I've also had trouble accessing hsapiens_gene_ensembl yesterday without updating the biomaRt package. I think ENSEMBL is making changes on the server side. Does anyone know more about this?
Best, Markus On Tue, 19 Dec 2017 at 16:17 Martin, Tiphaine <tiphaine.mar...@kcl.ac.uk> wrote: > Hi, > > > Could you inform me which modification you did in biomaRt ? or in ENSEMBL ? > > Indeed, I have my R package (coMET) use biomaRt to access to data. From > the last update in BiomaRt (12/14/2017), I have a new error message. > > > Do you change the name of database associated with ENSEMBL ? > > > This is my error message > > Unexpected format to the list of available marts. > Please check the following URL manually, and try ?listMarts for advice. > > http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt > > When I look at the list of dataset, I have > > <MartURLLocation database="ensembl_mart_91" default="1" > displayName="Ensembl Genes 91" host="grch37.ensembl.org" > includeDatasets="" martUser="" name="ENSEMBL_MART_ENSEMBL" > path="/biomart/martservice" port="80" serverVirtualSchema="default" > visible="1" /> > > > however, previously, the database name was hsapiens_gene_ensembl. > > Does it mean that you are going to change the name of database for each > new release ? > > How, I can have the name of databases from ENSEMBL stable between > different releases of ENSEMBL > > > Regards, > > Tiphaine > > > ---------------------------- > Tiphaine Martin > Research Associate | King's College > The Department of Twin Research & Genetic Epidemiology | Genetics & > Molecular Medicine Division > St Thomas' Hospital > 4th Floor, Block D, South Wing > SE1 7EH, London > United Kingdom > > Bioinformatician | The University of Western Australia, > Endocrinology & Diabetes, > Sir Charles Gairdner Hospital. > School of Medicine & Pharmacology, > The University of Western Australia, > Nedlands, Western Australia 6009. > > email : tiphaine.mar...@kcl.ac.uk > Fax: +44 (0) 207 188 6761 <+44%2020%207188%206761> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
