[Bioperl-l] For CVS developers-potentialpitfallwith"returnundef"

Chris Fields cjfields at uiuc.edu
Fri Jun 9 13:59:31 EDT 2006


I ran tests this morning on protgraph.t using bioperl-live, Mac OS X (Intel)
running perl 5.8.6 and all tests passed, but I haven't updated from CVS
since June 7th.  The test results are almost exactly alike; most failed
tests are from unexpected results (with exactly the same results for both
OS's).  A few look more serious: test 45 failed on both and tests 10 and 12
failed on linux (the only noticeable difference between the two) 
...

ok 10
not ok 11
# Test 11 got: '5' (t\protgraph.t at line 85)
#    Expected: '13'
ok 12
not ok 13
# Test 13 got: '5' (t\protgraph.t at line 94)
#    Expected: '13'
...

The line numbers seem to also be off by one (linux tests seem to have one
extra line); not sure if that means anything.

Here's the full WinXP protgraph.t results:

1..66
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
not ok 11
# Test 11 got: '5' (t\protgraph.t at line 85)
#    Expected: '13'
ok 12
not ok 13
# Test 13 got: '5' (t\protgraph.t at line 94)
#    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 112)
#    Expected: '0.027'
.not ok 21
# Test 21 got: '1' (t\protgraph.t at line 113)
#    Expected: ''
..ok 22
.ok 23
ok 24
..ok 25
.not ok 26
# Test 26 got: '1' (t\protgraph.t at line 121)
#    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 149)
#    Expected: '71'
ok 34
ok 35
not ok 36
# Test 36 got: '126' (t\protgraph.t at line 157)
#    Expected: '58'
.not ok 37
# Test 37 got: '1' (t\protgraph.t at line 162)
#    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 186
ok 46
ok 47
not ok 48
# Test 48 got: '75' (t\protgraph.t at line 211)
#    Expected: '72'
not ok 49
# Test 49 got: '343' (t\protgraph.t at line 227)
#    Expected: '72'
not ok 50
# Test 50 got: '368' (t\protgraph.t at line 228)
#    Expected: '74'
not ok 51
# Test 51 got: '344' (t\protgraph.t at line 232)
#    Expected: '73'
not ok 52
# Test 52 got: '368' (t\protgraph.t at line 233)
#    Expected: '74'
not ok 53
# Test 53 got: '432' (t\protgraph.t at line 247)
#    Expected: '72'
not ok 54
# Test 54 got: '461' (t\protgraph.t at line 248)
#    Expected: '74'
not ok 55
# Test 55 got: '434' (t\protgraph.t at line 252)
#    Expected: '74'
not ok 56
# Test 56 got: '463' (t\protgraph.t at line 253)
#    Expected: '76'
ok 57
ok 58
not ok 59
# Test 59 got: '437' (t\protgraph.t at line 262)
#    Expected: '3'
not ok 60
# Test 60 got: '467' (t\protgraph.t at line 263)
#    Expected: '4'
ok 61
ok 62
ok 63
ok 64
not ok 65
# Test 65 got: '440' (t\protgraph.t at line 274)
#    Expected: '3'
not ok 66
# Test 66 got: '472' (t\protgraph.t at line 275)
#    Expected: '5'  

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Heikki Lehvaslaiho
> Sent: Friday, June 09, 2006 3:07 AM
> To: bioperl-l at lists.open-bio.org
> Cc: Chris Fields; 'Brian Osborne'
> Subject: Re: [Bioperl-l] For CVS developers-
> potentialpitfallwith"returnundef"
> 
> 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  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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