[Bioperl-l] evalues/floating point tests

[Mark A. Jensen]

sounds good- MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "Mark A. Jensen" <maj at fortinbras.us>
Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Saturday, January 17, 2009 6:22 PM
Subject: Re: [Bioperl-l] evalues/floating point tests


> Oh, my guess is you'll see the same errors.  I didn't have a Windows  
> system to test on until yesterday so no changes were made until a  
> couple hours after RC3 was packaged up.  Unfortunately every test I've  
> seen has been from anything else but Windows.
> 
> A checkout and test of main trunk would help more, particularly after  
> the evalue and float_eq() commit (which may come down the pipe  
> tonight).  I can weed out the tests for modules not in the branch.
> 
> chris
> 
> On Jan 17, 2009, at 5:08 PM, Mark A. Jensen wrote:
> 
>> OK- I'll do a fresh build of RC3 and send the results- (I recall  
>> seeing the issue in the HSP tests some while back as well...)
>>
>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
>> >
>> To: "Mark A. Jensen" <maj at fortinbras.us>
>> Cc: "BioPerl List" <bioperl-l at lists.open-bio.org>
>> Sent: Saturday, January 17, 2009 5:22 PM
>> Subject: Re: [Bioperl-l] evalues/floating point tests
>>
>>
>>> Mark,
>>> If you have any additional errors post them here if you have time   
>>> (particularly for Strawberry Perl):
>>> http://www.bioperl.org/wiki/Release_1.6_Testing
>>> or you can send them in to me.  Related to Win installation I may  
>>> try  downloading ActivePerl for Mac OS X and test out PPM  
>>> connectivity if I  have time this weekend.
>>> I'm pretty sure the evalue issue has popped up before.  In fact,  
>>> Scott  Markel reported additional zeros appearing in evals, along  
>>> with file  name problems with Windows.
>>> chris
>>> On Jan 17, 2009, at 4:06 PM, Mark A. Jensen wrote:
>>>> I am getting these funky fails as well (ActiveState/Cygwin/Vista  
>>>> and  strawberry/Cygwin/Vista); I'm all for the kludge, should  
>>>> prevent a  LOT of chatter at support, but I can try to ferret out  
>>>> the  underlying issue.
>>>>
>>>> ----- Original Message ----- From: "Chris Fields" <cjfields at illinois.edu 
>>>>  >
>>>> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
>>>> Sent: Saturday, January 17, 2009 4:53 PM
>>>> Subject: [Bioperl-l] evalues/floating point tests
>>>>
>>>>
>>>>> I've noticed an odd issue when testing BioPerl on WinXP  
>>>>> yesterday   which doesn't appear to be popping up anywhere else.   
>>>>> When  comparing  floating point numbers, several tests fail like  
>>>>> the  following:
>>>>>
>>>>> #   Failed test at t\SearchIO\blast_pull.t line 40.
>>>>> #          got: '1e-23'
>>>>> #     expected: '1e-023'
>>>>>
>>>>> #   Failed test at t\SearchIO\blast_pull.t line 67.
>>>>> #          got: '6e-59'
>>>>> #     expected: '6e-059'
>>>>>
>>>>> These are generally in lines like (for the example above)
>>>>>
>>>>> is $result->get_parameter('expect'), 1e-23;
>>>>>
>>>>> I'm adding a method to Bio::Root::Test for comparing two  
>>>>> floating   point numbers based on equality:
>>>>>
>>>>> float_eq $float1, $float2, $message;
>>>>>
>>>>> This basically wraps is() but runs both values through   
>>>>> 'sprintf("%g",  $foo)' prior to the comparison; it has a  
>>>>> prototype  requiring two  values to be passed and an optional  
>>>>> message.  Any  objections to the  method name or adding this in?   
>>>>> I've already  converted many of the  tests in t/SearchIO over but  
>>>>> wanted to pass  it by the group prior to  an actual commit.
>>>>>
>>>>> chris
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>
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