[Bioperl-l] WinXP test results

Chris Fields cjfields at uiuc.edu
Mon Sep 25 18:26:13 UTC 2006

> Thanks Nathan. I think what I'll do is say that Bio::Graph* is
> deprecated with this release and simply drop t/protgraph.t. Nonetheless,
> is it possible for you to require Class::AutoClass 1.01 for Bio::Graph*?
> Is everyone happy with saying the perl requirements are 5.6.1 for all
> platforms except WindowsXP, which needs ActivePerl 5.8+?
> In that case, how close are install-related things (Makefile.PL, PPDs et
> al.) to being ready?
> I think the Bio::DB::SeqFeature failures are sufficient to delay RC1
> however. Sorry, I had forgotten about them. Chris/Nathan, are you
> looking into it? Shall I take a look as well?

I have a feeling the BioDBSeqFeature_BDB.t tests fail based on issues with
the perl installation, not with Bioperl itself.  There are some funky things
going on with tempfile and tempdir creation/removal that are
Windows-specific and, I think, are related to permissions issues:

Set up gcc environment - 3.4.2 (mingw-special)
Error in tempdir() using
C:\Temp\Bio::DB::SeqFeature::Store::berkeleydb_XXXXXX: Could not create
directory C:\Temp\Bio::DB::S
eqFeature::Store::berkeleydb_j59apk: Invalid argument at
Bio/DB/SeqFeature/Store/berkeleydb.pm line 252
not ok 1
# Failed test 1 in t/BioDBSeqFeature.t at line 57
not ok 2
# Failed test 2 in t/BioDBSeqFeature.t at line 45
not ok 3
# Failed test 3 in t/BioDBSeqFeature.t at line 45 fail #2
not ok 4
# Failed test 4 in t/BioDBSeqFeature.t at line 45 fail #3
not ok 5

Note that, when I run the regular BioDBSeqFeature.t tests, they pass, but at
the end...

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign

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