Typically, the problem just goes away if you cancel the update (there is a cancel button in the progress window), quit Fiji and restart it.

That is just a work-around, of course, while I am busy trying to fix things.

Found the problem, hold on while I clean up the code to fix it properly.

Unfortunately, the problem is more dramatic than I initially thought. So I fixed it, but of course the fix is only in the *new* version!

That means that you will have to cancel the infinite updating loop, restart Fiji, and update again. That should repair your updater.

Very sorry for the breakage!

Hi Johannes and all the others,
unfortunately the solution you propose doesn't work for me. Since the first time I canceled the loop I can't launch the updater anymore.. As I wrote in my first post (see below) when I restart FIJI or if run the command 'Update FIJI' from the Help menu I get the bootstrap.js macro but this is the end won't work (see below).

from first post [...] "I get message in an updater window that says "there was a problem checking whether everything is up-to-date. Start the updater?" If I do it, I get a bootstrap.js window. I follow the instructions (i.e. run the command Evaluate Javascript) and the following log 

Error: La fonction importPackage doit être appelée avec un package et non avec "[JavaClass ij]" (<Unknown source>#1) in <Unknown source> at line number 1 

It's in french but it says that the function importPackage needs to be called with a package and not with JavaClass." [...]

What should I do to repair the updater? I wouldn't like to have to re-install everything.
Thanks a lot for your help!
Claudio

Hi Claudio,

 Sorry I misunderstood your original message.. I thought that Fiji was asking if you wanted to update and that's what was causing bootstrap.js to pop up. I didn't realize it also pops up when you run Help > Update Fiji manually.

 Could you try updating from the command line? The wiki page (fiji.sc/Update_Fiji) explains how to do so.. basically you just want to run "imagej-winXX.exe --update update" and it should run the updater.

 If that doesn't work, the update site is hosted on the Fiji wiki itself (http://fiji.sc/update/). You should be able to manually download the updated .jars... but Johannes needs to chime in here, as I'm not sure which dependencies you need to update.

 Also, Johannes, I got the infinite updater bug this morning again.. :( maybe because I was downloading the fix? It worked for me to cancel and restart Fiji.

Hi Mark,
I tried to run the updater from the command prompt as you suggested but nothing happens.. Since I hav never used FIJI through the command line I may have done something wrong. Here is what I did exactly:
- in the command prompt I navigate into the folder where I have executable fiji or imagej-win64 files
- then I run the "imagej-win64.exe --update update" command as you suggested, but nothing happens.
How should I proceed? What can I do to repair the problem?

Thanks a lot!
Claudio

Hi Claudio,

 What you did sounds exactly right.. as far as I can tell, no message means everything is up to date. It will only update things that would have been marked for update in the updater though...

 Johannes - which are the relevant jars that need to be updated?

Hi Mark,
as a matter of fact when I restart FIJI I get exactly the same problem as before trying the update from the command line. It looks as there was nothing to update and nothing has been updated...
Claudio

Hi Claudio,

 It looks like there are some bugs with the ImageJ launcher on Windows. So try running:

"imagej-win64.exe --debug --update update"

instead. There were some recent changes to logging and it looks like they broke things on Windows at least, so behavior of the updater actually changes when --debug is specified.

This should tell you which jars need to be updated, but unfortunately I wasn't able to get them to actually update due to a problem harvesting command-line input. We'll get that fixed, but in the mean time you should be able to run this and least report back which jars it said needed output.

Let me know how that goes!

P.S. the new launcher tickets are:
https://github.com/imagej/imagej-launcher/issues/9
https://github.com/imagej/imagej-launcher/issues/10
https://github.com/imagej/imagej-launcher/issues/11

Hmm. This is really strange, in particular the error:

> Error: La fonction importPackage doit être appelée avec un package et non avec "[JavaClass ij]" (<Unknown source>#1) in <Unknown source> at line number 1 

We never call importPackage at all, only importClass. In fact, I would never call importPackage anyway because those wildcard imports cause way more trouble than the people who like them so much would like to admit.

Claudio, to get you back to a working state, I would like to suggest the following: import the bootstrap.js yourself by calling File>Import>URL... and typing http://update.imagej.net/bootstrap.js as URL. This should open the macro editor with the script that you should be able to call with Ctrl+J. If you still experience the problem with "importPackage", may I ask you to use the Fiji Package Maker via Plugins>Utilities>Make Fiji Package to make a .zip and upload it via Help>Upload Sample Image? I will try to fix this as soon as possible!

Hi Johannes,
firstly let me say thank you for spending so much of your time trying to fix this problem. Secondly, I tried to import the bootstrap.js by calling File>Import>URL... but I get the same problem as before. Finally, I tryied to use the Fiji Package Maker via Plugins>Utilities>Make Fiji Package to make a .zip but this also didn't want to work.. I get the following message appearing:

(Fiji Is Just) ImageJ 2.0.0-rc-2; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 32MB of 20000MB (<1%)
 
java.lang.NoClassDefFoundError: Could not initialize class fiji.packaging.ZipPackager
	at fiji.packaging.Package_Maker.run(Package_Maker.java:18)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)

I hope this helps to find the problem. It looks like everything we try gives no results...
Best
Claudio

Hi Mark,
as yuo suggested I tried to launch the updated from the command line using the debug version. Here is the message I get in the command line I hope it helps to find out what the problem is.

Microsoft Windows [Version 6.1.7601]
Copyright (c) 2009 Microsoft Corporation.  All rights reserved.

C:\Users\collinet>cd/d c:\fiji.app

c:\Fiji.app>imagej-win64.exe --debug --update update

c:\Fiji.app>JRE not found in 'c:\Fiji.app/jre'
JAVA_HOME contains a JRE: 'c:\Fiji.app/java/win64/jdk1.6.0_24//jre'
javaw -Xmx20000m -Dpatch.ij1=false -Dpython.cachedir.skip=true -Dplugins.dir=c:\
\Fiji.app -Xincgc -XX:PermSize=128m -Djava.class.path=c:\\Fiji.app/jars/imagej-l
auncher-3.1.0.jar -Dimagej.dir=c:\\Fiji.app -Dij.dir=c:\\Fiji.app -Dfiji.dir=c:\
\Fiji.app -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=c:\\Fiji.ap
p\\ImageJ-win64.exe -Dij.executable=c:\\Fiji.app\\ImageJ-win64.exe -Djava.librar
y.path=c:\\Fiji.app/lib/win64;c:\\Fiji.app/mm/win64 -Dsun.java2d.noddraw=true -D
ij.debug=true -Dscijava.log.level=debug net.imagej.launcher.ClassLauncher -class
path . -ijjarpath jars -ijjarpath plugins net.imagej.updater.CommandLine update
Using JAVA_HOME c:\Fiji.app/java/win64/jdk1.6.0_24//jre
Opening Java library c:\Fiji.app/java/win64/jdk1.6.0_24//jre/bin/server/jvm.dll
Adding option: -Djava.home=c:\Fiji.app/java/win64/jdk1.6.0_24/
ij1.plugin.dirs: null
$HOME/.plugins: C:\Users\collinet\.plugins does not exist
Launching main class net.imagej.updater.CommandLine with parameters [update]
Class loader = sun.misc.Launcher$AppClassLoader@3326b249
java.lang.ClassNotFoundException: net.imagej.updater.CommandLine
        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)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:231)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
java.lang.ClassNotFoundException: imagej.updater.CommandLine
        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)
        at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:237)
        at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:184)
        at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:76)
Class 'net.imagej.updater.CommandLine' was not found

Oh wow.

Last resort: can you just zip up your Fiji.app with any archiver you have handy (I usually recommend 7-Zip) and upload it with Help>Upload Sample File or share it in any other convenient way? I really would like to have a look at the current situation...

Hi Johannes,
I uploaded my fiji.app as .rar just now. Let me know if you received it.
Claudio

I got the .rar, and with that Fiji I can reproduce both problems!

Will keep you posted.

The 'importPackage' problem you reported is caused by ImageJ 1.x prefixing Javascript scripts with a line that actually fails.

So I put in a couple more levels of fallbacks into the fallback Javascript, and with the Fiji.app you gave me, I can get it into a working shape again: it opens the Javascript and Ctrl+J lets it run the remote updater correctly.

Could you please verify that my fix works on your side of the Atlantic, too?

Thank you very much.

For Curtis: the diff is here: https://github.com/fiji/fiji/commit/bc7da8b6ea70bf6840be0c0d1fa7bdfcbf7c2203

Hi Johannes,
it works also on the other side of the Atlantic! And now I can also read the very useful welcome message.
Thank you so much for your efforts!
All the best
Claudio

Great! I'll close this bug, then. Thank you for your patience with me, I think in the end Fiji became much more robust as a consequence!