[Bioperl-l] taxonomy nightmare

[Smithies, Russell]

We've upgraded BioPerl recently and now lots of stuff appears broken though I'm sure it's not as bad as it looks.
Under v1.5.2, the Bio::DB::Taxonomy worked fine but under 1.6.0 I'm deluged with errors.
AFAIK, there were no changes to Perl 5.8.8

Any help greatly appreciated!!!

Thanx,

Russell Smithies

-----------------------------------
#! /usr/local/bin/perl

use strict;
use warnings;
use Bio::DB::Taxonomy;
use Data::Dumper;

my $idx_dir = '/data/home/smithiesr/taxonomy';
my $TAXDIR =  "/data/home/smithiesr/taxdump";

my ($nodefile,$namesfile) = ("$TAXDIR/nodes.dmp","$TAXDIR/names.dmp");

my $db = new Bio::DB::Taxonomy(-source    => 'flatfile',
                               -nodesfile => $nodefile,
                               -namesfile => $namesfile,
                               -directory => $idx_dir,
					-force     => 1) or die $!;

my $human = $db->get_taxon(-name => 'Homo sapiens');
print Dumper $human;

-----------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Failed to load module Bio::DB::Taxonomy::flatfile. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Tree/Node.pm line 89
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Tree/Node.pm line 89.
Compilation failed in require at (eval 21) line 3.
        ...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Taxon.pm line 155.
Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Taxonomy/flatfile.pm line 89.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Taxonomy/flatfile.pm line 89.
Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 439.

STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:441
STACK: Bio::DB::Taxonomy::_load_tax_module /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Taxonomy.pm:264
STACK: Bio::DB::Taxonomy::new /usr/lib/perl5/site_perl/5.8.8/Bio/DB/Taxonomy.pm:115
STACK: taxonomyTest.pl:15
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