This message means that for some reason the garbage collector is taking an excessive amount of time (by default 98% of all CPU time of the process) and recovers very little memory in each run (by default 2% of the heap).

This effectively means that your program stops doing any progress and is busy running only the garbage collection at all time.

To prevent your application from soaking up CPU time without getting anything done, the JVM throws this Error so that you have a chance of diagnosing the problem.

The rare cases where I've seen this happen is where some code was creating tons of temporary objects and tons of weakly-referenced objects in an already very memory-constrained environment.

Check out the Java GC tuning guide, which is available for various Java versions and contains sections about this specific problem:

You need to modify the java parameters with the following function at the start of your script.

You may also need restart your environment first.

The Xmx flag controls the size of the Java runtime heap. You can increase this to a larger value which may allow your R code to run without hitting the ceiling:

Note that this should increase the heap only for the Java process called by your R script. Outside R, whatever heap size was being used by your Java should remain the same. You could also change it externally if you wanted to.

I know about Xmx but did not know how to do this from within the R console. For that, I found this useful blog post:

http://www.bramschoenmakers.nl/en/node/726

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