Fiji won't run even after a clean installation - ImageJ does though

I had my FIJI working fine until I installed MosaicSuite for FIJI - unfortunately I didn’t know about the issue with TrackMate before it was too late. I deleted the whole folder, downloaded the latest FIJI version, and unzipped it, but alas, no success in making FIJI working - I get the logo, and that’s all. I’ve done this process quite a few times, re-starting the computer and everything I could come up with, but to no avail.
I installed ImageJ, though, and it worked without any problem. I have no idea what is going on here. If anyone could help me with this situation, I’d appreciate it a lot!
Here’s the debug.exe log:

http://pastebin.com/da8sULd8

I’m running it on Windows 7 64x.
Thanks,
Rodrigo

This actually sounds like you’re being hit by a bug, described here, with the single instance listener function. I posted instructions in that bug report on how to find your temp directory and the offending file. If that is the problem, deleting the file should be sufficient to fix your installation.

If the file isn’t there, or deleting it doesn’t fix things for you, please let us know right away.

2 Likes

@hinerm How hard do you think it would be to add debug messages describing what is happening with respect to the single instance listener?

1 Like

Cool! It’s fixed!
Interesting. As you wrote in the instructions, it’s a bit annoying, this bug. I wouldn’t even dream on looking at anything about single instance listener!

Thank you for the help!

I actually ran into this today as well, when I went to test Fiji on a windows partition. Everything was working, then I decided to update and after that it didn’t start. Mark’s solution fixed it.

I know :cry: I’m very sorry for the inconvenience. If you happen to run into the problem again please let me know. I am still not sure how to reproduce the scenario where these files aren’t being cleaned up.

@ctrueden and I made the code a bit more robust, and provide better feedback

1 Like

Maybe we need to go back to calling System.exit

I would state it more strongly: we pushed a fix which I believe is highly likely to avoid this problem in the future.

1 Like

FYI, I was able to reproduce this with an up-to-date version of Fiji (specifically, imagej-legacy-0.19.0) on Windows 7 by running ImageJ-win64.exe (from the same folder or a different one) while Fiji/ImageJ is already running. The second instance shows the splash screen forever and doesn’t quit. Consequently, the .stub file is still locked even when the first Fiji instance is quit.

To be honest, I don’t quite understand how the single instance listener works and when that behavior was changed. IIRC, previously it was possible to start up two instances when running two distinct ImageJ-win64.exe, while the single instance listener was kicking in only when the same file (from the same folder) was started twice.

In Fiji, the single instance listener was unsupported until Johannes provided a new implementation in June 2015. The behavior was to trigger the single instance listener if ImageJ is launched from the same screen of the same display as a previous instance.

I can’t say I completely understand how the listener works, but in my digging I didn’t find any logic that checks executable of origin. I think the “screen” check could approximate that behavior. I found this logic to create unintuitive behavior (I started an ImageJ from the file browser, and then could not connect to it from the command line) and so removed the “screen” constraint.

I can see how when having multiple Fiji installations, e.g. with different update sites enabled or for different Java versions, it is reasonable to expect them to ignore each others’ running instances. But checking the display window is a fairly dirty and inaccurate way to provide that behavior. I think we just want to put something like a hash of the java classpath into the stub file. Does that sound reasonable?

Anyway I’ll do some tests in Windows and see if I can get a fix for the locking. Thanks, as always, for the report!

1 Like

Thanks again for this. I finally realized how dumb it is for the second instance to ever try and delete the stub file. I fixed this and am currently working on a release + upload

1 Like

Uploaded. @imagejan would you do me a huge favor and try to break the single instance listener again? :smile:

Hm, doesn’t seem to be fixed yet. I tested with two installations on Java 8, both updated to have imagej-legacy-0.19.1.jar from the Java-8 update site.

Below is the output of ImageJ-win64.exe --debug, if that helps:

[DEBUG] - class='org.scijava.plugins.scripting.java.MainJavaRunner', priority=-1
00.0, enabled=true, pluginType=JavaRunner
[DEBUG] - class='org.scijava.ui.dnd.FileDragAndDropHandler', priority=-100.0, en
abled=true, pluginType=DragAndDropHandler
[DEBUG] - class='io.scif.formats.qt.LegacyQTFormat', name='QuickTime', priority=
-100.0, enabled=true, pluginType=Format
[DEBUG] - class='org.scijava.app.SciJavaApp', name='SciJava', priority=-100.0, e
nabled=true, pluginType=App
[DEBUG] - class='io.scif.formats.JPEGTileFormat', name='Tile JPEG', priority=-10
0.0, enabled=true, pluginType=Format
[DEBUG] - class='org.scijava.ui.awt.AWTUI', name='awt', priority=-100.0, enabled
=true, pluginType=UserInterface
[DEBUG] - class='org.scijava.ui.swing.mdi.SwingMdiUI', name='swing-mdi', priorit
y=-100.0, enabled=true, pluginType=UserInterface
[DEBUG] - class='net.imagej.ops.map.MapIterableToIterable', priority=-101.0, ena
bled=true, pluginType=Map
[DEBUG] - class='org.scijava.text.io.TextIOPlugin', priority=-101.0, enabled=tru
e, pluginType=IOPlugin
[DEBUG] - class='net.imagej.plugins.tools.WandTool', name='Wand', description='W
and (tracing) tool', iconPath='/icons/tools/wand.png', priority=-110.0, enabled=
false, pluginType=Tool
[DEBUG] - class='net.imagej.ui.swing.tools.SwingTextTool', name='Text', descript
ion='Text tool', iconPath='/icons/tools/text.png', priority=-115.0, enabled=fals
e, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.ZoomTool', name='Zoom', description='M
agnifying glass (or use "+" and "-" keys)', iconPath='/icons/tools/zoom.png', pr
iority=-200.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.PanTool', name='Pan', description='Scr
olling tool (or press space bar and drag)', iconPath='/icons/tools/pan.png', pri
ority=-201.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.PaintBrushTool', name='Paintbrush', de
scription='Paintbrush Tool', iconPath='/icons/tools/paintbrush.png', priority=-3
00.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.PencilTool', name='Pencil', descriptio
n='Pencil Tool', iconPath='/icons/tools/pencil.png', priority=-301.0, enabled=tr
ue, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.SprayCanTool', name='SprayCan', label=
'Spray Can', description='Spray Can Tool', iconPath='/icons/tools/spray-can.png'
, priority=-303.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.FloodFillTool', name='FloodFill', labe
l='Flood Fill', description='Flood Fill Tool', iconPath='/icons/tools/flood-fill
.png', priority=-304.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.ArrowTool', name='Arrow', description=
'Arrow Tool', iconPath='/icons/tools/arrow.png', priority=-305.0, enabled=false,
 pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.FgColorTool', name='Foreground', iconP
ath='/icons/tools/blank.png', priority=-500.0, enabled=true, pluginType=Tool
[DEBUG] - class='net.imagej.plugins.tools.BgColorTool', name='Background', iconP
ath='/icons/tools/blankBlack.png', priority=-501.0, enabled=true, pluginType=Too
l
[DEBUG] - class='io.scif.ome.formats.OMETIFFFormat', priority=-9998.0, enabled=t
rue, pluginType=Format
[DEBUG] - class='io.scif.ome.formats.OMETIFFFormat$OMETIFFTranslator', priority=
-9998.0, enabled=true, pluginType=Translator
[DEBUG] - class='io.scif.formats.TIFFFormat$TIFFTranslator', priority=-9999.0, e
nabled=true, pluginType=Translator
[DEBUG] - class='org.scijava.module.process.LoadInputsPreprocessor', priority=-9
999.0, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='io.scif.formats.TIFFFormat', name='Tagged Image File Format', p
riority=-9999.0, enabled=true, pluginType=Format
[DEBUG] - class='org.scijava.ui.FilePreprocessor', priority=-9999.5, enabled=tru
e, pluginType=PreprocessorPlugin
[DEBUG] - class='io.scif.DefaultTranslator', priority=-10000.0, enabled=true, pl
uginType=Translator
[DEBUG] - class='net.imagej.legacy.plugin.MacroRecorderPostprocessor', priority=
-10000.0, enabled=true, pluginType=PostprocessorPlugin
[DEBUG] - class='net.imagej.legacy.ui.LegacyInputHarvester', priority=-10000.0,
enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='net.imagej.ops.math.ConstantToIIOutputRAI$Add', priority=-10000
.0, enabled=true, pluginType=Add
[DEBUG] - class='net.imagej.ops.math.ConstantToIIOutputRAI$Divide', priority=-10
000.0, enabled=true, pluginType=Divide
[DEBUG] - class='net.imagej.ops.math.ConstantToIIOutputRAI$Multiply', priority=-
10000.0, enabled=true, pluginType=Multiply
[DEBUG] - class='net.imagej.ops.math.ConstantToIIOutputRAI$Subtract', priority=-
10000.0, enabled=true, pluginType=Subtract
[DEBUG] - class='net.imagej.ops.thread.chunker.ChunkerInterleaved', priority=-10
000.0, enabled=true, pluginType=Chunker
[DEBUG] - class='net.imagej.ui.swing.overlay.DefaultJHotDrawAdapter', priority=-
10000.0, enabled=true, pluginType=JHotDrawAdapter
[DEBUG] - class='org.scijava.cache.DefaultCacheService', priority=-10000.0, enab
led=true, pluginType=Service
[DEBUG] - class='org.scijava.display.DisplayPostprocessor', priority=-10000.0, e
nabled=true, pluginType=PostprocessorPlugin
[DEBUG] - class='org.scijava.plugins.text.plain.PlainTextFormat', priority=-1000
0.0, enabled=true, pluginType=TextFormat
[DEBUG] - class='org.scijava.ui.awt.widget.AWTInputHarvester', priority=-10000.0
, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='org.scijava.ui.swing.widget.SwingInputHarvester', priority=-100
00.0, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='org.scijava.ui.swing.widget.SwingMdiInputHarvester', priority=-
10000.0, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='org.scijava.platform.DefaultPlatform', name='Default', priority
=-10000.0, enabled=true, pluginType=Platform
[DEBUG] - class='net.imagej.plugins.tools.AcceleratorHandler', name='Keyboard Sh
ortcuts', priority=-10000.0, enabled=true, pluginType=Tool
[DEBUG] - class='io.scif.formats.MinimalTIFFFormat', name='Minimal TIFF', priori
ty=-10000.0, enabled=true, pluginType=Format
[DEBUG] - class='org.scijava.module.process.SaveInputsPreprocessor', priority=-1
0001.0, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] - class='io.scif.formats.TIFFJAIFormat', name='Tagged Image File Format'
, priority=-10001.0, enabled=true, pluginType=Format
[DEBUG] - class='org.scijava.module.process.CheckInputsPreprocessor', priority=-
10002.0, enabled=true, pluginType=PreprocessorPlugin
[DEBUG] Created service 'org.scijava.plugin.DefaultPluginService' in 183 ms
[DEBUG] Creating service: org.scijava.module.DefaultModuleService
[DEBUG] Creating service: org.scijava.object.DefaultObjectService
[DEBUG] Created service 'org.scijava.object.DefaultObjectService' in 4 ms
[DEBUG] Creating service: org.scijava.prefs.DefaultPrefService
[DEBUG] Created service 'org.scijava.prefs.DefaultPrefService' in 2 ms
[DEBUG] Creating service: org.scijava.convert.DefaultConvertService
[DEBUG] Created service 'org.scijava.convert.DefaultConvertService' in 3 ms
[DEBUG] Created service 'org.scijava.module.DefaultModuleService' in 12 ms
[DEBUG] Created service 'org.scijava.command.DefaultCommandService' in 211 ms
[DEBUG] Creating service: org.scijava.options.DefaultOptionsService
[DEBUG] Created service 'org.scijava.options.DefaultOptionsService' in 1 ms
[DEBUG] Creating service: net.imagej.legacy.display.LegacyImageDisplayService
[DEBUG] Created service 'net.imagej.legacy.display.LegacyImageDisplayService' in
 4 ms
[DEBUG] Creating service: org.scijava.script.DefaultScriptService
[DEBUG] Created service 'org.scijava.script.DefaultScriptService' in 4 ms
[DEBUG] Creating service: org.scijava.app.DefaultStatusService
[DEBUG] Creating service: org.scijava.app.DefaultAppService
[DEBUG] Created service 'org.scijava.app.DefaultAppService' in 2 ms
[DEBUG] Created service 'org.scijava.app.DefaultStatusService' in 3 ms
[DEBUG] Creating service: io.scif.services.SCIFIODatasetService
[DEBUG] Created service 'io.scif.services.SCIFIODatasetService' in 6 ms
[DEBUG] Creating service: org.scijava.display.DefaultDisplayService
[DEBUG] Created service 'org.scijava.display.DefaultDisplayService' in 2 ms
[DEBUG] Creating service: org.scijava.menu.DefaultMenuService
[DEBUG] Created service 'org.scijava.menu.DefaultMenuService' in 1 ms
[DEBUG] Creating service: net.imagej.display.DefaultOverlayService
[DEBUG] Creating service: net.imagej.ui.awt.AWTRenderingService
[DEBUG] Created service 'net.imagej.ui.awt.AWTRenderingService' in 1 ms
[DEBUG] Created service 'net.imagej.display.DefaultOverlayService' in 5 ms
[DEBUG] Creating service: net.imagej.threshold.DefaultThresholdService
[DEBUG] Created service 'net.imagej.threshold.DefaultThresholdService' in 2 ms
[DEBUG] Found 9 ScriptLanguage plugins.
[DEBUG] Found 2 scripts
[INFO] Overriding About Pendent Drop; identifier: command:About_Pendent_Drop; ja
r: file:/C:/UTILIT~1/Fiji.app/plugins/pendent_drop-2.0.4.jar
[INFO] Overriding Pendent Drop; identifier: command:Goutte_pendante; jar: file:/
C:/UTILIT~1/Fiji.app/plugins/pendent_drop-2.0.4.jar
[INFO] Overriding Stitch Stacks via MIP; identifier: script:C:\UTILIT~1\Fiji.app
\plugins\Scripts\Plugins\FMI\Custom Scripts\Stitch_Stacks_via_MIP.py; jar: file:
/C:/UTILIT~1/Fiji.app/jars/scijava-common-2.53.0.jar
[DEBUG] Created service 'net.imagej.legacy.LegacyService' in 1089 ms
[DEBUG] Created service 'net.imagej.legacy.LegacyConsoleService' in 1091 ms
[DEBUG] Creating service: fiji.DefaultFijiService
[DEBUG] Created service 'fiji.DefaultFijiService' in 0 ms
[DEBUG] Creating service: org.scijava.console.DefaultConsoleService
[DEBUG] Created service 'org.scijava.console.DefaultConsoleService' in 2 ms
[DEBUG] Creating service: org.scijava.event.DefaultEventHistory
[DEBUG] Created service 'org.scijava.event.DefaultEventHistory' in 1 ms
[DEBUG] Creating service: org.scijava.input.DefaultInputService
[DEBUG] Created service 'org.scijava.input.DefaultInputService' in 2 ms
[DEBUG] Creating service: org.scijava.io.DefaultDataHandleService
[DEBUG] Found 1 DataHandle plugins.
[DEBUG] Created service 'org.scijava.io.DefaultDataHandleService' in 1 ms
[DEBUG] Creating service: org.scijava.io.DefaultIOService
[DEBUG] Created service 'org.scijava.io.DefaultIOService' in 1 ms
[DEBUG] Creating service: org.scijava.io.DefaultRecentFileService
Mär 10, 2016 5:50:38 PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0
x80000002. Windows RegCreateKeyEx(...) returned error code 5.
[DEBUG] Created service 'org.scijava.io.DefaultRecentFileService' in 8 ms
[DEBUG] Creating service: org.scijava.main.DefaultMainService
[DEBUG] Created service 'org.scijava.main.DefaultMainService' in 0 ms
[DEBUG] Creating service: org.scijava.platform.DefaultPlatformService
[DEBUG] Creating service: org.scijava.platform.DefaultAppEventService
[DEBUG] Created service 'org.scijava.platform.DefaultAppEventService' in 1 ms
[DEBUG] Found 2 Platform plugins.
[DEBUG] Configuring platform: org.scijava.plugins.platforms.windows.WindowsPlatf
orm
[DEBUG] Configuring platform: org.scijava.platform.DefaultPlatform
[DEBUG] Created service 'org.scijava.platform.DefaultPlatformService' in 5 ms
[DEBUG] Creating service: org.scijava.plugins.scripting.java.DefaultJavaService
[DEBUG] Created service 'org.scijava.plugins.scripting.java.DefaultJavaService'
in 0 ms
[DEBUG] Creating service: org.scijava.plugins.scripting.jython.DefaultJythonServ
ice
[DEBUG] Created service 'org.scijava.plugins.scripting.jython.DefaultJythonServi
ce' in 1 ms
[DEBUG] Creating service: org.scijava.script.DefaultScriptHeaderService
[DEBUG] Created service 'org.scijava.script.DefaultScriptHeaderService' in 0 ms
[DEBUG] Creating service: org.scijava.text.DefaultTextService
[DEBUG] Created service 'org.scijava.text.DefaultTextService' in 0 ms
[DEBUG] Creating service: org.scijava.tool.DefaultToolService
[DEBUG] Created service 'org.scijava.tool.DefaultToolService' in 3 ms
[DEBUG] Creating service: org.scijava.ui.DefaultUIService
[DEBUG] Created service 'org.scijava.ui.DefaultUIService' in 3 ms
[DEBUG] Creating service: org.scijava.ui.dnd.DefaultDragAndDropService
[DEBUG] Created service 'org.scijava.ui.dnd.DefaultDragAndDropService' in 2 ms
[DEBUG] Creating service: org.scijava.ui.swing.SwingIconService
[DEBUG] Created service 'org.scijava.ui.swing.SwingIconService' in 1 ms
[DEBUG] Creating service: org.scijava.welcome.DefaultWelcomeService
[DEBUG] Created service 'org.scijava.welcome.DefaultWelcomeService' in 1 ms
[DEBUG] Creating service: org.scijava.widget.DefaultWidgetService
[DEBUG] Found 22 InputWidget plugins.
[DEBUG] Created service 'org.scijava.widget.DefaultWidgetService' in 1 ms
[DEBUG] Creating service: org.scijava.cache.DefaultCacheService
[DEBUG] Created service 'org.scijava.cache.DefaultCacheService' in 0 ms
[DEBUG] Creating service: io.scif.DefaultMetadataService
[DEBUG] Created service 'io.scif.DefaultMetadataService' in 0 ms
[DEBUG] Creating service: io.scif.codec.DefaultCodecService
[DEBUG] Created service 'io.scif.codec.DefaultCodecService' in 0 ms
[DEBUG] Creating service: io.scif.formats.qt.DefaultQTJavaService
[DEBUG] Created service 'io.scif.formats.qt.DefaultQTJavaService' in 2 ms
[DEBUG] Creating service: io.scif.formats.tiff.DefaultTiffService
[DEBUG] Created service 'io.scif.formats.tiff.DefaultTiffService' in 2 ms
[DEBUG] Creating service: io.scif.gui.DefaultGUIService
[DEBUG] Created service 'io.scif.gui.DefaultGUIService' in 1 ms
[DEBUG] Creating service: io.scif.img.DefaultImgUtilityService
[DEBUG] Created service 'io.scif.img.DefaultImgUtilityService' in 4 ms
[DEBUG] Creating service: io.scif.img.cell.cache.MapDBCache
[DEBUG] Creating service: io.scif.refs.DefaultRefManagerService
[DEBUG] Created service 'io.scif.refs.DefaultRefManagerService' in 0 ms
[DEBUG] Created service 'io.scif.img.cell.cache.MapDBCache' in 4 ms
[DEBUG] Creating service: io.scif.img.converters.DefaultPlaneConverterService
[DEBUG] Created service 'io.scif.img.converters.DefaultPlaneConverterService' in
 0 ms
[DEBUG] Creating service: io.scif.io.DefaultNIOService
[DEBUG] Created service 'io.scif.io.DefaultNIOService' in 1 ms
[DEBUG] Creating service: io.scif.ome.services.DefaultOMEMetadataService
[DEBUG] Creating service: io.scif.services.DefaultFormatService
[DEBUG] Created service 'io.scif.services.DefaultFormatService' in 5 ms
[DEBUG] Creating service: io.scif.ome.services.DefaultOMEXMLService
[DEBUG] Created service 'io.scif.ome.services.DefaultOMEXMLService' in 14 ms
[DEBUG] Created service 'io.scif.ome.services.DefaultOMEMetadataService' in 23 m
s
[DEBUG] Creating service: io.scif.services.DefaultDatasetIOService
[DEBUG] Created service 'io.scif.services.DefaultDatasetIOService' in 0 ms
[DEBUG] Creating service: io.scif.services.DefaultFilePatternService
[DEBUG] Created service 'io.scif.services.DefaultFilePatternService' in 1 ms
[DEBUG] Creating service: io.scif.services.DefaultLocationService
[DEBUG] Created service 'io.scif.services.DefaultLocationService' in 1 ms
[DEBUG] Creating service: io.scif.services.DefaultTranslatorService
[DEBUG] Created service 'io.scif.services.DefaultTranslatorService' in 0 ms
[DEBUG] Creating service: io.scif.services.JAIIIOServiceImpl
[DEBUG] Created service 'io.scif.services.JAIIIOServiceImpl' in 5 ms
[DEBUG] Creating service: io.scif.xml.DefaultXMLService
[DEBUG] Created service 'io.scif.xml.DefaultXMLService' in 84 ms
[DEBUG] Creating service: io.scif.services.DefaultInitializeService
[DEBUG] Created service 'io.scif.services.DefaultInitializeService' in 2 ms
[DEBUG] Creating service: net.imagej.lut.DefaultLUTService
[DEBUG] Created service 'net.imagej.lut.DefaultLUTService' in 1 ms
[DEBUG] Creating service: net.imagej.DefaultDatasetService
[DEBUG] Creating service: net.imagej.types.DefaultDataTypeService
[DEBUG] Found 11 DataType plugins.
[DEBUG] Created service 'net.imagej.types.DefaultDataTypeService' in 17 ms
[DEBUG] Created service 'net.imagej.DefaultDatasetService' in 20 ms
[DEBUG] Creating service: net.imagej.DefaultImgPlusService
[DEBUG] Created service 'net.imagej.DefaultImgPlusService' in 0 ms
[DEBUG] Creating service: net.imagej.animation.DefaultAnimationService
[DEBUG] Created service 'net.imagej.animation.DefaultAnimationService' in 2 ms
[DEBUG] Creating service: net.imagej.autoscale.DefaultAutoscaleService
[DEBUG] Created service 'net.imagej.autoscale.DefaultAutoscaleService' in 1 ms
[DEBUG] Creating service: net.imagej.display.DefaultImageDisplayService
[DEBUG] Created service 'net.imagej.display.DefaultImageDisplayService' in 0 ms
[DEBUG] Creating service: net.imagej.display.DefaultWindowService
[DEBUG] Created service 'net.imagej.display.DefaultWindowService' in 1 ms
[DEBUG] Creating service: net.imagej.display.DefaultZoomService
[DEBUG] Created service 'net.imagej.display.DefaultZoomService' in 0 ms
[DEBUG] Creating service: net.imagej.measure.DefaultMeasurementService
[DEBUG] Created service 'net.imagej.measure.DefaultMeasurementService' in 1 ms
[DEBUG] Creating service: net.imagej.measure.DefaultStatisticsService
[DEBUG] Created service 'net.imagej.measure.DefaultStatisticsService' in 1 ms
[DEBUG] Creating service: net.imagej.operator.DefaultCalculatorService
[DEBUG] Created service 'net.imagej.operator.DefaultCalculatorService' in 0 ms
[DEBUG] Creating service: net.imagej.ops.DefaultOpMatchingService
[DEBUG] Created service 'net.imagej.ops.DefaultOpMatchingService' in 2 ms
[DEBUG] Creating service: net.imagej.ops.DefaultOpService
[DEBUG] Creating service: net.imagej.ops.DefaultNamespaceService
[DEBUG] Created service 'net.imagej.ops.DefaultNamespaceService' in 0 ms
[DEBUG] Created service 'net.imagej.ops.DefaultOpService' in 13 ms
[DEBUG] Creating service: net.imagej.sampler.DefaultSamplerService
[DEBUG] Created service 'net.imagej.sampler.DefaultSamplerService' in 1 ms
[DEBUG] Creating service: net.imagej.ui.DefaultImageJUIService
[DEBUG] Created service 'net.imagej.ui.DefaultImageJUIService' in 0 ms
[DEBUG] Creating service: net.imagej.ui.awt.AWTScreenCaptureService
[DEBUG] Created service 'net.imagej.ui.awt.AWTScreenCaptureService' in 0 ms
[DEBUG] Creating service: net.imagej.ui.swing.overlay.JHotDrawService
[DEBUG] Created service 'net.imagej.ui.swing.overlay.JHotDrawService' in 1 ms
[DEBUG] Creating service: net.imagej.ui.swing.script.DefaultLanguageSupportServi
ce
[DEBUG] Created service 'net.imagej.ui.swing.script.DefaultLanguageSupportServic
e' in 1 ms
[DEBUG] Creating service: net.imagej.updater.DefaultUpdateService
[DEBUG] Created service 'net.imagej.updater.DefaultUpdateService' in 3 ms
[DEBUG] Creating service: net.imagej.updater.DefaultUploaderService
[DEBUG] Created service 'net.imagej.updater.DefaultUploaderService' in 0 ms
[DEBUG] Creating service: net.imagej.display.DummyScreenCaptureService
[DEBUG] Created service 'net.imagej.display.DummyScreenCaptureService' in 1 ms
[DEBUG] Creating service: net.imagej.render.DummyRenderingService
[DEBUG] Created service 'net.imagej.render.DummyRenderingService' in 0 ms
[DEBUG] publish(
        context = org.scijava.Context@33cbfa57
        consumed = false,null,null), called from non-EDT Thread:null

That is disappointing. I just want to clarify what steps you’re taking. I expect it’s something like:

  1. Close all your running ImageJ instances.
  2. Check to see if the stub file is there. Delete it if it is.
  3. Start an ImageJ

And when you start another ImageJ at this instance, the splash screen starts but the application hangs?

Yes, that’s correct. I was making sure there’s no *.stub file present, then starting ImageJ and trying to start a second instance. I tried both starting a second instance from a different installation as well as from the very same file, and in between deleting the newly created stub file.

Did you manually delete the stub file while ImageJ was running? That shouldn’t be necessary… but if you did that, the expected behavior is that opening a new ImageJ would open a new instance.

Anyway I can’t reproduce any problem on Windows. :frowning: I tried multiple installs, with the fiji and imagej.exes, and can not get Fiji to hang on launch. It either closes nicely or opens a new instance, as appropriate.

Do you have any additional update sites enabled on any of your installs…?

Finally reproduced. I’ll fix it today, hopefully forever this time!

OK, fix uploaded. Please let me know if anyone still runs into this problem after updating.

2 Likes

where is the .stub file located again? the first link is gone now and I have this problem.

Sorry for the missing Fiji BugZilla pages. It is still in my backlog of things to do to restore those. They will be back again, someday.

In the meantime, you can peruse the Internet Archive’s mirror of that page.