R studio terminates after loading rjava for shiny app

chengyineng · June 27, 2018, 2:58pm

My R studio terminates when I try to run r library(RJDBC), which requires r library(rJava) on shiny app locally. I couldn't open my shiny app at all. I couldn't see the error message at all (if any) since the termination window blocks the view.

My R studio version is 1.1.453; R version is 3.5.0; java version is 10.0.1.

I have been stuck with this problem for a couple of weeks and am not familiar with Java language. Greatly appreciate any pointers. Thank you!

josh · June 27, 2018, 3:08pm

What version of rJava are you using?

It looks like there were fixes to support Java 10.

github.com/s-u/rJava

JAVAH is incorrectly required for JDK 10+

opened 12:29PM - 22 Apr 18 UTC

closed 04:58AM - 23 Apr 18 UTC

JuhaszIstvan

Hello, the installation of the current version of rJava dies because the l…ack of JAVAH definition in the envornment variables when the java vendor is openJDK (1.8 and 11) Background: Curiously, you have implemented workarounds that handle this issue: https://github.com/s-u/rJava/commit/7558bfd61aacd03329991ced356fc452258f5807 But it still failes on opensuse/openjdk-18 and 11 : ``` interpreter : '/usr/bin/java' archiver : '/usr/bin/jar' compiler : '/usr/bin/javac' header prep.: '' cpp flags : '-I/usr/lib64/jvm/java-11-openjdk-11/include' java libs : '-L/usr/lib64/jvm/java-11-openjdk-11/lib/server -ljvm' configure: error: One or more Java configuration variables are not set. Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. ``` I apologise for opening a separate ticket for every facet of this issue, I believe in being specific.

chengyineng · June 27, 2018, 5:06pm

I am using rJava_0.9-10. I just removed my JAVAH path in terminal and did R CMD javareconf, but that didn't do the trick. When I use rJava outside shiny app, it runs just fine. (as in running library(rJava) doesn't produce any errors). But when I start using shiny server, it terminates. Not sure what else I should do.