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

[Chris Fields]

Also, remember if you are installing from svn you are installing from the bleeding edge code.  IIRC the last svn co I made had several tests failing for various reasons; nothing that should affect your installation, but something to be aware of.

chris

On Feb 3, 2010, at 1:55 PM, Mark A. Jensen wrote:

> I'll jump in to +1 on this; the Build will make sure you have all the necessary prequisites, and install those automatically (I *think* it still does this....). It will also do comprehensive tests. These will save MANY headaches down the road.
> 
> [I speak as someone who didn't build in the beginning, until one day Dave Messina
> blithely said to me "why don't you just run ./Build test ?". Three days later, I was back up...]
> 
> ----- Original Message ----- From: "Scott Cain" <scott at scottcain.net>
> To: "Lacey Sanderson" <laceyanne_sanderson at shaw.ca>
> Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at lists.open-bio.org>
> Sent: Wednesday, February 03, 2010 2:49 PM
> Subject: Re: [Bioperl-l] After Checkout of Bioperl-live version doesn't seem tochange
> 
> 
> 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
> 
> 
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