[Biopython] Bug#751277: python-biopython: FTBFS on mips* powerpc s390x

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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