[BioC] Problems with biomaRt

[James W. MacDonald]

It's working for me:

 > library(biomaRt)
 > mart <- useMart("ensembl","hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > sessionInfo()
R version 2.9.0 (2009-04-17)
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 datasets  utils     methods   base

other attached packages:
[1] biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.98-1 XML_2.5-1
 > Sys.time()
[1] "2009-07-13 09:17:58 EDT"

Maybe try again?

Best,

Jim



michael watson (IAH-C) wrote:
> 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 
> 
>  
> 
> Please consider the environment and don't print this e-mail unless you
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> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826