[BioSQL-l] installation.....IO/String problem

[Chris Fields]

On Aug 13, 2008, at 3:54 PM, Peter wrote:

> On Wed, Aug 13, 2008 at 9:13 PM, mrphysh at juno.com <mrphysh at juno.com>  
> wrote:
>>
>> I am having trouble with database retrieval from online databases.
>> This is an install problem.(?)..I am running Linux (Ubuntu).........
>> I did these, following the documentation.  from cpan>
>> install Bundle::CPAN
>>
>> install Module::Build  #one of the many help files said to do this
>> install Bundle;;BioPerl
>> force install B/BI/BIRNEY/bioperl-1.4.tar.gz
>> ...
>> can't open file /usr/local/lib/perl/5.8.8/auto/Bio/.packlist:   
>> permission denied at /usr/share/perl/5.8/ExtUtils?Install.pm line 209
>> writing /usr/local/lib/perl/5.8.8/auto/Bio/.packlist
>> make:  ***  [pure_site_install  error13
>>  /usr/bin/make_install   --- NOT OKAY
>>       you may have to u to root to install the package
>
> This is the BioSQL mailing list, not the BioPerl mailing list, so you
> are asking the wrong people.
>
> However, this looks like a simple permissions problem - havee you
> tried to install this as the root user (e.g. use "sudo cpan" to start
> cpan) or have you configured it to install under your home directory
> where you should have write permissions?
>
> Peter

I think this is also a bioperl versioning issue.  Module::Build is  
(oddly) calling for the old BioPerl version (1.4) which is way out-of- 
date.

You should try installing bioperl 1.5.2 or bioperl-live for this; see  
here:

http://www.bioperl.org/wiki/Installing_BioPerl
http://www.bioperl.org/wiki/Core_package

chris