[Bioperl-l] parsing a phyloxml file

Chris Fields cjfields at illinois.edu
Wed Jan 28 12:10:32 EST 2009


Chrysanthi,

Make sure to keep the mail list in your replies.

Did you update the libxml2 library (http://xmlsoft.org/) to at least  
libxml2-2.6.21?  Make sure you don't have libxml instead (aka libxml  
v1).  Most repos (apt, yum, fink, macports) have the updated version.

I believe XML::LibXML will compile if you have an older libxml  
version, but it will skip Reader and other modules that don't have a  
minimum libxml library present (and older versions of Reader are not  
API-compliant if I recall correctly).

chris

On Jan 28, 2009, at 10:59 AM, Chrysanthi A. wrote:

> I updated the version but I am getting again the same error. Why? Is  
> there another way in order to parse a phyloxml file?
>
> Thanks a lot,
>
> Chrysanthi.
>
>
> 2009/1/28 Chris Fields <cjfields at illinois.edu>
>
> 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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