[Bioperl-l] WinXP test results

Chris Fields cjfields at uiuc.edu
Mon Sep 25 14:09:33 EDT 2006


...
> 
> The BioDBSeqFeature tests are the same fails already reported by Chris,
> but I also get fails in t/protograph.t. Further details at the bottom of
> this e-mail.

I think there is an issue with tempfile/tempdir creation in WinXP that is
hidden for the most part unless verbose is set.  The BioDBSeqFeature  tests
don't work b/c it can't create a tempdir and dies early on.  Other
scripts/tests which create tempfiles don't have the same issue, though.
It's something that needs looking into but I haven't had time for it.

I think it may be related to the way perl is set up on WinXP.  It's not a
killer bug but will lead to an accumulation of temp files and temp dirs
wherever TEMP is set.

> Running ActivePerl 5.6.1:
> Trying to get Bioperl installed on ActivePerl 5.6.1 is a total pain
> (which I still failed to do, even after a few days of trying). There are
> several reasons, a few dependencies (and more than a few dependencies of
> Bioperl dependencies) for which there are no PPD's for Perl 5.6 to
> install via PPM. Installing via CPAN, didn't work for me since nmake
> dies with many test suites. Therfore, we should probably recommend
> ActivePerl 5.8 for Windows.

Randy Kobes still has a repository strictly used for perl 5.6.1; I'm not
sure about the others.  I agree, though; we should only support ActivePerl
5.8 or above, especially if it is a real chore getting bioperl running on
it.

BTW, I did get it up-and-running using perl 5.6.1, but I also found it to be
too much trouble compared to v 5.8.

> I'll add the test results to http://www.bioperl.org/wiki/Release_1.5.2
> shortly.
> 
> Cheers
> Nath

Note that the protgraph.t issue was resolved (you need the newest
Class::Autoclass, 1.01), but we don't plan on doing anything about it as we
plan on deprecating the Bio::Graph modules.  We're awaiting word from Nat
Goodman to get his opinion on the matter.

Chris


> C:\bioperl-live>perl -I. -w t/protgraph.t
> 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'
> 
> 
> 
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