[Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange

[Lacey Sanderson]

Okay, running Build from the base of the bioperl-live directory Worked.

Version is now 1.0069 !!

For all users, even after re-logging in...

Thanks!
Lacey

On 3-Feb-10, at 1:49 PM, Scott Cain wrote:

> Hi Lacey,
>
> In order for it to be available to all users, I would suggest you go
> through the "normal" installation procedure:
>
> perl Build.PL
> ./Build
> ./Build test
> sudo ./Build install --uninst 1
>
> Scott
>
>
> On Wed, Feb 3, 2010 at 2:38 PM, Lacey Sanderson
> <laceyanne_sanderson at shaw.ca> wrote:
>> Okay,
>>>
>>> directly from the command line (don't relogin)
>>>
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>>> $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>
>> That gives me the correct version... For that user until I log out...
>>
>> I sudoed in to .profile and added the line directly but that  
>> doesn't seem to
>> have helped.
>>
>> How would I tell perl to look in the same place for Bioperl for ALL  
>> users?
>>
>> Lacey
>>
>> On 3-Feb-10, at 12:34 PM, Mark A. Jensen wrote:
>>
>>> Well, that's progress. It hard to debug these things remotely, but  
>>> now
>>> you can at least work around the problem by using the -I flag. The  
>>> next
>>> weak link I would try to eliminate is the append to the .profile  
>>> file.
>>> Just
>>> do directly from the command line (don't relogin)
>>>
>>> $ export
>>> PERL5LIB=/usr/local/share/applications/Bioperl/bioperl-live: 
>>> $PERL5LIB
>>> $ perl -MBio::Perl -e 'print Bio::Perl->VERSION'
>>>
>>> If this gives 1.0069, then the problem is in that append (and, you  
>>> can
>>> also do your work!).
>>> (If you're a sudoer, I'd just edit that file directly.)
>>>
>>> cheers MAJ
>>> ----- Original Message ----- From: "Lacey Sanderson"
>>> <laceyanne_sanderson at shaw.ca>
>>> To: "Mark A. Jensen" <maj at fortinbras.us>
>>> Cc: <bioperl-l at lists.open-bio.org>
>>> Sent: Wednesday, February 03, 2010 1:21 PM
>>> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version  
>>> doesn't
>>> seem tochange
>>>
>>>
>>>> That gives me the 1.069 that I was wanting so the problem seems  
>>>> to be
>>>>  that perl is finding the wrong installation by default...
>>>>
>>>> Lacey
>>>>
>>>> On 3-Feb-10, at 12:14 PM, Mark A. Jensen wrote:
>>>>
>>>>> perl -MBio::Perl -I/usr/local/share/applications/Bioperl/ 
>>>>> bioperl- live
>>>>> -le 'print Bio::Perl->VERSION;'
>>>>
>>>>
>>>
>>
>> ---------------------------------
>> Lacey Sanderson
>> Bioinformaticist
>> Pulse Crop Breeding and Genetics
>> Department of Plant Sciences
>> University of Saskatchewan.
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

---------------------------------
Lacey Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Department of Plant Sciences
University of Saskatchewan.