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.

I don't have any particular insight here, but you may want to install rJava from source, or try the stats-rosuda-devel mailing list. — Ian Fellows
I did ask on the list and just received an answer. I'll add it to the original question above. — Tod
Thanks for updating that with Simon's answer. It's easier to read if it's not in code-format with lateral scrolling. — IRTFM
@java_xof - you got it backwards - Linux is where this mess comes from - we have to jump through quite a few hoops to get Linux flags to work. On Macs things are frameworks so no complicated flags are needed at all. However, Oracle just took the Linux setup and put it on OS X which is why it's so broken. Oracle now essentially requires Linux fixes on OS X where no fixes where needed which is why it doesn't work. — Simon Urbanek
@SimonUrbanek - don't get mad, cool, make pace not war; for me and my colleagues we try to avoid any Java app working on linux, nevertheless we wrote few small Java apps which are working both on MS Win and Linux, but there are always problems with MAC OS; that is if we would chose commercial os we would chose linux (maybe on few desktops would be win), that's all - keep in mind that I've never being using MAC OS... cheers and pace to all os'es!! — java_xof

phamnamlong phamnamlong · Accepted Answer · 2013-10-03T05:18:09

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

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

2 Answers