Fiji won't boot after update

[Knecht, David]

I ran the Fiji updater today and now Fiji won’t boot in OS X 10.10.5.  I tried to download a fresh copy and the download site did not find a file.  Is this a known problem?  Dave

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200


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[Menelaos Symeonides]

Same issue here. Two different computers, one Windows 7 x64, one Windows 10 x64, just updated Fiji.64bit and after the update I can no longer launch it. I also extracted an untouched Fiji zip I had, ran it, updated it, and got the exact same behavior, so something is broken in the latest update.

I ran it in debug mode and got this:

JRE not found in 'C:\FIJI~1.64B/jre'
JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
Available RAM: 5995MB, using 3/4 of that: 4497MB
java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar -Dimagej.dir=C:\\FIJI~1.64B -Dij.dir=C:\\FIJI~1.64B -Dfiji.dir=C:\\FIJI~1.64B -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64 -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath C:\\FIJI~1.64B/jars/ij-1.50b.jar fiji.Main -port7
Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
Opening Java library C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
Launching main class fiji.Main with parameters [-port7]
Class loader = sun.misc.Launcher$AppClassLoader@138d107f
ij1.plugin.dirs: null
$HOME/.plugins: C:\Users\Mel\.plugins does not exist
Launching main class net.imagej.Main with parameters [-port7]
Class loader = sun.misc.Launcher$AppClassLoader@138d107f
Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
Not Eclipse because first entry is: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
[DEBUG] Creating service: org.scijava.event.DefaultEventService
[DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
[DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
[DEBUG] Creating service: org.scijava.thread.DefaultThreadService
[DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
[DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
[DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
[DEBUG] Creating service: net.imagej.legacy.LegacyService
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyConsoleService
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
        at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
        at org.scijava.Context.<init>(Context.java:267)
        at org.scijava.Context.<init>(Context.java:224)
        at org.scijava.Context.<init>(Context.java:163)
        at org.scijava.Context.<init>(Context.java:149)
        at net.imagej.ImageJ.<init>(ImageJ.java:79)
        at net.imagej.Main.launch(Main.java:61)
        at net.imagej.Main.main(Main.java:73)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at fiji.Main.main(Main.java:173)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyService
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
        at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
        at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
        ... 29 more
Caused by: java.lang.NoClassDefFoundError: Lnet/imagej/threshold/ThresholdService;
        at java.lang.Class.getDeclaredFields0(Native Method)
        at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
        at java.lang.Class.getDeclaredFields(Class.java:1743)
        at org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
        at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
        at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
        at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
        at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
        ... 32 more
Caused by: java.lang.ClassNotFoundException: net.imagej.threshold.ThresholdService
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        ... 40 more

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[Menelaos Symeonides]

I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
over and does not report needing any updates. I copied this over my
existing/"broken" Fiji folder and it now launches fine, but upon update
it had to remove 4 outdated packages. Works fine now, same exact
behavior on both computers I mentioned.

On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:

> Same issue here. Two different computers, one Windows 7 x64, one Windows 10 x64, just updated Fiji.64bit and after the update I can no longer launch it. I also extracted an untouched Fiji zip I had, ran it, updated it, and got the exact same behavior, so something is broken in the latest update.
>
> I ran it in debug mode and got this:
>
> JRE not found in 'C:\FIJI~1.64B/jre'
> JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
> Available RAM: 5995MB, using 3/4 of that: 4497MB
> java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar -Dimagej.dir=C:\\FIJI~1.64B -Dij.dir=C:\\FIJI~1.64B -Dfiji.dir=C:\\FIJI~1.64B -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64 -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -classpath C:\\FIJI~1.64B/jars/ij-1.50b.jar fiji.Main -port7
> Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
> Opening Java library C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
> Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
> Launching main class fiji.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> ij1.plugin.dirs: null
> $HOME/.plugins: C:\Users\Mel\.plugins does not exist
> Launching main class net.imagej.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
> Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> Not Eclipse because first entry is: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> [DEBUG] Creating service: org.scijava.event.DefaultEventService
> [DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
> [DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
> [DEBUG] Creating service: org.scijava.thread.DefaultThreadService
> [DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
> [DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
> [DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
> [DEBUG] Creating service: net.imagej.legacy.LegacyService
> Error while executing the main() method of class 'net.imagej.Main':
> java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyConsoleService
>          at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>          at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>          at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
>          at org.scijava.Context.<init>(Context.java:267)
>          at org.scijava.Context.<init>(Context.java:224)
>          at org.scijava.Context.<init>(Context.java:163)
>          at org.scijava.Context.<init>(Context.java:149)
>          at net.imagej.ImageJ.<init>(ImageJ.java:79)
>          at net.imagej.Main.launch(Main.java:61)
>          at net.imagej.Main.main(Main.java:73)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at fiji.Main.main(Main.java:173)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>          at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
> Caused by: java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyService
>          at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>          at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
>          at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>          ... 29 more
> Caused by: java.lang.NoClassDefFoundError: Lnet/imagej/threshold/ThresholdService;
>          at java.lang.Class.getDeclaredFields0(Native Method)
>          at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
>          at java.lang.Class.getDeclaredFields(Class.java:1743)
>          at org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
>          at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
>          at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
>          at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
>          at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>          ... 32 more
> Caused by: java.lang.ClassNotFoundException: net.imagej.threshold.ThresholdService
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>          at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>          ... 40 more
>
>

--
Menelaos Symeonides
University of Vermont
Cell & Molecular Biology Graduate Program
Department of Microbiology and Molecular Genetics
318 Stafford Hall
95 Carrigan Dr
Burlington, VT 05405
[hidden email]
Phone: [phone]

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[Jan Eglinger]

Hi all,

 >> I also extracted an untouched Fiji zip I had, ran
 >> it, updated it, and got the exact same behavior, so something is
 >> broken in the latest update.

This happens because the updater automatically downloads some core
component files (imagej-common.jar and imagej-ops.jar) but quits before
showing the dialog allowing to download the newly added
imagej-deprecated.jar.
See https://github.com/imagej/imagej-ops/issues/201

As a workaround, you can run the following command from the command prompt:
     ImageJ-win64.exe --update update jars/imagej-deprecated.jar

This will install the required file. After that, just start ImageJ/Fiji
as usual.

Hope that helps.
Jan



On 15.09.2015 00:32, Menelaos Symeonides wrote:

> I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
> over and does not report needing any updates. I copied this over my
> existing/"broken" Fiji folder and it now launches fine, but upon update
> it had to remove 4 outdated packages. Works fine now, same exact
> behavior on both computers I mentioned.
>
> On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:
>> Same issue here. Two different computers, one Windows 7 x64, one
>> Windows 10 x64, just updated Fiji.64bit and after the update I can no
>> longer launch it. I also extracted an untouched Fiji zip I had, ran
>> it, updated it, and got the exact same behavior, so something is
>> broken in the latest update.
>>
>> I ran it in debug mode and got this:
>>
>> JRE not found in 'C:\FIJI~1.64B/jre'
>> JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
>> Available RAM: 5995MB, using 3/4 of that: 4497MB
>> java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B
>> -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ
>> -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar
>> -Dimagej.dir=C:\\FIJI~1.64B -Dij.dir=C:\\FIJI~1.64B
>> -Dfiji.dir=C:\\FIJI~1.64B -Dfiji.defaultLibPath=bin/server/jvm.dll
>> -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe
>> -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe
>> -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64
>> -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug
>> net.imagej.launcher.ClassLauncher -classpath
>> C:\\FIJI~1.64B/jars/ij-1.50b.jar fiji.Main -port7
>> Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
>> Opening Java library
>> C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
>> Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
>> Launching main class fiji.Main with parameters [-port7]
>> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
>> ij1.plugin.dirs: null
>> $HOME/.plugins: C:\Users\Mel\.plugins does not exist
>> Launching main class net.imagej.Main with parameters [-port7]
>> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
>> Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
>> Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
>> Not Eclipse because first entry is:
>> file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
>> [DEBUG] Creating service: org.scijava.event.DefaultEventService
>> [DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
>> [DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
>> [DEBUG] Creating service: org.scijava.thread.DefaultThreadService
>> [DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
>> [DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
>> [DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
>> [DEBUG] Creating service: net.imagej.legacy.LegacyService
>> Error while executing the main() method of class 'net.imagej.Main':
>> java.lang.IllegalArgumentException: Invalid service:
>> net.imagej.legacy.LegacyConsoleService
>>          at
>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>>
>>          at
>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>>          at
>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>>          at
>> org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
>>          at org.scijava.Context.<init>(Context.java:267)
>>          at org.scijava.Context.<init>(Context.java:224)
>>          at org.scijava.Context.<init>(Context.java:163)
>>          at org.scijava.Context.<init>(Context.java:149)
>>          at net.imagej.ImageJ.<init>(ImageJ.java:79)
>>          at net.imagej.Main.launch(Main.java:61)
>>          at net.imagej.Main.main(Main.java:73)
>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>          at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>
>>          at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>          at
>> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>          at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>
>>          at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>          at fiji.Main.main(Main.java:173)
>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>          at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>
>>          at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>
>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>          at
>> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>> Caused by: java.lang.IllegalArgumentException: Invalid service:
>> net.imagej.legacy.LegacyService
>>          at
>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>>
>>          at
>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>>          at
>> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
>>
>>          at
>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>>
>>          ... 29 more
>> Caused by: java.lang.NoClassDefFoundError:
>> Lnet/imagej/threshold/ThresholdService;
>>          at java.lang.Class.getDeclaredFields0(Native Method)
>>          at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
>>          at java.lang.Class.getDeclaredFields(Class.java:1743)
>>          at
>> org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
>>          at
>> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
>>          at
>> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
>>          at
>> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
>>
>>          at
>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>>
>>          ... 32 more
>> Caused by: java.lang.ClassNotFoundException:
>> net.imagej.threshold.ThresholdService
>>          at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>>          at java.security.AccessController.doPrivileged(Native Method)
>>          at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>          at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>>          at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>>          at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>>          ... 40 more
>>
>>
>

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[ctrueden]

Hi everyone,

Thanks for the helpful analysis, Menelaos and Jan!

I have been unable to reproduce this breakage with any of my Fiji
installations, but I instituted a workaround which I hope avoids the
problem for now.

Unfortunately, due to how the ImageJ Updater works, it's not the first time
this issue has cropped up, and it probably won't be the last.

See the mentioned issue [1] for technical discussion if you are interested
in the details.

Regards,
Curtis

[1] https://github.com/imagej/imagej-ops/issues/201

On Tue, Sep 15, 2015 at 3:01 AM, Jan Eglinger <[hidden email]>
wrote:

> Hi all,
>
> >> I also extracted an untouched Fiji zip I had, ran
> >> it, updated it, and got the exact same behavior, so something is
> >> broken in the latest update.
>
> This happens because the updater automatically downloads some core
> component files (imagej-common.jar and imagej-ops.jar) but quits before
> showing the dialog allowing to download the newly added
> imagej-deprecated.jar.
> See https://github.com/imagej/imagej-ops/issues/201
>
> As a workaround, you can run the following command from the command prompt:
>     ImageJ-win64.exe --update update jars/imagej-deprecated.jar
>
> This will install the required file. After that, just start ImageJ/Fiji as
> usual.
>
> Hope that helps.
> Jan
>
>
>
>
> On 15.09.2015 00:32, Menelaos Symeonides wrote:
>
>> I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
>> over and does not report needing any updates. I copied this over my
>> existing/"broken" Fiji folder and it now launches fine, but upon update
>> it had to remove 4 outdated packages. Works fine now, same exact
>> behavior on both computers I mentioned.
>>
>> On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:
>>
>>> Same issue here. Two different computers, one Windows 7 x64, one
>>> Windows 10 x64, just updated Fiji.64bit and after the update I can no
>>> longer launch it. I also extracted an untouched Fiji zip I had, ran
>>> it, updated it, and got the exact same behavior, so something is
>>> broken in the latest update.
>>>
>>> I ran it in debug mode and got this:
>>>
>>> JRE not found in 'C:\FIJI~1.64B/jre'
>>> JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
>>> Available RAM: 5995MB, using 3/4 of that: 4497MB
>>> java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B
>>> -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ
>>> -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar
>>> -Dimagej.dir=C:\\FIJI~1.64B -Dij.dir=C:\\FIJI~1.64B
>>> -Dfiji.dir=C:\\FIJI~1.64B -Dfiji.defaultLibPath=bin/server/jvm.dll
>>> -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe
>>> -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe
>>> -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64
>>> -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug
>>> net.imagej.launcher.ClassLauncher -classpath
>>> C:\\FIJI~1.64B/jars/ij-1.50b.jar fiji.Main -port7
>>> Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
>>> Opening Java library
>>> C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
>>> Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
>>> Launching main class fiji.Main with parameters [-port7]
>>> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
>>> ij1.plugin.dirs: null
>>> $HOME/.plugins: C:\Users\Mel\.plugins does not exist
>>> Launching main class net.imagej.Main with parameters [-port7]
>>> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
>>> Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
>>> Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
>>> Not Eclipse because first entry is:
>>> file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
>>> [DEBUG] Creating service: org.scijava.event.DefaultEventService
>>> [DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
>>> [DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
>>> [DEBUG] Creating service: org.scijava.thread.DefaultThreadService
>>> [DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
>>> [DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
>>> [DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
>>> [DEBUG] Creating service: net.imagej.legacy.LegacyService
>>> Error while executing the main() method of class 'net.imagej.Main':
>>> java.lang.IllegalArgumentException: Invalid service:
>>> net.imagej.legacy.LegacyConsoleService
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>>>
>>>          at
>>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>>>          at
>>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>>>          at
>>> org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
>>>          at org.scijava.Context.<init>(Context.java:267)
>>>          at org.scijava.Context.<init>(Context.java:224)
>>>          at org.scijava.Context.<init>(Context.java:163)
>>>          at org.scijava.Context.<init>(Context.java:149)
>>>          at net.imagej.ImageJ.<init>(ImageJ.java:79)
>>>          at net.imagej.Main.launch(Main.java:61)
>>>          at net.imagej.Main.main(Main.java:73)
>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>          at
>>>
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>>          at
>>>
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>>          at
>>> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>>>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>>>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>          at
>>>
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>>          at
>>>
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>>          at fiji.Main.main(Main.java:173)
>>>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>>>          at
>>>
>>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>>
>>>          at
>>>
>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>>
>>>          at java.lang.reflect.Method.invoke(Method.java:597)
>>>          at
>>> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>>>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>>>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>>> Caused by: java.lang.IllegalArgumentException: Invalid service:
>>> net.imagej.legacy.LegacyService
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>>>
>>>          at
>>> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
>>>
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>>>
>>>          ... 29 more
>>> Caused by: java.lang.NoClassDefFoundError:
>>> Lnet/imagej/threshold/ThresholdService;
>>>          at java.lang.Class.getDeclaredFields0(Native Method)
>>>          at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
>>>          at java.lang.Class.getDeclaredFields(Class.java:1743)
>>>          at
>>> org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
>>>          at
>>> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
>>>          at
>>> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
>>>
>>>          at
>>>
>>> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>>>
>>>          ... 32 more
>>> Caused by: java.lang.ClassNotFoundException:
>>> net.imagej.threshold.ThresholdService
>>>          at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>>>          at java.security.AccessController.doPrivileged(Native Method)
>>>          at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>>>          at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>>>          at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>>>          at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>>>          ... 40 more
>>>
>>>
>>>
>>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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[Knecht, David]

I am still stuck.  Also, when I try to download a new copy of Fiji, I get this:
HTTP ERROR 404

Problem accessing /job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-macosx.dmg. Reason:

    Not Found

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Sep 15, 2015, at 4:01 AM, Jan Eglinger <[hidden email]<mailto:[hidden email]>> wrote:

Hi all,

>> I also extracted an untouched Fiji zip I had, ran
>> it, updated it, and got the exact same behavior, so something is
>> broken in the latest update.

This happens because the updater automatically downloads some core component files (imagej-common.jar and imagej-ops.jar) but quits before showing the dialog allowing to download the newly added imagej-deprecated.jar.
See https://github.com/imagej/imagej-ops/issues/201

As a workaround, you can run the following command from the command prompt:
   ImageJ-win64.exe --update update jars/imagej-deprecated.jar

This will install the required file. After that, just start ImageJ/Fiji as usual.

Hope that helps.
Jan



On 15.09.2015 00:32, Menelaos Symeonides wrote:
I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
over and does not report needing any updates. I copied this over my
existing/"broken" Fiji folder and it now launches fine, but upon update
it had to remove 4 outdated packages. Works fine now, same exact
behavior on both computers I mentioned.

On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:
Same issue here. Two different computers, one Windows 7 x64, one
Windows 10 x64, just updated Fiji.64bit and after the update I can no
longer launch it. I also extracted an untouched Fiji zip I had, ran
it, updated it, and got the exact same behavior, so something is
broken in the latest update.

I ran it in debug mode and got this:

JRE not found in 'C:\FIJI~1.64B/jre'
JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
Available RAM: 5995MB, using 3/4 of that: 4497MB
java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
-Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ
-Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar<smb://FIJI~1.64B/jars/imagej-launcher-3.1.6.jar>
-Dimagej.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dij.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
-Dfiji.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dfiji.defaultLibPath=bin/server/jvm.dll
-Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
-Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
-Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64<smb://FIJI~1.64B/lib/win64;C://FIJI~1.64B/mm/win64>
-Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug
net.imagej.launcher.ClassLauncher -classpath
C:\\FIJI~1.64B/jars/ij-1.50b.jar<smb://FIJI~1.64B/jars/ij-1.50b.jar> fiji.Main -port7
Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
Opening Java library
C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
Launching main class fiji.Main with parameters [-port7]
Class loader = sun.misc.Launcher$AppClassLoader@138d107f
ij1.plugin.dirs: null
$HOME/.plugins: C:\Users\Mel\.plugins does not exist
Launching main class net.imagej.Main with parameters [-port7]
Class loader = sun.misc.Launcher$AppClassLoader@138d107f
Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
Not Eclipse because first entry is:
file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
[DEBUG] Creating service: org.scijava.event.DefaultEventService
[DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
[DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
[DEBUG] Creating service: org.scijava.thread.DefaultThreadService
[DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
[DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
[DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
[DEBUG] Creating service: net.imagej.legacy.LegacyService
Error while executing the main() method of class 'net.imagej.Main':
java.lang.IllegalArgumentException: Invalid service:
net.imagej.legacy.LegacyConsoleService
        at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)

        at
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
        at
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
        at
org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
        at org.scijava.Context.<init>(Context.java:267)
        at org.scijava.Context.<init>(Context.java:224)
        at org.scijava.Context.<init>(Context.java:163)
        at org.scijava.Context.<init>(Context.java:149)
        at net.imagej.ImageJ.<init>(ImageJ.java:79)
        at net.imagej.Main.launch(Main.java:61)
        at net.imagej.Main.main(Main.java:73)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)
        at
net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)
        at fiji.Main.main(Main.java:173)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)

        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

        at java.lang.reflect.Method.invoke(Method.java:597)
        at
net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Caused by: java.lang.IllegalArgumentException: Invalid service:
net.imagej.legacy.LegacyService
        at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)

        at
org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
        at
org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)

        at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)

        ... 29 more
Caused by: java.lang.NoClassDefFoundError:
Lnet/imagej/threshold/ThresholdService;
        at java.lang.Class.getDeclaredFields0(Native Method)
        at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
        at java.lang.Class.getDeclaredFields(Class.java:1743)
        at
org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
        at
org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
        at
org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
        at
org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)

        at
org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)

        ... 32 more
Caused by: java.lang.ClassNotFoundException:
net.imagej.threshold.ThresholdService
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        ... 40 more





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[Jan Eglinger]

Hi David,

on OS X, can you please try starting Terminal, and then running:

     /path/to/your/Fiji.app/Contents/MacOS/ImageJ-macosx --update update

(of course after replacing the correct path)
and see if that helps??

Cheers,
Jan


On 15.09.2015 16:07, Knecht, David wrote:

> I am still stuck.  Also, when I try to download a new copy of Fiji, I get this:
> HTTP ERROR 404
>
> Problem accessing /job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-macosx.dmg. Reason:
>
>      Not Found
>
> Dr. David Knecht
> Professor of Molecular and Cell Biology
> Core Microscopy Facility Director
> University of Connecticut
> 91 N. Eagleville Rd.
> Storrs, CT 06269
> 860-486-2200
>
> On Sep 15, 2015, at 4:01 AM, Jan Eglinger <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi all,
>
>>> I also extracted an untouched Fiji zip I had, ran
>>> it, updated it, and got the exact same behavior, so something is
>>> broken in the latest update.
>
> This happens because the updater automatically downloads some core component files (imagej-common.jar and imagej-ops.jar) but quits before showing the dialog allowing to download the newly added imagej-deprecated.jar.
> See https://github.com/imagej/imagej-ops/issues/201
>
> As a workaround, you can run the following command from the command prompt:
>     ImageJ-win64.exe --update update jars/imagej-deprecated.jar
>
> This will install the required file. After that, just start ImageJ/Fiji as usual.
>
> Hope that helps.
> Jan
>
>
>
> On 15.09.2015 00:32, Menelaos Symeonides wrote:
> I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
> over and does not report needing any updates. I copied this over my
> existing/"broken" Fiji folder and it now launches fine, but upon update
> it had to remove 4 outdated packages. Works fine now, same exact
> behavior on both computers I mentioned.
>
> On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:
> Same issue here. Two different computers, one Windows 7 x64, one
> Windows 10 x64, just updated Fiji.64bit and after the update I can no
> longer launch it. I also extracted an untouched Fiji zip I had, ran
> it, updated it, and got the exact same behavior, so something is
> broken in the latest update.
>
> I ran it in debug mode and got this:
>
> JRE not found in 'C:\FIJI~1.64B/jre'
> JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
> Available RAM: 5995MB, using 3/4 of that: 4497MB
> java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
> -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ
> -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar<smb://FIJI~1.64B/jars/imagej-launcher-3.1.6.jar>
> -Dimagej.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dij.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
> -Dfiji.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dfiji.defaultLibPath=bin/server/jvm.dll
> -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
> -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
> -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64<smb://FIJI~1.64B/lib/win64;C://FIJI~1.64B/mm/win64>
> -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug
> net.imagej.launcher.ClassLauncher -classpath
> C:\\FIJI~1.64B/jars/ij-1.50b.jar<smb://FIJI~1.64B/jars/ij-1.50b.jar> fiji.Main -port7
> Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
> Opening Java library
> C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
> Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
> Launching main class fiji.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> ij1.plugin.dirs: null
> $HOME/.plugins: C:\Users\Mel\.plugins does not exist
> Launching main class net.imagej.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
> Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> Not Eclipse because first entry is:
> file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> [DEBUG] Creating service: org.scijava.event.DefaultEventService
> [DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
> [DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
> [DEBUG] Creating service: org.scijava.thread.DefaultThreadService
> [DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
> [DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
> [DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
> [DEBUG] Creating service: net.imagej.legacy.LegacyService
> Error while executing the main() method of class 'net.imagej.Main':
> java.lang.IllegalArgumentException: Invalid service:
> net.imagej.legacy.LegacyConsoleService
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>          at
> org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
>          at org.scijava.Context.<init>(Context.java:267)
>          at org.scijava.Context.<init>(Context.java:224)
>          at org.scijava.Context.<init>(Context.java:163)
>          at org.scijava.Context.<init>(Context.java:149)
>          at net.imagej.ImageJ.<init>(ImageJ.java:79)
>          at net.imagej.Main.launch(Main.java:61)
>          at net.imagej.Main.main(Main.java:73)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at fiji.Main.main(Main.java:173)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
> Caused by: java.lang.IllegalArgumentException: Invalid service:
> net.imagej.legacy.LegacyService
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at
> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
>
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>
>          ... 29 more
> Caused by: java.lang.NoClassDefFoundError:
> Lnet/imagej/threshold/ThresholdService;
>          at java.lang.Class.getDeclaredFields0(Native Method)
>          at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
>          at java.lang.Class.getDeclaredFields(Class.java:1743)
>          at
> org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
>          at
> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
>          at
> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
>          at
> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
>
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>
>          ... 32 more
> Caused by: java.lang.ClassNotFoundException:
> net.imagej.threshold.ThresholdService
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>          at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>          ... 40 more
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jan Eglinger]

Hi David,

On 15.09.2015 16:07, Knecht, David wrote:
> I am still stuck.  Also, when I try to download a new copy of Fiji, I get this:
> HTTP ERROR 404
>
> Problem accessing /job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-macosx.dmg. Reason:
>
>      Not Found


There was a broken link on the Downloads page, I just fixed it [1]:

     http://fiji.sc/Downloads

Cheers,
Jan

[1]: http://fiji.sc/index.php?title=Downloads&diff=16511&oldid=16499

>
> On Sep 15, 2015, at 4:01 AM, Jan Eglinger <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi all,
>
>>> I also extracted an untouched Fiji zip I had, ran
>>> it, updated it, and got the exact same behavior, so something is
>>> broken in the latest update.
>
> This happens because the updater automatically downloads some core component files (imagej-common.jar and imagej-ops.jar) but quits before showing the dialog allowing to download the newly added imagej-deprecated.jar.
> See https://github.com/imagej/imagej-ops/issues/201
>
> As a workaround, you can run the following command from the command prompt:
>     ImageJ-win64.exe --update update jars/imagej-deprecated.jar
>
> This will install the required file. After that, just start ImageJ/Fiji as usual.
>
> Hope that helps.
> Jan
>
>
>
> On 15.09.2015 00:32, Menelaos Symeonides wrote:
> I downloaded a fresh Fiji.64bit zip just now, it launches fine over and
> over and does not report needing any updates. I copied this over my
> existing/"broken" Fiji folder and it now launches fine, but upon update
> it had to remove 4 outdated packages. Works fine now, same exact
> behavior on both computers I mentioned.
>
> On 9/14/2015 6:18 PM, Menelaos Symeonides wrote:
> Same issue here. Two different computers, one Windows 7 x64, one
> Windows 10 x64, just updated Fiji.64bit and after the update I can no
> longer launch it. I also extracted an untouched Fiji zip I had, ran
> it, updated it, and got the exact same behavior, so something is
> broken in the latest update.
>
> I ran it in debug mode and got this:
>
> JRE not found in 'C:\FIJI~1.64B/jre'
> JAVA_HOME contains a JRE: 'C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre'
> Available RAM: 5995MB, using 3/4 of that: 4497MB
> java -Dpython.cachedir.skip=true -Dplugins.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
> -Xmx4497m -Xincgc -XX:PermSize=128m -Dsun.java.command=ImageJ
> -Djava.class.path=C:\\FIJI~1.64B/jars/imagej-launcher-3.1.6.jar<smb://FIJI~1.64B/jars/imagej-launcher-3.1.6.jar>
> -Dimagej.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dij.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B>
> -Dfiji.dir=C:\\FIJI~1.64B<smb://FIJI~1.64B> -Dfiji.defaultLibPath=bin/server/jvm.dll
> -Dfiji.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
> -Dij.executable=C:\\Fiji.64bit\\fiji-win64.exe<smb://Fiji.64bit//fiji-win64.exe>
> -Djava.library.path=C:\\FIJI~1.64B/lib/win64;C:\\FIJI~1.64B/mm/win64<smb://FIJI~1.64B/lib/win64;C://FIJI~1.64B/mm/win64>
> -Dsun.java2d.noddraw=true -Dij.debug=true -Dscijava.log.level=debug
> net.imagej.launcher.ClassLauncher -classpath
> C:\\FIJI~1.64B/jars/ij-1.50b.jar<smb://FIJI~1.64B/jars/ij-1.50b.jar> fiji.Main -port7
> Using JAVA_HOME C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre
> Opening Java library
> C:\FIJI~1.64B/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
> Adding option: -Djava.home=C:\FIJI~1.64B/java/win64/jdk1.6.0_24/
> Launching main class fiji.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> ij1.plugin.dirs: null
> $HOME/.plugins: C:\Users\Mel\.plugins does not exist
> Launching main class net.imagej.Main with parameters [-port7]
> Class loader = sun.misc.Launcher$AppClassLoader@138d107f
> Checking class loader: sun.misc.Launcher$AppClassLoader@138d107f
> Checking URL: file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> Not Eclipse because first entry is:
> file:/C:/Fiji.64bit/jars/imagej-launcher-3.1.6.jar
> [DEBUG] Creating service: org.scijava.event.DefaultEventService
> [DEBUG] Creating service: org.scijava.log.slf4j.SLF4JLogService
> [DEBUG] Created service 'org.scijava.log.slf4j.SLF4JLogService' in 342 ms
> [DEBUG] Creating service: org.scijava.thread.DefaultThreadService
> [DEBUG] Created service 'org.scijava.thread.DefaultThreadService' in 2 ms
> [DEBUG] Created service 'org.scijava.event.DefaultEventService' in 409 ms
> [DEBUG] Creating service: net.imagej.legacy.LegacyConsoleService
> [DEBUG] Creating service: net.imagej.legacy.LegacyService
> Error while executing the main() method of class 'net.imagej.Main':
> java.lang.IllegalArgumentException: Invalid service:
> net.imagej.legacy.LegacyConsoleService
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
>          at
> org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
>          at org.scijava.Context.<init>(Context.java:267)
>          at org.scijava.Context.<init>(Context.java:224)
>          at org.scijava.Context.<init>(Context.java:163)
>          at org.scijava.Context.<init>(Context.java:149)
>          at net.imagej.ImageJ.<init>(ImageJ.java:79)
>          at net.imagej.Main.launch(Main.java:61)
>          at net.imagej.Main.main(Main.java:73)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at fiji.Main.main(Main.java:173)
>          at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>          at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>
>          at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>
>          at java.lang.reflect.Method.invoke(Method.java:597)
>          at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:258)
>          at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
>          at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
> Caused by: java.lang.IllegalArgumentException: Invalid service:
> net.imagej.legacy.LegacyService
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:280)
>
>          at
> org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
>          at
> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
>
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>
>          ... 29 more
> Caused by: java.lang.NoClassDefFoundError:
> Lnet/imagej/threshold/ThresholdService;
>          at java.lang.Class.getDeclaredFields0(Native Method)
>          at java.lang.Class.privateGetDeclaredFields(Class.java:2291)
>          at java.lang.Class.getDeclaredFields(Class.java:1743)
>          at
> org.scijava.util.ClassUtils.cacheAnnotatedObjects(ClassUtils.java:507)
>          at
> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:405)
>          at
> org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:379)
>          at
> org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:315)
>
>          at
> org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
>
>          ... 32 more
> Caused by: java.lang.ClassNotFoundException:
> net.imagej.threshold.ThresholdService
>          at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>          at java.security.AccessController.doPrivileged(Native Method)
>          at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>          at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>          at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>          ... 40 more
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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