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Error when connecting NetLogo 6.0 and R #1282

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plopezmp opened this issue Jan 11, 2017 · 39 comments
Closed

Error when connecting NetLogo 6.0 and R #1282

plopezmp opened this issue Jan 11, 2017 · 39 comments

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@plopezmp
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Trying to call Netlogo 6.0 from R 3.3.2 on MacOSX 10.11.6 (Capitan)

After,

library("RNetLogo")

nl.path <- getwd()

NLStart(nl.path)
gives me the following exception/error:

java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:249)
Caused by: java.lang.ClassNotFoundException
at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 2 more
It seems some kind of problem with Java, RJavaClassLoader,

I would ask you to help me solve this issue.

Thank you very much

@mrerrormessage
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mrerrormessage commented Jan 11, 2017

Hi! The RJava package hasn't been updated for NetLogo 6. At this point, you can use RJava with NetLogo 5.3.1, but it will not work with NetLogo 6. NetLogo 5.3.1 is still available for download here.

While the r extension was included with NetLogo 6, we don't support the RJava package for R at this point. In the next few weeks, the development team here at the CCL will discuss supporting this long-term, as it appears it's actively used.

@plopezmp
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plopezmp commented Jan 11, 2017 via email

@mrerrormessage
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In the process of discussing support for the rJava package, we're trying to understand the features that rJava offers which aren't available in the NetLogo R extension. Do you or others have any use cases you can share with us?

@plopezmp
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plopezmp commented Jan 23, 2017 via email

@daimpi
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daimpi commented Jan 30, 2017

I haven't personally worked with the NetLogo R extension or RNetLogo yet, due to our model still being in an early development stage, but we're planing to use RNetLogo in the near future. From what I understand the NetLogo R extension is used to do R calculations from within NetLogo while RNetLogo is used to control NetLogo from within R (i.e. the other way around). The latter seems to be particularly suited for in-depth model analysis, calibration and automated run control. We're looking forward to utilize at least some of the simpler analyzing methods like Morris Screening and Full factorial design as described in this article for our NetLogo model in the near future. I've contacted Jan Thiele (the author of RNetLogo) and he said he's planing to update RNetLogo for the NetLogo 6 api, but he can't give a time-estimate yet as the development is confined to his free time.

@mrerrormessage
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My understanding is that rNetLogo has been updated for NetLogo 6.0. Is this correct? If so, can I close this issue?

@plopezmp
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plopezmp commented Feb 27, 2017 via email

@elenanitodelbosque
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I am having the same problems using RNetlogo 6.0.1

> Sys.setenv(NOAWT=1)     # to run RNetLogo in headless mode disable AWT before loading RNetlogo
> library(RNetLogo)
> setwd("/Applications/NetLogo 6.0.1/Java")
> nl.path <- getwd()
> NLStart(nl.path, gui=FALSE)
java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Class.java:249)
Caused by: java.lang.ClassNotFoundException
    at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
    ... 2 more

> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.4

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RNetLogo_1.0-3 igraph_1.0.1   rJava_0.9-8   

loaded via a namespace (and not attached):
[1] magrittr_1.5 tools_3.3.3 

Can anyone help me solve the problem?

@ashleyasmus
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I am having the exact same problem as @elenanitodelbosque. @mrerrormessage, do you know if there is a fix to this issue? I have tried updating R, RStudio, Java, and all the like. Then I tried installing an old version of RNetLogo from cran-archive and found it was no longer compatible with java...!

R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:
character(0)

other attached packages:
[1] RNetLogo_1.0-4

loaded via a namespace (and not attached):
[1] compiler_3.4.0 magrittr_1.5 graphics_3.4.0 tools_3.4.0 igraph_1.0.1 utils_3.4.0 grDevices_3.4.0 stats_3.4.0
[9] datasets_3.4.0 methods_3.4.0 rJava_0.9-8 base_3.4.0

@mrerrormessage
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@ashleyasmus - I assume you're running NetLogo 6.0.1? If so, the below advice applies to you as well.

@elenanitodelbosque, sorry it's taken so long to get back to you.

The newer versions of NetLogo have a versioned NetLogo jar which needs to be provided to NLStart (in RNetLogo 1.0.3 and later). An example is given on page 3&4 of the RNetLogo Manual. On mac, this looks like:

library(RNetLogo)
NLStart("/Applications/NetLogo 6.0.1/Java", gui = FALSE, nl.jarname = "netlogo-6.0.1.jar")  # these strings can be stored in variables, of course)
# ... etc.

On windows:

library(RNetLogo)
NLStart("C:/Program Files/NetLogo 6.0.1/app", gui = FALSE, nl.jarname = "netlogo-6.0.1.jar")
# ... etc

Note that each time you change your version of NetLogo, you will need to adjust both the nl.path and the nl.jarname to have the latest version number.

@ashleyasmus
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ashleyasmus commented May 17, 2017

Hi @mrerrormessage ! Thanks for the quick reply.
Unfortunately, I have tried pointing to the exact JAR with no luck. I moved to a friend's Mac Machine to see if I would have more success, but alas, no dice. I checked to be sure the jar file name and path name were the same as you suggest.

NLStart("/Applications/NetLogo 6.0.1/Java", gui = FALSE, nl.jarname = "netlogo-6.0.1.jar") # these strings can be stored in variables, of course)
java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
Caused by: java.lang.ClassNotFoundException
at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 2 more

Interestingly, I had issues with R asking me to install an old version of Java (version 6) when I loaded RNetLogo's library. But, it looks like RStudio is still reaching for the new version of Java (8). I wonder if (& am worried that) there is some deeper incompatibility going on that requires a terminal fix.

Here is the new session info:

J("java.lang.System","getProperty","java.version")
[1] "1.8.0_131"

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] RNetLogo_1.0-3 igraph_1.0.1 rJava_0.9-8

loaded via a namespace (and not attached):
[1] magrittr_1.5 tools_3.3.2

@ashleyasmus
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I have done a terrible job keeping track of all I've done, but running this sudo command in Terminal on Mac OS fixed the problem for me:
sudo ln -f -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib

Thanks to this website.

I wish I could re-create this issue for others, maybe @elenanitodelbosque will be helped by this??

Yowza. Java!

@mrerrormessage
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@ashleyasmus glad to hear you've found a solution! I had been wondering whether there were possible java version issues involved. NetLogo (6.0 and later) requires Java 8 to run (Java 6 won't work), but you must also tell R where to find "libjvm.dylib". There are several ways to do that, and your command looks like it does the trick nicely.

@itcarroll
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Suggestions on the Windows version of the fix @ashleyasmus found for macOS? I'm getting a nearly identical error:

java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
    at java.lang.Class.forName0(Native Method)
    at java.lang.Class.forName(Unknown Source)
Caused by: java.lang.ClassNotFoundException
    at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
... 2 more

@itcarroll
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Uh... not sure what happened. I tried using NLStart from outside RStudio (in 64bit R), which worked. I also tried doing library(rJava); .jinit() from within RStudio, which also worked. Then, I tried NLStart again from within RStudio ... and it worked. I don't know what changed ...

@elenanitodelbosque
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elenanitodelbosque commented May 31, 2017

Hi, thanks for the help. Sadly I'm still having the same issues.
I tried specifying nl.jarname to NLStart but had the same error as @ashleyasmus
`

Sys.setenv(NOAWT=1) # to run RNetLogo in headless mode disable AWT before loading RNetlogo
library(RNetLogo)
NLStart("C:/Program Files/NetLogo 6.0.1/app", gui = FALSE, nl.jarname = "netlogo-6.0.1.jar")
java.lang.UnsupportedClassVersionError: org/nlogo/workspace/Controllable : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:295)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:249)
`

Then I tried the terminal command line from @ashleyasmus and back to running NLStart with RStudio but got the same error as shown above.
As suggested by @itcarroll I tried the same from outside RStudio (in 64bit R 3.3.3) but again the same error
Sorry for the late reply! Someone has any other suggestion?
E.

@mrerrormessage
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@elenanitodelbosque , your problem looks like a java incompatibility instead of a problem locating the jar file. Run the following in R:

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

If the result does not start with "1.8.0", you are using an older, incompatible version of Java. To correct this, install the latest JDK / JRE from Oracle. You may additionally need to configure JAVA_HOME within R or reinstall rJava. this blog post describes how to fix a similar error.

@haoyangz
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haoyangz commented Jan 6, 2018

I encountered a similar but not quite the same error (it's org/nlogo/api/Exceptions$Handler):

java.lang.NoClassDefFoundError: org/nlogo/api/Exceptions$Handler
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:249)
Caused by: java.lang.ClassNotFoundException
	at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 2 more

The command I ran is:

library(RNetLogo)
NLStart("/Applications/NetLogo_5.3.1/Java", gui = FALSE, nl.jarname = "NetLogo.jar")

I checked the file /Applications/NetLogo_5.3.1/Java/NetLogo.jar does exist. I am using NetLogo 5.3.1. .jcall("java/lang/System", "S", "getProperty", "java.runtime.version") returnes version 1.6.0_65-b14-468.

Could anyone help please?

@jalapic
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jalapic commented Mar 30, 2018

I get the same issue when connecting to NetLogo 6.0.3 from RStudio on Windows. The error message I get is:

java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Unknown Source)
Caused by: java.lang.ClassNotFoundException
	at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	at java.lang.ClassLoader.loadClass(Unknown Source)
	... 2 more

@elskevdv
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@jalapic Are you using Java 9 by any chance? I was getting this error under Ubuntu 17.10, NetLogo 6.0.3, rJava 0.9-9 and RNetLogo 1.0-4, and going back to Java 8 from Java 9 fixed it.

@cschwem2er
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I receive the same error as @jalapic.

java -version
java version "1.8.0_171"
Java(TM) SE Runtime Environment (build 1.8.0_171-b11)
Java HotSpot(TM) 64-Bit Server VM (build 25.171-b11, mixed mode)

@vonjd
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vonjd commented Jul 15, 2018

I am encountering the same error. I reinstalled everything, so I use the latest versions of all packages, JAVA etc. Any idea what to do now?

@vonjd
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vonjd commented Sep 16, 2018

Is this project dead? Would be a pity...

@LaCuneta
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@vonjd I just setup and ran a test model through RNetLogo on macOS and Windows 7, so it should still work. Unfortunately there are a lot of different pieces that need to fit together (NetLogo, R, RNetLogo, rJava, and Java). Here is a list of things to check:

  • NetLogo uses Java 8, so I'd recommend using that with RNetLogo and rJava (the library RNetLogo uses). It might be possible to use a later one, but I don't think it'd be worth the time to try.
  • Make sure you have a Java 8 JDK installed, not just a Java runtime. Again, I think this is to appease the rJava library.
  • You need to make sure you're using the 64 bit versions of R, NetLogo, and Java JDK (or all 32 bit if that's what your machine supports).
    • I've seen comments saying that having both 32 and 64 bit Java JDKs is necessary for rJava, but I had only the 64 bit one installed on my machines.
  • Check your JAVA_HOME environment variable before running R, and make sure it points to the correct JDK install. echo $JAVA_HOME on macOS, echo %JAVA_HOME% on Windows. I've seen some comments saying having JAVA_HOME set isn't necessary, and others saying it is. I had it set on the Windows 7 machine I was using.
    • You should be able to check inside an R console by running Sys.getenv("JAVA_HOME"). If it points to a place that isn't your Java 8 SDK, that's a likely source problems.
  • Make sure you have the appropriate NetLogo paths for RNetLogo - nl.path="/Applications/NetLogo 6.0.4/Java" for macOS, nl.path="C:/Program Files/NetLogo 6.0.4/app" for Windows.
  • Make sure you're using the correct versioned jar name - nl.jarname="netlogo-6.0.4.jar"

Finally, if you need to use NetLogo 5.3.1, you might have to downgrade to an older version of RNetLogo. I'm not knowledgeable enough with R to give instructions, but it looks like source packages of the older versions are available.

@vonjd
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vonjd commented Sep 22, 2019

@LaCuneta: With NLStart(nl.path = "C:/Program Files/NetLogo 6.0.4/app", gui = TRUE, nl.jarname = "netlogo-6.0.4.jar") it works! Thank you!

@rbtlm640
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Hello! I tried following the advices given above. I have NetLogo 6.0.4 and R3.6.
I have this code:

library(rJava)
library(RNetLogo)
Sys.setenv(JAVA_HOME = "C:/Program Files/Java/jdk1.8.0_231/")
Sys.getenv("JAVA_HOME")

#testing rjava
.jinit(classpath = NULL,
       parameters = getOption("java.parameters"),silent = FALSE, force.init = FALSE)
s <- .jnew("java/lang/String",
           "Hello World!")
print(s)

#loading Netlogo

NLStart(nl.path="C:/Program Files/NetLogo 6.0.4/app", gui = FALSE,
         nl.obj ="my.netlogo1", nl.jarname="netlogo-6.0.4.jar")

and I get this:

Sys.getenv("JAVA_HOME")
[1] "C:/Program Files/Java/jdk1.8.0_231/

> .jinit(classpath = NULL,
+        parameters = getOption("java.parameters"),silent = FALSE, force.init = FALSE)
[1] 0
> s <- .jnew("java/lang/String",
+            "Hello World!")
> print(s)
[1] "Java-Object{Hello World!}"

> NLStart(nl.path = "C:/Program Files/NetLogo 6.0.4/app", gui = TRUE, nl.jarname = "netlogo-6.0.4.jar")
java.lang.NoClassDefFoundError: org/nlogo/workspace/Controllable
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:348)
Caused by: java.lang.ClassNotFoundException
	at RJavaClassLoader.findClass(RJavaClassLoader.java:383)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
	... 2 more

@knbknb
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knbknb commented Apr 30, 2021

Newer Linux versions have Java 11 (or Java 14, or ...) installed. In order to switch to OpenJDK 8.
it sometimes also helps to run R CMD javareconf as root.

 sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
Java version     : 1.8.0_292
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/lib/jvm/default-java/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-EyP6DW/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

Check where /usr/lib/jvm/default-java points to . It should now point to the directory /usr/lib/jvm/java-8-openjdk-amd64 (or similar).

For me, a reinstallation of the rJava R package was not needed. Current version of Netlogo, v6.2.0, can be started with NLstart(). However, models cannot be loaded with NLLoadModel(). Now trying v6.0.4 ...

It has to be RNetLogo 6.0.4.

@DavidSchultner
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Newer Linux versions have Java 11 (or Java 14, or ...) installed. In order to switch to OpenJDK 8.
it sometimes also helps to run R CMD javareconf as root.

 sudo R CMD javareconf
Java interpreter : /usr/lib/jvm/default-java/jre/bin/java
Java version     : 1.8.0_292
Java home path   : /usr/lib/jvm/default-java
Java compiler    : /usr/lib/jvm/default-java/bin/javac
Java headers gen.: /usr/lib/jvm/default-java/bin/javah
Java archive tool: /usr/lib/jvm/default-java/bin/jar

trying to compile and link a JNI program 
detected JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
detected JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux     -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-EyP6DW/r-base-4.0.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c conftest.c -o conftest.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o conftest.so conftest.o -L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm -L/usr/lib/R/lib -lR


JAVA_HOME        : /usr/lib/jvm/default-java
Java library path: $(JAVA_HOME)/jre/lib/amd64/server
JNI cpp flags    : -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JNI linker flags : -L$(JAVA_HOME)/jre/lib/amd64/server -ljvm
Updating Java configuration in /usr/lib/R
Done.

Check where /usr/lib/jvm/default-java points to . It should now point to the directory /usr/lib/jvm/java-8-openjdk-amd64 (or similar).

For me, a reinstallation of the rJava R package was not needed. Current version of Netlogo, v6.2.0, can be started with NLstart(). However, models cannot be loaded with NLLoadModel(). Now trying v6.0.4 ...

It has to be RNetLogo 6.0.4.

Any progress with this? I too cannot load models with NLLoadModel() with Netlogo 6.2.0 on Mac OS and Netlogo 5.3.1 did not work either. Would be grateful for hints if there's a working version

@LaCuneta
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@DavidSchultner Have you tried the nlrx package? It can run NetLogo models from R, and I believe it supports NetLogo 6.2.0.

@DavidSchultner
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@LaCuneta thanks - the nlrx has been discontinued as well...

@LaCuneta
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@DavidSchultner Hmm I don't see any mention of that in the nlrx docs and it looks like there were updates as recently as last month to it. Where are you seeing that it's discontinued? I do see this issue in their repo about the package being archived on CRAN, but it contains a workaround to load it from a different source.

@DavidSchultner
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@LaCuneta loading via GitHub worked, thanks so much! I gave up too soon

@kmbarn4
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kmbarn4 commented Mar 9, 2023

Hi! I have been running into similar issues using Java when trying to run rNetlogo. @mrerrormessage how do I tell R where to find "libjvm.dylib"? Can I do this within R without using the terminal?

Also, now when I try running NLStart, I do not get an error message in the R console but I get an error message pop up saying:
"Error in setting cp. Class path is
:C/Users/civitellolabuser/Documents/R/win-library/3.5/rJava/java/boot;C:\Users\civitellolabuser\Documents\R\win-library\3.5\RNetlogo\java;C:\Users\civitellolabuser\Documents\R\win-library\3.5\RNetlogo\java\RNetlogo.jar"

Do you know what this could mean?

@brandesNW
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brandesNW commented Mar 9, 2023 via email

@kmbarn4
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kmbarn4 commented Mar 9, 2023 via email

@brandesNW
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brandesNW commented Mar 9, 2023 via email

@brandesNW
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brandesNW commented Mar 9, 2023 via email

@kmbarn4
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kmbarn4 commented Mar 23, 2023 via email

@brandesNW
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brandesNW commented Mar 24, 2023 via email

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