[BioC] Biomart useDataset error

[sdurinck@ebi.ac.uk]

Hi Aedin,

You should upgrade biomaRt and use the latest version (1.5.10, see
developmental packages).

Best,
Steffen

> Dear BioC and Steffen
> I'd be grateful for your help.  I getting an xmlTreeParse error with
> useDataset()
> Thanks
> Aedin
>
>  > listDatasets(mart)
>                       dataset    version
> 1      mmusculus_gene_ensembl    NCBIM34
> 2  tnigroviridis_gene_ensembl TETRAODON7
> 3      frubripes_gene_ensembl      FUGU4
> 4  dmelanogaster_gene_ensembl      BDGP4
> 5        ggallus_gene_ensembl    WASHUC1
> 6    scerevisiae_gene_ensembl       SGD1
> 7       agambiae_gene_ensembl     AgamP3
> 8     mdomestica_gene_ensembl    BROADO2
> 9    rnorvegicus_gene_ensembl    RGSC3.4
> 10    amellifera_gene_ensembl    AMEL2.0
> 11       btaurus_gene_ensembl   Btau_2.0
> 12 cintestinalis_gene_ensembl       JGI2
> 13      celegans_gene_ensembl     CEL150
> 14      hsapiens_gene_ensembl     NCBI35
> 15   xtropicalis_gene_ensembl       JGI4
> 16   cfamiliaris_gene_ensembl    BROADD1
> 17      mmulatta_gene_ensembl   MMUL_0_1
> 18  ptroglodytes_gene_ensembl    CHIMP1A
> 19        drerio_gene_ensembl     ZFISH5
>
>  > mart<-useDataset(dataset="hsapiens_gene_ensembl", mart=mart)
> Reading database configuration of: hsapiens_gene_ensembl
> Entity: line 1: parser error : Start tag expected, '<' not found
> NA
> ^
> Error in .Call("RS_XML_ParseTree", as.character(file), handlers,
> as.logical(ignoreBlanks),  :
>         error in creating parser for NA
>
>  > traceback()
> 3: .Call("RS_XML_ParseTree", as.character(file), handlers,
> as.logical(ignoreBlanks),
>        as.logical(replaceEntities), as.logical(asText), as.logical(trim),
>        as.logical(validate), as.logical(getDTD), as.logical(isURL),
>        as.logical(addAttributeNamespaces), as.logical(useInternalNodes),
>        FALSE, as.logical(isSchema))
> 2: xmlTreeParse(res[1, ])
> 1: useDataset(dataset = "hsapiens_gene_ensembl", mart = mart)
>
>  > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-redhat-linux-gnu
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
> other attached packages:
>  biomaRt      XML   RMySQL      DBI
>  "1.4.0" "0.99-6"  "0.5-7" "0.1-10"
>
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