[Debian-med-packaging] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x

Mon Aug 18 11:43:10 UTC 2014

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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