[Bioperl-l] TreeIO problem

Mikel Ega pik at sindominio.net
Thu Apr 15 06:13:20 EDT 2004

Hello people;

First of all, Bioperl is great. I have just started using it for one of
my projects and I'm amazed. 

I have a problem with the TreeIO class. I just want to write a newick
tree in SVG format, so I got this code from the api and put it in this
little script:


use Bio::TreeIO;

my $in = new Bio::TreeIO(-file => 'input', -format => 'newick');
my $out = new Bio::TreeIO(-file => '>output', -format => 'svggraph');

  while( my $tree = $in->next_tree ) {
      my $svg_xml = $out->write_tree($tree);


And the following exception was given:

MSG: Failed to load module Bio::TreeIO::svggraph. Can't locate
SVG/Graph.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.3
/usr/local/share/perl/5.8.3 /usr/lib/perl5 /usr/share/perl5
/usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at
/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. BEGIN
failed--compilation aborted at
/usr/local/share/perl/5.8.3/Bio/TreeIO/svggraph.pm line 78. Compilation
failed in require at /usr/local/share/perl/5.8.3/Bio/Root/Root.pm line

STACK Bio::Root::Root::_load_module
/usr/local/share/perl/5.8.3/Bio/Root/Root.pm:396 STACK (eval)
/usr/local/share/perl/5.8.3/Bio/TreeIO.pm:227 STACK
/usr/local/share/perl/5.8.3/Bio/TreeIO.pm:226 STACK Bio::TreeIO::new
/usr/local/share/perl/5.8.3/Bio/TreeIO.pm:126 STACK toplevel ./svg.pl:6

So I have installed all the SVG related modules via CPAN but I receive
the same error, and I cannot figure out what should I do next.

Thank you for your time, 

Mikel Egaña.

PS: I'm using bioperl 1.4 in Debian Sarge.

-->pik at lolita (Debian Sarge-Kernel 2.4.20) 


-->"Don Quijote se salva cuando se echa a 
   los caminos a ser apaleado" (Francisco Umbral)

More information about the Bioperl-l mailing list