hail.java.FatalError: NoSuchMethodError: breeze.linalg.DenseVector$.canSetD()Lbreeze/generic/UFunc$InPlaceImpl2

Those two tests are failing because you don’t have the R and Plink test dependencies installed and on your path. See Running the Tests at bottom of Getting Started.

Do you get your original error if you increase the Java stack size as described here?

Do you get your original error using Spark 2.02?