RNetLogo not working on Mac Yosemite

Question

I just tried this, but I got this error message. Any ideas about how to fix it? I am using the R version 3.1.1, RNetLogo_1.0-1, the platform is x86_64-apple-darwin13.1.0 (64-bit), Java 7 update 60.

Sys.setenv(NOAWT=1)
library(JGR)
Sys.unsetenv("NOAWT")

JGR()
library(RNetLogo)

nl.path <- "/Applications/NetLogo 5.1.0"
NLStart(nl.path) 
Error in .jnew("nlcon/Preprocess") : 
  java.lang.UnsupportedClassVersionError: nlcon/Preprocess : Unsupported major.minor version 51.0

Did you read Details section of `?NLStart` regarding use in OSX? I ask because it fairly clearly states this should not work outside the JGR environment. I also see not evidence that you followed the directions to execute `Sys.setenv(NOAWT=1)` — IRTFM, Oct 28 '14 at 21:43
Same problem here. https://groups.yahoo.com/neo/groups/netlogo-users/conversations/topics/16067 suggests that updating to Java 7 should have made the grade but it does not work on my side either (Maverick, RNetLogo_1.0-1, Java 8) — Martin Van der Linden, Oct 30 '14 at 18:33
You installed Java 8, but are you sure that are actually successfully using it? It should not be possible for Java 8 to give a “Unsupported major.minor version 51.0” error. — Seth Tisue, Nov 01 '14 at 01:21

score 3 · Answer 1 · answered Nov 04 '14 at 19:58

You need at least Java 7.

I have missed to update the requirements in the package description to Java >= 7. Sorry for that. The CRAN maintainers ask me to clean up the package, i.e. update to Java 7 and remove support for old Java and NetLogo versions.

If older Java should be used, get old RNetLogo version (e.g. 1.0-0) from CRAN archive.

Best wishes, Jan

score 2 · Answer 2 · answered Oct 28 '14 at 23:31

2

What version of RNetLogo are you using? According to http://cran.r-project.org/web/packages/RNetLogo/news.html , RNetLogo version 0.9-6 fixed a bug that caused the "Unsupported major.minor version 51.0" version error.

answered Oct 28 '14 at 23:31

Seth Tisue

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I am using RNetLogo_1.0-1 – sdaza Oct 29 '14 at 07:39
I wonder if the authors accidentally reintroduced the bug. It's easy for add-on authors to forget to compile their code so it works with old Java versions. – Seth Tisue Oct 29 '14 at 11:54

score 2 · Answer 3 · answered Nov 02 '14 at 07:13

please check which Java version is used by R. I checked it on one of my Ubuntu installation with Java 7 without any problem. Yes, support for very old Java and NetLogo versions have been removed with 1.0-1 as requested by CRAN maintainers (that's not a bug).

Please execute the following functions in R to check which Java is active:

    library(rJava)
    .jinit()
    .jcall("java/lang/System", "S", "getProperty", "java.vm.version")
    .jcall("java/lang/System", "S", "getProperty", "java.vm.name")
    .jcall("java/lang/System", "S", "getProperty", "java.vm.info")
    .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
    .jcall("java/lang/System", "S", "getProperty", "sun.arch.data.model")

Cheers, Jan

How did you set up rJava after its installation? I am still stuck here: https://github.com/s-u/rJava/issues/37 — sdaza, Dec 06 '14 at 15:49

score 2 · Answer 4 · edited May 23 '17 at 11:54

Wanted to put this as a comment, but I lost my right to commenting by awarding a bounty to the question and getting below 50 rep... :-S

@Jan : I executed the functions you mentioned and got the following

[1] 0
     .jcall("java/lang/System", "S", "getProperty", "java.vm.version")
[1] "20.65-b04-462"
     .jcall("java/lang/System", "S", "getProperty", "java.vm.name")
[1] "Java HotSpot(TM) 64-Bit Server VM"
     .jcall("java/lang/System", "S", "getProperty", "java.vm.info")
[1] "mixed mode"
     .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.6.0_65-b14-462-11M4609"
     .jcall("java/lang/System", "S", "getProperty", "sun.arch.data.model")
[1] "64"

I understand that R might not be picking up the right Java version. I also get the error message

Error in .jnew("nlcon/Preprocess") : 
  java.lang.UnsupportedClassVersionError: nlcon/Preprocess : Unsupported major.minor version 51.0

Am I understanding correctly that version 51.0 corresponds to some update of Java 7? Should there be a problem with Java 7? Do we really need to make sure R finds and uses Java 8? I guess that R is still trying to use Java 7 suggest there is something wrong? Any idea how to fix this?

Edit following last answer by Jan

@Jan : thanks for following up on the question. I might chose to go back to older versions of RNetLogo if it solves the problem. The thing is I installed Java 8, so I would expect R to use it, but somehow it seems that it does not. For clarity, I'll start another question in order to figure out how to solve this ( see Getting R to use newer versions of java).

This being said from Getting R to use newer versions of java and the fact that the error message in R mentions version 51 I understand that I am indeed using Java 7, so there should be no problem with RNetLogo right?

Not sure if it works on Mac but have you tried R CMD javareconf (see also here: http://r.789695.n4.nabble.com/Can-t-get-R-to-recognize-Java-for-rJava-installation-td4553023.html) — Jan C. Thiele, Nov 08 '14 at 20:36
Thanks for the suggestion. I'll look into this when I get back to my mac next week. — Martin Van der Linden, Nov 08 '14 at 21:07
I have got the same problem, and R CMD javareconf didn't change anything. I still get R pointing to Java Runtime Version 1.6.0, even though system("java -version") yields "java version 1.7.0." — Kenji, Nov 14 '14 at 16:14
Thanks for all the suggestions. I have tried different ways to do it, but I am still not able change the java version R is using (1.6.0) :( — sdaza, Dec 02 '14 at 17:42
The problem has to do with rJava. Here some details: https://github.com/s-u/rJava/issues/37 — sdaza, Dec 06 '14 at 15:46
It seems for now the best solution is to use Windows: I haven't had any problems with Java 8 using Windows. — sdaza, Dec 18 '14 at 16:31

sdaza · Answer 5 · 2015-10-21T16:03:38.393

After several weeks trying to fix it, RNetLogo is finally working on my laptop with Yosemite and The Capitan. Here you have technical details regarding the solution: https://github.com/s-u/rJava/issues/37

This is what I did (remember that I use R in terminal):

Install Java 8 (http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
Install Java 6 from Mac (http://support.apple.com/kb/DL1572)
It is necessary to define correctly the java home directory. I used /Library/Java/Home, but it could be another. You can use eclipse IDE (preferences, installed jREs) to define the directory.
Reconfigure R using sudo R CMD javareconf -n in terminal
In terminal, set the path to lijvm.dylib

jvm = 'ls /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/jre/lib/server/lijvm.dylib' sudo install_name_tool -id "$jvm" "$jvm"

Install rJava as source install.packages("rJava", type="source")
You can check in the terminal to make sure you have linked rJava against 1.8 and not 1.6.

DYLD_PRINT_LIBRARIES=1 R library(rJava) .jinit() .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")

Then, install RNetLogo. That's it.

I followed the method laid out by sdaza. Everything works hunky dory when using R and JGR through the terminal. However when I try the same using the R console or RStudio, not only does RNetLogo not work, rJava is no longer found. Anybody else have the same experience? — invictus, Jun 18 '15 at 20:38
That worked perfectly on Linux as well. The key steps: (1) make sure that `/usr/lib/jvm/default-java` links to the correct Java, then (2) `sudo R CMD javareconf` as root; (3) reinstall `rJava` and then re-start R; (4) reinstall `RNetLogo`. — akhmed, Aug 20 '15 at 19:11

RNetLogo not working on Mac Yosemite

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