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'm pretty certain this error is related to issues with the Ensembl biomart server, but I'm currently not seeing this when I run your code, so maybe it's been fixed already. 

If you experience it again, you can always try one of the Ensembl mirror sites to see if they're working, like this:

mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", 
                dataset = "hsapiens_gene_ensembl", 
                host = "useast.ensembl.org")

You can also use asia.ensembl.org and uswest.ensembl.org for the host argument.

Unfortunately, it looks like the main ensembl.org server doesn't work either - at least for me. Throughout this weekend I have been having the same error with what looks like the communication error with BioMart to annotate my data.  Does anyone have a solution for this? or if not, a way to revert to the earlier version somehow so BioMart can be used?

source("http://bioconductor.org/biocLite.R")
biocLite("biomaRt")
require(biomaRt)

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "mmusculus_gene_ensembl",
                         host = 'ensembl.org')

t2g <- biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",
                                     "external_gene_name","chromosome_name", "entrezgene",
                                     "ucsc"), mart = mart)

Output then is:

Error in biomaRt::getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id",  : 
  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: Unknown MySQL server host 'ensdbweb-1-vip' (1) at /ensemblweb/www/www_88/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.

Hello,

I am afraid that we had a DOS attack affecting our www.ensembl.org marts on Friday.

The services were restored shortly after the attack.

Apologies for any inconveniences caused. 

Kind Regards,

Thomas

I saw the same error yesterday - it went away this morning. There was no note of an outage on the blog, but it looks like that's what it was.