[Bioperl-l] parsing a phyloxml file

Chris Fields cjfields at illinois.edu
Wed Jan 28 11:23:28 EST 2009


On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote:

> Hi,
>
> I am trying to parse a phyloxml file but I get the message error  
> below:
>
> Bio::TreeIO: phyloxml cannot be found
> Exception
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use
> XML::LibXML::Reader module - your libxml2 is compiled without reader
> support! at
> /System/Library/Perl/5.8.8/darwin-thread-multi-2level/XML/LibXML/ 
> Reader.pm
> line 17

Helps to read the error message.  You need an updated XML::LibXML, a  
version that has XML::LibXML::Reader support.  It requires an up-to- 
date libxml.  See:

http://search.cpan.org/~pajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION

chris




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