[BioC] biomaRt - current devel version of biomaRt+RCurl don't work

[Wolfgang Huber]

Hi

just to warn all users of the development version of biomaRt, please 
wait a few days before updating your RCurl, the current devel versions 
of these two packages do not work together. We are sorting it out.

An example for the error that is produced, with RCurl_0.97-2 and 
biomaRt_2.1.0, is shown below. With a previous version of RCurl, the 
problem should not arise.


library("biomaRt")
mart = useMart("ensembl")
ensembl = useDataset("hsapiens_gene_ensembl",
     mart=mart)
EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
utr = getSequence(id=EGsub, seqType="3utr",
     mart=ensembl, type="entrezgene")

CAGCAGTCAGGGGTCAGGTGTCAGGCCCGTCGGAGCT...   25
CTGCAGCTTTTGCCTTGGTTCTTCCTAGTGCCTACAA...  102
TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG...   87
TCCACCCCGCCCGGCCGCCCTCGTCTTGTGCGCCGTG...   87
                                                          V1
1                                           HTTP/1.1 200 OK
2                       Date: Thu, 28 May 2009 11:57:58 GMT
3 Server: Apache/2.2.9 (Debian) mod_perl/2.0.4 Perl/v5.10.0
4                                         Connection: close
5                                Transfer-Encoding: chunked
6                                  Content-Type: text/plain

Errore in getBM(c(seqType, type), filters = type, values = id, mart = 
mart,  :
   The query to the BioMart webservice returned an invalid result: the 
number of columns in the result table does not equal the number of 
attributes in the query. Please report this to the mailing list.


 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-28 r48665)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=C              LC_NUMERIC=C            LC_TIME=C 

  [4] LC_COLLATE=C            LC_MONETARY=C 
LC_MESSAGES=it_IT.UTF-8
  [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C 

[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.1.0  fortunes_1.3-6

loaded via a namespace (and not attached):
[1] RCurl_0.97-2 XML_2.3-0
 >


-- 

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber