[Bioperl-l] tests failing miserably

[Hilmar Lapp]

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
-------------------------------------------------------------