[Bioperl-l] tests failing miserably

Hilmar Lapp hlapp at gnf.org
Thu May 15 12:07:06 EDT 2003 

The hmmer tests pass meanwhile. Over the long run I'd agree though - if there is no functionality difference then we'll deprecate the old parser.

In fact, to hide such moves from legacy scripts, I thought could we masquerade  the old parser to be in fact the new one, by delegation, or re-blessing or whatever? Same applies to Bio::Tools::Blast.pm

      -hilmar

-----Original Message-----
From:	Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
Sent:	Thu 5/15/2003 6:30 AM
To:	Hilmar Lapp
Cc:	Bioperl
Subject:	Re: [Bioperl-l] tests failing miserably
The tree stuff needs me to back out my changes - I've still not been able
to make time to fix the bug I was intending to fix there.  This is root of
the molphy and tree tests failing.

Somewhere a month or so ago some feature changes went in - that broke
Bio::Tools::HMMer code for some reason.  I am actually a proponent of
dropping those modules anyways if SearchIO::hmmer will fit the bill for
most people.  Ewan wrote Tools::HMMer and I know old versions of it run
Pfam, but I don't know if I really want to support 2 HMMer parsers
(actually there 3 since the fugu group committed a quick hack in
Bio::Tools::Hmmpfam).

-jason

On Wed, 14 May 2003, 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
> >
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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