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

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Sat Dec 29 01:11:22 CET 2012

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?


-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
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/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected" 
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

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