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Henrik Kinnemann
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10
@henrik-kinnemann-280
Last seen 10.6 years ago
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
