Hi, I had the same error some days ago - but it seems ok now.
Arne
Paul Leo
Sent by: bioconductor-bounces@r-project.org
12/21/2010 01:55 AM
To
bioconductor
cc
Subject
[BioC] BioMart connection problem
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
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