JAVA_HOME not defined but it is #236
Description
Verify
- if you cannot compile/install , read https://github.com/lindenb/jvarkit/wiki/Compilation before submitting a new issue
- the version of java
JAVA
Subject of the issue
Describe your issue here.
I downloaded the precompiled jar to use
Your environment
- version of jvarkit
e5a6a83 - version of java
java -version
openjdk version "17.0.7" 2023-04-18
OpenJDK Runtime Environment (build 17.0.7+7-Ubuntu-0ubuntu122.04.2)
OpenJDK 64-Bit Server VM (build 17.0.7+7-Ubuntu-0ubuntu122.04.2, mixed mode, sharing)
- the value of
${JAVA_HOME}
echo $JAVA_HOME
/usr/lib/jvm/java-17-openjdk-amd64
- which OS
Ubuntu 22.04.2 LTS
Steps to reproduce
when I launch a command, I get
[WARN][OpenJdkCompiler]JAVA_HOME is not defined
[WARN][OpenJdkCompiler]JAVA_HOME is not defined
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by htsjdk.samtools.util.CloserUtil (file:/home/alessandro/Documents/MAexperiment/GATK/JVARKIT/jvarkit.jar) to method com.sun.xml.internal.stream.XMLEventReaderImpl.close()
WARNING: Please consider reporting this to the maintainers of htsjdk.samtools.util.CloserUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
However, it completes anyway. I suspect there might be an issue of dependency? Since by default, Ubuntu install Java 11 and you have compiled your jar with Java 17.
Hope this helps (it's not really an issue for me at the moment because the command worked anyway).