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Chris Fields | 18 Sep 14:05
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Species.t tests failing with bioperl-live

I'm getting a couple of failed tests with

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign
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Chris Fields | 18 Sep 14:15
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Re: Species.t tests failing with bioperl-live


On Sep 18, 2008, at 7:07 AM, Chris Fields wrote:

> I'm getting a couple of failed tests with

Um, that was supposed to be:

I'm getting a couple of failed tests with Species.t; I think these are  
due to the last commit to Bio::Species:

http://code.open-bio.org/svnweb/index.cgi/bioperl/revision/?rev=14793

Tests pass after commenting out that line.

chris
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Chris Fields | 24 Sep 03:23
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Bio::Species bug, was Species.t tests failing with bioperl-live

I'm reposting this in case it was lost (or forgotten).  I'll file it  
as a bug if it's not addressed fairly soonish, but I would consider  
this a serious blocker for a 1.6 release.  Any help would be   
appreciated.

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?

chris

Begin forwarded message:

> From: Chris Fields <cjfields <at> illinois.edu>
> Date: September 18, 2008 7:15:03 AM CDT
> To: Chris Fields <cjfields <at> illinois.edu>
> Cc: BioPerl List <bioperl-l <at> lists.open-bio.org>
> Subject: Re: [Bioperl-l] Species.t tests failing with bioperl-live
>
>
> On Sep 18, 2008, at 7:07 AM, Chris Fields wrote:
>
>> I'm getting a couple of failed tests with
>
>
> Um, that was supposed to be:
>
> I'm getting a couple of failed tests with Species.t; I think these  
> are due to the last commit to Bio::Species:
(Continue reading)

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Sendu Bala | 26 Sep 10:26
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Re: Bio::Species bug, was Species.t tests failing with bioperl-live

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?
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Chris Fields | 26 Sep 14:20
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Re: Bio::Species bug, was Species.t tests failing with bioperl-live


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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Sendu Bala | 26 Sep 15:45
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Re: Bio::Species bug, was Species.t tests failing with bioperl-live

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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Chris Fields | 26 Sep 16:54
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Re: Bio::Species bug, was Species.t tests failing with bioperl-live


On Sep 26, 2008, at 8:45 AM, Sendu Bala wrote:

> 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

Probably something that will go away when we quit using Bio::Species  
altogether (in favor of Bio::Taxon) after 1.6.   I'm not sure whether  
it will be worth the trouble, but it's worth discussing.
(Continue reading)

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George Hartzell | 27 Sep 02:21
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Re: Bio::Species bug, was Species.t tests failing with bioperl-live

Chris Fields writes:
 > 
 > On Sep 26, 2008, at 8:45 AM, Sendu Bala wrote:
 > 
 > > 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
 > 
 > Probably something that will go away when we quit using Bio::Species  
 > altogether (in favor of Bio::Taxon) after 1.6.   I'm not sure whether
(Continue reading)

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