RNetLogo diagnostics

Matthew Malishev^1*

¹ Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA, USA, 30322

*Corresponding author: matthew.malishev@gmail.com

🔗 Github

Versions:

• R 3.5.0
• RStudio 1.1.453
• rJava 0.9-10
• RNetLogo 1.0-4
• JGR 3.4.1
• Netlogo 6.0.4

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File extensions:
.R
.Rmd
.nlogo
.csv
.pdf
.rtf
.html

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🐷 Troubleshooting steps for diagnosing Java, rJava, and RNetLogo errors when setting up NetLogo model in RStudio for Mac OSX (10+).

First set Netlogo paths in R

# setup netlogo in r  
ver <-"6.0.4" # type in Netlogo version
nl.path <- "<netlogo path>" ; nl.path # set path to Netlogo program location
model.path <- "<netlogo model path>" # set path to Netlogo model    
nl.model <- "<netlogo model>" # netlogo model. file = .nlogo  

nl.path <- paste0(nl.path,"NetLogo ",ver,"/Java/"); nl.path
model.path <- paste0(,"/"); model.path   

1️⃣ Installing compiler toolchain for Mac OSX
2️⃣ If rJava error persists, run the following in Terminal (sources: https://stackoverflow.com/questions/30738974/rjava-load-error-in-rstudio-r-after-upgrading-to-osx-yosemite and http://paulklemm.com/blog/2015-02-20-run-rjava-with-rstudio-under-osx-10-dot-10/):
sudo ln -s $(/usr/libexec/java_home)/jre/lib/server/libjvm.dylib /usr/local/lib
3️⃣ Java troubleshooting. Run the following code in R (tests are sequential):

# java troubleshooting. tests are sequential. 
# https://stackoverflow.com/questions/14915898/rnetlogo-function-nlstart-fails-to-launch-gui

test.java <- 1 # 1 = run java diagnostics  

if(test.java==1){
  # test 1  
  # test java is working
  .jinit() 
  .jnew( "java/awt/Point", 10L, 10L )
  f <- .jnew("java/awt/Frame","Hello")
  .jcall(f,"setVisible",TRUE)
  
  # test 2
  component <- .jnull()
  component <- .jcast(component, new.class = "java/awt/Component")
  message <- .jnew("java/lang/String","This is a JOptionPane test from rJava.")
  message <- .jcast(message, new.class = "java/lang/Object")
  title <- .jnew("java/lang/String","Test")
  type <- .jnew("java/lang/Integer", as.integer(2))
  f <- .jnew("javax/swing/JOptionPane")
  .jcall(f,"showMessageDialog", component, message, title, .jsimplify(type))
  
  # test 3
  .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")
  
  # test 4
  .jcall("java/lang/System", "S", "getProperty", "java.awt.headless")
  Sys.getenv("NOAWT")
}

4️⃣ GCC compiler in R(unconfirmed)
5️⃣ Running Netlogo 6.0.+
6️⃣ The following error in R when executing NLStart() means you have successfully navigated the rJava errors, but are running into a Java issue that's preventing R from generating the NetLogo GUI from R:

java.awt.HeadlessException
    at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
    at java.awt.Window.<init>(Window.java:536)
    at java.awt.Frame.<init>(Frame.java:420)
    at java.awt.Frame.<init>(Frame.java:385)
    at javax.swing.SwingUtilities$SharedOwnerFrame.<init>(SwingUtilities.java:1758)
    at javax.swing.SwingUtilities.getSharedOwnerFrame(SwingUtilities.java:1833)
    at javax.swing.JOptionPane.getRootFrame(JOptionPane.java:1696)
    at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:863)
    at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:666)
    at javax.swing.JOptionPane.showMessageDialog(JOptionPane.java:637)
    at nlcon.NLink.<init>(NLink.java:109)  

For the above error, the NLStart() function should run successfully with gui=F, which launches a headless GUI mode.
NLStart(nl.path,gui=F,nl.jarname = paste0("netlogo-",ver,".jar")) # open netlogo

7️⃣ If none of the above steps work in R/RStudio, you can run Netlogo from JGR, the Java version of R.

In R/RStudio, run the following:

install.packages('JGR',,'http://www.rforge.net/')  
library(JGR)  
JGR::JGR()# open JGR  

Then run the normal NLLoad() and NLStart() functions in JGR to launch Netlogo.

Attempted diagnostics:

25-9-18

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

2. Attempted with both NL v. 5.3.0 and 6.0.4

ver <-"6.0.4" # type in Netlogo version  
nl.path <- "/Users/malishev/Documents/Melbourne Uni/Programs/" ; nl.path # set path to Netlogo program location

nl.path <- paste0(nl.path,"NetLogo ",ver,"/"); nl.path # opt 1
nl.path <- paste0(nl.path,"NetLogo ",ver,"/Java/"); nl.path # opt 2 
nl.path <- paste0(nl.path,"NetLogo ",ver,"/Java"); nl.path # opt 3 

model.path <- paste0(wd,"/"); model.path # set path to Netlogo model  
nl.model <- "DEB_INF_IBM_almost_working2.nlogo" # name of Netlogo model
NLStart(nl.path,nl.jarname = paste0("netlogo-",ver,".jar")) # open netlogo

References

• Compiler toolchain for Mac OSX
• Diagnosing rjava error: link 1 and link 2
• Running RNetlogo in JGR
• 2018 Git post summarising current troubleshooting notes
• Java troubleshooting