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

Sendu Bala bix at sendu.me.uk
Fri Sep 26 09:45:21 EDT 2008


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


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