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rJava provides a low-level bridge between R and Java (via JNI). It allows to create objects, call methods and access fields of Java objects from R. rJava release versions can be obtained from CRAN - usually install. packages("rJava") in R will do the trick.
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
On OSX El Capitan 10.11, the user doesn't have permission to write to /usr/lib. So instead, use the following command:
sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
You can load the libjvm.dylib explictly, by run like
dyn.load('/Library/Java/JavaVirtualMachines/jdk1.8.0_66.jdk/Contents/Home/jre/lib/server/libjvm.dylib')
library(rJava)
On macOS High Sierra (10.13.1) and Java Version 9 you have to use a slightly different JVM path (notice the missing jre folder in the path compared to the instructions for earlier Java versions):
sudo ln -f -s $(/usr/libexec/java_home)/lib/server/libjvm.dylib /usr/local/lib
You also have to notify R about the JVM:
MY_R_VERSION=$(Rscript -e "cat(with(R.version, sprintf('%s.%s', major, substring(minor, 1, 1))))")
ln -s /usr/local/lib/libjvm.dylib /Library/Frameworks/R.framework/Versions/$MY_R_VERSION/Resources/lib/
Following command works:
sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
After that, in RStudio, loading rJava works through loading of the "xlsx" package.
library("xlsx")
P.S. #1 Environment: Mac OS X El Capitan 10.11.3+ with RStudio 0.99.491+ and R 3.2.3+. (I've now tested this also on macOS Sierra (10.12) and R.3.3.1.)
P.S. #2 I find that openxlsx is much faster and doesn't rely on Java to work, so I'm now using that package. Hope that helps others.
You should be able to use the CRAN rJava, without needing to recompile rJava or do any additional steps by linking the shared library to the R frameworks library directory.
sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /Library/Frameworks/R.framework/Libraries
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