rJava throws OutOfMemoryError

Question

I am building a large species distribution model using the package "dismo" in the latest version of r. When I go to process the basic model using the code:

me <- maxent(x=train, p=p)

I get the following error:

> Error in .jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout,
> :    java.lang.OutOfMemoryError: unable to create new native thread

There is some discussion in stackoverflow and the internet about this error but none seem to address how to resolve the issue in the r code. Any input on this issue would be appreciated.

I don't know about r and rjava, so I'm not sure how tje JVM is beiong run, but it must be if Java is running. The JVM can take parameters telling it how much memory to use. So, that may be a clue for you to look. — Darius X.
– Darius X., Commented Mar 14, 2013 at 2:39
I had similar errors and I had to increase allocated memory using > options(java.parameters = "-Xmx200m") — Farhan Ahmed
– Farhan Ahmed, Commented Apr 20, 2013 at 0:48
Worth noting that for the increase in memory to be effective it has to be done before the JVM in enabled: bramschoenmakers.nl/en/node/726 — Ben
– Ben, Commented Apr 24, 2013 at 4:05

I Del Toro · Accepted Answer · 2013-07-11 00:08:23Z

from the dismo package: If you want to give MaxEnt (the Java virtual machine that runs it) more memory, you can do that by running something like this (for 1 GB) before you load the dismo library.

options(java.parameters = "-Xmx1g" )

Some people have reported problems when using this function on a Mac (Apple) computer. Specifically, the following error message occurs:

Error in .jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout, : java.lang.InternalError: Can’t start the AWT because
Java was started on the first thread. Make sure StartOnFirstThread is not specified in your application’s Info.plist or on the command line.

This is a known problem with certain Java applications on Macs. There are two work-arounds that we are aware of:

1) run Sys.setenv(NOAWT=TRUE) before running library rJava (this is what dismo does if rJava is not loaded). 2) use the JGR interface (a Java based R GUI). You can install JGR from here:

Collectives™ on Stack Overflow

rJava throws OutOfMemoryError

1 Answer 1

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

Comments

Your Answer

Sign up or log in

Post as a guest

Related