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