[Bioperl-l] TreeIO problem

[Jason Stajich]

And you did install SVG::Graph... which pulls in a bunch of dependancies:

 Math::Derivative
 Math::Spline
 Tree::DAG_Node


What does 'perldoc SVG::Graph' report?

If I do the install via the cpan shell I get all the dependancies too.
-jason

On Thu, 15 Apr 2004, Mikel [ISO-8859-1] Ega wrote:

> 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:
>
> ------------------------------------------------------------------------
> #!/usr/bin/perl
>
> 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
> 394.
>
> 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
> Bio::TreeIO::_load_format_module
> /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)
>
> -->http://sindominio.net/~pik
>
> -->"Don Quijote se salva cuando se echa a
>    los caminos a ser apaleado" (Francisco Umbral)
> -------------------------------------------------
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu