Hi Johan,

Thanks for reporting this. It looks like this is caused by an error in a
configuration of the Ensembl side which they need to fix, I will contact
them about this issue.

Here's a quick workaround to make your queries work again until Ensembl
fixes the configuration file:

mart <- useMart("ENSEMBL_MART_ENSEMBL", host="may2012.archive.ensembl.org")
mart@host="http://may2012.archive.ensembl.org:80/biomart/martservice"
mart = useDataset("mmusculus_gene_ensembl",mart=mart)

This should enable you to do your queries on the may2012 archive.

Here's a more detailed report on what is exactly wrong in the current
Ensembl configuration file and how to find this:

listMarts(host="may2012.archive.ensembl.org",verbose=TRUE,includeHosts=TRUE)

gives

Attempting web service request:
http://may2012.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
$biomart
[1] "ENSEMBL_MART_ENSEMBL" "ENSEMBL_MART_SNP"     "ENSEMBL_MART_FUNCGEN"
[4] "ENSEMBL_MART_VEGA"    "REACTOME"             "pride"

$version
[1] "Ensembl Genes 67"      "Ensembl Variation 67"  "Ensembl Regulation 67"
[4] "Vega 47"               "REACTOME (CSHL US)"    "PRIDE (EBI UK)"

$host
[1] "archive.ensembl.org" "archive.ensembl.org" "archive.ensembl.org"
[4] "archive.ensembl.org" "reactome.oicr.on.ca" "www.ebi.ac.uk"

Notice that the host is changed from may2012.archive.ensembl.org to just
archive.ensembl.org  so this is pointing to the wrong URL making the
useMart trying to connect to  archive.ensembl.org instead of
may2012.archive.ensembl.org.

Cheers,
Steffen


On Wed, Jan 9, 2013 at 6:31 AM, J.H. Brandsma <j.h.brandsma@erasmusmc.nl>wrote:

> mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", host="
> may2012.archive.ensembl.org")
>

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