Question: biomaRt error in useMart
0
2.5 years ago by
Germany
vedran.franke0 wrote:

When I run the following command:

    mart = useMart("ensembl", dataset="mmusculus_gene_ensembl")

I get the following error:

    Error: 1: Entity 'copy' not defined

I have never seen an error like this, and have no idea what might have caused it.

Thank you in advance.

biomart • 993 views
modified 2.5 years ago by Mike Smith4.0k • written 2.5 years ago by vedran.franke0
Answer: biomaRt error in useMart
3
2.5 years ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

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
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by Mike Smith4.0k