[Bioperl-l] Bio::Species bug, was Species.t tests failing with bioperl-live
cjfields at illinois.edu
Fri Sep 26 10:54:55 EDT 2008
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:
>> 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
> 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.
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