[Bioperl-l] RC2 test results on WinXP

Chris Fields cjfields at uiuc.edu
Wed Oct 18 14:10:07 UTC 2006

> Nathan Haigh wrote:
> > I get all tests passing except for BioDBSeqFeature_mysql which fails all
> > tests (1-46).
> >
> > During perl Makefile.PL I get:
> > "I see you have Berkeleydb installed. I will create the DBD tests for
> > Bio::DB::SeqFeature::Store..."
> >
> > I notice under the "needs investigation" there is mention about tests
> > been generated even if DBD::mysql isn't installed. I assume this is the
> > problem?
> Probably. I'm looking into it. Not sure why it wasn't causing a problem
> before now.

Funny, I don't have problems with the BioDBSeqFeature_mysql tests on WinXP
because 'perl Makefile.PL' doesn't detect my MySQL installation, so the
MySQL-based tests don't run even though I have DBD::mysql installed.  I
thought this might just be a WinXP issue, but apparently not.  If I can get
to it I'll run a few checks.

>  > If this is the problem should DBD::mysql be added to the
>  > dependencies in Makefile.PL?
> No. You can use the modules in question without mysql (presumably; ie.
> you have a different sql setup), so it makes no sense to warn people
> they don't have a module they absolutely do not need.

Agreed, though I don't know if other relational DB's are supported like

> > Is there an easy way to find out what tests are being skipped due to
> > absent modules?
> Ideally, when the skip occurs the test script will issue a message. I
> think that happens in most, if not all cases.

Yes, though we may run into the same issue we had with XEMBL tests not
reporting the reasons it skipped.  Each test suite should run an eval{} to
check the required modules, then only skip blocks of tests that rely on
those modules.  I think we have caught most of those, but who knows w/o
doing a complete test suite audit?

Our eventual complete switchover to Test::More should hopefully clean these
up.  I don't consider it a pressing issue for this release, though Sendu may
feel differently.

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

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