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Bug 1218 - Fiji crashes after recent update
Fiji crashes after recent update
Status: NEEDSINFO
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2016-01-29 07:49 CST by Aryeh Weiss
Modified: 2016-01-30 13:09 CST
2 users (show)

See Also:

Attachments
debug output (25.73 KB, application/zip)
2016-01-29 07:55 CST, Aryeh Weiss

Description Aryeh Weiss 2016-01-29 07:49:47 CST 
After a recent update (last week, around 27-01-16), Fiji started crashing. I cannot reproduce a single sequence of actions that cause this, but often a garbled pop-up window will occur before the crash. The pop-up is an expected window (eg, a warnign that only 32-bit windows are supported by some plug-in). 
I ran Fiji in debug mode, and  will upload that using the upload image-file command.
Here is that tail end of the debug output:
[DEBUG] publish(
	context = org.scijava.Context@7b5b8a7f
	consumed = false
	progress = -1
	maximum = -1
	status = Command finished: Up-to-date check
	warning = false,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@7b5b8a7f
	consumed = false
	focus = false,null,null), called from non-EDT Thread:null
[DEBUG] publish(
	context = org.scijava.Context@7b5b8a7f
	consumed = false
	focus = true,null,null), called from non-EDT Thread:null
Abort trap: 6



Note that I updated Java to 1.8.0._71 (I had been running 1.8.0_66).

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.11.3
  java.version => 1.8.0_71
  java.vendor => Oracle Corporation
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.8.0_71-b15
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 25.71-b15
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.8
  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: /Library/Java/JavaVirtualMachines/jdk1.8.0_71.jdk/Contents/Home/jre/
  imagej.dir => /Applications/local/fiji/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20160121135533)
Fiji: http://update.fiji.sc/ (last check:20160126202757)
Java-8: http://sites.imagej.net/Java-8/ (last check:20160127225850)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20160128045832)
BAR: http://sites.imagej.net/Tiago/ (last check:20160125203808)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20160129042646)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20160114141156)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20151207234930)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150303000629)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20151013151911)
GDSC: http://sites.imagej.net/GDSC/ (last check:20160113130152)
GDSC-SMLM: http://sites.imagej.net/GDSC-SMLM/ (last check:20160125165326)
IJPB-plugins: http://sites.imagej.net/IJPB-plugins/ (last check:20160112132924)
LOCI: http://sites.imagej.net/LOCI/ (last check:20150429005912)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723175558)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20160105155554)
PTBIOP: http://biop.epfl.ch/Fiji-Update/ (last check:20151204162832)
RT-Multiview-Deconvolution: http://sites.imagej.net/RT-Multiview-Deconvolution/ (last check:20150703182824)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20160112082758)
3D: http://sites.imagej.net/3D/ (last check:20160127225850)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221170506)

Files not up-to-date:
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Comment 1 Aryeh Weiss 2016-01-29 07:55:54 CST 
Created attachment 277
debug output

Debug output to which I referred.
Comment 2 Mark Hiner 2016-01-29 09:14:28 CST 
Hi Aryeh,

So nothing jumps out to me in the debug messages about what's going wrong.

Last week we did change the OSX launcher to fix Java detection and allow bundled Javas on Mac (so we can start shipping Fiji with Java 8).

Would you mind testing with a bundled Java 1.8.0_66 and see if it's a 1.8.0_71 problem?

If you download this bundle:
http://downloads.imagej.net/java/macosx.tar.gz

and unzip it to your Fiji.app/java/ directory, then it should be picked up when Fiji launches.

Let me know if that's not clear or if Fiji doesn't actually start with 1.8.0_66.

Thanks as always!
Comment 3 Aryeh Weiss 2016-01-30 10:54:19 CST 
Hi Mark,

Thanks for your reply.

The problem first appeared the I was still using 1.8.0_66. I upgraded to 1.8.0_71 in the hope that this would resolve the problem. However, the behaviour did not change. 

I am now downloading your bundle and a fresh Fiji. The downloads are really slow, so it will take some time.
Comment 4 Aryeh Weiss 2016-01-30 12:31:11 CST 
My most recent backup for Fiji.app was 19-Jan-2016. 
When I restored that and ran it with 1.8.0_71, the program did not crash.

There is one change in behaviour since the update that may be relevant.
With the old version, when I launched Fiji, it opened a new icon, and if I launched again, a second instance opened up.

After the update, only one copy of Fiji opens.
Comment 5 Aryeh Weiss 2016-01-30 13:07:54 CST 
I ran the updater on my backup form 19-Jan-2016. However, I excluded files from the ImageJ update site. The problem has not re-appeared. 
The two files that are not up-to-date are ImageJ-mocosx and ImageJ-launcher.

I then update ImageJ-macosx alone. It crashed, but much later than before. 
I ran the droplet finder on something. Then running update-imagej crashed it.

Same result when I added the ImageJ-launcher update.  I cannot run all of the combinations right now, but the problem appears to be in one of those two files.
Comment 6 Aryeh Weiss 2016-01-30 13:09:06 CST 
I ran the updater on my backup form 19-Jan-2016. However, I excluded files from the ImageJ update site. The problem has not re-appeared. 
The two files that are not up-to-date are ImageJ-mocosx and ImageJ-launcher.

I then update ImageJ-macosx alone. It crashed, but much later than before. 
I ran the droplet finder on something. Then running update-imagej crashed it.

Same result when I added the ImageJ-launcher update.  I cannot run all of the combinations right now, but the problem appears to be in one of those two files.