I'm having problems connecting to biomaRt through R.

 

useMart reports an error and claims either the service is down or I am
not connected to the internet:

 

> mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl")

Error in value[[3L]](cond) : 

  Request to BioMart web service failed. Verify if you are still
connected to the internet.  Alternatively the BioMart web service is
temporarily down.

 

But R can connect to martservice just fine:

 

> download.file(url="http://www.biomart.org/biomart/martservice",
destfile="test.html")

trying URL 'http://www.biomart.org/biomart/martservice'

Content type 'text/plain' length 200 bytes

opened URL

downloaded 5810 bytes

 

So the problem is not R, it is biomaRt.

 

Any help appreciated

 

Mick

 

> sessionInfo()

R version 2.9.1 (2009-06-26) 

i386-pc-mingw32 

 

locale:

LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

 

attached base packages:

[1] tools     stats     graphics  grDevices utils     datasets  methods
base     

 

other attached packages:

[1] CORNA_1.1      XML_2.5-3      GEOquery_2.8.0 RCurl_0.98-1
bitops_1.0-4.1 biomaRt_2.0.0  Biobase_2.4.1

 

Head of Bioinformatics
Institute for Animal Health
Compton
Berks
RG20 7NN
01635 578411 

 

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