[Bioperl-l] 0.7.1 X-platform results for OpenBSD 2.8 i386 (AlignIO
failing)
Heikki Lehvaslaiho
heikki@ebi.ac.uk
Tue, 12 Jun 2001 14:09:53 +0100
Jason Stajich wrote:
>
> Ack, my stupidity strikes again. Test before commit, test before
> commit...
>
> Ialso fixed the t/Clustalw.t problems...
Jason, we are working on same modules now. I am getting merge
conflicts all the time. (My fault, I have been keeping my changes
private and not committed them.)
> Hmm, using private state outside the class is bad, any objections to
> adding an 'order' method rather than using private state here?
>
> I guess this won't be part of the branch since it necessitates an api
> change, but on the main trunk?
There is a method get_seq_by_pos(); only in the main trunk. I've
started using it to fix the clustaw.t problems.
-Heikki
> On Tue, 12 Jun 2001, Heikki Lehvaslaiho wrote:
>
> >
> > Fixed.
> >
> > The tests are accessing private data variables directly and they were
> > not using the recently added underscore in the variable name (as in
> > '_order').
> > The head of bioperl live has a method for this so this will not happen
> > again.
> >
> > -Heikki
> >
> > chris dagdigian wrote:
> > >
> > > output of 'make test'
> > > =================================
> > > Failed Test Status Wstat Total Fail Failed List of failed
> > > -------------------------------------------------------------------------------
> > > t/AlignIO.t 18 10 55.56% 2, 4, 6, 8, 10, 12-13,
> > > 15-16, 18
> > > 24 subtests skipped.
> > > Failed 1/60 test scripts, 98.33% okay. 10/991 subtests failed, 98.99% okay.
> > > *** Error code 255
> > >
> > > Stop in /home/dag/bioperl/branch-07 (line 1152 of Makefile).
> > >
> > > output of 'perl t/AlignIO.t'
> > >
> > > ============================
> > >
> > > cvs:branch-07 {139} perl t/AlignIO.t
> > > 1..18
> > > ok 1
> > > not ok 2
> > > # Test 2 got: <UNDEF> (t/AlignIO.t at line 21)
> > > # Expected: '1433_LYCES-9-246'
> > > ok 3
> > > not ok 4
> > > # Test 4 got: <UNDEF> (t/AlignIO.t at line 27)
> > > # Expected: '1433_LYCES-9-246' ( failed pfam input test)
> > > ok 5
> > > not ok 6
> > > # Test 6 got: <UNDEF> (t/AlignIO.t at line 36)
> > > # Expected: '1433_LYCES-9-246' ( failed msf input test)
> > > ok 7
> > > not ok 8
> > > # Test 8 got: <UNDEF> (t/AlignIO.t at line 47)
> > > # Expected: 'AK1H_ECOLI-114-431' ( failed fasta input test )
> > > ok 9
> > > not ok 10
> > > # Test 10 got: <UNDEF> (t/AlignIO.t at line 57)
> > > # Expected: 'AK1H_ECOLI-114-431' ( failed selex format test )
> > > ok 11
> > > not ok 12
> > > # Test 12 got: <UNDEF> (t/AlignIO.t at line 65)
> > > # Expected: 'AK1H_ECOLI-1-318' ( failed mase input test )
> > > not ok 13
> > > # Test 13 got: <UNDEF> (t/AlignIO.t at line 69)
> > > # Expected: 'P04777-1-33' ( failed prodom input test )
> > > ok 14
> > > not ok 15
> > > # Test 15 got: <UNDEF> (t/AlignIO.t at line 79)
> > > # Expected: 'P04777-1-33' ( failed clustalw (.aln) output test - was )
> > > not ok 16
> > > # Test 16 got: <UNDEF> (t/AlignIO.t at line 85)
> > > # Expected: 'AK1H_ECOLI-114-431' ( failed filehandle input test )
> > > ok 17
> > > not ok 18
> > > # Test 18 got: <UNDEF> (t/AlignIO.t at line 94)
> > > # Expected: 'ALEU_HORVU -60-360' (failed BLAST bl2seq format test)
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > --
> > ______ _/ _/_____________________________________________________
> > _/ _/ 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/
--
______ _/ _/_____________________________________________________
_/ _/ 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
___ _/_/_/_/_/________________________________________________________