BioMart error

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swang ▴ 120

@swang-1798

Last seen 10.1 years ago

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ADD COMMENT • link updated 16.6 years ago by James W. MacDonald 67k • written 16.6 years ago by swang ▴ 120

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 12 hours ago

United States

Hi Shiliang, swang wrote: > Hi, > > I installed the newest R version 2.6.2. and the newest biomaRt version > biomaRt_1.12.2 > I got the following error. Would someone please tell me what wrong with this > package? > > package 'RCurl' successfully unpacked and MD5 sums checked > package 'XML' successfully unpacked and MD5 sums checked > The downloaded packages are in > > C:\Users\swang.UNCSPH\AppData\Local\Temp\RtmpJjs9mF\downloaded_packa ges > updating HTML package descriptions >> library(biomaRt) > Loading required package: RCurl >> ensembl = useMart("ensembl") > Error in .Call("RS_XML_ParseTree", as.character(file), handlers, > as.logical(ignoreBlanks), > : > error in creating parser for <html> > <body> > <meta http-equiv="refresh" content="0;URL= > <a href=" http:="" www.ebi.ac.uk="" errors="" failure.html"="" rel="nofollow">http://www.ebi.ac.uk/errors/failure.html"> > </body> > </body> >> listMarts() > Error in .Call("RS_XML_ParseTree", as.character(file), handlers, > as.logical(ignoreBlanks), > : > error in creating parser for <html> > <body> > <meta http-equiv="refresh" content="0;URL= > <a href=" http:="" www.ebi.ac.uk="" errors="" failure.html"="" rel="nofollow">http://www.ebi.ac.uk/errors/failure.html"> > </body> > </body> >> sessionInfo() > R version 2.6.2 (2008-02-08) > i386-pc-mingw32 > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] biomaRt_1.12.2 RCurl_0.8-1 > loaded via a namespace (and not attached): > [1] tools_2.6.2 XML_1.7-3 That's a very old version of XML (I have XML_1.93-2.1). Try updating and running again. Best, Jim > > Thanks > > Shiliang > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

ADD COMMENT • link 16.6 years ago James W. MacDonald 67k

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