[BioC] biomaRt xMLTreeParse error

[sdurinck@ebi.ac.uk]

Hi Matt,

This is due to an unexpected change in the Ensembl BioMart database and I
have fixed that in the BioMart version available from the devel
repository.

Note however that we are trying to remove the dependency on RMySQL and
currently are updating the biomaRt package to do queries over HTTP (will
be the default) in addition to the use of MySQL.  Some functions are not
yet updated and might give some errors for the next few days.  The
functions you are trying to use should already work properly.

best,
Steffen


> Dear list,
>
> I'm attempting to use the biomaRt library to annotate a microarray data
> set, and get the following error message (refer below).  This code
> (replacing 'ensembl_mart_37' with 'ensembl_mart_36') worked fine a week
> ago, so perhaps the latest ENSEMBL release (16/2/6) is causing biomaRt
> some trouble?
>
> Many thanks,
>
> Matt Ritchie
>
>  > library(biomaRt)
> Loading required package: RMySQL
> Loading required package: DBI
> Loading required package: XML
>  > listMarts()
> [1] "ensembl_mart_37" "vega_mart_37"    "snp_mart_37"     "msd_mart_4"
> [5] "uniprot_mart_17"
>  > mart<-useMart("ensembl_mart_37")
> connected to:  ensembl_mart_37
>  > 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('mmusculus_gene_ensembl', mart=mart)
> Reading database configuration of: mmusculus_gene_ensembl
> Entity: line 1: parser error : Start tag expected, '<' not found
> NA
> ^
> Error in xmlTreeParse(res[1, ]) : error in creating parser for NA
>  > sessionInfo()
> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
> other attached packages:
>  biomaRt      XML   RMySQL      DBI fortunes
>  "1.5.2" "0.97-8"  "0.5-5"  "0.1-9"  "1.2-0"
>
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