[Bioperl-guts-l] [Bug 2706] bioperl-live install issue

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Dec 10 06:03:47 EST 2008


http://bugzilla.open-bio.org/show_bug.cgi?id=2706





------- Comment #1 from online at davemessina.com  2008-12-10 06:03 EST -------
Sorry you're having trouble with this, Sean.

I just followed your procedure on my Linux box and did not see the same
problem.

A coupld of things you might try:
- moving your cpan MyConfig.pm elsewhere and reconfiguring cpan from scratch. I
know you posted your conf before and there wasn't anything about UNINST, but I
suggest this because the error you're getting shows that Build is trying to
uninstall the system copy of Bio::WebAgent.

'Shadowing' means having multiple versions of the same module installed on your
system, and one would hide, or 'shadow' the other one. keeping it from being
used.

One way of preventing this problem is to only have one version on your system,
and so you can set cpan to remove any previously existing versions before
installing a new one.

Obviously in your case, you don't want to remove the system copy. You in fact
*do* want to 'shadow' the system installation of BioPerl with your personal
copy. (You'll need to make sure your personal copy comes first in @INC for this
to work by setting PERL5LIB to point to your copy.)

- checking if your versions of CPAN and Module::Build are up to date.


In any case, for most of the core functionality of BioPerl, you don't actually
need to 'install' it. The bioperl-live distribution you downloaded has all of
the BioPerl modules at the root level of the directory, so if you set your
PERL5LIB environmental variable to the bioperl-live, you should then be able to
write code using bioperl.


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