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Bug 1036 - version skew in scifio-ome-xml-0.12.1-SNAPSHOT.jar ?
version skew in scifio-ome-xml-0.12.1-SNAPSHOT.jar ?
Status: RESOLVED WONTFIX
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-03-26 03:44 CDT by Aryeh Weiss
Modified: 2015-04-06 17:18 CDT
3 users (show)

See Also:
Description Aryeh Weiss 2015-03-26 03:44:59 CDT 
When I start Fiji, I get teh following:
[INFO] Overriding Dump Stack; identifier: command:org.scijava.plugins.commands.debug.DumpStack; jar: file:/C:/Users/User/Desktop/Fiji.app/jars/scijava-plugins-commands-0.1.7.jar
[ERROR] Cannot create plugin: class='io.scif.ome.translators.TIFFTranslator$OMETIFFTranslator', priority=100.0, enabled=true, pluginType=FromOMETranslator
java.lang.NoClassDefFoundError: ome/units/quantity/Length
	at java.lang.Class.getDeclaredMethods0(Native Method)
	at java.lang.Class.privateGetDeclaredMethods(Class.java:2427)
	at java.lang.Class.getDeclaredMethods(Class.java:1791)
	at org.scijava.util.ClassUtils.getAnnotatedMethods(ClassUtils.java:329)
	at org.scijava.util.ClassUtils.getAnnotatedMethods(ClassUtils.java:290)
	at org.scijava.event.DefaultEventService.subscribe(DefaultEventService.java:109)
	at org.scijava.Context.subscribeToEvents(Context.java:455)
                             ... and a bunch more

If I select the scifio update site, then it does not happen. Note that in each case, ImageJ2 data structures are not enabled, and use SCIFIO is not checked.

When I looked for the class in th plugin  that cannot be created, here is what I found
The class io.scif.ome.translators.TIFFTranslator$OMETIFFTranslator is contained in /C:/Users/User/Desktop/Fiji.app/jars/scifio-ome-xml-0.12.1-SNAPSHOT.jar

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: C:\Users\User\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\User\Desktop\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150319191059)
Fiji: http://fiji.sc/update/ (last check:20150325052333)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20150325062001)
Angiogenesis: http://sites.imagej.net/Angiogenesis/ (last check:20141016170027)
BAR: http://sites.imagej.net/Tiago/ (last check:20150321154850)
BigDataViewer: http://sites.imagej.net/Pietzsch/ (last check:20141221170506)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20150325032644)
Biomedgroup: http://sites.imagej.net/Biomedgroup/ (last check:20150324130527)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20150323111050)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20150303000629)
CMCI-EMBL: http://sites.imagej.net/Miura/ (last check:20140718170940)
IMCF Uni Basel: http://sites.imagej.net/UniBas-IMCF/ (last check:20150211003144)
LOCI: http://sites.imagej.net/LOCI/ (last check:20141210215338)
Morphology: http://sites.imagej.net/Landini/ (last check:20140723175558)
MOSAIC ToolSuite: http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite/ (last check:20150227210151)
NucleusJ: http://sites.imagej.net/PouletAxel/ (last check:20141101113602)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20150325102024)
TrackMate-dev: http://sites.imagej.net/TrackMate-dev/ (last check:20150129185028)

Files not up-to-date:
  db371381 (LOCAL_ONLY) 20140814110352 jars/Lib/UserDict$py.class
  21df2233 (LOCAL_ONLY) 20140814110352 jars/Lib/ntpath$py.class
  ad5ffe6a (LOCAL_ONLY) 20140814110352 jars/Lib/os$py.class
  ba7f97ee (LOCAL_ONLY) 20140814110352 jars/Lib/stat$py.class
  7a73b6fb (LOCAL_ONLY) 20140814105912 jars/Lib/test/blob.jar
  29133ae4 (LOCAL_ONLY) 20140814105916 jars/Lib/test/bug1126/bug1126.jar
  5b9fc5a0 (LOCAL_ONLY) 20140814105912 jars/Lib/test/bug1239.jar
  bb7c5f9c (LOCAL_ONLY) 20140814105912 jars/Lib/test/bug1373.jar
  cf1ee310 (LOCAL_ONLY) 20140814105912 jars/Lib/test/classimport.jar
  77d237d9 (LOCAL_ONLY) 20140814105912 jars/Lib/test/classimport_Lib.jar
  46dddace (LOCAL_ONLY) 20140814105912 jars/Lib/test/syspath_import.jar
  1ad3be0d (LOCAL_ONLY) 20140626093922 jars/jpedalSTD.jar
  febb9d05 (LOCAL_ONLY) 20141106100238 macros/toolsets/LineAndProfileTool.txt
  c8a61322 (LOCAL_ONLY) 20141106100238 plugins/Droplet_.jar
  cd6ef325 (LOCAL_ONLY) 20150201094243 plugins/FigureJ_.jar
  85f658a2 (LOCAL_ONLY) 20141106100238 plugins/IJ_Ed2.jar
  5cccefae (LOCAL_ONLY) 20140626100456 plugins/Morphology/AnnularClosing.txt
  763870ef (LOCAL_ONLY) 20140626100456 plugins/Morphology/AnnularDilation.txt
  da5dc033 (LOCAL_ONLY) 20140626100456 plugins/Morphology/BinaryDilateTest.txt
  9f2b4ef9 (LOCAL_ONLY) 20140626100456 plugins/Morphology/BinaryErodeTest.txt
  3f39caaf (LOCAL_ONLY) 20140626100456 plugins/Morphology/BinaryFilterReconstruct.txt
  d3c84f8c (LOCAL_ONLY) 20140626100456 plugins/Morphology/BinaryLabelMacro.txt
  36e4a042 (LOCAL_ONLY) 20140626100456 plugins/Morphology/BinaryPrune.txt
  3e83cc61 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Boundary4.txt
  9d64440e (LOCAL_ONLY) 20140626100456 plugins/Morphology/Boundary8_.txt
  42967771 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Catalogue_Particles.txt
  f53a898e (LOCAL_ONLY) 20140626100456 plugins/Morphology/CloseByReconstructionTopHat.txt
  6e8c39c9 (LOCAL_ONLY) 20140626100456 plugins/Morphology/CloseByReconstruction_.txt
  1c33105a (LOCAL_ONLY) 20140626100456 plugins/Morphology/ConvexHull1.txt
  7cb69fdf (LOCAL_ONLY) 20140626100456 plugins/Morphology/ConvexHull2.txt
  b19cb415 (LOCAL_ONLY) 20140626100456 plugins/Morphology/ConvexHull3.txt
  bd22187f (LOCAL_ONLY) 20140626100456 plugins/Morphology/Corners.txt
  d463ee86 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Delete_ZeroArea.txt
  8df2eb76 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Diagonal8to4.txt
  e428a0f5 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Domes_stack.txt
  925d3d8c (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawBoundingBox.txt
  63c4cd27 (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawBoundingCircle.txt
  b97f945a (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawConvexHulls.txt
  2adcfe94 (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawFeret&Breadth.txt
  b60f4365 (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawMinR&MaxR.txt
  12880837 (LOCAL_ONLY) 20140626100456 plugins/Morphology/DrawROIs.txt
  288ace7a (LOCAL_ONLY) 20140626100456 plugins/Morphology/EDM_16bits.txt
  71d10273 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Euler.txt
  63757672 (LOCAL_ONLY) 20140626100455 plugins/Morphology/Extended_Maxima.txt
  285e4c16 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Extended_Minima.txt
  e60a415f (LOCAL_ONLY) 20140626100456 plugins/Morphology/FillHolesReconstruct.txt
  fafe8afd (LOCAL_ONLY) 20140626100455 plugins/Morphology/Fill_Border_Holes.txt
  0d5a39d8 (LOCAL_ONLY) 20140626100455 plugins/Morphology/Fill_Greyscale_Holes.txt
  75041650 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyBlackTopHatByReconstruction_.txt
  a1118d5c (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyWhiteTopHatByReconstruction_.txt
  579b5383 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleCentreFilter.txt
  0a50379d (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleKillBorders.txt
  d3047959 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleProperAutomedian.txt
  b4d94111 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleProperClose.txt
  44d81a95 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleProperOpen.txt
  4d7e6035 (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleTopHat.txt
  cb2dc22a (LOCAL_ONLY) 20140626100456 plugins/Morphology/GreyscaleWell.txt
  282495a6 (LOCAL_ONLY) 20140626100455 plugins/Morphology/H-break.txt
  38dbe775 (LOCAL_ONLY) 20140626100456 plugins/Morphology/HMaxima_Transform.txt
  3dc157cf (LOCAL_ONLY) 20140626100456 plugins/Morphology/HMinima_Transform.txt
  af3183b2 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Hole_Counter.txt
  930ee9e1 (LOCAL_ONLY) 20140626100456 plugins/Morphology/HomotopicMarking.txt
  3429c4f3 (LOCAL_ONLY) 20140626100455 plugins/Morphology/Hysteresis.txt
  2511df4c (LOCAL_ONLY) 20140626100456 plugins/Morphology/Impose_Minimum.txt
  6be72748 (LOCAL_ONLY) 20140626100455 plugins/Morphology/Influence_Zones.txt
  5859277c (LOCAL_ONLY) 20140626100456 plugins/Morphology/KeepLargestParticle.txt
  559e475f (LOCAL_ONLY) 20140626100456 plugins/Morphology/KeepLargestParticlePixels_.txt
  4605ad0a (LOCAL_ONLY) 20140626100456 plugins/Morphology/KeepParticlesInRange.txt
  43259a0b (LOCAL_ONLY) 20140626100456 plugins/Morphology/LocalMaxima.txt
  c0207001 (LOCAL_ONLY) 20140626100456 plugins/Morphology/LocalMinMax.txt
  b2139bd8 (LOCAL_ONLY) 20140626100456 plugins/Morphology/LocalMinima.txt
  05f0502d (LOCAL_ONLY) 20140626100456 plugins/Morphology/MCentroids.txt
  b3ea5e05 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MinimaDynamic.txt
  57e4bbaa (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological2Derivative1.txt
  35b51e7e (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological2Derivative2.txt
  ef809632 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological2Derivative3.txt
  372d50f9 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalContrastTopHat.txt
  86d43a13 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalExternalGradient.txt
  66d657f2 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalGradient3.txt
  2cd67873 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalGradientBeucher.txt
  b141cc35 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalInternalGradient.txt
  babf8d91 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalSharpGradient.txt
  7e05ec43 (LOCAL_ONLY) 20140626100456 plugins/Morphology/MorphologicalSmoothing1.txt
  df30c851 (LOCAL_ONLY) 20140626100455 plugins/Morphology/MorphologicalSmoothing2.txt
  80eff432 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological_Clustering.txt
  e031d1be (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological_PCA.txt
  44b58573 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological_SelfDualCentre.txt
  d733fce9 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Morphological_contrast.txt
  1f7a4f93 (LOCAL_ONLY) 20140626100455 plugins/Morphology/Morphological_contrast_thr.txt
  c40dcb5d (LOCAL_ONLY) 20140626100456 plugins/Morphology/MultiscaleGradient.txt
  2d9a97b5 (LOCAL_ONLY) 20140626100456 plugins/Morphology/NumberParticles8_.txt
  cd6cf4de (LOCAL_ONLY) 20140626100456 plugins/Morphology/OpenByReconstructionTopHat.txt
  12b00e10 (LOCAL_ONLY) 20140626100456 plugins/Morphology/OpenByReconstruction_.txt
  8fdf1b15 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Parameter_Matrix.txt
  65c22a1e (LOCAL_ONLY) 20140626100456 plugins/Morphology/ParticleHoleArea.txt
  9a713d79 (LOCAL_ONLY) 20140626100456 plugins/Morphology/ParticleHoleNumber.txt
  9c0a7763 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Particle_Data_Map.txt
  77e227c2 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Particles8ToCalibratedUnits.txt
  c1d65ec7 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Plot_BivariateGraphs.txt
  e8ea53cb (LOCAL_ONLY) 20140626100456 plugins/Morphology/Plot_Histograms.txt
  ce077644 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Prune1.txt
  c4126534 (LOCAL_ONLY) 20140626100455 plugins/Morphology/PruneAll.txt
  916ac5a4 (LOCAL_ONLY) 20140626100456 plugins/Morphology/RegionalMinMax.txt
  3dcf6fa2 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Regional_Maxima.txt
  bc61499e (LOCAL_ONLY) 20140626100456 plugins/Morphology/Regional_Minima.txt
  358d5270 (LOCAL_ONLY) 20140626100456 plugins/Morphology/SelfComplementaryTopHat.txt
  e13f5159 (LOCAL_ONLY) 20140626100456 plugins/Morphology/SelfDualReconstruction_.txt
  64886ac9 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Skeleton1.txt
  64fa451e (LOCAL_ONLY) 20140626100456 plugins/Morphology/Skeleton2.txt
  809a6770 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Skeleton3.txt
  16447730 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Skeleton4.txt
  b2242712 (LOCAL_ONLY) 20140626100456 plugins/Morphology/SkeletonFiltering.txt
  5d0400a0 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Summarize_Results.txt
  ab0b29c3 (LOCAL_ONLY) 20140626100456 plugins/Morphology/Thin_Results_Table.txt
  090f96c1 (LOCAL_ONLY) 20140626100456 plugins/Morphology/UnbiasedCounting.txt
  fecf6a46 (LOCAL_ONLY) 20140626100455 plugins/Morphology/UnbiasedParticleArea.txt
  19a9433c (LOCAL_ONLY) 20140626100456 plugins/Morphology/Viscous_Geodesic_Reconstruction.txt
  8fcd9dfd (MODIFIED) 20140626100748 plugins/Morphology/morphology_collection.jar
  2dbeb38d (LOCAL_ONLY) 20141106100238 plugins/PDF_MacroExt.jar
  f4cd91ea (LOCAL_ONLY) 20141126132110 plugins/StackSorter.class
  203df37a (LOCAL_ONLY) 20141007122052 plugins/Utilities/Time_Series_Analyzer.jar
  01c76d73 (LOCAL_ONLY) 20150201094243 plugins/action_bar.jar
Comment 1 Mark Hiner 2015-03-26 09:14:15 CDT 
Hi Aryeh,

 The Bio-Formats update site enables Bio-Formats 5.1 and thus has to ship updated components that use the new API (such as a modified scifio-ome-xml).

 If any other update site ships its own version of Bio-Formats but doesn't also override the components that have been updated to 5.1, there will be dependency skew.

 If any other update site ships its own version of the updated components without also reverting Bio-Formats to 5.0.x, there will be dependency skew.

The NoClassDefFound is specifying a class (ome.units.quantity.Length) added in Bio-Formats 5.1. Thus you must have another update site enabled that is overwriting Bio-Formats 5.1 with 5.0 without similarly reverting scifio-ome-xml. Turning on the SCIFIO-dev update site fixes the problem by accident, by overwriting the scifio-ome-xml.jar with one compatible with Bio-Formats 5.0.

Knowing this, I looked for what update site was providing the Bio-Formats ome-xml.jar[1]. SCIFIO-dev actually provides its own copy of Bio-Formats 5.0 to avoid skew like this. However, it looks like TrackMate-dev provides an ome-xml.jar without also updating scifio-ome-xml.

So TrackMate-dev is incompatible with Bio-Formats update site. The resolution is to disable one of the two until TrackMate-dev is updated to use Bio-Formats 5.1.

I also filed an issue for the updater to warn about conflicts[2] when update sites provide the same artifacts.

[1] http://imagej.net/Bug_reporting_best_practices#Disable_problematic_update_sites

[2] https://github.com/imagej/imagej-ui-swing/issues/36
Comment 2 Curtis Rueden 2015-04-06 17:18:04 CDT 
The funniest part is that TrackMate does not actually _need_ the ome-xml library anymore. So I removed the linkage:

https://github.com/fiji/TrackMate/commit/ba0aa52c9528110b43b97099051fdd155e792145

But the ome-xml JAR file should still be marked "obsolete (unshadowing)" from the TrackMate-dev update site. Then this problem will go away in this particular case!