Gfilui

I am not able to install the rJava package in R.

If I run sudo R CMD javareconf:

*** JAVA_HOME is not a valid path, ignoring
Java interpreter : /usr/bin/java
Java version : 1.8.0_161
Java home path : /usr/lib/jvm/java-8-oracle/jre
Java compiler : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/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/amd64/server -ljvm
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I/usr/lib/jvm/java-8- 
oracle/jre/../include -I/usr/lib/jvm/java-8- 
oracle/jre/../include/linux 
-fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat - 
Werror=format-security -D_FORTIFY_SOURCE=2 -g -c conftest.c -o 
conftest.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o 
conftest.so conftest.o -L/usr/lib/jvm/java-8- 
oracle/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR

JAVA_HOME : /usr/lib/jvm/java-8-oracle/jre
Java library path: $(JAVA_HOME)/lib/amd64/server
JNI cpp flags : -I$(JAVA_HOME)/../include - 
I$(JAVA_HOME)/../include/linux
JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

I have also ran the following commands:

export JAVA_HOME=/usr/lib/jvm/java-8-oracle
export PATH=$PATH:$JAVA_HOME/bin

but I don't really know what it is supposed to do...

Finally, it has to be mentioned that

• if I install and run rJava (using library(rJava)) in sudo mode everything is ok.



• 
  

  if I run rJava in normal user mode with

  
  
  

  library(rJava)
  

  
  
  

  I get the following error:

  
  
  

  library(rJava)
  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 '/home/marc/R/x86_64-pc-linux- 
  gnu-library/3.4/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
  

  
  


• 
  

  If I try to install rJava in normal user mode I get the same error as the previous when testing if package can be loaded:

  
  
  

  ** testing if installed package can be loaded
  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 '/home/marc/R/x86_64-pc-linux- 
  gnu-library/3.4/rJava/libs/rJava.so':
  libjvm.so: cannot open shared object file: No such file or directory
  Error: loading failed
  Execution halted
  

  
  

Any help would be welcome.

Try:

update-alternatives --config java

This gave an output like this:

• 2 /usr/lib/jvm/java-8-oracle/jre/bin/java

Add to your /etc/environment

JAVA_HOME='/usr/lib/jvm/java-8-oracle'

And then remove and reinstall r-base:

sudo apt-get remove r-base

sudo apt-get install r-base

Now try install rJava again.