Hi Jim,

I updated the packages as recommended, and still have the same error.

> library(biomaRt)
> sessionInfo()
R version 2.10.1 RC (2009-12-06 r50681)
i686-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.3-0 XML_2.6-0
> ensembl <- useMart("ensembl", "hsapiens_gene_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.
>

Can you tell me what curl and xml are on your system?
I have
$ xml2-config --version
2.7.5
$ curl --version
curl 7.19.7 (i686-pc-linux-gnu) libcurl/7.19.7
Protocols: tftp ftp telnet dict http file
Features: IPv6 Largefile

Best,
Cristobal



El 7 de diciembre de 2009 14:37, James W. MacDonald
<jmacdon@med.umich.edu>escribió:

> Hi Cristobal,
>
>
> Cristobal Fresno Rodríguez wrote:
>
>> 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?
>>
>
> Possibly. You have a previous version of R and a current version of biomaRt
> and RCurl. This works for me with packages installed using biocLite():
>
> > library(biomaRt)
> > ensembl <- useMart("ensembl", "hsapiens_gene_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)
>  affy_hg_u133_plus_2 entrezgene
> 1           202763_at        836
> 2           202763_at         NA
> 3         209310_s_at        837
> 4         209310_s_at         NA
> 5           207500_at        838
> 6           207500_at         NA
> > > > sessionInfo()
> R version 2.10.0 Patched (2009-11-05 r50317)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
>
> other attached packages:
> [1] biomaRt_2.2.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.2-1 XML_2.6-0
>
> Best,
>
> Jim
>
>>
>>
>>  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
>>
>>        [[alternative HTML version deleted]]
>>
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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
> **********************************************************
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