[R-sig-hpc] multicore and AnnotaionDBI (bioconductor) problem

[Morten Hansen]

I am trying to use mclapply from package multicore on a Bioconductor function, but I get an error with the function mget from library AnnotationDbi.

When I run the following code:

	# You need to install Biobase from http://www.bioconductor.org
	require( Biobase )
	require( hgu95av2.db )
	
	getSymbol <- function ( x ) {
		return( AnnotationDbi::mget( x , hgu95av2SYMBOL ) )
	}	

	x <- list( "36090_at" , "38785_at" )

	mclapply( x , getSymbol )

I get this error:

[[1]]
[1] "Error in sqliteExecStatement(con, statement, bind.data) : \n  RS-DBI driver: (invalid dbManager handle)\n"

[[2]]
[1] "Error in sqliteExecStatement(con, statement, bind.data) : \n  RS-DBI driver: (invalid dbManager handle)\n"

It work fine with lapply instead of mclapply:

[[1]]
[[1]]$`36090_at`
[1] "TBL2"


[[2]]
[[2]]$`38785_at`
[1] "MUC1"

This could of course be a problem in the AnnotationDbi::mget function, but it looks like multicore is having some problem with RS-DBI driver.

Any suggestions?

Regards -

Morten Hansen
MD, Ph.D. student
ICMM
Panum Institute
Blegdamsvej 3B
DK-2200 Copenhagen N