The following command produces the error message mentioned below:
> mart = useMart("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
Referring to the help function everything should be okay if the URL within the eror message produces the following output:
<MartRegistry>
<MartURLLocation database="ensembl_mart_95" default="1" displayName="Ensembl Genes 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
<MartURLLocation database="mouse_mart_95" default="" displayName="Mouse strains 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_MOUSE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
<MartURLLocation database="sequence_mart_95" default="" displayName="Sequence" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SEQUENCE" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
<MartURLLocation database="ontology_mart_95" default="" displayName="Ontology" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_ONTOLOGY" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
<MartURLLocation database="genomic_features_mart_95" default="" displayName="Genomic features 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_GENOMIC" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="" />
<MartURLLocation database="snp_mart_95" default="" displayName="Ensembl Variation 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_SNP" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
<MartURLLocation database="regulation_mart_95" default="" displayName="Ensembl Regulation 95" host="www.ensembl.org" includeDatasets="" martUser="" name="ENSEMBL_MART_FUNCGEN" path="/biomart/martservice" port="80" serverVirtualSchema="default" visible="1" />
</MartRegistry>
I use version 2.36.1 . Any idea how to solve this issue?
Frank
This is odd, because you're getting the correct result in the browser, so it isn't a fundamental connection problem either at your end or with Ensembl. Your code also works fine for me.
You could try using one of the mirror sites e.g.
The usage of another mirror (here: useast) works perfectly whereas the same command without a mentioned mirror on the same system still does not work. It is strange, but it solves at least the problem.
Thanks! Frank