Latest upgrade of Numpy breaks tests of other packages (Was: Bug#848758: python-skbio: FTBFS: Test failures)

[Andreas Tille]

[Debian Science maintainers and Debian Med packaging in CC as warning]

Hi Sandro,

it seems the recent upgrade of numpy has broken some tests in other
packages like for instance this one in python-skbio.  I wonder whether
you are either able to suggest patches to get the tests working with the
new interface of numpy again or whether it might be sensible to revert
the upgrade of python-numpy to the previous version considering that we
are quite close to the freeze.

Kind regards

        Andreas.

On Mon, Dec 19, 2016 at 10:19:10PM +0100, Lucas Nussbaum wrote:
> Source: python-skbio
> Version: 0.5.1-1
> Severity: serious
> Tags: stretch sid
> User: debian-qa at lists.debian.org
> Usertags: qa-ftbfs-20161219 qa-ftbfs
> Justification: FTBFS on amd64
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
> 
> Relevant part (hopefully):
> >     multiple_comparisons_correction=None)
> >   File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", line 971, in ancom
> >     _logratio_mat = _log_compare(mat.values, cats.values, significance_test)
> >   File "/<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py", line 1084, in _log_compare
> >     arr=ratio)
> >   File "/usr/lib/python3/dist-packages/numpy/lib/shape_base.py", line 133, in apply_along_axis
> >     if res.shape == ():
> > AttributeError: 'F_onewayResult' object has no attribute 'shape'
> > 
> > ----------------------------------------------------------------------
> > Ran 2238 tests in 42.139s
> > 
> > FAILED (SKIP=30, errors=15)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose 
> > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned exit code 13
> > debian/rules:22: recipe for target 'override_dh_auto_test' failed
> 
> The full build log is available from:
>    http://aws-logs.debian.net/2016/12/19/python-skbio_0.5.1-1_unstable.log
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
> 
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