eipi10 eipi10 - 5 months ago 26
Java Question

rJava load error in RStudio/R after "upgrading" to OSX Yosemite

I recently "upgraded" from OSX Mountain Lion to Yosemite and from R 3.1.3 to 3.2. Immediately after the upgrade, when I opened R or RStudio I got a pop-up message saying that I needed to install Java 6. In addition, loading

rJava
or any package that depends on rJava (e.g.,
xlsx
) caused RStudio to crash (R also crashed when I tried this by opening
R.app
directly).

After trying a few fixes found on Stack Overflow and elsewhere (more details below), I am at a point where loading
rJava
or any package that depends on
rJava
no longer causes R to crash, but results in the following error:

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’


However, if I invoke R from the command line and then load
rJava
or any package that depends on
rJava
, it seems to work (or at least I don't get any error messages).

I've tried a number of different attempted fixes, some of them a few times, and can't quite remember exactly what I did in what order (didn't realize this would be such a morass and wasn't really keeping track), but here's the gist of it:


  • Added the following to my
    .bash_profile
    (per this SO answer):


    export JAVA_HOME="/usr/libexec/java_home -v 1.8"

    export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/server

  • Reconfigured java from the command line as follows:


    sudo R CMD javareconf -n

  • Checked
    options("java.home")
    and discovered this was set to
    NULL
    . I tried setting it to the following (per this SO question):


    options("java.home"="/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre")

  • Installed the latest Java Development Kit and reinstalled
    rJava
    from source (can't remember where I found that one).



At some point while trying all of these, I was able to load
rJava
without crashing R, but instead got the error message posted above. In addition, when I quit RStudio, it would seem to close normally, but then an "RStudio quit unexpectedly" message would pop up, indicating that the program had crashed while trying to close.

I finally decided to install Java for OS X 2014-001 (Java 6), as I seemed to be running out of options. Now, when I opened R or RStudio the "This software needs Java 6" pop-up message no longer appeared. However, I was still getting the
.onLoad failed in loadNamespace() for 'rJava'
error message posted above.

In reviewing some of the posts I'd already looked at, I noticed another SO answer that I'd missed before, which recommended opening RStudio with the following command line code that gives RStudio the correct path to java:


LD_LIBRARY_PATH=$(/usr/libexec/java_home)/jre/lib/server: open -a RStudio


That opened an RStudio window and I was also able to load
rJava
and packages that depend on it without getting an error.

Lastly, I tried running R from the command line (which I hadn't done before). It turns out that on the command line, loading
rJava
or any package that depends on
rJava
works and does not throw any errors.

So, I can now get
rJava
to work if I open RStudio from the command line with the code that gives RStudio the java path (as noted above). However, I'd like to find a way to fix the underlying problem, whatever it may be, so that RStudio can be opened in the usual Mac way, without needing a command line kludge. I'm also concerned that having an old version of Java installed could cause problems down the road.

Does anyone have any ideas about how to diagnose and solve this issue?

Answer

I had the same problem and went through the same steps as you. The final step to allow starting RStudio through Finder/Spotlight was to link libjvm.dylib to /usr/local/lib:

sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

-f flag is added to force overwriting existing file/link