[Bioperl-l] evalues/floating point tests

Chris Fields cjfields at illinois.edu
Sat Jan 17 17:22:31 EST 2009


If you have any additional errors post them here if you have time  
(particularly for Strawberry Perl):


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.


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

More information about the Bioperl-l mailing list