The `GO.db` package comes with an sqlite database file. It looks like there is an issue calling the sqlite database from MonetDB. On Thu, May 12, 2016 at 9:38 AM, Willem Ligtenberg < willem.ligtenberg@openanalytics.eu> wrote:

Hi,

I am trying to run some R code in database. Most of it is going pretty well, but I seem to have stumbled on a bug. I cannot load the following package, which is a dependency for some of my code. WGCNA

I have been chasing it down, and it seems to be due to an error when trying to load GO.db. I get the following error: Error in .local(conn, statement, ...) : Unable to execute statement 'SELECT * FROM tmp_test();'. Server says '!Error running R expression. Error message: Error in as.data.frame((function() { : '.

Digging a bit further it seems to be due to the following statement: dbconn <- dbFileConnect(dbfile)

Error can be reproduced using: functionDef <- paste( "CREATE FUNCTION tmp_test() ", "RETURNS TABLE(output STRING)", "LANGUAGE R ", "{", "library(AnnotationDbi)", "datacache <- new.env(hash=TRUE, parent=emptyenv())", "pkgname <- 'GO.db'", "libname <- .libPaths()[1]", "dbfile <- system.file('extdata', 'GO.sqlite', package=pkgname, lib.loc=libname)", "assign('dbfile', dbfile, envir=datacache)", "dbconn <- dbFileConnect(dbfile)", "};", sep = "\n")

dbGetQuery(conn, functionDef)

dbGetQuery(conn, "SELECT * FROM tmp_test();")

By the way, installing GO.db from within MonetDB works just fine. And can be done using the following R code: source("https://bioconductor.org/biocLite.R") biocLite("GO.db")

Hints on how to resolve this are greatly appreciated.

Kind regards,

Willem _______________________________________________ users-list mailing list users-list@monetdb.org https://www.monetdb.org/mailman/listinfo/users-list