[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
More information about the Bioconductor
mailing list