[BioC] Biomart useDataset error

Aedin Culhane aedin at jimmy.harvard.edu
Thu Mar 2 22:28:39 CET 2006


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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