[Bioperl-l] tests failing miserably

Heikki Lehvaslaiho heikki at ebi.ac.uk
Thu May 15 11:43:46 EDT 2003


The CoordinateMapper.t error comes from Bio::Coordinate::Util and is
caused by a change in consensus string from an Bio::SimpleAlign object
(that is, compared to 1.2 branch). I'll look into it later unless
someone understands what is going on in there better and can fix it
quickly.

	-Heikki

On Thu, 2003-05-15 at 02:48, Hilmar Lapp wrote:
> I've got Genpred.t, Pictogram.t, est2genome.t, and hmmer.t fixed. In  
> SeqFeature.t there is one test left that fails which I'm looking into,  
> everything else passes. I'm clueless wrt CoordinateMapper.t, Molphy.t,  
> and Tree.t, and being short of time I won't touch them. I'll give the  
> Sim4.t failures a try, unless someone else wants to take that on.
> 
> 	-hilmar
> 
> On Wednesday, May 14, 2003, at 03:16  PM, Hilmar Lapp wrote:
> 
> > These failures have been there now since more than 2 weeks. Either  
> > this is specific to my system (perl 5.6.0, Mac OSX 10.2.5), or I'm  
> > playing the bad guy now pulling out the whistle. This is after a fresh  
> > cvs update.
> >
> > Failed Test          Stat Wstat Total Fail  Failed  List of Failed
> > ----------------------------------------------------------------------- 
> > --------
> > t/CoordinateMapper.t  255 65280   170    2   1.18%  169-170
> > t/Genpred.t                        34   ??       %  ??
> > t/Molphy.t            255 65280    17    0   0.00%  ??
> > t/Pictogram.t           2   512     2    2 100.00%  1-2
> > t/SeqFeature.t                     66    5   7.58%  13-14 17-18 61
> > t/Sim4.t                           27   24  88.89%  35 38 41 44 52 55  
> > 58 61 69
> >                                                     72 75 78 86 89 92  
> > 95 103
> >                                                     106 109 112 120  
> > 123 126 129
> > t/Tree.t                           10    4  40.00%  4-5 8-9
> > t/est2genome.t                     60   25  41.67%  4 37-60
> > t/hmmer.t                         134    2   1.49%  130 134
> > 15 subtests skipped.
> > Failed 9/149 test scripts, 93.96% okay. -39/6872 subtests failed,  
> > 100.57% okay.
> >
> > CoordinateMapper.t:
> > t/CoordinateMapper...........ok 168/170Can't call method "start" on an  
> > undefined value at blib/lib/Bio/Coordinate/Utils.pm line 136.
> > t/CoordinateMapper...........dubious
> >         Test returned status 255 (wstat 65280, 0xff00)
> > DIED. FAILED tests 169-170
> >         Failed 2/170 tests, 98.82% okay
> >
> > Genpred.t: I fixed this. (Msg: Don't know which tests failed: got 35  
> > ok, expected 34)
> >
> > Molphy.t:
> > t/Molphy.....................ok 1/17Modification of non-creatable  
> > array value attempted, subscript -8 at  
> > blib/lib/Bio/TreeIO/TreeEventBuilder.pm line 242.
> > t/Molphy.....................dubious
> >         Test returned status 255 (wstat 65280, 0xff00)
> >         after all the subtests completed successfully
> >
> > Pictogram.t: I fixed this. (no graceful skip if SVG.pm not installed)
> >
> > Seqfeature.t:
> > not ok 13
> > # Test 13 got: <UNDEF> (t/SeqFeature.t at line 103)
> > #    Expected: 'exon'
> > not ok 14
> > # Test 14 got: <UNDEF> (t/SeqFeature.t at line 104)
> > #    Expected: 'internal'
> > not ok 17
> > # Test 17 got: <UNDEF> (t/SeqFeature.t at line 107)
> > #    Expected: 'other'
> > not ok 18
> > # Test 18 got: <UNDEF> (t/SeqFeature.t at line 108)
> > #    Expected: 'program_a'
> > not ok 61
> > # Test 61 got: '1' (t/SeqFeature.t at line 284)
> > #    Expected: '1595'
> >
> > Sim4.t:
> > lots of warnings in the form
> > -------------------- WARNING ---------------------
> > MSG: Did not defined the number of conserved matches in the HSP  
> > assuming conserved == identical (118)
> > ---------------------------------------------------
> >
> > Failures are all 0/1 mismatches like
> > not ok 112
> > # Test 112 got: '0' (t/Sim4.t at line 217)
> > #     Expected: '1'
> >
> > Tree.t:
> >
> > not ok 4
> > # Failed test 4 in t/Tree.t at line 76
> > not ok 5
> > # Failed test 5 in t/Tree.t at line 79
> > not ok 8
> > # Test 8 got: '-1' (t/Tree.t at line 100)
> > #   Expected: '0'
> > not ok 9
> > # Test 9 got: '-1' (t/Tree.t at line 103)
> > #   Expected: '1'
> > -------------------- WARNING ---------------------
> > MSG: Node requested for reroot is already the root node!
> > ---------------------------------------------------
> >
> > est2genome.t:
> >
> > not ok 4
> > # Failed test 4 in t/est2genome.t at line 56
> >
> > The rest of the failures stem from the fact that it only prints 36  
> > tests, not 60 as expected.
> >
> > hmmer.t:
> >
> > ok 121
> >
> > -------------------- WARNING ---------------------
> > MSG: Could not find SEED 33 103 unit even though I am reading it in.  
> > ugh!
> > ---------------------------------------------------
> >
> > -------------------- WARNING ---------------------
> > MSG: Could not find SEED 124 194 unit even though I am reading it in.  
> > ugh!
> > ---------------------------------------------------
> > ok 122
> >
> > -------------------- WARNING ---------------------
> > MSG: Could not find Methylase_M 280 481 unit even though I am reading  
> > it in. ugh!
> > ---------------------------------------------------
> >
> > not ok 130
> > # Test 130 got: <UNDEF> (t/hmmer.t at line 267)
> > #     Expected: '-105.2'
> > not ok 134
> > # Test 134 got: '0' (t/hmmer.t at line 279)
> > #     Expected: '604'
> >
> >
> > Quite frankly I have little clue as to what is going on in those that  
> > I haven't fixed (all except 2). A couple of them look like old  
> > features that used to work, so it smells like a knock-on effect that  
> > some recent change caused. Maybe someone who changed something  
> > recently has an idea where to start?
> >
> > 	-hilmar
> >
> > -- 
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at bioperl.org
> > http://pw600a.bioperl.org/mailman/listinfo/bioperl-l
> >
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_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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