[Bioperl-l] Variation_IO.t [was: External dependencies]
Jason Stajich
jason@chg.mc.duke.edu
Mon, 18 Dec 2000 17:57:15 -0500 (EST)
On Mon, 18 Dec 2000, Ewan Birney wrote:
> 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...
yeah, build is up to date, but the sgi machine I can get on is running
with Text::Wrap module version 97.011701, perl 5.004_04 ( which I know
Heikki said causes problems). We can always skip tests if Text::Wrap
version is not at least > 97.011701.
-jason
>
>
> >
> > 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>.
> -----------------------------------------------------------------
>
>
Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/