Hi,

I'm trying to use biomaRt but get the following error, when I try getBM
statement but the connectivity seems ok according to listMarts().

library("biomaRt")
listMarts()[1:4,]
              biomart
             version
1             ensembl               ENSEMBL 56 GENES (SANGER UK)
2                 snp          ENSEMBL 56 VARIATION  (SANGER UK)
3 functional_genomics ENSEMBL 56 FUNCTIONAL GENOMICS (SANGER UK)
4                vega                       VEGA 36  (SANGER UK)
ensembl = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
Checking attributes ... ok
Checking filters ... ok
affyids = c("202763_at", "209310_s_at", "207500_at")
getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters =
"affy_hg_u133_plus_2", values = affyids, mart = 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.
Calls: getBM ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>


I search a little bit and found that on the postForm call on getBM got the
error; probably RCurl compatibility issue?


> sessionInfo()
R version 2.9.2 (2009-08-24)
i486-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.2.0 rkward_0.5.1

loaded via a namespace (and not attached):
[1] RCurl_1.3-0 tools_2.9.2 XML_2.6-0


Thanks,

Cristobal

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