Fix the libjvm.so file not found error

I encounter this problem whenever I try to use rJava on Ubuntu + Rstudio, so I decided to write it down.

You’ll see this error message if you try to load the rJava package or anything else that depends on it (psData in my case):

> library(psData)
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/anh/Rlibs/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
Error: package or namespace load failed for ‘psData’

The issue boils down to Rstudio being unable to find the shared file libjvm.so. We need to include the path towards libjvm.so (i.e. the Java library folder) in LD_LIBRARY_PATH, the environment variable that points Ubuntu and its application towards shared library.

A wrinke: If we set LD_LIBRARY_PATH in /etc/environment, library(rjava) can be loaded via terminal R. However, Rstudio doesn’t look into /etc/environment and thus is still not aware of the new LD_LIBRARY_PATH.

The upshot: Set LD_LIBRARY_PATH in ~/.profile to make it available to all desktop applications, including Rstudio (as suggested by Ubuntu wiki article on persistent environment variable).

Instructions:

• Inside ~/.profile, add the path to libjvm.so to LD_LIBRARY_PATH (you may have a different path from mine):

export LD_LIBRARY_PATH=/usr/lib/jvm/java-7-oracle/lib/amd64:/usr/lib/jvm/java-7-oracle/jre/lib/amd64/server

• Log out and in or restart your computer so that Ubuntu reloads ~/.profile.
• Then make R update its java configuration:

sudo R CMD javareconf

That’s it. library(rJava) should run after restarting Rstudio.