Hi Andreas, Jakub, On Fri, Jun 13, 2014 at 1:55 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi BioPython developers, > > I have updated the Debian package to version 1.64 (BTW, it is fine to > ping debian-...@lists.debian.org about new upstream versions - we might > become more quick in packaging new versions).
Good point. I used to email the Phillipe & Charles when there was a change I anticipated might cause trouble. Should we just email debian-...@lists.debian.org after each new Biopython release? If so we can add that to our build process: http://biopython.org/wiki/Building_a_release > Thanks for adopting the patches we sended to you. > No problem - while some of your tweaks are Debian specific, where it makes sense to incorporate fixes into Biopython we try to do that. > Since the Debian package is built on different hardware architectures, > we were facing different problems in the test suite. Here you have an > overview about all build logs: > > > https://buildd.debian.org/status/package.php?p=python-biopython&suite=unstable > > Jakub Wilk was kind enough to point to the real problems of the tests > which can be read below (since the end of the build log does not say > a lot). > > It would be great if you give some advise how to deal with these > problems. Most of these are tests where we call an external command line tool (i.e. muscle, dnal, dialign2-2). The purpose of the tests is in part to check our command line wrappers are current (and catch any API changes), but also in many cases to check we can parse the current output (to catch any format changes). I would *guess* that some of these platforms have problems in these underlying tools - or a very different version is being tested? i.e. Older than the mainstream platforms. -- The final category of failures was from test_Cluster.py under powerpc and s390x, under Python 3.4, which suggests it could be something in the C code for Bio.Cluster - probably Python 3 specific. >From line 138-141, clusterid, error, nfound = kcluster(data, nclusters=nclusters, mask=mask, weight=weight, transpose=0, npass=100, method='a', dist='e') Line 210-212, distance = clusterdistance(data, mask=mask, weight=weight, index1=c1, index2=c2, dist='e', method='a', transpose=0) Line 289-290, tree = treecluster(data=data1, mask=mask1, weight=weight1, transpose=0, method='a', dist='e') Line 555-557, clusterid, celldata = somcluster(data=data, mask=mask, weight=weight, transpose=0, nxgrid=10, nygrid=10, inittau=0.02, niter=100, dist='e') This all give the following error via C function distance_converter in Bio/Cluster/clustermodule.c ValueError: distance should be a single character Yet in all those examples, dist='e' which is a single character... The good news is I can reproduce a related problem on Mac OS X under Python 3.3 and 3.4 where this error is not raised: Test branch: https://github.com/peterjc/biopython/tree/cluster_single_char This commit makes the error messages more explicit: https://github.com/peterjc/biopython/commit/fa597040cfb7e5f18d55257367397e88274563b8 This commit verifies the errors are thrown (and they are not under Python 3 on the Mac): https://github.com/peterjc/biopython/commit/5b99854a82f08321ad78feaf0b362002d2d1fd2b I'm going to have to pass this one to Michiel to look at... but it looks like a glitch in the bytes vs unicode handling, which for some reason mostly works - but breaks under some unusual platforms? Thanks, Peter -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
