[Bioperl-l] Bio::Species bug, was Species.t tests failing with bioperl-live
hartzell at alerce.com
Fri Sep 26 20:21:41 EDT 2008
Chris Fields writes:
> On Sep 26, 2008, at 8:45 AM, Sendu Bala wrote:
> > Chris Fields wrote:
> >> On Sep 26, 2008, at 3:26 AM, Sendu Bala wrote:
> >>> Chris Fields wrote:
> >>>> The last commit to Bio::Species, which was an effort to fix a
> >>>> memory leak, has unfortunately broken Species.t tests. The
> >>>> relevant commit used weaken(); my guess is something is being
> >>>> garbage collected way too early. Any ideas?
> >>> Was that last commit motivated by a bug report, and/or is there an
> >>> associated test? If not, perhaps it can just be reverted?
> >> Here's the relevant list thread:
> >> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/17541/focus=17550
> >> The proposed patch was George's, which gets rid of the leak but
> >> causes the Species.t failures. I say we revert the patch, but
> >> we'll still need to address the original problem addressed by
> >> Rutger Vos, i.e. that there is a significant memory leak in
> >> Bio::Species.
> > Thanks. Rather than revert I've kludged it for now. Everything
> > should be fine, it's just that I fear my solution isn't 'correct'
> > and could mess things up we don't happen to have tests for.
> > See http://bugzilla.open-bio.org/show_bug.cgi?id=2594
> Probably something that will go away when we quit using Bio::Species
> altogether (in favor of Bio::Taxon) after 1.6. I'm not sure whether
> it will be worth the trouble, but it's worth discussing.
> Anyway, I'm still a bit unfamiliar with some aspects of Bio::Species
> (and I'm pretty busy ATM) so it make take a few days.
I can try to take a look at it again and see if there's a way to make
it work [more] correctly.
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