[BioC] trouble getting connection to Ensembl using biomaRt

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


Hello,

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
</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)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.ISO-8859-1;LC_NUMERIC=C;LC_TIME=en_US.ISO-8859-1;LC_COLLATE=en_US.ISO-8859-1;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-1;LC_PAPER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.ISO-8859-1;LC_IDENTIFICATION=C

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.

Cheers,

Joern



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