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ClearVolume / imglib2-clearvolume

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java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT #16

Closed haesleinhuepf closed 5 years ago

haesleinhuepf commented 5 years ago

Hey guys,

I just wanted to check if the current build works inside Fiji, before we update the update site. However, when trying to open T1-head.tif in ClearVolume, this error message comes up. I just downloaded the recent master branch (2019-03-25), and used mvn install to install it to my Fiji.

Do I have to install some additional Jogamp dependency manually?

Cheers, Robert

(Fiji Is Just) ImageJ 2.0.0-rc-71/1.52i; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 61MB of 12101MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748) Caused by: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:299) ... 5 more Caused by: java.lang.NoClassDefFoundError: com/jogamp/newt/awt/NewtCanvasAWT at de.mpicbg.jug.plugins.ClearVolumePlugin.run(ClearVolumePlugin.java:90) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.lang.ClassNotFoundException: com.jogamp.newt.awt.NewtCanvasAWT at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 10 more

imagejan commented 5 years ago

When running Plugins > Utilities > Find Jar For Class, I get:

The class com.jogamp.newt.awt.NewtCanvasAWT is contained in /[...]/Fiji.app/jars/jogl-all-2.3.2.jar

... and jogl-all-2.3.2.jar seems to be shipped by the Java-8 update site. Is there any third-party update site introducing version skew for you?

skalarproduktraum commented 5 years ago

Hi guys,

the same problem occurs with scenery and the reason is the installer plugin's inability to figure out natives. CV does not have too many dependencies, and we copied them manually to fix this. In sciview, this is done by a script.

As this has nothing to do with imglib2-clearvolume, I'll close this for now.

Edit: @imagejan jogl 2.3.2 is also the most recent version, as development seems to have halted.