[Bioperl-l] Can't locate IO/String.pm._._..install problem

mrphysh at juno.com mrphysh at juno.com
Tue Aug 12 10:30:36 EDT 2008


I am studying bioperl and making progress.  I have been struggling with the database retrieval from 
on-line databases.  This is an example................

#!/usr/bin/perl -w
 
use Bio::Perl;

 
$seq_object = get_sequence('swiss',"ROA1_HUMAN");
 
write_sequence(">roa1.fasta",'fasta',$seq_object);

exit;

This script gives

Can't locate IO/String.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.8 /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at ee_bpo.pl line 12.
BEGIN failed--compilation aborted at ee_bpo.pl line 12.

I have chased around with the paths in @INC, using "use lib'.

This is an install problem.  The original installation was with perl Makefile.pl.  I reinstalled over the old with cpan.  stuff like this:
cpan> o conf prerequisites_policy follow
cpan> i /bioperl/
cpan> install Bundle::BioPerl
cpan> install B/BI/BIRNEY/bioperl-1.2.1.tar.gz
cpan> force install B/BI/BIRNEY/bioperl-1.2.1.tar.gz
This all seemed to proceed smoothly.

this guy did not produce an error.
use Bio::Perl;

I am almost thinking that the problem is with the perl. But regular ftp through perl works:

use Net::FTP;#I found this in usr/share/perl/5.8.8/Net
As a perl command this module seems to work.

I looked in the archives and found nothing.  I think I have done my homework.  any ideas?

I run Ubuntu on a pentium III (and love it).  the version of Ubuntu is new.  the Perl (and MySQL) came with the OS: perl 5.8.8

John Brigham in Denver.


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