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

[Rutger Vos]

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