Hi I'm getting the following error with biomaRt: > marts <- listMarts() > index <- grep("ensembl", marts) > mart <- useMart(marts[index]) connected to: ensembl_mart_38 > mart <- useDataset(dataset = "hsapiens_gene_ensembl", mart = mart) Reading database configuration of: hsapiens_gene_ensembl Error in .Call("RS_XML_ParseTree", as.character(file), handlers, as.logical(ignoreBlanks), : error in creating parser for NA I searched the lists and found this error may be fixed in the devel release, but I can only find the .tar.gz for the devel release, not a .zip. I'm using R version 2.2.1 (on Windows XP), which I guess also may be a problem Thanks Mick

Hi Mick, michael watson (IAH-C) wrote: > Hi > > I'm getting the following error with biomaRt: > > >>marts <- listMarts() >>index <- grep("ensembl", marts) >>mart <- useMart(marts[index]) > > connected to: ensembl_mart_38 > >>mart <- useDataset(dataset = "hsapiens_gene_ensembl", mart = mart) > > Reading database configuration of: hsapiens_gene_ensembl > Error in .Call("RS_XML_ParseTree", as.character(file), handlers, > as.logical(ignoreBlanks), : > error in creating parser for NA > > I searched the lists and found this error may be fixed in the devel > release, but I can only find the .tar.gz for the devel release, not a > .zip. > > I'm using R version 2.2.1 (on Windows XP), which I guess also may be a > problem Have you tried upgrading to R-2.3.1 and using the release version? You are using a fairly old version of biomaRt. If the fix is truly only in the devel version (I would bet the list entry you read was from before the release of BioC 1.8, so what was devel then is release now), you will need to get R-2.4.0dev, as well as get set up to build source packages. This isn't the most trivial thing to do, but it is nice to have the capability to build source packages so you aren't dependent on someone else to build the binary for you. The canonical information for how to get set up is here: http://www.murdoch-sutherland.com/Rtools/ Also, there are some good hints from the folks in Seattle here: http://wiki.fhcrc.org/bioc/HowTo/Build_R_on_Windows Note that you need all of this stuff to build R from source on Windows (including building the install package if you want to get hardcore), but you only need a subset if you just want to build and install packages. HTH, Jim > > Thanks > Mick > > _______________________________________________ > 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.