On Fri, Jul 17, 2009 at 3:52 AM, Marek Szuba <[email protected]> wrote:
> > On Thu, 16 Jul 2009 12:57:28 +0900 > Namshin Kim <[email protected]> wrote: > > > If you check annotation_hg18_megatest.py, you can see "sys.exit('wrong > > query')". The reason why I put this into this code is that pygr > > should NOT return slice object with NEGATIVE coordinates. But, some > > of NLMSA results falled into this part if you run megatest in > > Python2.4 and latest Pyrex. > At least it's something that is obviously wrong, rather than having > two subtly different versions of output... Is there, in your opinion, an > easy way of getting rid of such artifacts so that the comparison > performed in megatests can succeed? > Python2.4 and latest Pyrex give errors, not different version of output. Correct output (Collection and SQLTableClustered versions are same) is from Python2.5 and latest Pyrex. I think we may have to downgrade Pyrex if we want to use Python2.4. > > By the way, could you possibly push all the changes you've recently > made to megatest code to GitHub, for the benefit of those without > direct access to our new megatest machine? I had updated two database tables (pygr_snp126_hg18 and pygr_snp126_chrY_hg18) and three pre-calculated output files. The only thing we need to update is to get rid of "sys.exit" in annotation_hg18_megatest.py. I will update downloadable files in http://biodb.bioinformatics.ucla.edu. > > > > This error may not be the problem with the megatest, but it would be > > the problem with Python2.4 + latest Pyrex. > > > > Python2.5 + latest Pyrex works very well for all full version of > > megatest. > Looks like there is a pretty clear lesson coming out of this debacle... > We need megatests run on buildbots, at least once in a while. That way > we could guarantee that at least for a specific combination of > dependencies, megatests are supported by all set-ups Pygr itself runs > on. > > -- > MS > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "pygr-dev" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/pygr-dev?hl=en -~----------~----~----~----~------~----~------~--~---
