Posted by
Jan Eglinger on
Sep 15, 2015; 7:56am
URL: http://imagej.273.s1.nabble.com/Fiji-won-t-boot-after-update-tp5014333p5014336.html
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/201As 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 it had to remove 4 outdated packages.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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