentation/summarizing_biom_tables
> BIOM_LICENSE }
> > build succeeded, 3 warnings.
> > make[1]: Leaving directory '/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg'
> >    dh_auto_test -i -O--buildsystem=pybuild
> >       pybuild --test --test-nose -i python{version} -p 2.7
> > I: pybuild pybuild:212: cp -r /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/examples
> /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/tests
> /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build
> > I: pybuild base:184: cd /<<BUILDDIR>>/python-biom-
> format-2.1.5+dfsg/.pybuild/pythonX.Y_2.7/build; python2.7 -m nose tests
> > ............................................................
> ............................................................
> ............................................................
> ............................................................
> ...........S.............
> > ----------------------------------------------------------------------
> > Ran 265 tests in 3.736s
> >
> > OK (SKIP=1)
> >       pybuild --test --test-nose -i python{version} -p 3.5
> > I: pybuild pybuild:212: cp -r /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/examples
> /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/tests
> /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build
> > I: pybuild base:184: cd /<<BUILDDIR>>/python-biom-
> format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose tests
> > ............................................................
> ............................................................
> ............................................................
> ............................................................
> ...........S......F......
> > ======================================================================
> > FAIL: test_generate_subsamples (tests.test_util.UtilTests)
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "/<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/
> pythonX.Y_3.5/build/tests/test_util.py", line 58, in
> test_generate_subsamples
> >     (3, 1, 1)})
> > AssertionError: Items in the second set but not the first:
> > (3, 0, 0)
> >
> > ----------------------------------------------------------------------
> > Ran 265 tests in 3.575s
> >
> > FAILED (SKIP=1, failures=1)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1:
> cd /<<BUILDDIR>>/python-biom-format-2.1.5+dfsg/.pybuild/pythonX.Y_3.5/build;
> python3.5 -m nose tests
> > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5
> returned exit code 13
> > debian/rules:18: recipe for target 'build-indep' failed
> > make: *** [build-indep] Error 25
> > dpkg-buildpackage: error: debian/rules build-indep gave error exit
> status 2
> > ------------------------------------------------------------
> --------------------
> >
> > The failure happens randomly on the single-CPU KVM/QEMU virtual machines
> > I use as autobuilders. The approximate failure rate is about 1%.
> >
> > I attach several build logs (made on different autobuilders).
> >
> > If you could not reproduce this using sbuild on a single CPU virtual
> > machine (as I did), of course trying a lot of times (because of the
> > failure rate above), please do not downgrade or mark as unreproducible,
> > I would then consider giving you access to a virtual machine on which
> > I can reproduce it so that you can as well. (In such case, please
> > contact me off-list for details).
> >
> > Thanks.
>
>
>
>
>
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at lists.alioth.debian.org
> > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/
> debian-med-packaging
>
>
> --
> http://fam-tille.de
>
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