Running gradlew on sortsamrefname returns zip END header not found errors

Verify

if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue Followed http://lindenb.github.io/jvarkit/SortSamRefName.html
the version of java 11.0.3

Subject of the issue

Running gradlew on sortsamrefname returns zip END header not found errors

Your environment

version of jvarkit: Commit hash: bc9dafd6f630b8895f4fb8a860edf138347a8451

version of java

$ java -version
java version "11.0.3" 2019-04-16 LTS
Java(TM) SE Runtime Environment 18.9 (build 11.0.3+12-LTS)
Java HotSpot(TM) 64-Bit Server VM 18.9 (build 11.0.3+12-LTS, mixed mode)

the value of ${JAVA_HOME}

$ echo ${JAVA_HOME}
/Library/Java/JavaVirtualMachines/jdk-11.0.3.jdk/Contents/Home

which OS

$ sw_vers
ProductName:    Mac OS X
ProductVersion: 10.14.5
BuildVersion:   18F132

Steps to reproduce

Following: http://lindenb.github.io/jvarkit/SortSamRefName.html

Run:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew sortsamrefname

Expected behaviour

java compiled executables should appear in dist

Actual behaviour

gradle fails with the following output

$ ./gradlew sortsamrefname                        
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/org/tukaani/xz/1.5/xz-1.5.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar; zip END header not found
[ant:javac] error: error reading /Users/<username>/git/<foldername>/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar; zip END header not found
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8

> Task :sortsamrefname FAILED
Downloading http://central.maven.org/maven2/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar to /Users/<username>/git/<foldername>/jvarkit/lib/com/github/samtools/htsjdk/2.19.0/htsjdk-2.19.0.jar
Downloading http://central.maven.org/maven2/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar to /Users/<username>/git/<foldername>/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar
Downloading http://central.maven.org/maven2/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar to /Users/<username>/git/<foldername>/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar
Downloading http://central.maven.org/maven2/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar to /Users/<username>/git/<foldername>/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar
Downloading http://central.maven.org/maven2/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar to /Users/<username>/git/<foldername>/jvarkit/lib/org/apache/commons/commons-compress/1.4.1/commons-compress-1.4.1.jar
Downloading http://central.maven.org/maven2/org/tukaani/xz/1.5/xz-1.5.jar to /Users/<username>/git/<foldername>/jvarkit/lib/org/tukaani/xz/1.5/xz-1.5.jar
Downloading http://central.maven.org/maven2/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar to /Users/<username>/git/<foldername>/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.4/snappy-java-1.1.4.jar
Downloading http://central.maven.org/maven2/com/beust/jcommander/1.72/jcommander-1.72.jar to /Users/<username>/git/<foldername>/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar
Downloading http://central.maven.org/maven2/org/testng/testng/6.14.3/testng-6.14.3.jar to /Users/<username>/git/<foldername>/jvarkit/lib/org/testng/testng/6.14.3/testng-6.14.3.jar

FAILURE: Build failed with an exception.

* Where:
Build file '/Users/<username>/git/<foldername>/jvarkit/build.gradle' line: 599

* What went wrong:
Execution failed for sortsamrefname com.github.lindenb.jvarkit.tools.misc.SortSamRefName.
> Compile 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. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 1s
1 actionable task: 1 executed

lindenb / jvarkit