For the past couple of days, I needed to install rJava package on my Mac, and boy did I know how complicated the process would turn out to be! I vaguely knew about the mess that is java and Mac OS, but I didn’t care that much until now, because (1) most of my development work has been done in my company environment (Linux) which I ssh into and is pretty well managed by folks more qualified to do so than me and (2) for my personal work (i.e., blogging, R package development, etc.), I didn’t need to touch java so far (or so I think).

Then I thought of writing a wrapper function that makes a connection from within R to a company database¹. I had a snippet of code that does the job, and I decided to turn it into an R function and include it to my personal R package. Among other things, the code required rJava package, and that’s how I entered this mess that is java and Mac OS.

Since I’m no expert there, I’m not going to try to explain each step I took, but basically, I searched for similar problems and solution, and I ended up following the awesome instruction given here. I should’ve taken screenshots of the error/ok messages that I got through this whole process, but long story short, I accidentally dropped “lib” at the end of this line where LDFLAGS² is being set, and it took a while to figure out what I was doing wrong:

"LDFLAGS = -L/usr/local/lib -L/Users/user_name/opt/clang+llvm-4.0.1-x86_64-apple-macosx10.9.0/lib -lomp"

Once I fixed the error, rJava was installed successfully, and the database connection wrapper function is added to the personal package. Special thanks to the author of the above blog post and the author of the rJava package!