Ask questionsFiji crashes on startup after update with some kind of "Access Denied" error

Hi all,

as discussed with @ndefrancesco on Fiji starts now with a black console window showing an error message. Some installations also freeze at that point: image

The error number "5" often stands for "Access denied" and Nicos suggestion of running Fiji with administrator priviledges would solve this issue confirm that. However, in the light of recent events to the server where the update sites are hosted, I would prefer running Fiji without administrator preiviledges.

  1. Does anyone know what Fiji is trying to change at the System configuration?

  2. Can we undo the rollout of this exe file and stick to the old one until the issue is solved?


Cheers, Robert


Answer questions refack

3. The fact that Fiji hangs at startup on some systems with the new launcher, but not with the old launcher, is a critical new bug, which we still don't understand. @haesleinhuepf On your affected system, please rename ImageJ-win64.exe to debug.exe and run it, to see what's happening in more detail. If there's nothing helpful there, you can then generate a thread dump (ctrl+pause) to see if things are deadlocked on the Java side. Please paste any interesting findings here on this issue.

I'm seeing the above mentioned quick crash issue after updating just now (running on Windows 10 64bit Insider build 20185). Following is the console output after renaming to debug.exe:

Detected Fiji
Using JRE from ImageJ.cfg: D:\bin\tools\fiji/jre
Found Java options in ImageJ.cfg: '-Xmx7560m -cp ij.jar'
JRE not found in 'D:\bin\tools\fiji/jre'
JAVA_HOME contains a JRE: 'D:\bin\tools\fiji/java/win64/jdk1.8.0_172//jre'
java -Xmx7560m -Dpython.cachedir.skip=true -Dplugins.dir=D:\\bin\\tools\\fiji -Xincgc -XX:PermSize=128m -Djava.class.path=D:\\bin\\tools\\fiji/jars/imagej-launcher-5.0.3.jar -Dimagej.dir=D:\\bin\\tools\\fiji -Dij.dir=D:\\bin\\tools\\fiji -Dfiji.dir=D:\\bin\\tools\\fiji -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=D:\\bin\\tools\\fiji\\debug.exe -Dij.executable=D:\\bin\\tools\\fiji\\debug.exe -Djava.library.path=D:\\bin\\tools\\fiji/lib/win64;D:\\bin\\tools\\fiji/mm/win64 -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath D:\\bin\\tools\\fiji/jars/ij-1.53c.jar fiji.Main -port7
Using JAVA_HOME D:\bin\tools\fiji/java/win64/jdk1.8.0_172//jre
Opening Java library D:\bin\tools\fiji/java/win64/jdk1.8.0_172//jre/bin/server/jvm.dll
Java HotSpot(TM) 64-Bit Server VM warning: ignoring option PermSize=128m; support was removed in 8.0
Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
Adding option: -Djava.home=D:\bin\tools\fiji/java/win64/jdk1.8.0_172/
Launching main class fiji.Main with parameters [-port7]
Class loader = sun.misc.Launcher$AppClassLoader@c387f44
java.lang.ClassNotFoundException: fiji.Main
        at java.lang.ClassLoader.loadClass(
        at sun.misc.Launcher$AppClassLoader.loadClass(
        at java.lang.ClassLoader.loadClass(
        at net.imagej.launcher.ClassLauncher.launch(
        at net.imagej.launcher.ClassLauncher.main(
        at net.imagej.launcher.ClassLauncher.launch(
        at net.imagej.launcher.ClassLauncher.main(

P.S. Invoking the SNAPHOST launcher mentioned above gets the app to start.


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Refael Ackermann (רפאל פלחי) refack Cambridge, MA FOSS worker bee Invested in the success of Node.js Proud adopted father of GYP3
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