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Build Error: Java "unchecked conversion" error when building with gradle

Dear community,

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.

Laurens

Answers

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