[BioC] trouble getting connection to Ensembl using biomaRt

[James W. MacDonald]

Hi Joern,

I can't connect using the Rcurl interface, but the RMySQL interface is 
working. I assume the webserver is down right now.

Best,

Jim



Joern Toedling wrote:
> 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
> 
> _______________________________________________
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623