Hey Mac OSX users with Java 1.8 installed. Did R just request a Java 1.6 installation and then promptly crash your session? If so, read on...
A few days ago I was attempting to use the mallet package for topic models and I found that typing
caused two things to happen:
The operating system launches a dialog asking whether I would like to download Java 1.6
The R session crashes (regardless of what I did about the dialog)
This seems to be a general problem for packages that depends on the rJava package.
I'm running the latest Mac OSX (Yosemite 10.10.1) and have installed the latest Java
$ java -version
java version "1.8.0" Java(TM) SE Runtime Environment (build 1.8.0-b132) Java HotSpot(TM) 64-Bit Server VM (build 25.0-b70, mixed mode)
and the latest R
$ R --version
R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin13.4.0 (64-bit)
But for some reason with R, it's Java 1.6 (which is no longer even being updated) or bust.
The fix (maybe)
The trail of bug reports starts here, but before you delve into those and bother Simon Urbanek as much as I did, try the following:
Download and install Apple's Java version 1.6 like you were asked to.
Reconfigure your R installation by typing
sudo R CMD javareconf
in a Terminal window. (Thanks to commenter Benjamin for pointing out that there shouldn't have been a -n flag in this line)
Trigger a recompile by reinstalling rJava by typing
Now if you relauch R and load your package it should use your shiny new Java 1.8 and not crash any R sessions.
For this to work you may have to set (or have something else set) some environment variables too. See the comments below for my settings.
Just give up. Six years later it still seldom works. I now find it
quicker and much less exasperating to write out shell commands to run
the Java code with
system2. Heck it's probably more efficient to
rewrite the Java in C++ and call it with