README: R setup for running tests may need OS X update
open | Created 2018-11-02 | Last updated 2018-11-02| Posted by jmthibault79 | See in Github

DeveloperDoc UserDoc bug

Documentation request


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.

R installation itself

Expected: brew install R would install R with all necessary core functionality.
Actual: brew install R installed a version of R without X11 support. The binary I downloaded from CRAN had the proper support.

R package installation

Expected 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.

Return to top