[Bioperl-l] 0.7.1 X-platform results for OpenBSD 2.8 i386 (AlignIO failing)

[Jason Stajich]

Ack, my stupidity strikes again.  Test before commit, test before
commit... 

Ialso fixed the t/Clustalw.t problems...

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?

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)
> > 
> > _______________________________________________
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> > 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/