[Bioperl-l] strange error in the beginners howto

[Brian Osborne]

Matthew,

First, let's distinguish "warning" and "error". Errors stop execution of the app or script, what you're seeing is a warning, your script actually completes. Does the warning vanish if you remove "-w"?

Second, seems like this is a Perl version thing:

http://www.sysarchitects.com/bioperl

BIO

On Jan 4, 2013, at 1:55 PM, "Thornton, Matthew" <Matthew.Thornton at med.usc.edu> wrote:

> Hello,
> 
> I am working through the first part of the BioPerl beginners howto and I am getting an error and I was wondering if you could tell me what is wrong.
> 
> I made the seqio.pl script:
> 
> #!/bin/perl -w
> 
> use Bio::Seq;
> 
> $seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",                        
>                          -display_id => "#12345",                        
>                          -desc => "example 1",                        
>                          -alphabet => "dna" );
> 
> print $seq_obj->seq();
> 
> I execute the script and I get this error:
> 
> gserver at gserver:~/bio$ perl seqio.pl 
> Replacement list is longer than search list at /usr/local/share/perl/5.14.2/Bio/Range.pm line 251.
> aaaatgggggggggggccccgttgserver at gserver:~/bio$
> 
> Is there something wrong with my installation?
> 
> Any help is greatly appreciated.
> 
> Thanks!
> 
> 
> Matthew E. Thornton
> 
> 
> 
> Laboratory Technician III
> Broad Center for Stem Cell and Regenerative Medicine
> University of Southern California
> 1501 San Pablo St. ZNI
> Los Angeles, CA 90089-2821
> ph.:323-442-1688
> fx.:323-442-4040
> matthew.thornton at med.usc.edu
> 

Brian O.
--
Brian Osborne, PhD
BioTeam: http://bioteam.net
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