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 <[email protected]> wrote:
>
> Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
> To: "Peter Cock" <[email protected]>
> Cc: "Dejan Latinovic" <[email protected]>, "Michiel de Hoon"
> <[email protected]>, "Biopython discussion list"
> <[email protected]>, "[email protected]"
> <[email protected]>, "[email protected]"
> <[email protected]>
> 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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