I am having trouble using biomaRt. Any ideas as to what might be happening?
Error message below.
Thanks
> library(biomaRt)
> listMarts(host="www.ensembl.org")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> human<-useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.28.0 edgeR_3.14.0 limma_3.28.5
loaded via a namespace (and not attached):
[1] IRanges_2.6.0 parallel_3.3.0 DBI_0.4-1 tools_3.3.0 RCurl_1.95-4.8 Biobase_2.32.0 AnnotationDbi_1.34.3
[8] RSQLite_1.0.0 S4Vectors_0.10.1 BiocGenerics_0.18.0 stats4_3.3.0 bitops_1.0-6 XML_3.98-1.4
>
The error also happens to me.