Error: Loading openVA using R and RScript

[rrwen]

When I load openVA using R in a command line terminal, the R session is immediately killed.

Working Example (Expected Behaviour)

This will work in RStudio without any problems, loading the openVA package.

library(openVA)

Not Working Example (Unexpected Behaviour)

However, in a terminal, this will not work:

R -e "library(openVA)"

Neither will this (assuming the contents of run.R only has library(openVA) on the first line:

RScript run.R

In all cases above, a message stating killed R will occur immediately.

Suspicion

It seems like InSilicoVA is the culprit, as the following does work:

R -e "library(InterVA4)"
R -e "library(InterVA5)"
R -e "library(Tariff)"

But this does not:

R -e "library(InSilicoVA)"

Use Case

I am hoping to run scheduled CRON jobs to code VA records in a scheduled manner - thus needing to run openVA via the Rscript or R commands in the terminal.

System Specs

• Mac OS Ventura 13.4.1 (c)
• Apple M1
• 16 GB RAM
• 256GB SSD
• R v4.3.1
  • openVA 1.1.1
    • InSilicova v1.4.0
    • InterVA4 v1.7.6
    • InterVA5 v1.1.3
    • Tariff v1.0.5
    • nbc4va (not installed)

[richardli]

All the commands work for me on both an M1 and M2 mac that I have, with R 4.2.1 and 4.3.0. So I cannot reproduce the error.

If the issue is with InSilicoVA, maybe check if you can run R -e "library(rJava)" in case the issue you experience is with rJava package. Otherwise it might be a issue with your system setup.

[rrwen]

Thanks for looking into this!

Looks like R -e "library(rJava)" does produce the same error Killed: 9 - maybe it is my Java version or the way I installed Java.

Do you remember which version of java you have and how you installed it? I usually use brew to install on Mac

[richardli]

I have the following:

% java -version
java version "17.0.2" 2022-01-18 LTS
Java(TM) SE Runtime Environment (build 17.0.2+8-LTS-86)
Java HotSpot(TM) 64-Bit Server VM (build 17.0.2+8-LTS-86, mixed mode, sharing)

Setting up R with Java sometimes require a bit of manual fiddling with the system set up. I don't think I did anything more complicated than R CMD javareconf on the fresh mac...but I would probably go try if someone has the same issue in the rJava package's github repo...

[rrwen]

Update - I have a different java version installed with Homebrew:

% java --version
openjdk 20.0.1 2023-04-18
OpenJDK Runtime Environment Homebrew (build 20.0.1)
OpenJDK 64-Bit Server VM Homebrew (build 20.0.1, mixed mode, sharing)

I will try a different version of java and see if this still occurs.

[rrwen]

I retried with OpenJDK 17 install using Homebrew (brew install openjdk@17 and ran R CMD javareconf), but the error still occurs - so it looks like it may not be a version issue

I will look into the rJava package's repo for more clues