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NicoKiaru / ABBA-Python

How to use Aligning Big Brains and Atlases with Python
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Rat atlas fails (win installer) #12

Closed NicoKiaru closed 1 year ago

NicoKiaru commented 1 year ago

Windows installer

java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw error
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at ch.epfl.biop.atlas.scijava.AtlasChooserCommand.run(AtlasChooserCommand.java:72)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: java.lang.RuntimeException: Module threw error
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:130)
    ... 6 more
Caused by: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBContext
    at ch.epfl.biop.atlas.rat.waxholm.spraguedawley.v4.WaxholmSpragueDawleyRatV4Ontology.initialize(WaxholmSpragueDawleyRatV4Ontology.java:59)
    at ch.epfl.biop.atlas.rat.waxholm.spraguedawley.v4p1.WaxholmSpragueDawleyRatV4p1Atlas.initialize(WaxholmSpragueDawleyRatV4p1Atlas.java:54)
    at ch.epfl.biop.atlas.rat.waxholm.spraguedawley.v4p1.command.WaxholmSpragueDawleyRatV4p1Command.run(WaxholmSpragueDawleyRatV4p1Command.java:70)
    at org.scijava.command.CommandModule.run(CommandModule.java:196)
    at org.scijava.module.ModuleRunner.run(ModuleRunner.java:163)
    at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124)
    ... 6 more
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBContext
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522)
    ... 12 more
NicoKiaru commented 1 year ago

Solved by using jdk 8 instead of jdk 11. So long for the potential perf improvements.