[BioC] biomaRt - current devel version of biomaRt+RCurl don't work
Paul Leo
p.leo at uq.edu.au
Fri May 29 06:56:42 CEST 2009
I (and I assume most) have no problem with the "standard" config below.
Worth depreciating ?
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_AU.UTF-8;LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_AU.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_0.94-1 XML_1.95-3
>
-----Original Message-----
From: James Bullard <bullard at berkeley.edu>
To: whuber at embl.de
Cc: Bioconductor <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] biomaRt - current devel version of biomaRt+RCurl
don't work
Date: Thu, 28 May 2009 14:00:04 -0700
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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