[Bioperl-l] evalues/floating point tests
Mark A. Jensen
maj at fortinbras.us
Sat Jan 17 18:08:13 EST 2009
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
>>> # 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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