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

[James Bullard]

Hi, I am having problems with biomaRt and based on Wolfgang's post it  
looks like I shouldn't be (or am I being completely naive?):

Thanks, jim

 > library("biomaRt")
 > mart = useMart("ensembl")
 > ensembl = useDataset("hsapiens_gene_ensembl",
+    mart=mart)
Checking attributes ... ok
Checking filters ... ok
 > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
 > utr = getSequence(id=EGsub, seqType="3utr",
+    mart=ensembl, type="entrezgene")
CA ..... I cut out a lot of the sequence ...  
GTGCCCTGCCTTGCACCTCCGCCTTATTTTCTGC	87
                                                          V1
1                                           HTTP/1.1 200 OK
2                       Date: Thu, 28 May 2009 20:56:08 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
Error 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 2.9.0 Patched (2009-05-28 r48678)
x86_64-unknown-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 
= 
C 
;LC_MESSAGES 
= 
en_US 
.UTF 
-8 
;LC_PAPER 
= 
en_US 
.UTF 
-8 
;LC_NAME 
= 
C 
;LC_ADDRESS 
=C;LC_TELEPHONE=C;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_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.95-1 tools_2.9.0  XML_2.3-0


On May 28, 2009, at 5:01 AM, Wolfgang Huber wrote:

> 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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