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 <andr...@an3as.eu> wrote: Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x To: "Michiel de Hoon" <mjldeh...@yahoo.com>, debian-powe...@lists.debian.org, debian-m...@lists.debian.org, debian-s...@lists.debian.org Cc: "Peter Cock" <p.j.a.c...@googlemail.com>, "Dejan Latinovic" <dejan.latino...@imgtec.com>, "Biopython discussion list" <biopyt...@lists.open-bio.org>, "751...@bugs.debian.org" <751...@bugs.debian.org>, "biopython-...@biopython.org" <biopython-...@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 <andr...@an3as.eu> wrote: > > Subject: Re: Bug#751277: python-biopython: FTBFS on mips* powerpc s390x > To: "Peter Cock" <p.j.a.c...@googlemail.com> > Cc: "Dejan Latinovic" <dejan.latino...@imgtec.com>, "Michiel de Hoon" <mjldeh...@yahoo.com>, "Biopython discussion list" <biopyt...@lists.open-bio.org>, "751...@bugs.debian.org" <751...@bugs.debian.org>, "biopython-...@biopython.org" <biopython-...@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 -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". 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