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

Chris Fields cjfields at illinois.edu
Fri Sep 26 08:20:45 EDT 2008


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.

chris


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