[BioC] biomaRt error and no devel package for windows?

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 14 15:37:15 CEST 2006

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:


Also, there are some good hints from the folks in Seattle here:


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.



> Thanks
> Mick
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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