[Bioperl-l] BioPerl on Linux....

James Thompson tex at biosysadmin.com
Tue Nov 2 01:08:57 EST 2004


It sounds like something went seriously wrong in your attempted installation,
here's what my /usr/local/lib/perl5/site_perl/5.8.5/Bio directory has 41 files
in it.

I wouldn't worry to much about uninstalling, just repeat the installation and
it should overwrite all of the old modules. Bioperl does depend on a few external
modules, so try installing Bundle::BioPerl to grab the external dependencies.

One thing that you should try is downloading the tarball (or grabbing it from
your ~/.cpan/sources directory), unzipping it, running make and then make test.
Look at what tests fail, then send e-mail to the list. That extra information
will allow us to help you better.

Best of luck. :)

James Thompson

On Mon, 1 Nov 2004, Peter G Carswell wrote:

> Hello,
> I am running Fedora core 1 on my laptop. Today I attempted to install 
> bioperl-1.4, using the CPAN shell. Everything seemed to go well, just a 
> couple of failed tests. So I did a 'force install' on 
> B/BI/BIRNEY/bioperl-1.4.tar.gz. It finished and I quit the shell. I 
> created a simple test:
> #!/bin/bin/perl
> use Bio::Perl
> and ran the script "perl test.pl". It created the output:
> Can't locate Bio/Perl.pm in @INC ....
> I looked in the path "/usr/lib/perl5/site_perl/5.8.3", the installation 
> directory, and could find no Perl.pm in the Bio directory. In ./Bio/ 
> were the directories 'Factory' and 'Tools'. Under ./Bundle/ there was a 
> BioPerl.pm, but as I have not used BioPer extensively, I was unsure as 
> where these files should fall. I was looking at some of the tutorial 
> scripts and followed there lead as to using the perl command "use 
> Bio::Perl".
> What I would like to do is reinstall, but is there a CPAN shell command 
> to unistall the previous version? Any pointers?
> Thanks for your help.
> pete

More information about the Bioperl-l mailing list