[Bioperl-l] taxonomy nightmare

[Chris Fields]

You may have a version of perl that either doesn't include Scalar::Util or includes a broken version.  Try installing Scalar::Util from CPAN to see if it fixes the problem.

Here's a link on the problem:

http://www.perlmonks.org/?node_id=424737

chris

On May 24, 2010, at 5:01 PM, Smithies, Russell wrote:

> 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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