[Bioperl-l] bioperl-live install issue on unix

[Kevin Brown]

It's trying to unlink the installed Bio::Perl module (notice the path to
the module ends with Bio/module_name.pm) and failing as you don't have
permission to delete files from /usr/local/lib/perl5/site_perl/5.8.7/ as
that is a system directory and generally reserved for root to write to.

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Sean O'Keeffe
> Sent: Tuesday, December 09, 2008 10:25 AM
> To: bioperl-l at portal.open-bio.org
> Subject: [Bioperl-l] bioperl-live install issue on unix
> 
> Hi all,
> 
> I've just downloaded bioperl-live with svn. All fine.
> Tried doing a local install in a personal module area like so:
> 
> 'cd /home/okeeffe/bioperl-live; perl Build.PL --install_base
> /home/okeeffe/bioperl; ./Build install'
> 
> and got the following error at the install stage:
> ...
> Manifying /home/okeeffe/bioperl/lib/perl5/Bio/WebAgent.pm
> Unlinking 
> /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm (shadowing?)
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!
> WARNING: WARNING: Failed chmod(438,
> /usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm): Operation not
> permitted
> 
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!
> ERROR: Cannot unlink
> '/usr/local/lib/perl5/site_perl/5.8.7/Bio/WebAgent.pm': Permission
> denied
> !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
> !!!!!!!!!!
> 
> 
> What is shadowing? Why is it trying to unlink a system-wide 
> perl module?
> Perl is v5.8.7
> Thanks,
> Sean.
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