[Bioperl-l] Problem about slashes and backslahes in library paths

Chris Fields cjfields at illinois.edu
Sat Oct 31 10:10:16 EDT 2009

On Oct 31, 2009, at 8:55 AM, Robert Bradbury wrote:

> On Fri, Oct 30, 2009 at 11:23 AM, MathGon <dfog22 at hotmail.com> wrote:
>> Can't locate Bio/PrimarySeq.pm in @INC (@INC contains H:/Perl64/ 
>> site/lib/
>> H:Perl64/site.lib .) at H:\script.pl line 10
> Well, you've got a "mixed" pathname in @INC.  Anything that starts  
> with  L:
> would be a windows path while the use of forward slashes (/) is a  
> Linux
> path.  I'd suggest changing the script (or the environment which  
> sets @INC)
> so it uses only Windows or Linux paths.

Also, that last directory is a bit odd: H:Perl64/site.lib

Regardless, the message means the perl executable used from command  
line or called from the shebang line can't find BioPerl in @INC.   
Another way to check is using 'perldoc -l Bio::Root::Root'; replace  
Bio::Root::Root with any BioPerl module.  You can set PERL5LIB to  
point at your local BioPerl directory, but for Windows you really  
should install it.  It should work using PPM or CPAN with ActivePerl  
and CPAN with Strawberry Perl.

> There may be some Perl scripts that one is supposed to run to setup  
> the @INC
> variable correctly for ones current system (presumably depends on the
> supplier of Perl for your Windows installation).
> Or you could switch to Linux which I would consider to be a much more
> Perl/BioPerl friendly environment.  Because, IMO, sticking with  
> Windows is
> like boarding the Titanic as it is about to sail out of the harbor.
> Robert

Ah, let's not start that up here, please?  The more users we have the  
better.  I much prefer to use Ubuntu 9.10 and OS X, but some of the  
devs (me included) have put a decent amount of work trying to get  
things working on WinXP (to the point of having a local VM).


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