Hi Steffen , hi Johannes,

I consistently get the same error. Something must have changed because 
before some days it worked fine. Maybe I have to update.

Wasco

Am 8/10/2011 5:17 PM, schrieb Steffen Durinck:
> Hi Wasco,
>
> This works for me, maybe the server was temporarily down, any chance 
> you can try again?
>
> Steffen
>
> On Wed, Aug 10, 2011 at 5:16 AM, Wasco Wruck <wasco.wruck@charite.de 
> <mailto:wasco.wruck@charite.de>> wrote:
>
>     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; <title>FEHLER: Die
>     angeforderte URL konnte nicht gefunden werden</title> <style
>     type="text/css"><!--   /*
>     2                                                                
>                                                                      
>                                                                      
>                                                      Stylesheet for
>     Squid Error pages
>     3                                                                
>                                                                      
>                                                                      
>                                             Adapted from design by
>     Free CSS Templates
>     4 http://www.freecsstemplates.org
>     5                                                                
>                                                                      
>                                                                      
>                    Released for free under a Creative Commons
>     Attribution 2.5 License
>     6                                                                
>                                                                      
>                                                                      
>                                                                      
>                  */
>     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 <tel:%2B49%2030%20450%20536237>
>     wasco.wruck@charite.de <mailto:wasco.wruck@charite.de>
>
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>
>


-- 

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


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