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Bug 795 - update sites that kill fiji
update sites that kill fiji
Status: RESOLVED MOVED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: Johannes Schindelin
Depends on:
Blocks:
 
Reported: 2014-06-17 06:04 CDT by Aryeh Weiss
Modified: 2015-04-15 12:39 CDT
6 users (show)

See Also:

Attachments
SCIFIO-dev startup log (2.77 KB, text/plain)
2014-06-17 07:01 CDT, Mark Hiner
lllt startup error log (2.77 KB, text/plain)
2014-06-17 07:02 CDT, Mark Hiner

Description Aryeh Weiss 2014-06-17 06:04:03 CDT 
As of 17-6-2014, I identified 3 update sites tha kill fiji (ie, cause it to fail to launch) on openSuse 13.1 .

trackmate
scifio-dev
LLLT

Each of these individually  will cause Fiji to fail to launch. 
I verified that when all except these are selected, Fiji launches.

The biomed update site produces a duplication error with IJ-blob-1.2.jar

I saved the stderr output for the failed execution after adding scifio-dev and after LLLT
However, i donot see how to attach those files, so I will email them separately.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.11.10-11-desktop
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/hila/Downloads/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  imagej.dir => /home/hila/Downloads/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140616163006)
Fiji: http://fiji.sc/update/ (last check:20140616190925)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20140411041644)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20140611105952)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140519212603)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131221011857)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140328125917)
CMP-BIA tools: http://sites.imagej.net/CMP-BIA/ (last check:20140423173817)
FFMPEG: http://fiji.sc/~schindelin/ffmpeg-plugins/ (last check:20130606182449)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20140616185733)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20140526174644)
ImageJ Latex: http://sites.imagej.net/Yul.liuyu/ (last check:20130817015011)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20140521190037)

Files not up-to-date:
  6e312829 (NOT_INSTALLED) 20140616191117 jars/bsh.jar
Comment 1 Aryeh Weiss 2014-06-17 06:07:08 CDT 
I tried uploading the two log files using "upload a sample image"
Please let me know if that worked.
Comment 2 Mark Hiner 2014-06-17 07:01:30 CDT 
Created attachment 163
SCIFIO-dev startup log
Comment 3 Mark Hiner 2014-06-17 07:02:03 CDT 
Created attachment 164
lllt startup error log
Comment 4 Mark Hiner 2014-06-17 07:04:35 CDT 
Thanks for testing Aryeh! This is great information.

>However, i donot see how to attach those files, so I will email them separately.

There should be an "Attachments" section right above "Additional Comments".. and in there is an "Add an attachment" link that takes you to an upload page.

I went ahead and uploaded the two logs you took though.

I'll take care of updating SCIFIO-dev today.
Comment 5 Mark Hiner 2014-06-19 14:54:04 CDT 
The SCIFIO-dev update site is now fixed.

Also opened a new ticket to mitigate these problems in the long term: https://github.com/imagej/imagej-updater/issues/30
Comment 6 Mark Hiner 2014-06-19 15:09:04 CDT 
Note that, in the mean time, the LLTT update site (http://sites.imagej.net/Alex-krull/jars/) has many ImgLib2 SNAPSHOT jars, and would probably be fixed by updating dependencies to the latest releases.

It looks like TrackMate-dev's dependencies are based off pom-fiji, which I believe is always a snapshot. It also is using pom-imagej 2.31 which uses pom-scijava 2.18. So if we update the stack (release pom-imagej 2.33 which depends on pom-scijava 2.20) I'm assuming the TrackMate site will work again as long as it isn't pulling in any other dependencies... (at a glance, everything else looks fine in https://github.com/fiji/TrackMate/blob/e61e7acc30affe729aad3b09e5d2caa7c9608494/pom.xml)
Comment 7 Curtis Rueden 2014-06-23 16:05:27 CDT 
Johannes recently fixed TrackMate-dev, so the only remaining problem site is LLTT, which has not been updated in over a year.

The plan is to add some logic to the ImageJ Updater to prevent clashes between libraries in these situations. See https://github.com/imagej/imagej-updater/issues/30 for details. Johannes plans to tackle it later this week, hopefully tomorrow.
Comment 8 Aryeh Weiss 2014-06-24 02:18:00 CDT 
I can confirm that adding trackmate-dev on my OSX system no longer breaks Fiji.
Comment 9 Jean-Yves Tinevez 2014-06-24 02:52:17 CDT 
I confirm as well that it does not break Fiji. 
Plus I get the v2.3.1-SNAPSHOT of TrackMate, which is exactly what is expected.
Awesome guys!
Comment 10 Johannes Schindelin 2014-06-24 08:15:00 CDT 
Aryeh, J-Y: Thanks for all your help!

We are not *quite* out of the woods yet, but the upcoming updater change that will respect SemVer (http://semver.org/) when handling artifacts from the ImageJ update site, even LLLT should be "fixed"...
Comment 11 Thorsten W. 2014-07-12 05:27:09 CDT 
Hi,

I've resolved the duplication error with ijblob!

Thank you for reporting!

Cheers,
Thorsten
Comment 12 Jean-Yves Tinevez 2015-04-14 01:57:56 CDT 
Can we close this one?
Comment 13 Curtis Rueden 2015-04-15 12:39:56 CDT 
Unfortunately, the relevant issue (https://github.com/imagej/imagej-updater/issues/30) was never addressed. So the possibility of update sites killing ImageJ2 remains a very real threat.

That said, I'm closing this bug as "MOVED" since we have an appropriate issue on GitHub, and Aryeh's specific clashes are now long resolved.