The main Ensembl website is down for maintenance a the moment. If you go to it in a web browser you get redirected to a page telling you this. The same thing happens when you run a query in biomaRt
and the current release version doesn't cope very well and you get that unhelpful error message.
The current devel version of biomaRt
handles this a bit better e.g.
> mart = useMart("ensembl", dataset="mmusculus_gene_ensembl")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
You can still use the Ensembl mirror sites, if you are happy to install the developmental version of biomaRt
. This requires a version 2.31.8 or newer of biomaRt
You can then do:
mart = useMart("ensembl",
dataset="mmusculus_gene_ensembl",
host = "asia.ensembl.org",
ensemblRedirect = FALSE)
> mart
Object of class 'Mart':
Using the ENSEMBL_MART_ENSEMBL BioMart database
Using the mmusculus_gene_ensembl dataset