Question: biomaRt error in useMart
gravatar for vedran.franke
24 months ago by
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 • 829 views
ADD COMMENTlink modified 24 months ago by Mike Smith3.3k • written 24 months ago by vedran.franke0
Answer: biomaRt error in useMart
gravatar for Mike Smith
24 months ago by
Mike Smith3.3k
EMBL Heidelberg / de.NBI
Mike Smith3.3k 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.

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", 
               host = "", 
               ensemblRedirect = FALSE)
> mart
Object of class 'Mart':
 Using the ENSEMBL_MART_ENSEMBL BioMart database
 Using the mmusculus_gene_ensembl dataset
ADD COMMENTlink modified 24 months ago • written 24 months ago by Mike Smith3.3k
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