rJava support

[weshinsley]

This seems to work!

options(didehpc.use_java = TRUE)
options(didehpc.java_home = "\\\\fi--san03\\homes\\wrh1\\jre")

(java_home here points to a JVM I made; it can be left blank to take the cluster's favourite)

options(didehpc.cluster = 'fi--didemrchnb')
packages <- c("rJava", "bartMachine")
ctx <- context::context_save("contexts", packages = packages, sources = "test.R")
obj <- didehpc::queue_didehpc(ctx)
t <- obj$enqueue(testj())

where test.R says:

testj <- function() {
  library(rJava)
  options(java.parameters = "-Xmx5g")
  library(bartMachine)
  paste0(getOption("java.parameters"), " : ",Sys.getenv("JAVA_HOME"))
}

And the result is:-

Welcome to bartMachine v1.2.3! You have 0.51GB memory available.

If you run out of memory, restart R, and use e.g.
'options(java.parameters = "-Xmx5g")' for 5GB of RAM before you call
'library(bartMachine)'.

This is fine - except that bartMachine only says we've got 0.51GB, not the 5Gb we asked for. This is because the two library commands in testj() are not actually doing anything - the libraries are already loaded by didehpc, hence the options are set too late.

The work-around for now is: after running the above once to provision the packages, set packages <- c() and recreate the context. Longer term, we should pass java.parameters formally as a configuration parameter.

[richfitz]

can you please run devtools::document() to regenerate the docs?

[weshinsley]

Done - I've run devtools:document(), which has updated man\didehpc_config.Rd