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

[Jason Stajich]

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...

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
> ___ _/_/_/_/_/________________________________________________________
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/