[BioC] Biomart mysql error...

[Jesper Ryge]

thanx laurent :-)


----- Original Message -----
From: Laurent Gautier <lgautier at gmail.com>
Date: Monday, December 1, 2008 7:16 pm
Subject: Re: [BioC] Biomart mysql error...
To: Jesper.Ryge at ki.se
Cc: "bioconductor mail list bioconductor at stat.math.ethz.ch" 
<bioconductor at stat.math.ethz.ch>

> 
> The issue is likely on the server end (updates of the database 
> structure).
> I think that sql=TRUE will "only" provide a faster data retrieval.
> 
> You can keep=FALSE in the meanwhile.

hm, could be. but the problem persisted since friday and its still there... i wanted to update 
annotation from the whole affy_rat230 chip so its a rather big query and i assume mysql 
handle this better... ill brace myself with patience, but should it take so long to correct if its 
an error in their end (ensembl database update or something)? does anybody know if this is 
the case and when it will be up and running again?

cheers,
jesper 

> 
> 
> Jesper Ryge wrote:
> > Hi
> > 
> > im running into a biomaRt problem when i use the mysql=T in 
> useMart which has worked 
> > very well earlier on my computer (MacPro3,1 )???  Here is a short 
> illustration: 
> > 
> >> library(biomaRt)
> > 
> >>  mart <- useMart("ensembl" 
> ,dataset="rnorvegicus_gene_ensembl",mysql=T)> connected to:  
> ensembl 
> > Reading database configuration of: rnorvegicus_gene_ensembl 
> > Checking attributes and filters ... ok
> > Checking main tables ... ok
> > 
> >> test <- 
> > 
> 
getBM(attributes=c("ensembl_gene_id","external_gene_id","description"),filters="affy_rat230_
> 2",values=c("1367452_at","1367453_at"), mart=mart)
> > Error in mysqlExecStatement(conn, statement, ...) : 
> >   RS-DBI driver: (could not run statement: Table 
> 'ensembl_mart_51.ox_AFFY_Rat230_2__dm' 
> > doesn't exist)
> > 
> > the samme session run with mysql=F works fine! 
> > 
> >> sessionInfo()
> > R version 2.8.0 (2008-10-20) 
> > i386-apple-darwin9.5.0 
> > 
> > locale:
> > C/UTF-8/C/C/C/C
> > 
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   
> base     
> > 
> > other attached packages:
> > [1] RMySQL_0.6-1   DBI_0.2-4      biomaRt_1.16.0
> > 
> > loaded via a namespace (and not attached):
> > [1] RCurl_0.92-0 XML_1.98-1  
> > 
> > any help highly appreciated:-)
> > 
> > cheers,
> > jesper Ryge
> > karolinska Institutet
> > 
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