[Bioperl-l] malloc errors while using Bio::SeqIO?

[Christopher Fields]

I'm pretty sure it's not due to a particular version of weaken(), though it does 
sound like a circular references issue.  I have tried this with perl 5.8.6, 5.8.8, 
and 5.10 (all Mac OS, either 10.4 or 10.5); all have the same memory leak 
issues.  

You can try using SeqBuilder to get rid of the Bio::Species object.  I'll give that a 
try when I can.  Unfortunately my laptop is now with the local Apple geniuses 
awaiting a motherboard, so I can't get to it right away (I'll give it a try on my 
wife's laptop).

chris

---- Original message ----
>Date: Sat, 9 Aug 2008 10:47:33 -0700
>From: "Rutger Vos" <rvos at interchange.ubc.ca>  
>Subject: Re: [Bioperl-l] malloc errors while using Bio::SeqIO?  
>To: "Hilmar Lapp" <hlapp at gmx.net>
>Cc: Chris Fields <cjfields at illinois.edu>, bioperl list <bioperl-l at lists.open-
bio.org>
>
>I am sure my version of weaken() works as advertised. Is there a way
>to turn off species storing from outside the code base or do you mean
>I go and start commenting bits out in Bio::SeqIO::genbank (or
>wherever)?
>
>On Sat, Aug 9, 2008 at 9:00 AM, Hilmar Lapp <hlapp at gmx.net> wrote:
>> This smells of circular references somewhere. I think the first point I
>> would go looking is the species storing - does the problem go away if you
>> turn that off? Maybe the version of weaken() is at play here?
>>
>>        -hilmar
>>
>> On Aug 9, 2008, at 10:15 AM, Chris Fields wrote:
>>
>>> Forgot to mention, maybe we can file this as a bug?  It's a pretty serious
>>> one but it should be easy to narrow down; the change had to be 
introduced
>>> fairly recently.
>>>
>>> chris
>>>
>>> On Aug 9, 2008, at 7:58 AM, Dave Messina wrote:
>>>
>>>>>
>>>>> I seem to vaguely recall that even if perl free()'s memory that doesn't
>>>>> necessarily mean that the memory is returned to the OS for the runtime
>>>>> of
>>>>> the program
>>>>
>>>>
>>>> I believe that's correct.
>>>>
>>>>
>>>>
>>>>> What OS are you on? I'm running perl 5.8.6 on OS X 10.4.11 intel.
>>>>>
>>>>
>>>> perl 5.10 or 5.8.8 on OS X 10.5.4 Intel.
>>>>
>>>>
>>>> Dave
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>> Christopher Fields
>>> Postdoctoral Researcher
>>> Lab of Dr. Marie-Claude Hofmann
>>> College of Veterinary Medicine
>>> University of Illinois Urbana-Champaign
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> 
=================================================
==========
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> 
=================================================
==========
>>
>>
>>
>>
>
>
>
>-- 
>Dr. Rutger A. Vos
>Department of zoology
>University of British Columbia
>http://www.nexml.org
>http://rutgervos.blogspot.com
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