Maxent X11 error using Biomod2 from Ubuntu server
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Dino B.
Jul 30, 2017, 7:41:27 AM7/30/17
to Maxent
I'm trying running Maxent from Biomod2 in an Ubuntu 14.04 server with RStudio remote access. This is the script:
> library (biomod2)
> library (raster)
> library (rJava)
> setwd("~/data/Maxent")
> ExplVar = stack("~/Climatecurrent/Tiff/bio_1",
"~/Climatecurrent/Tiff/bio_8",
"~/Climatecurrent/Tiff/bio_9",
"~/Climatecurrent/Tiff/bio_10",
"~/Climatecurrent/Tiff/bio_11",
"~/Climatecurrent/Tiff/bio_12",
"~/Climatecurrent/Tiff/bio_16",
"~/Climatecurrent/Tiff/bio_17",
"~/Climatecurrent/Tiff/bio_18",
"~/Climatecurrent/Tiff/bio_19")
> spLIST <- c("map6234",
"map19358",
"map42190",
"map5143",
"map41788",
"map41299",
"map42395",
"map41695",
"map16672",
"map41291",
"map29684",
"map41686",
"map899",
"map20025",
"map41661",
"map23062")
> for (i in 1:length(spLIST)){
> spFILEcal <- read.csv(paste("~/Occurrences 30 min", "/", spLIST[i],
> ".csv", sep=""),sep=",",dec=".",header=F)
> myRespName = "V3"
> myResp <- as.numeric(spFILEcal[, myRespName])
> myRespCoord = spFILEcal[c("V1","V2")]
> myBiomodDataTrial <- BIOMOD_FormatingData(resp.var = myResp,
expl.var = ExplVar,
resp.xy = myRespCoord,
resp.name = myRespName,
PA.nb.rep = 3,
PA.nb.absences = 10000,
PA.strategy = 'sre',
PA.sre.quant = 0.025,
PA.table = NULL,
na.rm = TRUE)
> myBiomodOption <- BIOMOD_ModelingOptions(MAXENT.Phillips = list(visible=F))
> myBiomodModelOutTrial <- BIOMOD_Modeling (myBiomodDataTrial, models = 'MAXENT.Phillips',
models.options = myBiomodOption, NbRunEval=3, DataSplit=80,
Prevalence=0.5,
VarImport=3,
models.eval.meth = c('TSS','ROC'),
SaveObj = TRUE,
rescal.all.models = TRUE,
do.full.models = FALSE,
modeling.id= paste(spLIST[i],"Trial",sep=""))
}
I made this script after this tutorial: https://r-forge.r-project.org/scm/viewvc.php/*checkout*/pkg/biomod2/inst/doc/Multi_species_computation.pdf?root=biomod
I keep getting this error:
> Model=MAXENT.Phillips Creating Maxent Temp Proj Data.. Running
> Maxent...
> Exception in thread "main" java.lang.InternalError: Can't
> connect to X11 window server using ':0' as the value of the DISPLAY
> variable. at sun.awt.X11GraphicsEnvironment.initDisplay(Native
> Method) at
> sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
> at
> sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:110)
> at java.security.AccessController.doPrivileged(Native Method) at
> sun.awt.X11GraphicsEnvironment.<clinit>(X11GraphicsEnvironment.java:74)
> at java.lang.Class.forName0(Native Method) at
> java.lang.Class.forName(Class.java:195) at
> java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:102)
> at
> java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:81)
> at sun.awt.X11.XToolkit.<clinit>(XToolkit.java:120) at
> java.lang.Class.forName0(Native Method) at
> java.lang.Class.forName(Class.java:195) at
> java.awt.Toolkit$2.run(Toolkit.java:869) at
> java.security.AccessController.doPrivileged(Native Method) at
> java.awt.Toolkit.getDefaultToolkit(Toolkit.java:861) at
> sun.swing.SwingUtilities2.getSystemMnemonicKeyMask(SwingUtilities2.java:1928)
> at
> javax.swing.plaf.basic.BasicLookAndFeel.initComponentDefaults(BasicLookAndFeel.java:752)
> at
> javax.swing.plaf.metal.MetalLookAndFeel.initComponentDefaults(MetalLookAndFeel.java:433)
> at
> javax.swing.plaf.basic.BasicLookAndFeel.getDefaults(BasicLookAndFeel.java:148)
> at
> javax.swing.plaf.metal.MetalLookAndFeel.getDefaults(MetalLookAndFeel.java:1588)
> at javax.swing.UIManager.setLookAndFeel(UIManager.java:536) at
> javax.swing.UIManager.setLookAndFeel(UIManager.java:576) at
> javax.swing.UIManager.initializeDefaultLAF(UIManager.java:1345) at
> javax.swing.UIManager.initialize(UIManager.java:1455) at
> javax.swing.UIManager.maybeInitialize(UIManager.java:1422) at
> javax.swing.UIManager.getUI(UIManager.java:1003) at
> javax.swing.JPanel.updateUI(JPanel.java:126) at
> javax.swing.JPanel.<init>(JPanel.java:86) at
> javax.swing.JPanel.<init>(JPanel.java:109) at
> javax.swing.JPanel.<init>(JPanel.java:117) at
> ptolemy.plot.PlotBox.<init>(PlotBox.java:245) at
> ptolemy.plot.Plot.<init>(Plot.java:214) at
> ptolemy.plot.MyPlot.<init>(MyPlot.java:22) at
> density.Runner.initPlots(Runner.java:2366) at
> density.Runner.writeCumulativeIndex(Runner.java:1832) at
> density.Runner.start(Runner.java:470) at
> density.MaxEnt.main(MaxEnt.java:36)
From what I could find on google and other questions (https://stackoverflow.com/questions/10165761/java-cant-connect-to-x11-window-server-using-localhost10-0-as-the-value-of-t), this problem seems to be caused by the remote access on the server, but I'm incapable of understanding why am I getting it on this specific case and how to fix it.
The point is: how can I stop maxent from calling X11? I can't install it on the server.
Rita Castilho
May 15, 2018, 7:07:29 PM5/15/18
to Maxent
Hi, Have you solved your problem? I have exactly the same one...
Thanks,
Rita
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