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Bug 136 - Get DOS code to manually remove updated files when reboot Fiji after update. This occurs on my Vista machine but not XP machine. Might update to Win7, should that make a difference.
Get DOS code to manually remove updated files when reboot Fiji after update. ...
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-02-08 15:38 CST by Dave Schneider
Modified: 2011-03-23 15:59 CDT
1 user (show)

See Also:

Description Dave Schneider 2010-02-08 15:38:12 CST
[Enter details of the problem or bug and how to reproduce it here.]

Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows Vista
  os.version => 6.0
  java.version => 1.6.0_16
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_16-b01
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 14.2-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \
Comment 1 Dave Schneider 2010-02-08 15:45:27 CST
After updates are applied, a DOS window opens when I reboot Fiji. The window states that I need to manually remove certain files (the ones that were replaced or otherwise removed in the updates). Everything works fine after I do this and reboot Fiji again. This is only a problem on my machine running Vista Professional Edition and not on my XP Professional. I could upgrade to Win 7 if that makes a difference.
Comment 2 Johannes Schindelin 2010-02-09 10:52:18 CST
What files do you have to remove? What error message did it display? Without vital information like this, you ask me to guess, and I refuse to do that.
Comment 3 Dave Schneider 2010-02-09 17:34:30 CST
(In reply to comment #2)
> What files do you have to remove? What error message did it display? Without
> vital information like this, you ask me to guess, and I refuse to do that.

I'll try to replicate this again and write this information down. To do so I deleted the Fiji program folder and re-extracted the original download to C:\Program Files\.

I start Fiji and go to Help>Update Fiji. This opens the Fiji Updater window and ends with "jars/jython2.2.1/jython.jar"..."Uninstall it". I Apply changes and it states update is successful. Upon restart I get a DOS window that states "Could not remove C:\Progra~1\Fiji.app/jars/jython2.2.1/jython.jar". 

If I close the window, restart Fiji, the DOS window does not come up. However, I get the same update suggestion. 

If instead I close Fiji and the DOS window, manually remove the jython.jar from its folder, then no DOS window appears upon restarting Fiji and Fiji is reported as up to date.

This behavior is exactly the same as when I first downloaded Fiji (approximately 2010.02.02) BUT it involved numerous plugin files and a few jar files instead of just the one reported this time. Previously, when multiple files needed updating, I would recieve the "Could not remove..." statement for just one file at a time; i.e., I would not get the next file in need of deleting until I restarted Fiji again. Once I got through all those manual deletions Fiji seemed to work just fine until the next updates. I think there were two or three updates since that time and, except for the very last update, all others required manual removal of updated files. The very last update (2010.02.07 or 08) did not behave this way but worked without requiring manual removal of any files.

I hope this helps. I'm sorry I can't recall all the files that this previously involved. But the behavior, though involving only one file this time, seems still to occur today (2010.02.09).
Comment 4 Dave Schneider 2010-02-11 16:08:05 CST
Another update today replicates original problem.

Start Fiji and allow updater to run.

Fiji updater window:
"plugins/TrakEM2_.jar...update it
plugins/mpicbg_.jar...update it"

Applied changes. Restart Fiji

1st DOS window <window autocloses after ~60s>:
"Could not move C:\Progra~1\Fiji.app/update/plugins/TrkEM2_.jar to C:\Progra~1\Fiji.app/plugins/TrakEM2_jar: File exists."

Try starting Fiji again. 2nd DOS window <autocloses after ~60s>:
"Could not remove old version of C:\Progra~1\Fiji.app/plugins/mpicbg_.jar. Please remove manually!"

Restarting Fiji results in second DOS window again.

Removed mpicbg_.jar manually.

Restart Fiji and get 1st DOS window.

Removed TrakEM2_.jar and Fiji restarts normally and is up-to-date.

I'm starting to think the difficulties are related to the user control protection of Vista. Vista gives me a window "Destination Folder Access Denied" everytime I try to delete something from Fiji. I press the "Continue" button to confirm the intended deletion of the file which then brings up an "User Account Control" window asking me to confirm that I started this action. These must be steps that the Fiji update process cannot overcome. Perhaps upgrading to Windows 7 will alleviate the update hassel I'm experiencing.
Comment 5 Johannes Schindelin 2011-03-23 15:59:23 CDT
I very much hope that you excuse the long delay in answering, but I equally hope that I managed to fix the issue in the meantime. If not, please let me know and reopen the bug. I will have to reproduce this somehow (which involves me physically being in front of a machine that has the same OS as you have...)