[Bioperl-l] WinXP test results

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Sep 26 03:23:13 EDT 2006


Chris Fields wrote:
> ...
>   
>> 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)
> 1..43
> 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
>   
Hope it's not trying to create a path with colons in it!?

> 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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