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Bug 1159 - toxic fiji updater
toxic fiji updater
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-09-15 08:09 CDT by vbindoka
Modified: 2015-09-15 08:51 CDT
3 users (show)

See Also:
Description vbindoka 2015-09-15 08:09:43 CDT 
as folks have mentions RE OSX and the daily updater, I can tell you I've just had to reload fiji from scratch.
Not a quick fix, since I have many plugins and settings to restore by hand!

PLEASE STIOP THE TOXIC UPDATER UNTIL THE PROBLEM IS FIXED

You will notice I'm running win7-64 NOT OSX.... [so it affects all, it seems]

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\SEP201~1/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\SEP201~1

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150914115303)
Fiji: http://update.fiji.sc/ (last check:20150910163236)

Files not up-to-date:
  6d337b7a (LOCAL_ONLY) 20140730142734 plugins/Accurate_Gaussian_Blur.class
  6e9d50db (LOCAL_ONLY) 20140320051924 plugins/Adjustable_Watershed.class
  306ad943 (LOCAL_ONLY) 20150721115948 plugins/Align3_TP.jar
  12ec0761 (LOCAL_ONLY) 20120224100622 plugins/Align_RGB_planes.class
  f98ce4f3 (LOCAL_ONLY) 20150721120238 plugins/Auto_Align_2.jar
  b0398adb (LOCAL_ONLY) 20141028073350 plugins/DeconvolutionLab/DeconvolutionLab_.jar
  aaeffc0c (LOCAL_ONLY) 20141222071308 plugins/FFMPEG_IO.jar
  11326750 (LOCAL_ONLY) 20050408103628 plugins/FFT1D.class
  18f23277 (LOCAL_ONLY) 20050408103628 plugins/FourierSpace.class
  44693e65 (LOCAL_ONLY) 20150325121214 plugins/Frac_Lac.jar
  348da731 (LOCAL_ONLY) 20141126044659 plugins/GHT_.jar
  15a0aac2 (LOCAL_ONLY) 20050408150536 plugins/GibsonPSF.class
  52861b7c (LOCAL_ONLY) 20050408150244 plugins/GibsonPSFF.class
  62fcee4a (LOCAL_ONLY) 20150216122311 plugins/HDF5_Vibez.jar
  f481dc68 (LOCAL_ONLY) 20120817074900 plugins/Hybrid_2D_Filters.class
  6b2de3e5 (LOCAL_ONLY) 20120817084143 plugins/Hybrid_3D_Filters.class
  e9cb6eb7 (LOCAL_ONLY) 20150115083713 plugins/Image_CorrelationJ_1o.class
  077159f3 (LOCAL_ONLY) 20150716125422 plugins/Image_Stabilizer.class
  55624188 (LOCAL_ONLY) 20150716125430 plugins/Image_Stabilizer_Log_Applier.class
  d6bc39b9 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins.jar
  04b38ca7 (LOCAL_ONLY) 20141023044548 plugins/Jay_Plugins2.jar
  71ae5c42 (LOCAL_ONLY) 20140509130342 plugins/KalmanOpenStackFilter_.class
  d0d470a1 (LOCAL_ONLY) 20150910042624 plugins/MIST_.jar
  53c5c1ad (LOCAL_ONLY) 20141103073745 plugins/NL_Means_.jar
  21927175 (LOCAL_ONLY) 20140808090713 plugins/PIV_.jar
  b3b13b1f (LOCAL_ONLY) 20050408150244 plugins/PSFCredits$1.class
  cb99705d (LOCAL_ONLY) 20050408150244 plugins/PSFCredits.class
  de90b917 (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG$1.class
  e33950eb (LOCAL_ONLY) 20050408150536 plugins/PSFCreditsG.class
  9f2412ff (LOCAL_ONLY) 20141028082626 plugins/PSF_Generator.jar
  5a3abd78 (LOCAL_ONLY) 20050408150536 plugins/PSF_Gibson_.class
  65b190f7 (LOCAL_ONLY) 20121002063426 plugins/PSF_Simple_.class
  12289f6e (LOCAL_ONLY) 20110916093010 plugins/PureDenoise_.jar
  2d4a0cba (LOCAL_ONLY) 20150804045930 plugins/Thunder_STORM.jar
  69b16199 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4.class
  f0990b22 (LOCAL_ONLY) 20050408103628 plugins/WaveDaub4Filter.class
  27901023 (LOCAL_ONLY) 20050408152652 plugins/Wavelet_Deconvolution_.class
  7ad8e0c0 (LOCAL_ONLY) 20150406040305 plugins/gdsc_smlm-0.3.1-SNAPSHOT.jar
  71331805 (LOCAL_ONLY) 20140314082430 plugins/jacop_.jar
  9bbfb280 (LOCAL_ONLY) 20140225135257 plugins/octane2_.jar
Comment 1 Jan Eglinger 2015-09-15 08:16:10 CDT 
I don't know what you are refering to by mentioning "folks" and "RE OSX", but as mentioned on the ImageJ mailing list [1], there's a recent update that breaks Fiji on all platforms.

A workaround to fix existing installations is to run the following command from the command prompt:

    ImageJ-win64.exe --update update jars/imagej-deprecated.jar

See also: https://github.com/imagej/imagej-ops/issues/201


[1]: http://imagej.1557.x6.nabble.com/Fiji-won-t-boot-after-update-td5014333.html
Comment 2 Curtis Rueden 2015-09-15 08:51:52 CDT 
I cannot reproduce this, so I cannot test. However, I have tweaked the metadata to -- I hope! -- avoid this issue for now.

For details, see https://github.com/imagej/imagej-ops/issues/201

And you can fix a broken installation using the instructions posted by Jan. There should be no need to install from scratch, unless that is easier for you.