[Bioperl-l] parsing a phyloxml file

Chrysanthi A. chrysain at gmail.com
Thu Jan 29 16:24:55 EST 2009


Hi,

Yes, I updated library with the last version of libxml2 (2.6.27), but I get
again the same problem? Trying to parse files of nexus or newick format, I
do not have any problem.. I read in the bioperl wiki that "the phyloxml tree
format will be supported in the next release".. So, I am supposing that
maybe the problem is with the format tha I am using. Am I right? Which is
the newest version? Is there another way to parse the file?

Thanks a lot for your help,

Chrysanthi


2009/1/28 Chris Fields <cjfields at illinois.edu>

> 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<http://search.cpan.org/%7Epajas/XML-LibXML-1.69/lib/XML/LibXML/Reader.pod#DESCRIPTION>
>>
>> chris
>>
>>
>>
>>
>


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