Build error: failed to create jvarkit.jar object

lindenb / jvarkit

Java utilities for Bioinformatics

https://jvarkit.readthedocs.io/

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Build error: failed to create jvarkit.jar object #238

Closed Gilquin closed 1 year ago

Gilquin commented 1 year ago

Subject of the issue

Error encountered during compilation when running:

./gradlew jvarkit

Your environment

version of jvarkit: https://github.com/lindenb/jvarkit/tree/3d336e522b2862e7f9490bbdfc80b219e68532e2

version of java:

$ java --version
openjdk 11.0.16 2022-07-19
OpenJDK Runtime Environment (build 11.0.16+8-post-Debian-1deb11u1)
OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Debian-1deb11u1, mixed mode, sharing)

the value of ${JAVA_HOME}: undefined.

which OS:

Distributor ID: Debian
Description:    Debian GNU/Linux 11 (bullseye)
Release:    11
Codename:   bullseye

Steps to reproduce

Follow the documentation steps.

Expected behaviour

The jvarkit.jar should be created without errors.

Actual behaviour

Build fails with error:

[ant:javac] ./jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/tbi2bed/VcfTbiToBed.java:216:
error: package com.github.lindenb.jvarkit.tools.vcfregulomedb does not exist

See corresponding scan for complete report and log.

lindenb commented 1 year ago

@Gilquin hi laurent.

It works on my machine using the branch 'dev' and a fresh install:

git clone -b dev "https://github.com/lindenb/jvarkit.git"

could you please try with this branch ?

Gilquin commented 1 year ago

Hello,

Unfortunately, I get two new errors this time:

[ant:javac] /home/lgilquin/softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/VcfSpringBeanVariantAnnotator.java:35: error: cannot access ApplicationContext
[ant:javac] import org.springframework.context.ApplicationContext;
[ant:javac]                                   ^
[ant:javac]   bad class file: /home/lgilquin/softwares/jvarkit/lib/org/springframework/spring-context/6.0.9/spring-context-6.0.9.jar(/org/springframework/context/ApplicationContext.class)
[ant:javac]     class file has wrong version 61.0, should be 55.0
[ant:javac]     Please remove or make sure it appears in the correct subdirectory of the classpath.
[ant:javac] /home/lgilquin/softwares/jvarkit/src/main/java/com/github/lindenb/jvarkit/variant/VcfSpringBeanVariantAnnotator.java:36: error: cannot access FileSystemXmlApplicationContext
[ant:javac] import org.springframework.context.support.FileSystemXmlApplicationContext;
[ant:javac]                                           ^
[ant:javac]   bad class file: /home/lgilquin/softwares/jvarkit/lib/org/springframework/spring-context/6.0.9/spring-context-6.0.9.jar(/org/springframework/context/support/FileSystemXmlApplicationContext.class)
[ant:javac]     class file has wrong version 61.0, should be 55.0
[ant:javac]     Please remove or make sure it appears in the correct subdirectory of the classpath.

Here is the new scan

EDIT: Doesn't Spring Framework 6 requires Java 17 or higher ?

lindenb commented 1 year ago

yes please, try with java 17:

https://stackoverflow.com/questions/74648576/spring-class-file-has-wrong-version-61-0-should-be-55-0

lindenb commented 1 year ago

BTW a pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .

Gilquin commented 1 year ago

BTW a pre-compiled jar is available at https://uncloud.univ-nantes.fr/index.php/s/4sL77oWR2BFzSBH .

Yes, I saw that option, thanks!

yes please, try with java 17:

https://stackoverflow.com/questions/74648576/spring-class-file-has-wrong-version-61-0-should-be-55-0

I will try with java 17 later on. I will close the issue.