[Bioperl-l] Variation_IO.t [was: External dependencies]
Heikki Lehvaslaiho
heikki@ebi.ac.uk
Tue, 19 Dec 2000 10:09:57 +0000
Jason,
Could you cvs update and try again. I added the quotes around -id and
put in the test the dependency to Text::Wrap 98. I can not test this
properly as my systems all have the latest Text::Wrap module.
-Heikki
Jason Stajich wrote:
>
> 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/
--
______ _/ _/_____________________________________________________
_/ _/ 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
___ _/_/_/_/_/________________________________________________________