"Unable to run a simple JNI program" error message when installing rJava on R 3.6 for ubuntu bionic beaver

Question

I have the very common problem that rJava does not install correctly on Ubuntu. This problem has been dsicussed in multiple places here, here, here, to name a few.

The basic problem is that on installing the rJava package, the following error message is produced

configure: error: Unable to run a simple JNI program. Make sure you have configured R with Java support (see R documentation) and check config.log for failure reason.
Warning in system(cmd) : error in running command
ERROR: configuration failed for package ‘rJava’
* removing ‘/home/jonno/R/x86_64-pc-linux-gnu-library/3.6/rJava’

There are various closely related solutions to this problem. Most of them use sudo R CMD javareconf to configure Java for R (also a -e variant). Some suggest setting the JAVA_HOME path in the environment variables (others say not to). Others suggest uninstalling and re-installing R whilst others suggest installing rJava from cran. There are several who reccomend update alternatives. There are other variants of these solutions.

I have tried combinations of all of the above, and have got nowhere, so am clearly doing something wrong.

entering echo $JAVA_HOME returns

/usr/lib/jvm/java-11-openjdk-amd64

my etc/environment looks like this

PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/$
MKL_THREADING_LAYER=GNU
JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64"

When I run R CMD javaconf, it looks like this

Java interpreter : /usr/lib/jvm/java-11-openjdk-amd64/java
Java version     : 11.0.4
Java home path   : /usr/lib/jvm/java-11-openjdk-amd64
Java compiler    : /usr/lib/jvm/java-11-openjdk-amd64/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/lib/jvm/java-11-openjdk-amd64/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/java-11-openjdk-amd64/include -I/usr/lib/jvm/java-11-openjdk-amd64/include/linux    -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/java-11-openjdk-amd64/lib/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/java-11-openjdk-amd64
Java library path: $(JAVA_HOME)/lib/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

What am I doing wrong and how do I get rJava to install properly?

EDIT:

having managed to successfully install rJava using sudo apt-get install r-cran-rjava I know get the following error

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

Answer 1

I've investigated with the original poster (we work at the same place) and the problem is that in OpenJDK11 they moved around some of the .so files that the JVM lives in, specifically libjvm.so which in the Ubuntu package is now in /usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server/.

This means that even if you install the Ubuntu package for rJava with apt install r-cran-rjava it fails when you try to library(rJava).

The solution is to add /usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server/ to your $LD_LIBRARY_PATH by adding:

export LD_LIBRARY_PATH=/usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server:$LD_LIBRARY_PATH

to the end of your ~/.bashrc and starting a new shell (or source ~/.bashrc).

This is something we had to fix for our central installs of OpenJDK e.g. here: https://github.com/UCL-RITS/rcps-buildscripts/blob/master/adoptopenjdk-11.0.3_install.sh#L46

If you want to make this work with Rstudio launched from Gnome, you need to add that directory to ldconfig.

As root (or with sudo) create a file in /etc/ld.so.conf.d/ which you should call something with a .conf extension e.g. java.conf which contains the line:

/usr/lib/jvm/java-1.11.0-openjdk-amd64/lib/server

And then as root run

ldconfig -v

This should add the directory to the locations that executables launched through GNOME search for. This particular part of the problem (GNOME ignoring settings in bashrc) has been a problem in Ubuntu since at least 9.04 (https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/366728/).