DeveloperDoc UserDoc bug
I was unable to successfully follow the R setup instructions required to run integration tests locally. I don't know whether this is a general concern regarding initial setup on Mac OS X High Sierra 10.13.6, or the problem is specific to my system.
brew install R would install R with all necessary core functionality.
brew install R installed a version of R without X11 support. The binary I downloaded from CRAN had the proper support.
sudo Rscript scripts/docker/gatkbase/install_R_packages.R would install the necessary packages for R scripts needed.
Actual: Failure to compile source packages, with an error like
clang: error: unsupported option '-fopenmp'. I made some attempts to update my local
clang but was unsuccessful. Instead, I installed the packages at the R prompt:
$ R > install.packages('ggplot2') > install.packages('reshape') > install.packages('gplots') > install.packages('gridExtra') > install.packages('gsalib') > install.packages('data.table') > quit()
After doing so, my test run
TEST_TYPE=integration ./gradlew shadowJar test succeeded.