[BioC] problems when connecting to biomaRt database

[Wolfgang Huber]

Lina,

Please update your R and your biomaRt to a more recent version. Ensembl
is an online resource that regularly has new releases that change its
content (and just has one this week), and hence the biomaRt package
needed changes to keep pace with it.

 Best wishes
 Wolfgang

Lina Hultin-Rosenberg wrote:
> 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,
> problem! 
> 
> ______________________________________________________________________
>> 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)
> i686-pc-linux-gnu
> 
> 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"
> __________________________________________________________________________
> 
> Sincerely,
> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber