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

[Heikki Lehvaslaiho]

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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-- 
______ _/      _/_____________________________________________________
      _/      _/                      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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