[Bioperl-l] [Gmod-gbrowse] Non-root installation: problem with Module::Builder versions

[Brian Osborne]

Neil,

Try setting the environmental variable PERL5LIB:

PERL5LIB

A colon-separated list of directories in which to look for Perl  
library files before looking in the standard library and the current  
directory. If PERL5LIB is not defined, PERLLIB is used. When running  
taint checks (because the script was running setuid or setgid, or the - 
T switch was used), neither variable is used. The script should  
instead say

     use lib "/my/directory";

Brian O.


On May 12, 2009, at 1:36 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Neil,
>
> I'm cross-posting your question to the BioPerl list as 1) it is more
> of a perl question than a GBrowse question, and 2) I don't know the
> answer.
>
> Dave C.
> GMOD Help Desk
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at SMBE & Arthropod Genomics:
>  http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>  http://www.k-state.edu/agc/symp2009/seminar.html
>
>
>
> On Thu, May 7, 2009 at 7:26 PM, Neil Saunders <neilfws at gmail.com>  
> wrote:
>> I'm trying to install the latest Gbrowse (1.99) on a machine where  
>> I do
>> not have root access (Ubuntu/dapper).
>>
>> I have set up non-root CPAN and installed all of the prerequisites,  
>> no
>> problems, in ~/lib/perl5.  However, when I try to install Gbrowse  
>> either
>> via CPAN or using the latest CVS Build script, I run into this  
>> problem:
>>
>> Global symbol "$VAR1" requires explicit package name at (eval 28)  
>> line
>> 1088, <GEN6> line 1.
>>        ...propagated at /usr/local/share/perl/5.8.7/Module/Build/ 
>> Base.pm line
>> 1002, <GEN6> line 1.
>> make: *** [all] Error 255
>>   LDS/GBrowse-1.99.tar.gz
>>   /usr/bin/make -- NOT OK
>>
>>
>> It seems that there are 2 versions of Module::Builder on the  
>> machine.  I
>> have installed a version from CPAN which is found in
>> ~/lib/perl5/site_perl/Module/.  However, from the above error it  
>> looks
>> as though the install is trying to use a system-wide version of
>> Module::Build in /usr/local/share/perl/5.8.7.
>>
>> Can anyone shed any light on either the error message, or a way to  
>> force
>> usage of my $HOME module, not the system one?
>>
>> thanks,
>> Neil Saunders
>> --
>>  Statistical Bioinformatics - Health
>>  CSIRO Mathematical and Information Sciences
>>  Locked Bag 17, North Ryde, NSW 1670, Australia
>>
>> http://friendfeed.com/neilfws
>>
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