Run rJava with RStudio under OSX 10.10, 10.11 (El Capitan) or 10.12 (Sierra)

The R script uses rJava and RJDBC packages to load tables from database. In Mac OS X, to correctly load this packages
requires the following steps borrowed from https://github.com/snowflakedb/dplyr-snowflakedb/wiki/Configuring-R-rJava-RJDBC-on-Mac-OS-X.
Steps have been modified to reflect problems (and it's solutions) reported here.

Overview

This is the list of software downloads needed in order to connect R via RJDBC to a database:

• Xcode Command Line Tools
• Java 6
• Java 8
• R
• rJava source package
• Database JDBC jar file
• RStudio (optional)

If you have any of this software already installed, you can skip that section.

Open Terminal.app

We'll change to the Downloads directory as we'll have to download some packages from the internet.

 cd $HOME/Downloads

Just to make debugging easier if something does not go as planned, log all output.

 script osx-rjava-install.log

Xcode Command Line Tools

We need Xcode Command Line Tools, by running this command we will invoke the downloader if not installed, otherwise it will report it is already installed.

 xcode-select --install

Java 6

Install the legacy Java 6 runtime which is needed despite us not going to use Java 6.

 curl -#ROL https://support.apple.com/downloads/DL1572/en_US/javaforosx.dmg
 open javaforosx.dmg

Now walk through the install to complete.

Java 8

Install Java 8. Note: newer versions may be available.

 curl -#ROL -b "oraclelicense=a"  http://download.oracle.com/otn-pub/java/jdk/8u111-b14/jdk-8u111-macosx-x64.dmg  
 open jdk-8u111-macosx-x64.dmg

Now walk through the install to complete.

We'll run these two commands to output Java installations and what the current command defaults to. They are informative only.

 /usr/libexec/java_home -V
 java -version

You should see something like this:

 bash-3.2$ /usr/libexec/java_home -V
 Matching Java Virtual Machines (5):
   1.8.0_111, x86_64:	"Java SE 8"	/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home
   1.8.0_25, x86_64:	"Java SE 8"	/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home
   1.6.0_65-b14-468, x86_64:	"Java SE 6"	/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
   1.6.0_65-b14-468, i386:	"Java SE 6"	/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
 
 /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home 
 bash-3.2$ java -version
 java version "1.8.0_111"
 Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
 Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode) ```

R for OS X

Download and install the R package for OS X.

 curl -#ROL https://cran.rstudio.com/bin/macosx/R-3.3.2.pkg
 open R-3.3.2.pkg

Now walk through the install to complete.

Now we need to tell R to use our Java 8 as it's JAVA_HOME

sudo R CMD javareconf

You should see output similar to

 Password:
 Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/bin/java
 Java version : 1.8.0_111
 Java home path : /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/jre
 Java compiler : /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/bin/javac
 Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/bin/javah
 Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/bin/jar
 Non-system Java on macOS

 trying to compile and link a JNI program
 detected JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
 detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
 clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c conftest.c -o conftest.o
 clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


 JAVA_HOME : /Library/Java/JavaVirtualMachines/jdk1.8.0_111.jdk/Contents/Home/jre
 Java library path: $(JAVA_HOME)/lib/server
 JNI cpp flags : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
 JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
 Updating Java configuration in /Library/Frameworks/R.framework/Resources
 Done.

Now install rJava from source and compile it against the Java 8 JDK. The 'unset JAVA_HOME' takes care of:

'checking JNI data types... configure: error: One or more JNI types differ from the corresponding native type.'  
error.

 unset JAVA_HOME
 R --quiet -e 'install.packages("rJava", type="source", repos="http://cran.us.r-project.org")'

Now let's check that rJava can be loaded correctly and returns the correct JDK version. This command should return the string 1.8.0_111-b14 (or whatever Java 8 version you installed).

 R --quiet -e 'library("rJava"); .jinit(); .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")'

Finish

Exit from the script logging.

exit

Using RStudio.app or R.app

A common error when trying to load rJava in RStudio is:

 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/3.3/Resources/library/rJava/libs/rJava.so':

There are three ways to get around this problem and use rJava with RStudio or R console (R.app) :

1 - Launching from the command line

You can launch it from the command line in Terminal.app like such:

LD_LIBRARY_PATH=`/usr/libexec/java_home`/jre/lib/server open -a rstudio

LD_LIBRARY_PATH=`/usr/libexec/java_home`/jre/lib/server open -a R

This is a known limitation with RStudio on OS X. See this link for more details: [https://support.rstudio.com/hc/communities/public/questions/200650933-rJava-fails-to-load-in-RStudio-Desktop-OS-X] (https://support.rstudio.com/hc/communities/public/questions/200650933-rJava-fails-to-load-in-RStudio-Desktop-OS-X)

2 - Make a symlink to libjvm.dylib

This is an alternate solution to loading RStudio, but must be updated any time you upgrade Java

+Based on this Stack Overflow thread, one can use the following to work around the libjvm.dylib loading issues.

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

3 - Load the library in the script (which is the used approach in the CohortEx R script)

Just a bit of code in your R script:

 if (Sys.info()['sysname'] == 'Darwin') {
   libjvm <- paste0(system2('/usr/libexec/java_home',stdout = TRUE)[1],'/jre/lib/server/libjvm.dylib')
   message (paste0('Load libjvm.dylib from: ',libjvm))
   dyn.load(libjvm)
 }

library(rJava)