[BioC] biomaRt package listMarts() error

[Sean Davis]

Is RMySQL installed?

If so, what happens when you do:

driv <- dbDriver('MySQL', force.reload=FALSE)
conn <-  
dbConnect(driv,user='anonymous',password='',host='ensembldb.ensembl.org' 
)
res <- dbGetQuery(conn,"show databases like '%mart%'")
dbDisconnect(conn)
res

Do you get something that lists the databases like:
ensembl_mart_27_1
ensembl_mart_28_1
....

Sean


On Jun 29, 2005, at 3:33 PM, Ye, Bin wrote:

> Hi, everyone,
>
> I met an error message when I using biomaRt package.
>> listMarts()
> Error in if (is.na(pattern)) { : argument is of length zero
> In addition: Warning message:
> is.na() applied to non-(list or vector) in: is.na(pattern)
>
> Does anyone know what's wrong? I'm running windows 2k, R 2.0.1,  
> bioconductor 1.6, and biomaRt 1.1.2.
>
> Thanks a lot!
>
>
> Bin
>
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