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

Sat Dec 17 22:53:23 UTC 2016

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 looking for now-outdated files...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.

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