[ImageJ-bugs] [Bug 1036] New: version skew in scifio-ome-xml-0.12.1-SNAPSHOT.jar ?

bugzilla at fiji.sc bugzilla at fiji.sc
Thu Mar 26 03:44:59 CDT 2015 

http://fiji.sc/bugzilla/show_bug.cgi?id=1036

            Bug ID: 1036
           Summary: version skew in scifio-ome-xml-0.12.1-SNAPSHOT.jar ?
           Product: Fiji
           Version: unspecified
          Hardware: PC
                OS: Windows
            Status: NEW
          Severity: normal
          Priority: P4
         Component: Plugins
          Assignee: imagej-bugs at imagej.net
          Reporter: aryeh at cc.huji.ac.il
                CC: aryeh at cc.huji.ac.il

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

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