How can I make rJava use the newer version of java on osx?

Question

I am following this tutorial on rJava: http://cran.r-project.org/web/packages/helloJavaWorld/vignettes/helloJavaWorld.pdf

I have made all the files as specified in t

Answer 1

I had a similar problem, but this solution didn't work for me. I eventually got it working, but now I'm not sure which of the things I changed solved the problem. Here's what I did:

1. I added the following lines to my .bash_profile:

   export JAVA_HOME="/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre"
   export LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server 
   export PATH=$PATH:$JAVA_HOME/bin
   

2. I set my java.home option and my DYLD_FALLBACK_LIBRARY_PATH environmental variable in R:

   options(java.home="/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk")
   Sys.setenv(DYLD_FALLBACK_LIBRARY_PATH="/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/jre/lib/server/")
   

3. I re-installed Apple's version of Java 1.6 just in case, as per this issue thread: https://github.com/s-u/rJava/issues/37

4. I reconfigured R's java settings. In Bash: R CMD javareconf
5. I ran R as root, and then installed rJava from source, directly from RForge. In Bash: sudo R. Then in the R session: install.packages('rJava',,'http://www.rforge.net/').

Installing from source was crucial to making rJava pick up on R's new Java settings. When I didn't install from source, rJava would install ok, but it would continue to use JRE 1.6. You can check which JRE rJava uses by running:

library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

Running R as root was crucial to making rJava install correctly from the RForge source. When I tried to run install.packages('rJava',,'http://www.rforge.net/') as User, I got the following error messages:

• If running R in the command line, rJava would not install correctly:

  checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this.
  ERROR: configuration failed for package ‘rJava’
  

• If running R as an application from Finder, rJava would install, but not load:

  > library(rJava) 
  Error : .onLoad failed in loadNamespace() for 'rJava', details:  
  call: dyn.load(file, DLLpath = DLLpath, ...) 
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so, 6): 
  Library not loaded: @rpath/libjvm.dylib 
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rJava/libs/rJava.so 
  Reason: image not found 
  Error: package or namespace load failed for ‘rJava’
  

Hopefully this answer will save someone else some time!

Edited to add: Two of my professors followed these instructions and ran into the following issue: rJava would work when running R in the command line, but would fail to load when running RStudio or the default Mac R app.

Joe Ramsey figured out the solution. He writes:

Apparently RStudio grumbles about having to use the default user/directory that Apple uses to open applications.

This article describes it: http://jeromyanglim.tumblr.com/post/34221143729/how-to-run-rstudio-from-the-command-line-on-osx

[To fix the issue] You go to the command line and type: open -a rstudio or open -a R

Edit number two: I just installed rJava on one of the school computers, running Ubuntu 14.04.4 LTS (64-bit). I was able to install rJava when running R as root. However, when I then tried to run R as user and load the package, I got a brand new loading error:

> library(rJava)
Error : .onLoad failed in loadNamespace() for 'rJava', details:
    call: dyn.load(file, DLLpath = DLLpath, ...)
    error: unable to load shared object '/home/lizziesilver/R/x86_64-pc-linux-gnu-library/3.2/rJava/libs/rJava.so':
    libjvm.so: cannot open shared object file: No such file or directory
  Error: package or namespace load failed for ‘rJava’

I checked the directory; rJava.so definitely existed. It turned out that I didn't have the right permissions for it:

...$ ls -l /home/lizziesilver/R/x86_64-pc-linux-gnu-library/3.2/rJava/libs/rJava.so
-rwxr-xr-x 1 root root 353325 Feb 26 16:58 /usr/lib/R/library/rJava/libs/rJava.so

So I changed the permissions: sudo chmod -R a+rX /home/lizziesilver/R/x86_64-pc-linux-gnu-library/3.2/rJava/

Then reconfigured R's java settings:

export LD_LIBRARY_PATH=/usr/lib/jvm/java-8-oracle/lib/amd64:/usr/lib/jvm/java-8-oracle/jre/lib/amd64/server
sudo R CMD javareconf

Now rJava loads, even when running R as user instead of root!

rJava: the package that keeps on giving (config errors)