[Bioperl-l] Extreme newbie question.

Kevin Brown Kevin.M.Brown at asu.edu
Thu Jun 25 14:54:19 EDT 2009


Please keep your replies on the list. 

> -----Original Message-----
> From: Adlai Burman [mailto:adlai at refenestration.com] 
> Sent: Thursday, June 25, 2009 11:39 AM
> To: Kevin Brown
> Subject: Re: [Bioperl-l] Extreme newbie question.
> 
> Thanks, Kevin.
> I did install everything using sudo. I will try again and pay  
> attention to the error log. I hope I did not introduce any conflicts  
> or weird path problems.
> 
> Adlai
> On Jun 25, 2009, at 5:21 PM, Kevin Brown wrote:
> 
> > http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
> >
> > Or http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink
> >
> > That error suggests that the install fails and you need to 
> figure out
> > why from the install error messages. I suspect you aren't doing the
> > install as root, but as a normal user who lacks the needed 
> permissions
> > to change files in certain directories.
> >
> >> -----Original Message-----
> >> From: bioperl-l-bounces at lists.open-bio.org
> >> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> >> Adlai Burman
> >> Sent: Wednesday, June 24, 2009 7:09 PM
> >> To: bioperl-l at lists.open-bio.org
> >> Subject: [Bioperl-l] Extreme newbie question.
> >>
> >> I have been trying to install BioPerl for a while now and after
> >> pummeling my hard drive (Mac OS 10.5 intel) with several 
> attempts at
> >> Fink installation, a >cpan installation and removing my .cpan
> >> folder I
> >> am still at square 0. I do not want to do anymore damage to my
> >> computer, yet I really need a working install (especially to
> >> interface
> >> with remote DBs like GenBank. Can anyone give me some advice here?
> >> After each attempt, I have tried to run perldoc bptutorial.pl and
> >> tried test scripts with "use Bio::Perl" in the headers and I just
> >> receive  error mesages like the following:
> >>
> >> Can't locate Bio/Perl.pm in @INC (@INC contains: 
> /home/users/dag/lib/
> >> perl5/ /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level
> >> /Library/
> >> Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-
> >> multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-
> >> thread-multi-2level /Library/Perl/5.8.8 /Library/Perl
> >> /Network/Library/
> >> Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /
> >> Network/Library/Perl 
> /System/Library/Perl/Extras/5.8.8/darwin-thread-
> >> multi-2level /System/Library/Perl/Extras/5.8.8 
> /Library/Perl/5.8.6 /
> >> Library/Perl/5.8.1 .) at trsh.pl line 1.
> >>
> >> I have been working from the OReilly book astering Perl for
> >> Bioinformatics and the INSTALL file and have scoured around the
> >> BioPerl website and am still stuck.
> >>
> >> Thanks in advance,
> >>
> >> Adlai
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> 
> 



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