Hi Michiel,
thanks for testing this. Just to let you know: I personally need to
admit that I do not feel capable to verify your test for the next couple
of weeks.
Just from my gut feling I'd say: If you find a workaround here that's
probably helpful to run the test suite successfully.
Thanks again
Andreas.
On Sat, Aug 23, 2014 at 06:47:00PM -0700, Michiel de Hoon wrote:
> 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 <andr...@an3as.eu> wrote:
>
> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
> To: "Peter Cock" <p.j.a.c...@googlemail.com>
> Cc: "Dejan Latinovic" <dejan.latino...@imgtec.com>, "Michiel de Hoon"
> <mjldeh...@yahoo.com>, "Biopython discussion list"
> <biopyt...@lists.open-bio.org>, "751...@bugs.debian.org"
> <751...@bugs.debian.org>, "biopython-...@biopython.org"
> <biopython-...@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
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
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