Thanks Rhoda, That's what I was looking for. Cheers Paul -----Original Message----- From: Rhoda Kinsella To: Paul Leo Cc: bioconductor Subject: Re: [BioC] BioMart connection problem Date: Tue, 21 Dec 2010 09:24:47 +0000 Hi Paul You can set your host to www.ensembl.org rather than accessing the www.biomart.org server. I hope that helps Regards Rhoda > listMarts(host="www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 60 2 ENSEMBL_MART_SNP Ensembl Variation 60 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 60 4 ENSEMBL_MART_VEGA Vega 40 5 REACTOME Reactome 6 wormbase215 WormBase 215 (CSHL US) 7 pride PRIDE (EBI UK) On 14 Dec 2010, at 07:44, Paul Leo wrote: > I've never actually seen this error, though it appears benign .. I > assume someone is flogging in poor BioMart server? > > If there a alternative mirror site? This has persisted for a few > hours ... > > > > > > library(biomaRt) > > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > > ann.refseq<-getBM(attributes = > > c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","description"), filters = "hgnc_symbol", values=gene.names, mart = mart) > Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", > "gene_biotype", : > Query ERROR: caught BioMart::Exception::Database: Could not connect > to > mysql database ensembl_mart_60: DBI > connect('database=ensembl_mart_60;host=dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 > > > sessionInfo() > > R version 2.13.0 Under development (unstable) (2010-11-03 r53517) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.7.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]