[Bioperl-l] Variation_IO.t [was: External dependencies]

[Ewan Birney]

On Mon, 18 Dec 2000, Jason Stajich wrote:

> I tested Variation_IO.t on irix 6.5, perl 5.004_04 
> 
> got this error for make test on Variation_IO.t
> t/Variation_IO......Ambiguous use of id => resolved to "id" => at
> blib/lib/Bio/Variation/SeqDiff.pm line 915.
> couldn't wrap
> 'I>TRTRAPGTQRPRAQHLPAPVCCCCSSSSSSSSSSSSSSSSSSSSKRLAPGSSSSSRVRMVLPKPIVEAPQATWSWMRNSNLHSRSRPWSATPREVASQSLEPPWPPARGCRSSCQHLRTRMTQLPHPRCPCWAPLSPA*'
> at /usr/share/lib/perl5/Text/Wrap.pm line 58, <GEN0> chunk 11.
> dubious
>         Test returned status 2 (wstat 512, 0x200)
> Number found where operator expected at (eval 103) line 1, near "*(512"
>         (Missing operator before 512?)
> DIED. FAILED tests 4-26
>         Failed 23/26 tests, 11.54% okay
> 
> perl5.004 or irix is actually really picky - complaining about dos
> linefeeds and is also  doing this for both DB.t and game.t in the BEGIN
> block where we tell it to skip this test, I am really not sure why this
> happens - in fact any print statement in the block seems to spawn
> uninitialized messages...

Hmmm. Are you up to date? I squashed some of these things 2 days ago...


> 
> t/game..............XML::Parser::PerlSAX not loaded. This means game test
> cannot be executed. Skipping
> Use of uninitialized value at t/game.t line 26.
> Use of uninitialized value at t/game.t line 27.
> Use of uninitialized value at t/game.t line 28.
> Use of uninitialized value at t/game.t line 29.
> ok
> 
> -jason
> On Sun, 17 Dec 2000, Heikki Lehvaslaiho wrote:
> 
> > We better move this discussion back to bioperl-l so that other can
> > help. I've never ran perl in a Mac.
> > 
> > It seems to me that either the XML modules are not installed properly
> > or the 
> > Variation_IO.t is not going through the motions as it should.
> > 
> > 	-Heikki
> > 
> > Todd Richmond wrote:
> > > 
> > > On 12/15/00 1:30 AM, "Heikki Lehvaslaiho" <heikki@ebi.ac.uk> wrote:
> > > 
> > > >
> > > > I think I know what is going on. In perl distribution 5.004 and before
> > > > Text::Wrap (version 97.011701) was able to wrap only on word boundary.
> > > > The latest version (98.112902) has this fixed.
> > > >
> > > 
> > > This indeed fixes the problem - however, it appears that not all of the
> > > tests are run. It starts with "1..26", then runs through the first 17 tests
> > > successfully and then just stops. Two new files are created:
> > > "mutations.out.xml" and "polymorphism.out.xml", but they are both empty. In
> > > addition, to run the tests on a Mac, I had to remove the "t/" from in front
> > > of the file names within Variation_IO.t, because otherwise it couldn't find
> > > them. This is probably a problem with the calling directory and differences
> > > between Unix and MacOS in defining what that is. Moving Variation_IO.t up
> > > one level outside of the "t" directory failed to fix the problem (which is
> > > where I assume the "make test" would have been run from).
> > > 
> > > --
> > > Dr Todd Richmond                 http://cellwall.stanford.edu/todd
> > > Carnegie Institution             email: todd@andrew2.stanford.edu
> > > Department of Plant Biology      fax: 1-650-325-6857
> > > 260 Panama Street                phone: 1-650-325-1521 x431
> > > Stanford, CA 94305
> > 
> > -- 
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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