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

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Sep 29 04:31:18 EDT 2006


Sorry. I was sloppy,

I fixed the Bio::DB::GFF issues, and Brian worked on BPpsilite.pm yesterday.
I have no problems with CytoMap. All tests pass.

	-Heikki



On Thursday 28 September 2006 21:23, 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
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign

-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  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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