[Bioperl-l] parsing a phyloxml file

Hilmar Lapp hlapp at gmx.net
Thu Jan 29 17:31:32 EST 2009


Chrysanthi,

if your error message still says

'XML::LibXML::Reader module - your libxml2 is compiled without reader  
support!'

then in all likelihood that is precisely your problem. NEXUS or newick  
are not XML formats and hence whether they work or not says nothing as  
to why you are getting this error.

Chris also indicates that after updating your libxml2 you will have to  
recompile and reinstall XML::LibXML so that it recognized and compiles  
with the newer libxml2 capabilities. Have you done that?

	-hilmar

On Jan 29, 2009, at 4:24 PM, Chrysanthi A. wrote:

> 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
>>>
>>>
>>>
>>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================





More information about the Bioperl-l mailing list