[Bioperl-l] problem with install

Mon Dec 14 14:22:40 UTC 2009

Thank you Jason.  I appreciate the help.

Eric

----- Original Message -----
From: Jason Stajich <jason at bioperl.org>
Date: Monday, December 14, 2009 12:10 am
Subject: Re: [Bioperl-l] problem with install
To: eric_donaldson at med.unc.edu
Cc: BioPerl List <bioperl-l at bioperl.org>

> Eric -
> please CC the bioperl list when responding so others can help - 
> I  
> can't be the only answerer.
> 
> But since your @INC message doesn't include /sw/lib/perl5/5.8.8/ 
> you  
> would need to make sure that is added to your PERL5LIB.
> There are some help docs on the perl sites I expect on how to 
> get your  
> PATHs in order.
> 
> Or you can just install via CPAN which will put it in the right 
> path -  
> there are docs on the bioperl website about installing via CPAN.
> 
> -jason
> On Dec 13, 2009, at 9:02 PM, eric_donaldson at med.unc.edu wrote:
> 
> > Hi Jason,
> >
> > The fink package did not have support for perl 5.10, so I 
> attempted  
> > to install the perl 5.8.6 package.
> >
> > When I attempted: locate Bio/SearchIO.pm
> > I got: -bash: $: command not found
> >
> > So even though I can find SearchIO.pm in 
> sw/lib/perl5/5.8.8/Bio/ 
> > SearchIO.pm  I cannot access it.  Do I need to use 
> the older version  
> > of perl?
> >
> > Would it be better to install with CPAN?  If so, can you 
> send me to  
> > a page that has instructions?
> >
> > Thank you so much!
> >
> > ERic
> >
> >
> > ----- Original Message -----
> > From: Jason Stajich <jason at bioperl.org>
> > Date: Sunday, December 13, 2009 11:10 pm
> > Subject: Re: [Bioperl-l] problem with install
> > To: eric_donaldson at med.unc.edu
> > Cc: BioPerl List <bioperl-l at bioperl.org>
> >
> >> So you installed perl-5.10 or using system perl?  I'm
> >> confused if you
> >> actually installed bioperl.pm or not via fink?
> >>
> >> It seems like since your @INC or $PERL5LIB points to
> >> /sw/lib/perl5
> >> which is one of the dirs it would have installed in, but I don't
> >> think
> >> you actually installed bioperl.
> >>
> >> you can try and do:
> >> $ locate Bio/SearchIO.pm
> >>
> >> We'll see if any of the other osx/fink gurus are on the list
> >> that can
> >> help or you can install it via CPAN I guess.
> >>
> >> -jason
> >> On Dec 13, 2009, at 6:39 PM, eric_donaldson at med.unc.edu wrote:
> >>
> >>>
> >>> I actually tried a different blastparser that uses
> >> BIO::SearchIO and
> >>> got the same message:
> >>>
> >>> Can't locate Bio/SearchIO.pm in @INC (@INC contains:
> >> /sw/lib/perl5/
> >>> darwin-thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin
> >> /
> >>> Library/Perl/Updates/5.10.0 
> /System/Library/Perl/5.10.0/darwin-
> >>
> >>> thread-multi-2level /System/Library/Perl/5.10.0
> >> /Library/Perl/5.10.0/
> >>> darwin-thread-multi-2level /Library/Perl/5.10.0
> >> /Network/Library/
> >>> Perl/5.10.0/darwin-thread-multi-2level
> >> /Network/Library/Perl/5.10.0 /
> >>> Network/Library/Perl 
> /System/Library/Perl/Extras/5.10.0/darwin-
> >>
> >>> thread-multi-2level /System/Library/Perl/Extras/5.10.0 .)
> >> at
> >>> blastparser.new.pl line 8.
> >>> BEGIN failed--compilation aborted at blastparser.new.pl line 8.
> >>>
> >>> I suspect there is a path problem, but am not savvy enough to
> >> know
> >>> how to fix it.  I am really just a hacker.... I have
> >> several scripts
> >>> that I use regularly and that I know how to modify, but am
> >> lost when
> >>> they don't work...
> >>>
> >>> Thanks for any help,
> >>>
> >>> Eric
> >>>
> >>> ----- Original Message -----
> >>> From: Jason Stajich <jason at bioperl.org>
> >>> Date: Sunday, December 13, 2009 8:24 pm
> >>> Subject: Re: [Bioperl-l] problem with install
> >>> To: eric_donaldson at med.unc.edu
> >>> Cc: bioperl-l at bioperl.org
> >>>
> >>>> Hi Eric -
> >>>>
> >>>> Bio::Tools::BPlite is no longer supported in Bioperl - it
> >>>> was
> >>>> deprecated several releases ago.
> >>>> It was replaced with Bio::SearchIO
> >>>>
> >>>> -jason
> >>>> On Dec 13, 2009, at 3:15 PM, eric_donaldson at med.unc.edu wrote:
> >>>>
> >>>>> Hello,
> >>>>>
> >>>>> Today I downloaded bioperl 1.61 on my new macbook pro using
> >>>> fink.  I
> >>>>> used the
> >>>>>
> >>>>> fink install bioperl.pm-588 as I could not get it to instal
> >>>> using
> >>>>> the perl version 5.10.
> >>>>>
> >>>>> But now I get an error when trying to run a bioperl script.
> >>>>>
> >>>>> Here is the error:
> >>>>>
> >>>>> Can't locate Bio/Tools/BPlite.pm in @INC (@INC contains:
> >>>> /sw/lib/
> >>>>> perl5/darwin-thread-multi-2level /sw/lib/perl5
> >>>> /sw/lib/perl5/darwin /
> >>>>> Library/Perl/Updates/5.10.0
> >> /System/Library/Perl/5.10.0/darwin-
> >>>>
> >>>>> thread-multi-2level /System/Library/Perl/5.10.0
> >>>> /Library/Perl/5.10.0/
> >>>>> darwin-thread-multi-2level /Library/Perl/5.10.0
> >>>> /Network/Library/
> >>>>> Perl/5.10.0/darwin-thread-multi-2level
> >>>> /Network/Library/Perl/5.10.0 /
> >>>>> Network/Library/Perl
> >> /System/Library/Perl/Extras/5.10.0/darwin-
> >>>>
> >>>>> thread-multi-2level /System/Library/Perl/Extras/5.10.0 .)
> >>>> at
> >>>>> blastparser.pl line 8.
> >>>>> BEGIN failed--compilation aborted at blastparser.pl line 8.
> >>>>>
> >>>>>
> >>>>> I am a novice at unix and bioperl so I do not know how
> >>>> to
> >>>>> troubleshoot this, would you please hleo me?
> >>>>>
> >>>>> Thank you,
> >>>>>
> >>>>> Eric
> >>>>>
> >>>>>
> >>>>> Eric F. Donaldson, Ph.D.
> >>>>> Research Assistant Professor, Ralph Baric Lab
> >>>>> University of North Carolina
> >>>>> Department of Epidemiology
> >>>>>
> >>>>>
> >>>>>
> >>>> <
> >>>>
> >> eric_donaldson.vcf>_______________________________________________>
> >>>> Bioperl-l mailing list
> >>>>> Bioperl-l at lists.open-bio.org
> >>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>
> >>>> --
> >>>> Jason Stajich
> >>>> jason.stajich at gmail.com
> >>>> jason at bioperl.org
> >>>>
> >>>>
> >>>
> >>> Eric F. Donaldson, Ph.D.
> >>> Research Assistant Professor, Ralph Baric Lab
> >>> University of North Carolina
> >>> Department of Epidemiology
> >>>
> >>>
> >>> <eric_donaldson.vcf>
> >>
> >> --
> >> Jason Stajich
> >> jason.stajich at gmail.com
> >> jason at bioperl.org
> >>
> >>
> >
> > Eric F. Donaldson, Ph.D.
> > Research Assistant Professor, Ralph Baric Lab
> > University of North Carolina
> > Department of Epidemiology
> >
> >
> > <eric_donaldson.vcf>
> 
> --
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
> 
> 

Eric F. Donaldson, Ph.D.
Research Assistant Professor, Ralph Baric Lab
University of North Carolina
Department of Epidemiology

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