[BioC] trouble getting connection to Ensembl using biomaRt

Joern Toedling toedling at ebi.ac.uk
Tue May 13 17:12:31 CEST 2008


since this afternoon I have trouble to get a connection to Ensembl using biomaRt. Has any noticed this before?

> ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
Entity: line 4: parser error : Opening and ending tag mismatch: meta line 3 and body
Entity: line 6: parser error : Premature end of data in tag html line 1

Error in .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks),  :
  error in creating parser for P¿

> sessionInfo()
R version 2.8.0 Under development (unstable) (2008-04-21 r45421)


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

other attached packages:
[1] biomaRt_1.15.0 RCurl_0.9-2    fortunes_1.3-3

loaded via a namespace (and not attached):
[1] XML_1.93-2

Will ask the Ensembl help desk as well.



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