Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Hi porters,
could you please be so kind to check this issue? It would be great to
find out why the test suite of biopython fails on these architectures.
Thanks a lot
Andreas.
On Mon, Aug 18, 2014 at 12:35:53AM -0700, Michiel de Hoon wrote:
> Hi Andreas,
>
> Without access to powerpc, I have no way to test the code.
> Can you try recompiling Biopython and checking what exactly happens inside the distance_converter function in Bio/Cluster/clustermodule.c ?
> For example, I am really wondering what strlen(data) inside this function returns on powerpc.
>
> Best,
> -Michiel.
>
> --------------------------------------------
> On Sat, 8/16/14, Andreas Tille <andreas@an3as.eu> wrote:
>
> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
> To: "Peter Cock" <p.j.a.cock@googlemail.com>
> Cc: "Dejan Latinovic" <Dejan.Latinovic@imgtec.com>, "Michiel de Hoon" <mjldehoon@yahoo.com>, "Biopython discussion list" <biopython@lists.open-bio.org>, "751277@bugs.debian.org" <751277@bugs.debian.org>, "biopython-dev@biopython.org" <biopython-dev@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
>
>
--
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