[Bioperl-l] Re: GFF3

[Allen Day]

doh!  my bad.

On Wed, 19 Jan 2005, Jason Stajich wrote:

> test count was off.
> 1..19
> [SNIP]
> ok 20
> ok 21
> ok 22
> 
> You can also try
> % make test_FeatureIO
> to run just a specific test within the test framework to look at things.
> 
> Fixed.
> On Jan 19, 2005, at 6:30 PM, Scott Cain wrote:
> 
> > Weird: when I run the FeatureIO test on the command line (via `perl
> > t/FeatureIO.t`), all tests pass.  When I run it as part of 'make test',
> > tests 20-22 fail.  Does anyone know why that sort of thing might  
> > happen?
> >
> > thanks,
> > Scott
> >
> > ----------------------------------------------------------------------
> > Scott Cain, Ph. D.				 	 cain at cshl.org
> > GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
> > ----------------------------------------------------------------------
> >
> >
> > On Wed, 19 Jan 2005, Allen Day wrote:
> >
> >> okay, let me know.  we should probably add some validation tests as  
> >> well,
> >> right now i'm just making sure the lines can be processed but don't  
> >> do any
> >> typechecking on the document.
> >>
> >> Rob, would you mind writing some tests into FeatureIO.t for your
> >> validation code?
> >>
> >> -allen
> >>
> >>
> >> On Wed, 19 Jan 2005, Scott Cain wrote:
> >>
> >>> I just did a cvs update and the last few tests are failing on MacOSX  
> >>> 10.3.
> >>> I'll try to sort it out over the next couple of days.
> >>>
> >>> Scott
> >>>
> >>> --------------------------------------------------------------------- 
> >>> -
> >>> Scott Cain, Ph. D.				 	 cain at cshl.org
> >>> GMOD Coordinator, http://www.gmod.org/			 (216)392-3087
> >>> --------------------------------------------------------------------- 
> >>> -
> >>>
> >>>
> >>> On Tue, 18 Jan 2005, Allen Day wrote:
> >>>
> >>>>> The first series of errors die because the feature ID=AB000114 in
> >>>>> t/data/knownGene.gff3 has several Dbxrefs separated with ';'  
> >>>>> instead of
> >>>>> ','
> >>>>
> >>>> i'm not getting these errors, are you are in sync with cvs HEAD?
> >>>>
> >>>>> The second failure is because  hybrid1.gff3 isn't in cvs
> >>>>
> >>>> gff files are in cvs now.
> >>>>
> >>>>>
> >>>>> Rob
> >>>>>
> >>>>>
> >>>>>
> >>>>> % perl -I. -w t/FeatureIO.t
> >>>>> 1..19
> >>>>> ok 1
> >>>>> ok 2
> >>>>> ok 3
> >>>>> ok 4
> >>>>> ok 5
> >>>>> ok 6
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 590, <GEN5> line 10.
> >>>>> Use of uninitialized value in substitution (s///) at
> >>>>> Bio/FeatureIO/gff.pm line 591, <GEN5> line 10.
> >>>>> Use of uninitialized value in split at Bio/FeatureIO/gff.pm line  
> >>>>> 593,
> >>>>> <GEN5> line 10.
> >>>>> ok 7
> >>>>> ok 8
> >>>>>
> >>>>> ------------- EXCEPTION  -------------
> >>>>> MSG: Could not open t/data/hybrid1.gff3: No such file or directory
> >>>>> STACK Bio::Root::IO::_initialize_io Bio/Root/IO.pm:314
> >>>>> STACK Bio::FeatureIO::_initialize Bio/FeatureIO.pm:345
> >>>>> STACK Bio::FeatureIO::gff::_initialize Bio/FeatureIO/gff.pm:92
> >>>>> STACK Bio::FeatureIO::new Bio/FeatureIO.pm:268
> >>>>> STACK Bio::FeatureIO::new Bio/FeatureIO.pm:288
> >>>>> STACK toplevel t/FeatureIO.t:83
> >>>>>
> >>>>> --------------------------------------
> >>>>>
> >>>>
> >>>
> >>
> >
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> >
> >
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>