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_COL LATE=en_US.ISO-8859-1;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-1;LC_PA PER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREM ENT=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

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@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-885 9-1;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

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_C OLLATE=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_MEASUR EMENT=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