[Bioperl-l] problems installing bioperl

Scott Cain cain at cshl.edu
Tue Dec 19 10:31:50 EST 2006

I really don't think the BioPerl version detection is wrong.  I actually
don't check Bio::Root::Version::VERSION in Makefile.PL, I check
Bio::Graphics::Panel->api_version.  When it doesn't find the correct
api_version, it gives a warning the BioPerl 1.5.2 is not installed.  I
have seen this happen when more than one BioPerl instance is installed
and `perl Makefile.PL` finds the wrong one first.  My suggestion is to
try reinstalling BioPerl and providing the --uninst 1 argument to remove
older versions of BioPerl:

  sudo ./Build install --uninst 1


On Tue, 2006-12-19 at 15:12 +0000, Sendu Bala wrote:
> Stephan Roessner wrote:
> > Dear support team,
> > 
> > I installed bioperl 1.5.2_100 on a ferdora machine to be able to use
> > gbrowse.
> > The installation seems to work (except of the test failures) but the
> > gbrowse installation tells me that BIO::pERL 1.0050021 is installed, but
> > of course it requires 1.52.
> > 
> > Is there a chance to find out what went wrong?
> Nothing went wrong with the Bioperl installation (well, expect there 
> shouldn't have been any test failures - can you post those please?). 
> gbrowse simply defined its Bioperl requirement incorrectly. If you tell 
> me exactly where you downloaded gbrowse from and how you went about 
> installing it, and provide the exact, complete error message you got 
> from it, I might be able help the authors fix the problem.
> Or I'm pretty sure they can figure it our for themselves :)
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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