Rjava-dependent package installation Segmentation error (kernel flushing)

Question

I am trying to reinstall a package that I could previously install and use. I created my own package after the computer unexpectedly restarted, and then I had problems downloading the rpgraph package. So I decided to uninstall it and reinstall. When I did this, I got the following error:

library(devtools) library(rJava) install_github("Albluca/rpgraph") Downloading GitHub repo Albluca/ rpgraph@master from URL https://api.github.com/repos/Albluca/rpgraph/zipball/master Installing rpgraph Running command /usr/lib/R/bin/R Arguments: CMD INSTALL /tmp/Rtmp5OrtLL/devtools505a703b3ccd/Albluca-rpgraph-de04f96 --library=/home/gonzalo/R/x86_64-pc-linux-gnu-library/3.4 --install-tests installing source package 'rpgraph' ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Segmentation fault (core dumped) ERROR: loading failed removing '/home/gonzalo/R/x86_64-pc-linux-gnu-library/3.4/rpgraph' Installation failed: run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout), stderr_line_callback = real_callback(stderr), stdout_callback = real_block_callback, stderr_callback = real_block_callback, echo_cmd = echo, echo = show, spinner = spinner, error_on_status = fail_on_status, timeout = timeout) : System command error` 

I tried reinstalling JAva and cran from scratch, but for some reason there is something in my system that avoids installing the package. In addition, since the error is not very informative, I have no idea how to narrow down where the problem is.

Thanks for any help you can provide.

Answer 1

I encountered the same problem when installing the vanneuler and wordnet libraries and solved the problem using the solution proposed by Kenneth. In my case, the -Xss2560k option was enough to solve:

export _JAVA_OPTIONS="-Xss2560k"

In addition: instead of running the export command from the terminal, the java parameter can be set directly from the R session using the following command:

options(java.parameters = "-Xss2560k")

Answer 2

This seems to be a bug in recent kernel versions, the same problem occurs with other R-libraries that include Java, as well as other software.

See https://lists.ubuntu.com/archives/ubuntu-devel-discuss/2017-June/017507.html and https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1698919 .

This workaround does the trick for me:

 export _JAVA_OPTIONS="-Xss2560k -Xmx2g"