[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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