[Bioperl-l] Bio::Species bug, was Species.t tests failing with bioperl-live

[Chris Fields]

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.

chris