Posted by
Knecht, David on
Sep 15, 2015; 2:07pm
URL: http://imagej.273.s1.nabble.com/Fiji-won-t-boot-after-update-tp5014333p5014341.html
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/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it had to remove 4 outdated packages.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<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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