[R-sig-DB] DBI:dbConnect () inherited method error for RMySQL v 0.5-11 driver

[Chris Cotsapas]

Hi David, thanks for your response:

David James wrote:
> Hi Chris,
> 
> The message seems to indicate a S4 dispatching error from the generic
> function dbConnect when given a drv = "MySQLConnection" and not
> with the mysql libraries themselves.   The idiom that you're using is 
> widely
> used, so I cannot see why it would fail, so I would try
> (1)  what's the output of
>     summary(drv, verbose = TRUE)
>     (you should see a full description of the MySQLDriver object)


> summary(drv, verbose = TRUE)
Error in function (classes, fdef, mtable)  :
         unable to find an inherited method for function "dbGetInfo",
for signatu re "MySQLDriver"


> (2)  try other dbConnect methods, namely
>      con <- dbConnect("MySQL")
>      con <- dbConnect(MySQL())

> con <- dbConnect("MySQL")
Error in function (classes, fdef, mtable)  :
         unable to find an inherited method for function "dbConnect",
for signatu re "character"
> con <- dbConnect(MySQL())
Error in function (classes, fdef, mtable)  :
         unable to find an inherited method for function "dbConnect",
for signatu re "MySQLDriver"
In addition: Warning message:
RS-DBI driver warning: (MySQL mismatch between compiled version 5.0.19
and runti me version 5.0.22)



> (3) What do you see if you type
>      getMethods("dbConnect")


> getMethods("dbConnect")
An object of class “MethodsList”
Slot "methods":
list()

Slot "argument":
drv

Slot "allMethods":
list()


This looks telling - there seem to be no methods associated with dbConnect?

Thanks!

Chris


>> I'm really not sure what to do with this: I've tried updating all mysql
>> Ubuntu packages, adding dev packages etc, to no avail. The database
>> itself is functional and accessible.
>>
>> I've also created a ~/.my.cnf file with appropriate entries, to no avail.
>>
>> Any hints or comments most welcome.
>>
>> Thanks
>>
>> Chris
>>
>> ## Error Log ##
>>
>> drv <- dbDriver("MySQL")
>>   Warning message:
>>   RS-DBI driver warning: (MySQL mismatch between compiled version
>> 5.0.19
>>   and runtime version 5.0.22)
>>
>> dbConnect(drv=drv)
>>   Error in function (classes, fdef, mtable)  :
>>        unable to find an inherited method for function "dbConnect", for
>>         signature "MySQLDriver"
>>
>> ## End ##
>>
>>
>>




-- 
Chris Cotsapas, PhD

Research Associate
Center for Human Genetic Research,
Massachusetts General Hospital
and
Broad Institute of Harvard and MIT

A: 185 Cambridge St CPZN 6818, Boston, MA, 02114
P: 1 617 643 1634 (MGH)/ 1 617 324 7176 (Broad)