[R-SIG-Mac] R 2.15.2, OS X 10.8.2, JGR

[Roy Mendelssohn - NOAA Federal]

Thanks.  But I am still stuck.  No matter which command I give, I  get the following:

> sudo R CMD javareconf
> Password:
> Java interpreter : /usr/bin/java
> Java version     : 1.6.0_29
> Java home path   : /Library/Java/JavaVirtualMachines/1.6.0_29-b11-402.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
> 

Note the Java home path.  But when I  do the following:

> bash-$ which java
> /usr/bin/java
> bash-$ java -version
> java version "1.7.0_06"
> Java(TM) SE Runtime Environment (build 1.7.0_06-b24)
> Java HotSpot(TM) 64-Bit Server VM (build 23.2-b09, mixed mode)
> 

So where is ti getting that the home path is to /Library/Java/JavaVirtualMachines/1.6.0_29-b11-402.jdk/Contents/Home?  Is there a file that I can hand edit to give R the correct values?

Thanks.

-Roy M.
On Dec 28, 2012, at 1:28 PM, Marc Schwartz <marc_schwartz at me.com> wro

> On Dec 28, 2012, at 3:05 PM, peter dalgaard <pdalgd at gmail.com> wrote:
> 
>> 
>> On Dec 28, 2012, at 20:40 , Roy Mendelssohn - NOAA Federal wrote:
>> 
>>> Hi All:
>>> 
>>> I recently upgraded my computer to 10.8.2, and my Java is now java 1.7 from Oracle.  I am running R 2.15.2, and now rjava and JGR don't work because what appears to be a problem with ipot.  I tried reinstalling rjava and got the following:
>> 
>> I can't remember this kind of stuff form one occasion to the next either, but wouldn't it be something with "sudo R CMD javareconf" ?
> 
> 
> 
> For Mountain Lion, it should be:
> 
>  sudo R CMD javareconf JAVA_CPPFLAGS=-I/System/Library/Frameworks/JavaVM.framework/Headers
> 
> Regards,
> 
> Marc Schwartz
> 

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
1352 Lighthouse Avenue
Pacific Grove, CA 93950-2097

e-mail: Roy.Mendelssohn at noaa.gov (Note new e-mail address)
voice: (831)-648-9029
fax: (831)-648-8440
www: http://www.pfeg.noaa.gov/

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"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.