[BioC] gene annotation with annotate() function

[Henrik Kinnemann]

Hallo,

within the last days I installed a couple of BioConductor Release 1.1
Packages (Biobase, AnnBuilder, annotate) for UNIX and WINDOWS. I would
like to query the pubmed database via R's "pubmed()" function, but
there's the following problem (on UNIX and WINDOWS installations):


> library(annotate)
Loading required package: Biobase 
Loading required package: methods 
Expanding the signature to include omitted arguments 
in definition: j = "missing" 

Attaching package `Biobase':


        The following object(s) are masked from package:base :

         split 

> pubmed("9695952")
Loading required package: XML 
[1] NA
Warning messages: 
1: XML Parsing Error:
http://www.ncbi.nih.gov/entrez/utils/pmfetch.fcgi?report=xml&mode=text&tool=bioconductor&db=PubMed&id=9695952:0:
xmlParseStartTag: invalid element name 
2: XML Parsing Error:
http://www.ncbi.nih.gov/entrez/utils/pmfetch.fcgi?report=xml&mode=text&tool=bioconductor&db=PubMed&id=9695952:0:
Extra content at the end of the document 


What could be the reason for this 'XML Parsing Error?

Could it be the proxy? I already tried to set the 'http_proxy' variable
in my UNIX shell before I started R - but no success!

Could it be a wrong installation of the 'libxml2' library written by
Daniel Veillard? I already installed 'libxml2-2.2.3', and afterwards I
downloaded and installed the appropriate R module via the command 'R CMD
INSTALL -l /meta/metasoft/R-1.5.0/lib/R/library
~/Software/R/XML_0.93-3.tar.gz' - but no success!

Currently, I don't have any further ideas how to solve the problem with
'XML Parsing Error'. Who could help me, please?

Kind regards in advance,
Henrik