[Bioperl-l] parsing a phyloxml file
cjfields at illinois.edu
Wed Jan 28 17:10:32 UTC 2009
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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).
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,
> 2009/1/28 Chris Fields <cjfields at illinois.edu>
> On Jan 28, 2009, at 9:40 AM, Chrysanthi A. wrote:
> I am trying to parse a phyloxml file but I get the message error
> Bio::TreeIO: phyloxml cannot be found
> ------------- EXCEPTION -------------
> MSG: Failed to load module Bio::TreeIO::phyloxml. Cannot use
> XML::LibXML::Reader module - your libxml2 is compiled without reader
> support! at
> 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:
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