Problems with execution (Java 11, solved using miniconda)

[evatosco]

Hello there!

I am trying to use VarNote and assess its functions, but I couldn't run it locally. My errors were these (using OpenJDK Runtime Environment (build 11.0.9.1+1-Ubuntu-0ubuntu1.20.04):

$ java -jar VarNote.jar
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
Exception in thread "main" java.lang.ExceptionInInitializerError
    at org.mulinlab.varnote.cmdline.VarNoteCommandLine.processAllCommandLinePrograms(VarNoteCommandLine.java:102)
    at org.mulinlab.varnote.cmdline.VarNoteCommandLine.extractCommandLineProgram(VarNoteCommandLine.java:59)
    at org.mulinlab.varnote.cmdline.VarNoteCommandLine.instanceMain(VarNoteCommandLine.java:44)
    at org.mulinlab.varnote.cmdline.VarNoteCommandLine.main(VarNoteCommandLine.java:40)
Caused by: java.lang.UnsupportedOperationException: No class provided, and an appropriate one cannot be found.
    at org.apache.logging.log4j.LogManager.callerClass(LogManager.java:555)
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:580)
    at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:567)
    at org.broadinstitute.barclay.argparser.ClassFinder.<clinit>(ClassFinder.java:29)
    ... 4 more

I've read here that Java Runtime Environment (JRE) version 8.0 or above is required for VarNote. So I tried to execute it with OpenJDK 8.0 using a conda environment. It seems like it works since it shows the Program Summary Table.

I've looked for the java error online and I found out here that it's probably because the jar file is trying to use a java class that was removed in java 9. I have no idea about programming, even less about java, but I just wanted to point this out just in case someone is having the exact same problem.

Happy Holidays everyone! Best wishes!

[mulinlab]

Hi, sorry for the late response, we will refactor the code to fix the Java version issue. Thanks.

[mulinlab]

The issue has been fixed in VarNote 1.2.0.