Hi,
This type of error was already posted BioMart connection problem but I don't see that it was resolved.
I've been using this code for a while:
require(biomaRt,quietly=T)
mart <- useMart(biomart="ensembl",dataset = "hsapiens_gene_ensembl")
df <- getBM(attributes = c("ensembl_gene_id"),mart=mart)
with no problems but now all of a sudden I'm getting this error:
Error in getBM(attributes = c("ensembl_gene_id"), mart = mart) :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_87: DBI connect('database=ensembl_mart_87;host=ensdbweb-1-vip;port=5316','ensro',...) failed: Too many connections at /ensemblweb/wwwmart/www_87/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
This persists even if change my code to:
mart <- useMart(biomart="ensembl",dataset = as.character(data.set),host="www.ensembl.org")
or:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",dataset = as.character(data.set),host="www.ensembl.org")
Any idea?
I am having this exact same issue today, and I've been unable to resolve it. Is this still thought to be related to DOS attacks?