biomaRt error in useMart
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@vedranfranke-7218
Last seen 6.0 years ago
Germany

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 • 1.6k views
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Mike Smith ★ 6.5k
@mike-smith
Last seen 7 hours ago
EMBL Heidelberg

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
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