[BioC] Biomart mysql error...

[Laurent Gautier]

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.



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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor