[Bioperl-l] For CVS developers-potentialpitfall with"returnundef"

Heikki Lehvaslaiho heikki at sanbi.ac.za
Fri Jun 9 04:06:30 EDT 2006


I am using:
   This is perl, v5.8.7 built for i486-linux-gnu-thread-multi
and I have Clone installed, but more than half the tests fail.

Something is badly wrong.


	-Heikki
bala ~/src/bioperl/core> perl -w t/protgraph.t
1..66
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
not ok 10
# Failed test 10 in t/protgraph.t at line 85
not ok 11
# Test 11 got: '5' (t/protgraph.t at line 86)
#    Expected: '13'
not ok 12
# Failed test 12 in t/protgraph.t at line 94
not ok 13
# Test 13 got: '5' (t/protgraph.t at line 95)
#    Expected: '13'
ok 14
ok 15
ok 16
ok 17
ok 18
ok 19
not ok 20
# Test 20 got: '0.013' (t/protgraph.t at line 113)
#    Expected: '0.027'
.not ok 21
# Test 21 got: '1' (t/protgraph.t at line 114)
#    Expected: ''
..ok 22
.ok 23
ok 24
..ok 25
.not ok 26
# Test 26 got: '1' (t/protgraph.t at line 122)
#    Expected: '5'
ok 27
ok 28
ok 29
ok 30
ok 31
ok 32
not ok 33
# Test 33 got: '139' (t/protgraph.t at line 150)
#    Expected: '71'
ok 34
ok 35
not ok 36
# Test 36 got: '126' (t/protgraph.t at line 158)
#    Expected: '58'
.not ok 37
# Test 37 got: '1' (t/protgraph.t at line 163)
#    Expected: '15'
ok 38
ok 39
ok 40
ok 41
ok 42
ok 43
ok 44
not ok 45
# Failed test 45 in t/protgraph.t at line 187
ok 46
ok 47
not ok 48
# Test 48 got: '75' (t/protgraph.t at line 212)
#    Expected: '72'
not ok 49
# Test 49 got: '343' (t/protgraph.t at line 228)
#    Expected: '72'
not ok 50
# Test 50 got: '368' (t/protgraph.t at line 229)
#    Expected: '74'
not ok 51
# Test 51 got: '344' (t/protgraph.t at line 233)
#    Expected: '73'
not ok 52
# Test 52 got: '368' (t/protgraph.t at line 234)
#    Expected: '74'
not ok 53
# Test 53 got: '432' (t/protgraph.t at line 248)
#    Expected: '72'
not ok 54
# Test 54 got: '461' (t/protgraph.t at line 249)
#    Expected: '74'
not ok 55
# Test 55 got: '434' (t/protgraph.t at line 253)
#    Expected: '74'
not ok 56
# Test 56 got: '463' (t/protgraph.t at line 254)
#    Expected: '76'
ok 57
ok 58
not ok 59
# Test 59 got: '437' (t/protgraph.t at line 263)
#    Expected: '3'
not ok 60
# Test 60 got: '467' (t/protgraph.t at line 264)
#    Expected: '4'
ok 61
ok 62
ok 63
ok 64
not ok 65
# Test 65 got: '440' (t/protgraph.t at line 275)
#    Expected: '3'
not ok 66
# Test 66 got: '472' (t/protgraph.t at line 276)
#    Expected: '5'


On Friday 09 June 2006 04:30, Chris Fields wrote:
> Yes; using ActiveState's PPM:
>
> ppm> query CLone
> Querying target 1 (ActivePerl 5.8.7.815)
>   1. Clone [0.20] recursively copy Perl datatypes
> ppm>
>
> v. 0.20 is the latest in CPAN.
>
> I can try some additional tests with the relevant modules to see what the
> problem is.
>
> Chris
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Brian Osborne
> > Sent: Thursday, June 08, 2006 2:42 PM
> > To: Chris Fields; 'Heikki Lehvaslaiho'; bioperl-l at lists.open-bio.org
> > Cc: Paul.Boutros at utoronto.ca; bioperl-l
> > Subject: Re: [Bioperl-l] For CVS developers-potentialpitfall
> > with"returnundef"
> >
> > Chris,
> >
> > Odd. protgraph.t passes all of its tests on my computer. Do you have the
> > Clone module installed?
> >
> > Brian O.
> >
> > On 6/8/06 3:28 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
> > > t/protgraph..........................FAILED tests 11, 13, 20-21, 26,
> > > 33, 36-37, 45, 48-56, 59-60, 65-66
> > > Failed 22/66 tests, 66.67% okay
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> _______________________________________________
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-- 
______ _/      _/_____________________________________________________
      _/      _/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
    _/_/_/_/_/  Associate Professor    skype: heikki_lehvaslaiho
   _/  _/  _/  SANBI, South African National Bioinformatics Institute
  _/  _/  _/  University of Western Cape, South Africa
     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
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