Error running MaxEnt from within 'biomod2' in R

Question

I am trying to fit some species distribution models using the biomod2 package in R.

I have compiled all of the required data such that biomod2 successfully fits models using all techniques except MaxEnt, which throws an error:

Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: running command 'java -mx512m -jar C:/Users/ajb273/inSync Share/PhD/Data/SDMs R/maxent.jar environmentallayers="Bushcrow/models/BushcrowFirstModeling/m_38411293/Back_swd.csv" samplesfile="Bushcrow/models/BushcrowFirstModeling/m_38411293/Sp_swd.csv" projectionlayers="Bushcrow/models/BushcrowFirstModeling/m_38411293/Predictions/Pred_swd.csv" outputdirectory="Bushcrow/models/BushcrowFirstModeling/Bushcrow_PA1_RUN10_MAXENT_outputs" outputformat=logistic  redoifexists visible=FALSE linear=TRUE quadratic=TRUE product=TRUE threshold=TRUE hinge=TRUE lq2lqptthreshold=80 l2lqthreshold=10 hingethreshold=15 beta_threshold=-1 beta_categorical=-1 beta_lqp=-1 beta_hinge=-1 defaultprevalence=0.5 autorun nowarnings notooltips noaddsamplestobackground' had status 1 
2: In file(file, "rt") :
   cannot open file 'Bushcrow/models/BushcrowFirstModeling/Bushcrow_PA1_RUN10_MAXENT_outputs/Bushcrow_PA1_RUN10_Pred_swd.csv': No such file or directory

I thought this might be because biomod2 wasn't managing to find MaxEnt or Java, but I have the rJava package loaded, and have tried running MaxEnt in the dismo package, in the same R session, and it runs fine.

Does anyone have any idea what might be going on?

Thanks, Andrew

Answer 1

I had a similar connection problem and finally managed to fix it thus:

Running biomod2 this is the result i was getting:

Model=MAXENT
    > MAXENT modeling...
        Creating Maxent Temp Proj Data...
 Getting predictions...Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file './BROWN.HARE/models/1703069163/BROWN.HARE_allData_RUN1_MAXENT_outputs/BROWN.HARE_allData_RUN1_Pred_swd.csv': No such file or directory

 Getting predictor contributions...Error in system(command = maxent.command, wait = TRUE, intern = TRUE) : 
  'java' not found

And so I looked to my folder pathways C:/A_R_ANALYSIS_ENGLAND And within that there was indeed the following

maxent.bat
maxent.jar

and also the folder containing Java with its 220mb application

..and then I checked and recoded all the references to folder pathways as stated in BIOMOD_ModelingOptions() to ensure all correct. However it still did not work.. until.. I came out of R, switched it all off, rebooted and then it did start working.

Answer 2

Just to let any users who are interested know, I finally solved this. It seems that MaxEnt in biomod2 will not accept spaces in the file path to the maxent.jar file, at least some of the time. I moved my files to a different directory without a space, and it now runs.