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

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 <[email protected]> wrote:

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