A new record ! my most arrives at BioC 7 days after I posted it... (on the 14 of DEC). Electrons must move slowly form Australia. -----Original Message----- From: Paul Leo To: bioconductor Subject: [BioC] BioMart connection problem Date: Tue, 14 Dec 2010 17:44:29 +1000 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 [[alternative HTML version deleted]]