[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x

[Andreas Tille]

Hi Peter,

On Thu, Aug 14, 2014 at 09:52:40AM +0100, Peter Cock wrote:
> >
> >   1. waiting for your confirmation / patch
> >   2. deactivating the specific test
> >   3. exclude mips for biopython
> >   4. ? any better idea ?
> >
> > In the current state all the work we spent in biopython over the last
> > monthes will not migrate to testing for the simple reason that the
> > current package in testing just does not run the test suite at build
> > time and moreover python3 is not supported.
> >
> > Kind regards
> >
> >      Andreas.
> 
> I would suggest (2), deactivate this test (at least for for mips) as
> the most practical short term solution for the Debian packages.
> Or if you prefer (3), don't target mips for the Biopython package
> (yet).
> 
> Medium term, I hope we can fix the C code to handle either
> Endian platform - option (1).

It seems after having fixed the issue caused by wise we have one
remaining problem:

  On powerpc[1] and s390x[2] test_Cluster fails even with Python 2.7 with:

======================================================================
ERROR: test_clusterdistance (test_Cluster.TestCluster)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 212, in test_clusterdistance
    method='a', transpose=0)
ValueError: method should be a single character

======================================================================
ERROR: test_kcluster (test_Cluster.TestCluster)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 141, in test_kcluster
    method='a', dist='e')
ValueError: method should be a single character

======================================================================
ERROR: test_somcluster (test_Cluster.TestCluster)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 557, in test_somcluster
    inittau=0.02, niter=100, dist='e')
ValueError: distance should be a single character

======================================================================
ERROR: test_treecluster (test_Cluster.TestCluster)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/«BUILDDIR»/python-biopython-1.64+dfsg/.pybuild/pythonX.Y_3.4/build/Tests/test_Cluster.py", line 290, in test_treecluster
    transpose=0, method='a', dist='e')
ValueError: method should be a single character

----------------------------------------------------------------------
Ran 210 tests in 293.712 seconds

FAILED (failures = 1)


On sparc[3] there is a problem with dialign but sparc is no release
architecture and wie might ignore this.  It might be a helpful hint
anyway.

Any hint for the test_Cluster problem?  If not I would also consider to
hide it cowardly under the carpet for the moment.  The new package is so
much better tested than the one in the testing distribution which does
not even dare about any unit tests and only for this reason reached the
testing distribution.

What do you think?

Kind regards

       Andreas.

scrool these links to the end to see the problem:

[1] https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=powerpc&ver=1.64%2Bdfsg-3&stamp=1408116532
[2] https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=s390x&ver=1.64%2Bdfsg-3&stamp=1408107524
[3] https://buildd.debian.org/status/fetch.php?pkg=python-biopython&arch=sparc&ver=1.64%2Bdfsg-3&stamp=1408130792

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