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 <andr...@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 <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-powerpc-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: https://lists.debian.org/20140818080110.gi5...@an3as.eu > -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
