[BioC] problems when connecting to biomaRt database

Lina Hultin-Rosenberg Lina.Hultin.Rosenberg at ebc.uu.se
Fri Dec 22 12:45:49 CET 2006

Dear all,

I have been using biomaRt to connect to ensembl and have previously done
that without any problems. Now when I tried again today I run into problems,
see code and error message below. I have also provided the output from
sessionInfo() below.

I would greatly appreciate some help with this, probably easily solved,

> library(biomaRt)
> ensembl = useMart("ensembl")
Error in validObject(.Object) : invalid class "Mart" object: invalid object
for slot "vschema" in class "Mart": got class "NULL", should be or extend
class "character"

> sessionInfo()
Version 2.3.1 (2006-06-01)

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

other attached packages:
 biomaRt    RCurl      XML
 "1.6.3"  "0.6-2" "0.99-8"

Lina Rosenberg

Lina Hultin Rosenberg
Msc Molecular Biotechnology
Evolutionary Biology Department
Uppsala University
Norbyvägen 18
752 36 Uppsala
Phone: +46-18-4716444
Email: lina.hultin.rosenberg at ebc.uu.se

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