[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 01:46:41 CET 2012
Yes i have the jdk. But I just stumbled on part of the problem (I have a feeling i know have to wrestle with 32-bit versus 64-bit versions).
I accidently gave the command:
> R CMD javareconf
without the sudo and the paths were being set correctly to the java 1.7 machine, but of course without permissions it would not overwrite the settings. I then instead did:
> export JAVA_HOME=`/usr/libexec/java_home -v 1.7`
> R CMD javareconf
That then echoed what I expected. Okay, so my question is I have been running R not R64. To use rJava, JGR etc do I need to run R64 and just install the binary or build from source? because even though now my paths are set correctly, iplots is still unhappy, and won't build either, because the compiler is trying to do 64-bits in a 32-bit program.
Thanks for any help.
On Dec 28, 2012, at 4:35 PM, Marc Schwartz <marc_schwartz at me.com> wrote:
> Did you install the 1.7 JRE only, or did you also install the JDK?
> If you did not also install the JDK, I believe that you need to do so. It is available here:
> Install that and then run the full javareconf command as I had in my reply below.
> On Dec 28, 2012, at 6:11 PM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
>> Thanks. But I am still stuck. No matter which command I give, I get the following:
>>> sudo R CMD javareconf
>>> 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
>>> 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
>>> Marc Schwartz
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
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)
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