rJava package in r-devel 3.5

rJava package used /usr/local/clang4 folder to search bin/clang compiler.

However clang4 is relatively old now. We will use most recent version of clang:

brew install llvm

clang 5.0.1 (at the time of writing this note) will be install in:
/usr/local/opt/llvm/bin/clang

Then, do:

cd /usr/local
sudo ln -s /usr/local/opt/llvm clang4

However, it fails to find the libomp
Do:
sudo ln -s /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libomp.dylib libomp.dylib

Now you can do in R:
install.packages("rJava")

Still two problems to solve:
- do not setup JAVA_HOME in your .profile or it will make an error when you load the library
- If you use Rstudio, you must enter these commands due to a bug in Rstudio

cd /usr/local/lib
sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjsig.dylib libjsig.dylib
sudo ln -s /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home/jre/lib/server/libjvm.dylib libjvm.dylib

replacing /Library/Java/JavaVirtualMachines/jdk1.8.0_162.jdk/Contents/Home with the return of 
echo $(/usr/libexec/java_home)

When you update java, you must do again this step.



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