[BioC] biomaRt - current devel version of biomaRt+RCurl don't work
Wolfgang Huber
huber at ebi.ac.uk
Thu May 28 14:01:02 CEST 2009
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
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