On Fri, Jun 13, 2014 at 11:05 PM, Andreas Tille <andr...@an3as.eu> wrote: > Hi Peter, > > thanks for your quick response. > > On Fri, Jun 13, 2014 at 02:57:37PM +0100, Peter Cock wrote: >> > 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? > > Yes, that's perfectly OK. It might happen that certain persons might be > busy with other things. I also see no point to waste the chance to make > new versions of BioPython even more popular - so let readers of the > Debian Med list know about what you are doing. > >> If so we can add that to our build process: >> http://biopython.org/wiki/Building_a_release > > +1
Done. We can add other Linux etc packaging contacts too... >> > 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. > > Usually all these tools are in sync. However, not all of these are > tested since most are missing unit tests - so BioPython is a great > test for these tools. Indirectly yes :) >> -- >> >> 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? > > I'll try to ask porters to check this patch on the different > architectures. I think Jakub is correct that the original problem is a big-endian issue, but it appears to have helped me spot a Python 3 specific problem in our error handling as well (the work on that branch). Thanks, Peter P.S. There is a problem with our mail server, which is being looked, at but some of these messages may have been lost and never appear on the Biopython archives :( -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org