[Biopython] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Michiel de Hoon
mjldehoon at yahoo.com
Sun Aug 24 01:47:00 UTC 2014
Hi Andreas,
I was able to replicate this bug on a PowerPC with Python 2.7, but only if I replace the single character into a single unicode character
(e.g. in line 212 of test_Cluster.py, if I replace method='a' by method=u'a').
Can you confirm that you get this bug with Python 2.7 even with simple strings rather than unicode?
Thanks,
-Michiel.
--------------------------------------------
On Sat, 8/16/14, Andreas Tille <andreas at an3as.eu> wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Peter Cock" <p.j.a.cock at googlemail.com>
Cc: "Dejan Latinovic" <Dejan.Latinovic at imgtec.com>, "Michiel de Hoon" <mjldehoon at yahoo.com>, "Biopython discussion list" <biopython at lists.open-bio.org>, "751277 at bugs.debian.org" <751277 at bugs.debian.org>, "biopython-dev at biopython.org" <biopython-dev at biopython.org>
Date: Saturday, August 16, 2014, 5:37 AM
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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