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

Sat Dec 17 12:34:49 UTC 2016

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looking for now-outdated files...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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