[BioC] biomaRt error

Iain Gallagher iaingallagher at btopenworld.com
Wed Jan 13 20:00:14 CET 2010


Hello List

Can anyone shed any light on the following biomaRt error? Has something changed at Ensembl?

> library(biomaRt)
> 
> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
Error: non-BioMart die(): 
not well-formed (invalid token) at line 1, column 11797, byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187

  does not seem to be XML, nor to identify a file name
> sessionInfo()
R version 2.10.1 (2009-12-14) 
x86_64-pc-linux-gnu 

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

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

other attached packages:
[1] biomaRt_2.2.0

loaded via a namespace (and not attached):
[1] RCurl_1.3-1 XML_2.6-0  
> 

Thanks

Iain




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