What is the correct method to install a JDK on Mac OS Lion?

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Hi,

    I'm using R.app on Mac OS Lion and when I attempt to build the 
rJava package from source I get the following error:

Checking whether JNI programs can be compiled... configure: error: 
Cannot compile a simple JNI program. See *config.log* for details.

Make sure you have Java Development Kit installed and correctly 
registered in R.
If in doubt, re-run "R CMD javareconf" as root.

ERROR: configuration failed for package 'rJava'
* removing 
'/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rJava'

On a fresh Mac OS install, executing the command: sudo R CMD javareconf 
fails with:

 "No Java runtime present, requesting install. Java interpreter doesn't 
work properly." and then initiates fetching of Apple's Java runtime.

executing the command, once the Java runtime is finished completes with 
the following output

Java interpreter : /usr/bin/java
Java version     : 1.6.0_26
Java home path   : 
/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java compiler    : /usr/bin/javac
Java headers gen.: /usr/bin/javah
Java archive tool: /usr/bin/jar
*Java library path:*
JNI linker flags : -framework JavaVM
JNI cpp flags    : -I$(JAVA_HOME)/include

Updating Java configuration in /Library/Frameworks/R.framework/Resources
Done.

Attempting to build the rJava package again results in the same error as 
before.

This causes me to ask a few questions:

1) Is the Java package that my Mac automatically downloaded from Apple 
the right package?
Yes
 If not which one should I use?
2) Above there is no Java Library path listed, is this part of my problem?
No, OS X doesn't need it
3) Where is the config.log that R.app generates?  Dredging around the 
Console.app and the likely places did not reveal it.

It is deleted after the installation. You want to use the unpacked tar ball.

But to your real issue - Apple doesn't provide headers inside the Java home anymore, so you want to re-run javareconf pointing to the framework:

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

(normally you don' t need sudo but if you used it once, you have to use it from then on).

Cheers,
Simon
For what it is worth I have tried 3 different version of R at this 
point: (R-2.13-branch, 
<http://r.research.att.com/R-2.13-branch-leopard.pkg>R-2.13-patched for 
Lion, R-devel)

Thanks for any help!

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