[BioSQL-l] problem loading NCBI_taxonomy database into BioSQL bioseqdb

[Hilmar Lapp]

On Sep 3, 2008, at 2:16 PM, Nick Matzke wrote:

> [...]
> mws2:~ nick$ perldoc -l DBI
>
> /usr/local/ActivePerl-5.10/site/lib/Bundle/DBI.pm

Can you pull up this file in an editor and see what's in there? I  
think this may just be the CPAN bundle definition (which modules to  
install together), but not the actual DBI module itself.

>
> mws2:~ nick$ sudo perldoc -l DBI
> Password:
>
> /usr/local/ActivePerl-5.10/site/lib/DBI.pm

If you inspect this one, it will probably be the actual DBI module.

So I suspect that your Perl module search paths aren't the same  
between executing as root or not. If you do 'perl -V' (capital-v) you  
will see the include path array (@INC) printed at the end. It should  
be identical whether under sudo or not, but I suspect that for you it  
will not be the same.

If that's indeed the case then the question is why is the path  
different. As the one for you as normal user is wrong, you can look  
into your shell initialization files (.tcshrc, .cshrc for csh/ 
tcsh; .profile, .bash_profile, .login for bash) whether you see  
anything there that aims to mess with PERL5LIB.

Or simply do 'echo $PERL5LIB' w/ and w/o sudo. Should be the same.

	-hilmar

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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