[BioC] BioMart connection problem

[Martin Morgan]

On 12/20/2010 05:04 PM, Paul Leo wrote:
> 
> 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.

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> 
> 
> 
> 
> -----Original Message-----
> From: Paul Leo <p.leo at uq.edu.au>
> To: bioconductor <bioconductor at stat.math.ethz.ch>
> 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  
> 
> 
> 
> 
> 
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