[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 05:12:38 CET 2012
Thanks!. I am an admin user, using javareconf with sudo overwrote the settings, just didn't find the java 1.7 settings. I had to su so that I could explicitly set JAVA_HOME and overwrite the settings, even though JAVA_HOME is set in my bash_profile. I mainly wrote that down for the record, in case anyone else runs into the problem.
rJava is one piece I did not try rebuilding. I will give that a go.
It is a shame that the Apple Java utility no longer exists, so that it is relatively easy to switch between Javas. My memory also is that you use to set JAVA_HOME to a location in the javavm.frameworks directory, but clearly not anymore.
Thanks again and happy new year.
-Roy
On Dec 28, 2012, at 7:51 PM, Simon Urbanek <simon.urbanek at r-project.org> wrote:
> On Dec 28, 2012, at 7:46 PM, Roy Mendelssohn - NOAA Federal wrote:
>
>> 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.
>
> "of course"? R is normally (i.e. from CRAN) installed so that admin users can modify settings. It will only fail if you messed with sudo before or you are not an admin user.
>
>
>> I then instead did:
>>
>>> su
>>> 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?
>
> You have to build rJava from sources with R64 because Oracle's Java is incompatible with anything Apple has supplied before -- see the Oracle 1.7 thread on stats-rosuda-devel (which is the mailing list for rJava and JGR). Oracle's Java doesn't support 32-bit anyway, so you have to use 64-bit R.
>
>
>> 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.
>>
>
> There is no compiler involved in iplots and there is no reason to mess with it (you were mistaken, iplots merely starts rJava which is where you get the JVM error - it has nothing to do with iplots, really) - there is no native code in there and it works with any Java, so just use the CRAN binary. The only piece you have to re-compile is rJava (and possibly JavaGD), everything else should work from CRAN. Just make sure you're using the 64-bit JGR launcher.
>
> Cheers,
> Simon
>
>
>
>> Thanks for any help.
>>
>> -Roy
>>
>> On Dec 28, 2012, at 4:35 PM, Marc Schwartz <marc_schwartz at me.com> wrote:
>>
>>> Roy,
>>>
>>> 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:
>>>
>>> http://www.oracle.com/technetwork/java/javase/downloads/jdk7-downloads-1880260.html
>>>
>>> Install that and then run the full javareconf command as I had in my reply below.
>>>
>>> Regards,
>>>
>>> Marc
>>>
>>> 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
>>>>> 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/
>>
>> "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.
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>>
>
**********************
"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/
"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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