[Bioperl-l] problem with install

[Jason Stajich]

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