[BioC] BioMart error

Mon Mar 3 15:39:12 CET 2008

Hi Shiliang,

swang wrote:
> Hi,
> 
> I installed the newest R version 2.6.2. and the newest biomaRt version
> biomaRt_1.12.2
> I got the following error. Would someone please tell me what wrong with this
> package?
> 
> package 'RCurl' successfully unpacked and MD5 sums checked
> package 'XML' successfully unpacked and MD5 sums checked
> The downloaded packages are in
> 
> C:\Users\swang.UNCSPH\AppData\Local\Temp\RtmpJjs9mF\downloaded_packages
> updating HTML package descriptions
>> library(biomaRt)
> Loading required package: RCurl
>>     ensembl = useMart("ensembl")
> Error in .Call("RS_XML_ParseTree", as.character(file), handlers,
> as.logical(ignoreBlanks),
> :
>   error in creating parser for <html>
> <body>
> <meta http-equiv="refresh" content='0;URL=
> http://www.ebi.ac.uk/errors/failure.html'>
> </body>
> </body>
>> listMarts()
> Error in .Call("RS_XML_ParseTree", as.character(file), handlers,
> as.logical(ignoreBlanks),
> :
>   error in creating parser for <html>
> <body>
> <meta http-equiv="refresh" content='0;URL=
> http://www.ebi.ac.uk/errors/failure.html'>
> </body>
> </body>
>> sessionInfo()
> R version 2.6.2 (2008-02-08)
> i386-pc-mingw32
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] biomaRt_1.12.2 RCurl_0.8-1
> loaded via a namespace (and not attached):
> [1] tools_2.6.2 XML_1.7-3

That's a very old version of XML (I have XML_1.93-2.1). Try updating and 
running again.

Best,

Jim

> 
> Thanks
> 
> Shiliang
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623