[Bioperl-l] Error: The extension 'Bio::SeqIO::staden::read' is not properly installed in path

CJay Horton jayhorton at gmail.com
Thu Mar 30 14:38:57 EST 2006


Hello Everyone,

I am using perl v5.8.0 and bioperl-1.4 on rh linux.

When i run this script:

#!/bin/perl -w

 use Bio::SeqIO;

 $seqio_obj = Bio::SeqIO->new(-file =>
"H12_SLC3R_Shelley_Sheridan.ab1", -format => "fasta" );

 $seq_obj = $seqio_obj->next_seq;

 while ($seq_obj = $seqio_obj->next_seq){
   # print the sequence
   print $seq_obj->seq,"\n";
 }
##########################################


I recieve the following error:

$ perl seqio.pl
The extension 'Bio::SeqIO::staden::read' is not properly installed in path:
  '/usr/lib/perl5/site_perl/5.8.0'

If this is a CPAN/distributed module, you may need to reinstall it on your
system.

To allow Inline to compile the module in a temporary cache, simply remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.

 at seqio.pl line 0
INIT failed--call queue aborted, <DATA> line 1.

#####################################

The only error I recall seeing during installation was during the perl
Make.PL for bioperl-ext and it was:
$ perl Makefile.PL
Checking if your kit is complete...
Looks good
Writing Makefile for Bio::Ext::Align
Found Staden io_lib "libread" in /usr/local/lib ...
Automatically using the Read.h found in /usr/local/include/io_lib ...
Writing Makefile for Bio::SeqIO::staden::read
Writing Makefile for Bio
One or more DATA sections were not processed by Inline.

#######################################

I manually moved the .h files into /usr/local/include/io_lib as
instructed by the bioperl-ext readme and installed and modules that
were required for each component to run(inline:MakeMaker, etc.)

Any direction would be greatly appreciated!



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