Install rJava in R 3.6 with MacOSX 10.13

Instal homebrew: https://brew.sh/index_fr

In terminal:

brew install --with-toolchain llvm

in .profile, add:

PATH="/usr/local/opt/llvm/bin:${PATH}"
LDFLAGS="-L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib"
CPPFLAGS="-I/usr/local/opt/llvm/include"
export LDFLAGS
export CPPFLAGS

Install the latest java jdk: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

Look at here: https://biostatsr.blogspot.fr/2018/02/set-javahome-to-correct-value-in-profile.html

In terminal, enter:

cd $(/usr/libexec/java_home)/jre/bin/
sudo ln $(/usr/libexec/java_home)/bin/javac javac
sudo ln $(/usr/libexec/java_home)/bin/javah javah
sudo ln $(/usr/libexec/java_home)/bin/jar jar

cd $(/usr/libexec/java_home)/jre/lib/

sudo ln $(/usr/libexec/java_home)/lib/tools.jar tools.jar

 cd $HOME

 sudo R CMD javareconf

And in R

install.packages("rJava")

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