[BioC] getBM returns error

Wed Aug 10 14:16:31 CEST 2011

Hi,

I am getting an error for a biomaRt getBM() call which used to work 
before. Has something changed in getBM() or the corresponding web 
services - or might there be firewall problems? I have the environment 
variable http_proxy set and other commands through the firewall, e.g. 
package installations work. Also getting the same information from 
biomart via wget and a xml query works through http_proxy. Here is the 
output:

 > library("biomaRt")
 > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
 > o=getBM(c("ensembl_gene_id", "ensembl_transcript_id", 
"illumina_humanwg_6_v2"), mart=mart)
                                                                                                                                                                                                                                                                                      V1
1 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" 
"http://www.w3.org/TR/html4/strict.dtd"> <html><head> <meta 
http-equiv="Content-Type" content="text/html; charset=utf-8"> 
<title>FEHLER: Die angeforderte URL konnte nicht gefunden werden</title> 
<style type="text/css"><!--   /*
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Stylesheet for Squid Error pages
3                                                                                                                                                                                                                                             
Adapted from design by Free CSS Templates
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http://www.freecsstemplates.org
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Released for free under a Creative Commons Attribution 2.5 License
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*/
Fehler in getBM(c("ensembl_gene_id", "ensembl_transcript_id", 
"illumina_humanwg_6_v2"),  :
   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 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

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

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

other attached packages:
[1] biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-1 XML_2.8-1

Best regards,
Wasco

-- 

Wasco Wruck
Institute of Pathology
Charite Campus Mitte
Charite - Universitaetsmedizin Berlin
Chariteplatz 1
10117 Berlin
+49 30 450 536237
wasco.wruck at charite.de