[BioC] Biomart mysql error...

Jesper Ryge Jesper.Ryge at ki.se
Mon Dec 1 19:04:28 CET 2008


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 <- 
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) 


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:-)

jesper Ryge
karolinska Institutet

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