[Biopython] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
Michiel de Hoon
mjldehoon at yahoo.com
Tue Aug 19 00:18:41 UTC 2014
> I can provide SSH access
> to a PowerMac G5 running 7.6 if you'd like to test this.
That would be great. Then I can test it.
Best,
-Michiel.
--------------------------------------------
On Mon, 8/18/14, David Gosselin <dave at appleside.org> wrote:
Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x
To: "Andreas Tille" <andreas at an3as.eu>
Cc: "Michiel de Hoon" <mjldehoon at yahoo.com>, "debian-powerpc at lists.debian.org" <debian-powerpc at lists.debian.org>, "debian-mips at lists.debian.org" <debian-mips at lists.debian.org>, "debian-s390 at lists.debian.org" <debian-s390 at lists.debian.org>, "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, 8:43 PM
I can provide SSH access
to a PowerMac G5 running 7.6 if you'd like to test this.
> On Aug 18, 2014, at
4:01, Andreas Tille <andreas at an3as.eu>
wrote:
>
> 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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