[Bioperl-l] Performance of Bio::Species

Sendu Bala bix at sendu.me.uk
Sat Nov 25 08:57:53 EST 2006


Chris Fields wrote:
> 
> On Nov 25, 2006, at 6:47 AM, Sendu Bala wrote:
> ...
> 
>> I think the Tree actually only keeps a ref to its root Node, which means
>> Nodes in general must keep hard refs to their Descendants. With that
>> constraint, I haven't been able to break the deadlock and get these
>> things to clean up.
>>
>> Hopefully I'm missing something obvious; please look into it.
> 
> I'm curious to see if this affects sequence parsing (i.e. SwissProt DB 
> parsing).  Does anyone know?  It sounds pretty serious.

Any time you create lots of Bio::Species objects the memory leak ought 
to arise.


> Sendu, could you commit a bug report for this?  I don't think this 
> should hold up rel 1.5.2 (it's a dev release) but it would be nice to 
> get it fixed.

http://bugzilla.open-bio.org/show_bug.cgi?id=2149


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