[Biopython] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Michiel de Hoon
mjldehoon at yahoo.com
Sat Aug 30 03:37:24 UTC 2014
Dear all,
With Dave kindly offering access to a PowerPC, I was able to fix this bug.
I have uploaded a fixed version of Bio/Cluster/clustermodule.c to the Biopython github repository; see
https://github.com/biopython/biopython/blob/master/Bio/Cluster/clustermodule.c
Can you try this version? This should solve the test failures.
Best,
-Michiel.
--------------------------------------------
On Mon, 8/18/14, Andreas Tille <andreas at an3as.eu> wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Michiel de Hoon" <mjldehoon at yahoo.com>, debian-powerpc at lists.debian.org, debian-mips at lists.debian.org, debian-s390 at lists.debian.org
Cc: "Peter Cock" <p.j.a.cock at googlemail.com>, "Dejan Latinovic" <Dejan.Latinovic at imgtec.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: Monday, August 18, 2014, 5:01 PM
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 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
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
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