[BioC] trouble getting connection to Ensembl using biomaRt

[Steffen Durinck]

Hi Joern,

Looks like their site is down

http://www.ensembl.org/biomart/martview

doesn't load in my browser either.

Cheers,
Steffen


----- Original Message -----
From: Joern Toedling <toedling at ebi.ac.uk>
Date: Tuesday, May 13, 2008 8:16 am
Subject: [BioC] trouble getting connection to Ensembl using biomaRt
To: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>

> 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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