Build Error: Java "unchecked conversion" error when building with gradle
I have checked out a clean copy of the GATK4 repository (commit #4233). Now I am trying to compile the framework on my machine, which runs Mac OS X 10.13.2.
I am in a conda environment which I created as described in the README.
Now, when running the command
./gradlew bundle I get the following error.
:createPythonPackageArchive UP-TO-DATE :compileJava /Users/ldam/gatk/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/inference/SimpleStrandSwitchVariantDetector.java:13: warning: [unchecked] unchecked conversion import org.broadinstitute.hellbender.tools.spark.sv.discovery.SvDiscoveryInputData; ^ required: List<String> found: List error: warnings found and -Werror specified 1 error 1 warning :compileJava FAILED FAILURE: Build failed with an exception. * What went wrong: Execution failed for task ':compileJava'. > Compilation failed; see the compiler error output for details. * Try: Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. BUILD FAILED Total time: 9.098 secs (gatk)
This is my Java version:
$ java -version java version "1.8.0_161" Java(TM) SE Runtime Environment (build 1.8.0_161-b12) Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
Is there anything I am missing in this build procedure? Any help is very much appreciated.