[Bioperl-l] tests failing miserably
Hilmar Lapp
hlapp at gnf.org
Wed May 14 19:48:03 EDT 2003
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
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>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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