Cannot install on Yosemite: homebrew-cask java 1.8.0_25, homebrew R 3.1.2

[mpodell]

Not sure this is a rJava problem but looking for help.

Installing R via homebrew gives me this message:

To enable rJava support, run the following command:
  R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
If you've installed a version of Java other than the default, you might need to instead use:
  R CMD javareconf JAVA_CPPFLAGS='-I/System/Library/Frameworks/JavaVM.framework/Headers -I/Library/Java/JavaVirtualMachines/jdk<version>.jdk/'
  (where <version> can be found by running `java -version` or `locate jni.h`)

Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

running either (subbing jdk1.8.0_25.jdk for <version>) fails not finding jni.h

java installs jni.h into

/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include

Since there was nothing at /System/Library/Frameworks/JavaVM.framework/Headers/ where javareconf seems to want to look for it, I created symlinks:

cd /System/Library/Frameworks/JavaVM.framework/Versions
sudo ln -nsf /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents ./CurrentJDK
cd /System/Library/Frameworks/JavaVM.framework
sudo ln -nsf Versions/CurrentJDK/Home/include/ ./Headers

and added

export JAVA_HOME = "/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home"

to ~/.bash_profile since without it javareconf says the JAVA_HOME is not a valid path. This allows javareconf to find jni.h using:

R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers -I/System/Library/Frameworks/JavaVM.framework/Headers/

but then javareconf fails because it can't find jni_md.h which is in /Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include/dawrin

looking at javareconf there is this code:

    ## only if we get jni.h we can try to find jni_md.h
    if test -n "${jinc}"; then
       JAVA_CPPFLAGS="-I${jinc}"
       jmdinc=''
       jmdirs=''
   ## we are not in configure, so we need to find the OS from R
   host_os=`echo 'cat(R.version$os)'|${R_HOME}/bin/R --vanilla --slave 2>/dev/null`
       ## put the most probable locations for each system in the first place
       case "${host_os}" in
         darwin*)  jmdirs=darwin;;
         linux*)   jmdirs=linux;;
         bsdi*)    jmdirs=bsdos;;
         osf*)     jmdirs=alpha;;
         solaris*) jmdirs=solaris;;
         freebsd*) jmdirs=freebsd; add_java_libs='-lpthread';;
       esac

I would think that this would allow javareconf to find the jni_md.h but that's not happening.

This may not be a rJava issue but since the R install said to run javareconf in order to enable rJava support, I thought I would post here, but then again, I know just enough to know that I know nothing about this stuff. I'm just bummed I can't get rJava installed in R.

Thanks for taking the time to read this.

[mpodell]

Update:

I can get rJava support complied if I pass the actual location of the jni.h file (duh):

JAVA_CPPFLAGS=/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/include`

to R CMD javareconf

seems that for Yosemite the help message for R should be modified as the current message below is inaccurate.

To enable rJava support, run the following command:
  R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
If you've installed a version of Java other than the default, you might need to instead use:
  R CMD javareconf JAVA_CPPFLAGS='-I/System/Library/Frameworks/JavaVM.framework/Headers -I/Library/Java/JavaVirtualMachines/jdk<version>.jdk/'
  (where <version> can be found by running `java -version` or `locate jni.h`)

[gwinstanley]

This still doesn't resolve the problem, as when the script detects what it assumes to be "system Java", it overrides the JAVA_CPPFLAGS to be -I/System/Library/Frameworks/JavaVM.framework/Headers instead of the custom value supplied. Looking at the script, the correct $JAVA_HOME/include folder should be detected ok once the non-system Java is detected correctly, but it would also need the $JAVA_HOME/include/darwin folder to be included for correct operation.

Unfortunately installing the Apple Java for OS X 2014-001 package doesn't work either, which I hoped would should provides the necessary headers in the expected locations.

The error remains the same, and it's clear the JAVA_CPPFLAGS are not being passed through correctly:

clang -I/usr/local/Cellar/r/3.1.2/R.framework/Resources/include -DNDEBUG -I/System/Library/Frameworks/JavaVM.framework/Headers -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include    -fPIC  -g -O2  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: 'jni.h' file not found
#include <jni.h>
         ^
1 error generated.

The simplest way to get it working seems to be to modify the script by preventing it detecting the host OS. For example, I simply modified the line if test "${hostos}" = "Darwin"; then to be ``if test "${hostos}" = "DarwinX"; then` and the script ran fine. However, I'm still experiencing issues with loading the rJava package within R, as follows:

> library(rJava)
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/usr/local/Cellar/r/3.1.2/R.framework/Versions/3.1/Resources/library/rJava/libs/rJava.so':
  dlopen(/usr/local/Cellar/r/3.1.2/R.framework/Versions/3.1/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: @rpath/libjvm.dylib
  Referenced from: /usr/local/Cellar/r/3.1.2/R.framework/Versions/3.1/Resources/library/rJava/libs/rJava.so
  Reason: image not found
Error: package or namespace load failed for ‘rJava’

[gwinstanley]

Ok, turns out for my case it was loading rJava correctly with the terminal version of R, but not in RStudio. For some reason the LD_LIBRARY_PATH configuration in RStudio was omitting the required JRE folder ($JAVA_HOME/jre/lib/server). I can now successfully load rJava in RStudio by launching it from the terminal after defining a suitable alias in my .bashrc:

alias rstudio='LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/server: open -a RStudio'

[yasirs]

@gwinstanley
What is $JAVA_HOME in OSX?
I get $ which java
/usr/bin/java
ls -alth /usr/bin/java
lrwxr-xr-x 1 root wheel 74B Oct 23 2013 /usr/bin/java -> /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java

[gwinstanley]

Good point @yasirs, I forgot to mention that I usually set the JAVA_HOME variable in my .zshenv/.bashrc file. This is the line I usually include in mine:

export JAVA_HOME=`/usr/libexec/java_home`

or if you want a specific version of Java (e.g. Java 8):

export JAVA_HOME=`/usr/libexec/java_home -v1.8`

[s-u]

@gwinstanley check with RStudio - one way to make sure that you have correct vars set is to use R CMD open -a RStudio or similar. Normally, RStudio should be using R's vars, but I'm not sure if they actually do. Either way, always test with R first to make sure it's not a bug in RStudio (which is not R).
Also do not set JAVA_HOME

As for configuration, with properly installed Oracle Java (do not set JAVA_HOME manually!) you should see something like

$ R CMD javareconf
Java interpreter : /usr/bin/java
Java version     : 1.8.0_20
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_20.jdk/Contents/Home/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on OS X

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_20.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_20.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_20.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_20.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

[gwinstanley]

I like the idea of launching from the R CMD ..., which should pick up the Java config from the R installation. Regarding JAVA_HOME though, I have three Java installations on my machine, so I have it set to configure many other items from the specific Java version I'm using. I found the standard javareconf script failed without both disabling the OS auto-detect for Darwin, and custom configuring JAVA_HOME & JAVA_CPPFLAGS. It would make sense if javareconf correctly detected this (e.g. using jdk1.8.0_xx), but it didn't work for me, hence the workaround I posted. That said, perhaps it's updated since I last tried (27 Nov 2014).

[gwinstanley]

So I've just upgraded to the latest Hombrew version of R (3.2.1_1) and latest Java (1.8.0_51), and I get the following using the recommended
R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers:
However, it works fine using my technique as shown above.

Java interpreter : /usr/bin/java
Java version     : 1.8.0_51
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents/Home/jre
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
Non-system Java on OS X

trying to compile and link a JNI program
detected JNI cpp flags    : -I/System/Library/Frameworks/JavaVM.framework/Headers
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
clang -I/usr/local/Cellar/r/3.2.1_1/R.framework/Resources/include -DNDEBUG -I/System/Library/Frameworks/JavaVM.framework/Headers -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include    -fPIC  -g -O2  -c conftest.c -o conftest.o
conftest.c:1:10: fatal error: 'jni.h' file not found
#include <jni.h>
         ^
1 error generated.
make: *** [conftest.o] Error 1
Unable to compile a JNI program


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.8.0_51.jdk/Contents/Home/jre
Java library path:
JNI cpp flags    :
JNI linker flags :

[gwinstanley]

BTW, if anyone's arrived at this thread still looking for a fix for the latest Java/rJava, I've created a gist for it.