Saturday, June 27, 2015

The rJava Nightmare

I like R. I like Java. I hate the rJava package, or more precisely I hate installing or updating it. Something (often multiple somethings) always goes wrong. I forget that for some reason I need to invoke root privileges when installing it. It needs a C++ library that I could swear I have, except I don't have the developer version of that library installed. Whatever. See this post from 2011 for a previous misadventure.

Today's battle was fought after a "successful" installation on my laptop. The good news: the package was installed, and RStudio knew it was installed. The bad news: neither RStudio, nor R run in a terminal, would let me load it. The key nugget in the error message: cannot open shared object file: No such file or directory
Now was definitely installed (as part of Oracle Java 8), so this was a matter of somehow breaking the news to R and/or RStudio. Search for "rJava" and "libjvm" on Google and you'll find a lot of hits, because I'm apparently not the first person to trip over this. Most solutions involving adding the requisite directory (which for me is ${JAVA_HOME}/jre/lib/amd64/server) to the LD_LIBRARY_PATH environment variable in your .profile file. I tried both that and .bashrc, with the result that R in a terminal agreed to load rJava but R running in RStudio still did not. Some of the posts I found said that this was expected if you made the tweeked .bashrc, but tweaking .profile instead was supposed to fix things. Except it didn't.

Fortunately, my laptop and desktop both run the same OS (Linux Mint), pretty much the same version, and rJava was working fine on the desktop. So the trick was to figure out how they differed. The route to does not appear in LD_LIBRARY_PATH on my PC, and is not mentioned in either of those profile files. It turns out that the path is set in the profile for R (/usr/lib/R/etc/ldpaths, to be specific), in the definition of a new variable R_JAVA_LD_LIBRARY_PATH. On the laptop, that was set to ${JAVA_HOME}/lib/amd64/server; on the PC, it was ${JAVA_HOME}/jre/lib/amd64/server. The latter path is correct on both the PC and the laptop. So I edited ldpaths on the laptop (as root), inserted the missing piece of the path, and lo and behold both R in a terminal and R inside RStudio could execute "library(rJava)" without bellyaching!

Note that, per my 2011 post, I had run sudo R CMD javareconf (more than once), with the correct value of the JAVA_HOME environment variable in place. Why that did not fix the path in ldpaths, and why the path was wrong in the first place, remain mysteries to me.

Update (12/30/16): I ran into the same problem, with a somewhat different cause. Updated details are in this post.

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