[Bioperl-l] Failing tests, was Re: Simplifications now possible with Perl 5.6.1requirement?

Chris Fields cjfields at uiuc.edu
Thu Sep 28 15:53:31 EDT 2006


I committed a fix for Bio::DB::GFF (extra quote), which fixed  
BioGraphics.t and BioDBGFF.t test failures.  The other two, CytoMap.t  
and BPpsilite.t, I haven't had a chance to look at and can't get  
until later tomorrow.

Chris

On Sep 28, 2006, at 2:23 PM, Chris Fields wrote:

> I'm getting a few failed tests on Mac OS X:
>
> Failed Test     Stat Wstat Total Fail  List of Failed
> ---------------------------------------------------------------------- 
> --
> -------
> t/BPpsilite.t      9  2304    11    6  9-11
> t/BioDBGFF.t     255 65280   276  552  1-276
> t/BioGraphics.t  255 65280    14   28  1-14
> t/CytoMap.t       22  5632   110   14  104-110
> 5 subtests skipped.
> Failed 4/241 test scripts. 300/12479 subtests failed.
> Files=241, Tests=12479, 413 wallclock secs (107.53 cusr + 14.85 csys
> = 122.38 CPU)
> Failed 4/241 test programs. 300/12479 subtests failed.
>
> This was from a clean checkout.
>
> Chris
>
>
> On Sep 28, 2006, at 1:51 PM, Heikki Lehvaslaiho wrote:
>
>> On Tuesday 26 September 2006 16:29, Chris Fields wrote:
>>>>> open my $FH, '>', $infile
>>>>> # instead of
>>>>> open FH, ">$infile";
>>>>
>>>> The latter form has caused at least one bug, so this is worth  
>>>> taking
>>>> note of.
>>>
>>> Agreed.  Localized filehandles cut down on a lot of problems.
>>>
>>
>> I've changed all file handles I could find into lexically scoped
>> ones. In many
>> cases the three argument form is used.
>>
>> 	-Heikki
>>
>> --
>> ______ _/      _/ 
>> _____________________________________________________
>>       _/      _/
>>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>>     _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
>>    _/  _/  _/  SANBI, South African National Bioinformatics Institute
>>   _/  _/  _/  University of Western Cape, South Africa
>>      _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
>> ___ _/_/_/_/_/ 
>> ________________________________________________________
>> _______________________________________________
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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