[Bioperl-l] evalues/floating point tests
cjfields at illinois.edu
Sat Jan 17 23:22:05 UTC 2009
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.
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
>> 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.
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
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