how to get rJava 0.9-3 to work on OS X 10.7.4 with Oracle Java 1.7?

Question

Is there anyone out there who has managed to get rJava 0.9-3 to work on OS X 10.7.4 with Oracle Java 1.7?

R version 2.15.2 (2012-10-26) -- "Trick or Treat" Platform
x86_64-apple-darwin9.8.0/x86_64 (64-bit)

java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02, mixed mode)

I've installed rJava using both the install.packages function and the command line install with R 2.15.2. I don't get any errors.

$ R CMD INSTALL rJava
* installing to library ‘/Library/Frameworks/R.framework/Versions/2.15/Resources/library’
* installing *binary* package ‘rJava’ ...

* DONE (rJava)
$ 

If I use Java Preferences to put 1.7 first on the list, but leave 1.6 "on", rJava always starts 1.6.

If I use Java Preferences to put 1.7 first and turn off 1.6, rJava does this:

> library(rJava)
> .jinit()
JavaVM: requested Java version ((null)) not available. Using Java at "" instead.
JavaVM: Failed to load JVM: /bundle/Libraries/libserver.dylib
JavaVM FATAL: Failed to load the jvm library.
Error in .jinit() : JNI_GetCreatedJavaVMs returned -1
> 

However, using the system function, R by itself finds Java 1.7.

> system("java -version")
java version "1.7.0_09"
Java(TM) SE Runtime Environment (build 1.7.0_09-b05)
Java HotSpot(TM) 64-Bit Server VM (build 23.5-b02, mixed mode)
> 

Does 1.7 need a special entry in /System/Library/Java/JavaConfig.plist ?

Does the Versions directory need tweaking for 1.7 ? It is weird that Current goes to A, which ends up with 1.7 while CurrentJDK is mapped to 1.6

$cd /System/Library/Frameworks/JavaVM.framework/Versions/
$ls -la
total 64
drwxr-xr-x  11 root  wheel  374 Sep 26 10:10 .
drwxr-xr-x  11 root  wheel  374 Nov 26 09:24 ..
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.4 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.4.2 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.5 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.5.0 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.6 -> CurrentJDK
lrwxr-xr-x   1 root  wheel   10 Sep 26 10:09 1.6.0 -> CurrentJDK
drwxr-xr-x   8 root  wheel  272 Nov 26 09:24 A
lrwxr-xr-x   1 root  wheel    1 Sep 26 10:09 Current -> A
lrwxr-xr-x   1 root  wheel   59 Sep 26 10:09 CurrentJDK -> /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents

Even with R CMD javareconf run with the path pointing to the 1.7 files directly or to the /usr/bin/java paths, rJava still can't find or start Java 1.7.

Does 1.7 need the JAVA_LD_LIBRARY_PATH variable set?

Makeconf:JAVA = /usr/bin/java
Makeconf:JAVAC = /usr/bin/javac
Makeconf:JAVAH = /usr/bin/javah
Makeconf:JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre
Makeconf:JAVA_LD_LIBRARY_PATH = 
Makeconf:JAVA_LIBS = -framework JavaVM
Makeconf:JAVA_CPPFLAGS = -I$(JAVA_HOME)/include

Makeconf:JAR = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/jar
Makeconf:JAVA = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/bin/java
Makeconf:JAVAC = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/javac
Makeconf:JAVAH = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/bin/javah
Makeconf:JAVA_HOME = /Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre
Makeconf:JAVA_LD_LIBRARY_PATH = 
Makeconf:JAVA_LIBS = -framework JavaVM
Makeconf:JAVA_CPPFLAGS = -I$(JAVA_HOME)/include

Thanks for any help

Update 1:

I asked this on the stats-rosuda-devel list and received the following response from Simon Urbanek. I don't think Windows and Linux have the same problems with needing compile from source for Java 1.7, since we're running this on Windows and Linux and didn't have to compile rJava. I'll report back once I have a chance to try this:

You are using the binary which is compiled against system Java (which on your system is 1.6) - so if you remove Java 1.6 you'll break it. If you want to use Java 1.7, you'll have to re-configure R for Java 1.7 and re-compile rJava to use those settings. Note that Oracle's Java lives in an entirely different place (/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk) than the system Java (/System/Library/Frameworks/JavaVM.framework), so it is not interchangeable.

In addition, Oracle Java 1.7 is not a framework, it's a big mess that was not really designed for OS X, so you have to set it by hand to settings like on Linux - it's pretty painful. Also it requires overrides ... so if you really want to go down the rabbit hole, this is what worked for me:

JAVA_LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server
JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server -ljvm'
JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/include/darwin'
R64 CMD javareconf

Then install rJava from sources (R64 -> install.packages("rJava",type='source')). Note that it's 64-bit only, so it will only work with 64-bit R.

Answer 1

This works for me:

The situation is that my Java directories were not configured correctly.

1) First run: sudo R CMD javareconf . It should the following:

Java interpreter : /usr/bin/java
Java version     : 1.7.0_40
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.7.0_40.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 progam 
detected JNI cpp flags    : -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/darwin
detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/../include -I/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/../include/darwin -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c conftest.c -o conftest.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o conftest.so conftest.o -L/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre/lib/server -ljvm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation


JAVA_HOME        : /Library/Java/JavaVirtualMachines/jdk1.7.0_40.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.

2) In R, run: install.packages("rJava",type='source') . Installation should returns DONE(rJava). Note that, I had to set

JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home

when I need to start R as root: sudo R. To run as a normal user, use

JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/jre

It happened to me that I did not set the symbolic links of the above /usr/bin/java* to the corresponding in Java 1.7 (directed to version 1.6 instead) and got all the frustration from there. Links should be like this: (it looks like only java, javac, javah, and jar are required in R).

$ ls -l /usr/bin/ja*
lrwxr-xr-x  1 root  wheel  71 Oct  3 11:44 /usr/bin/jar -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/jar
lrwxr-xr-x  1 root  wheel  77 Oct  3 12:14 /usr/bin/jarsigner -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/jarsigner
lrwxr-xr-x  1 root  wheel  72 Oct  3 11:44 /usr/bin/java -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/java
lrwxr-xr-x  1 root  wheel  73 Oct  3 11:42 /usr/bin/javac -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javac
lrwxr-xr-x  1 root  wheel  75 Oct  3 12:15 /usr/bin/javadoc -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javadoc
lrwxr-xr-x  1 root  wheel  73 Oct  3 11:44 /usr/bin/javah -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javah
lrwxr-xr-x  1 root  wheel  73 Oct  3 12:15 /usr/bin/javap -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javap
lrwxr-xr-x  1 root  wheel  74 Oct  3 12:15 /usr/bin/javaws -> /Library/Java/JavaVirtualMachines/jdk1.7.0_40.jdk/Contents/Home/bin/javaws

Answer 2

Finally, something worked!

Simon Urbanek : can you please put these instructions on the rJava website / cran install instructions...? This is the the first time I've been down this rabbit hole and I'm sure I'm not the only one.

JAVA_LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server JAVA_LIBS='-L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm' JAVA_CPPFLAGS='-I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin' R CMD javareconf
Java interpreter : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/bin/java
Java version     : 1.8.0_77
Java home path   : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home
Java compiler    : /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/javac
Java headers gen.: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/javah
Java archive tool: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/bin/jar
System Java on OS X

trying to compile and link a JNI program
detected JNI cpp flags    : -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin
detected JNI linker flags : -L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/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_77.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_77.jdk/Contents/Home
Java library path: /Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server
JNI cpp flags    : -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/include/darwin
JNI linker flags : -L/Library/Java/JavaVirtualMachines/jdk1.8.0_77.jdk/Contents/Home/jre/lib/server -ljvm
Updating Java configuration in /Library/Frameworks/R.framework/Resources
override rw-r--r--  root/admin for /Library/Frameworks/R.framework/Resources/etc/Makeconf? (y/n [n]) y
override rw-r--r--  root/admin for /Library/Frameworks/R.framework/Resources/etc/ldpaths? (y/n [n]) y
Done.

R CMD INSTALL rJava_0.9-9.tar.gz