Can't produce model with Maxent

[Yo Pinto]

Hello,I'm trying to produce a species model distribution of Tamandua tetradactyla with 300 localities and following the step-by-step of the Wallace vignette tutorial (https://wallaceecomod.github.io/vignettes/wallace_vignette.html). For some reazon when I run de model in Maxent using the feature clases L, LQ and H just as the tutorial says, the program turns all grey and stops working just when it is running the H1, as you can see in the picture. 

Is the first time it happens to me and I already had made other models with Wallace with out any problem. Does somebody knows what to do? 

[Gonzalo Pinilla-Buitrago]

Hi Yo Pinto,

I think that your issue is related to a bug on the maxnet package (this always happens randomly with the hinge class). Although, I'm not completely sure without seeing the error msg that you got in your r console. The workaround of this problem is using the maxent.jar option instead of maxnet. Keep in mind that you need to place the maxent.jar file in a specific place in your machine. This link is a good resource if you need help (https://github.com/wallaceEcoMod/wallace/tree/master#how-to-run-maxent-with-maxentjar).

Please let me know if the solution works for you.

Best,

Gonzalo 

[Sebastià JR]

Hello, 

I have the same problem, when running the model, after H1 it turns grey and this message error appears in R:

Warning: from glmnet Fortran code (error code -186); Convergence for 186th lambda value not reached after maxit=100000 iterations; solutions for larger lambdas returned

Warning: Error in intI: index larger than maximal 185

  104: stop

  103: intI

  102: subCsp_cols

  101: [

   96: [

   94: maxnet::maxnet

   93: modelTune.maxnet

   92: tuning

   91: ENMeval::ENMevaluate

   90: <reactive> [modules/mod_c6_maxent.R#94]

   74: mod.maxent

   73: observeEventHandler [/Library/Frameworks/R.framework/Versions/3.6/Resources/library/wallace/shiny/server.R#519]

    2: shiny::runApp

    1: run_wallace

I tried to reload the Wallace package but it keeps happening, 

Thank you, 

Sebastià

[Gonzalo Pinilla-Buitrago]

> Is the first time it happens to me and I already had made other models with Wallace with out any problem. Does somebody knows what to do? 

Hi Sebastià,

Did you try the workaround of using the maxent.jar option? Right now, it is the only way to get your models when maxnet has problems with the hinge class.

Please, let me know if this works for you.

Best,
Gonzalo

[Sebastià JR]

Hello,

When running the maxent.jar option this error appears in R:

> library(wallace)

> run_wallace()

Listening on http://127.0.0.1:5177

Loading required package: rJava

Warning in fun(libname, pkgname) :

  Cannot find JVM library '/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/server/libjvm.dylib'

Install Java and/or check JAVA_HOME (if in doubt, do NOT set it, it will be detected)

Error: package or namespace load failed for ‘rJava’:

 .onLoad failed in loadNamespace() for 'rJava', details:

  call: fun(libname, pkgname)

  error: JVM could not be found

I have the rJava package installed, but i do not know how to fix the problem. 

Best, 

Sebastià 

[Gonzalo Pinilla-Buitrago]

Hi Sebastià,

Unfortunately, you got a common and annoying problem for running maxent.jar on R. I think it is a problem between the Java version and the Mac OS version that you are using (although it looks like there are some issues of loading rJava on R v4). Which versions of these are you using (R, Java, MacOS)?

Maybe this link could be helpful (https://github.com/wallaceEcoMod/wallace/tree/master#rjava-and-java-versions-just-for-maxentjar-option).

Best,

Gonzalo 

[Sebastià JR]

Okey, I will take a look at the link, the versions I am using are: MacOs Mojave 10.14.6, R 4.0.0 GUI 1.71 and Java 8. May the problem disappear if I update to MacOs Catalina? i see the R 4.0 version is optimized for that MacOs version.

Thank you, 

Sebastià

[Gonzalo Pinilla-Buitrago]

Hi Sebastià,

Unfortunately, I can not help you too much with specific problems because I am not a mac user. The error that you got is similar to the report StackOverflow post, so maybe you just need to link your libjvm.dylib to /usr/local/lib.

Let me know if this works for you.

Best,

Gonzalo

[Jamie M. Kass]

As a Mac user, and frequent sufferer of rJava problems, I can tell you what works for me. Uninstall the current version of Java you have (check stackOverflow for the procedure). Download the latest Java version and JDK, making sure it matches your processor (32 or 64 bit). Reinstall rJava. It should load up now, and you should be able to use dismo::maxent().

Jamie

[Sebastià JR]

Hello, 

I think i finally fix that following your and other similar advises, but now another error appears... When trying to run Wallace with maxent.jar appears:

Warning: Error in rJava::.jnew: java.lang.ClassNotFoundException

  95: <Anonymous>

I am trying to find a solution... 

Thank you for your help even when it is not a "wallace problem" but mine i suppose.

Sebastià

[Gonzalo Pinilla-Buitrago]

Hi Sebastià,

Let us know if you are getting the same problem again. We will do our best to help you.

Thanks for using Wallace and for reporting this issue.

Best,

Gonzalo

[Dimitris Poursanidis]

What if downgrate R and use the previou one?

Have you try it?

[Jamie M. Kass]

I know it's been a long time since this post, but I'd like to emphasize that for those with Java problems, the other solution would be to just use maxnet instead, which does not rely on Java.

Jamie