Java woes...

[cvisintin]

boab/Dockerfile

Line 51 in 7baf111

openjdk-8-jdk \

This is installing multiple versions of JRE - 8 & 11. We need to force only the single version to install or somehow set the version to use to 8

[cvisintin]

We could try adding:
alternatives --set java /usr/lib/jvm/java-8-openjdk-amd64/jre

I don't think setting of JAVA_HOME is persisting through into the container

[jdyen]

This can be solved within an R session by updating the LD_LIBRARY_PATH with Sys.setenv(). This seems less than ideal, but I assume there's a way to add java-8 to the path more generally without breaking anything?

[cvisintin]

Can the LD_LIBRARY_PATH be set outside of a session? I think that is where we are running into trouble...

[jdyen]

It probably can be set globally but possibly shouldn't. Beyond me at this stage, but I'll do some googling.

[goldingn]

I would try setting LD_LIBRARY_PATH a .Rprofile file in the user's R home directory. The following R code will do that (R's R.home() function is needed to find the appropriate directory).

rprofile <- file.path(R.home(), ".Rprofile")
file.create(rprofile)
cat('Sys.setenv(LD_LIBRARY_PATH = <blahblahblah>)', file = rprofile)

Maybe it's worth wrapping this and other R things like #3 up in an R setup script to run in the dockerfile?

[goldingn]

I this this Rprofile approach means the environment variable is only set for R, not for other programs that might want to use java

[jdyen]

I've tried some variants of this, setting LD_LIBRARY_PATH and JAVA_HOME. It seems to break the rJava installation then, so it won't even install RNetLogo.

[jdyen]

I'm not sure this is the best route to go down. Why do we need Java 8? I suggest focusing on the NetLogo issue because everything else works: #4