[BioC] getBM weird error

[James W. MacDonald]

Hi Dick,

On 10/4/2012 2:25 PM, Dick Beyer wrote:
> I'm hoping someone might have a work-around for this getBM problem:
>
> library(biomaRt)
> mart <- useMart( "ensembl", dataset="mmusculus_gene_ensembl")
> tmp <- getBM(attributes=c("uniprot_swissprot_accession","ipi"), 
> filters="ipi", values="IPI00134704", mart=mart)
>
> Error in getBM(attributes = c("uniprot_swissprot_accession", "ipi"), 
> filters = "ipi",  :
>   Query ERROR: caught BioMart::Exception::Database: Could not connect 
> to mysql database ensembl_mart_68: DBI 
> connect('database=ensembl_mart_68;host=bmdccdb.oicr.on.ca;port=3306','bm_web',...) 
> failed: Host 'bmdcc1.oicr.on.ca' is blocked because of many connection 
> errors; unblock with 'mysqladmin flush-hosts' at 
> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm 
> line 98

That server looks borked. You could switch to the ensembl one:

 > mart <- useMart("ENSEMBL_MART_ENSEMBL","mmusculus_gene_ensembl", 
host="www.ensembl.org")
 > getBM(c("uniprot_swissprot_accession","ipi"), "ipi","IPI00124704", mart)
[1] uniprot_swissprot_accession ipi
<0 rows> (or 0-length row.names)

Best,

Jim


>
> Thanks much,
> Dick
> ******************************************************************************* 
>
> Richard P. Beyer, Ph.D.    University of Washington
> Tel.:(206) 616 7378    Env. & Occ. Health Sci. , Box 354695
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099