Hi, I had the same error some days ago - but it seems ok now.

  Arne




Paul Leo <p.leo@uq.edu.au> 
Sent by: bioconductor-bounces@r-project.org
12/21/2010 01:55 AM

To
bioconductor <bioconductor@stat.math.ethz.ch>
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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