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Bug 775 - bioformats missing jar
bioformats missing jar
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-06-12 04:35 CDT by brotkastennation
Modified: 2014-06-12 07:43 CDT
2 users (show)

See Also:
Description brotkastennation 2014-06-12 04:35:03 CDT 
Since yesterday's update bioformats are not working anymore.
It is requesting a common.jar file which is not available, a formats-common-5.0.2.jar is installed though.
This was done on a freshly compiled and updated distribution.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.14.6-1-ARCH
  java.version => 1.7.0_55
  java.vendor => Oracle Corporation
  java.runtime.name => OpenJDK Runtime Environment
  java.runtime.version => 1.7.0_55-b14
  java.vm.name => OpenJDK 64-Bit Server VM
  java.vm.version => 24.51-b03
  java.vm.vendor => Oracle Corporation
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.7
  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: /usr/lib/jvm/java-7-openjdk/jre
  imagej.dir => /opt/fiji-custom/fiji

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140611193802)

Files not up-to-date:
  7c30c48a (MODIFIED) 20140611122144 Contents/Info.plist
  6b82c620 (LOCAL_ONLY) 20140611122144 Contents/Resources/Fiji.icns
  e369d216 (MODIFIED) 20140611122144 README.md
  766b3f0c (LOCAL_ONLY) 20140611122144 images/fiji-logo-1.0-128x128.png
  5bec251f (LOCAL_ONLY) 20140611122144 images/fiji-logo-1.0-256x256.png
  78576254 (LOCAL_ONLY) 20140611122144 images/function.png
  1faaeed6 (MODIFIED) 20140611122144 images/icon-flat.png
  a02d5340 (MODIFIED) 20140611122144 images/icon.png
  499a3cd7 (LOCAL_ONLY) 20140611122144 images/var.png
  91ece67d (LOCAL_ONLY) 20140611122235 jars/JWlz-1.4.0.jar
  8168b41c (LOCAL_ONLY) 20140611122236 jars/VIB-lib-2.0.0-SNAPSHOT.jar
  2d4780f4 (LOCAL_ONLY) 20140611122236 jars/VectorString-1.0-SNAPSHOT.jar
  a70a2d61 (LOCAL_ONLY) 20140611122236 jars/args4j-2.0.25.jar
  5a0c7964 (LOCAL_ONLY) 20140611122236 jars/batik-1.8.jar
  79924510 (LOCAL_ONLY) 20140611122236 jars/bio-formats/formats-api-5.0.2.jar
  aa815682 (LOCAL_ONLY) 20140611122236 jars/bio-formats/formats-bsd-5.0.2.jar
  98d89e4c (LOCAL_ONLY) 20140611122236 jars/bio-formats/formats-common-5.0.2.jar
  b0dc6eac (LOCAL_ONLY) 20140611122236 jars/bio-formats/formats-gpl-5.0.2.jar
  0b99a39a (LOCAL_ONLY) 20140611122238 jars/bio-formats/mdbtools-java-5.0.2.jar
  caf9f3ae (LOCAL_ONLY) 20140611122238 jars/bio-formats/metakit-5.0.2.jar
  fc861d9e (LOCAL_ONLY) 20140611122238 jars/bio-formats/ome-poi-5.0.2.jar
  f9c55626 (LOCAL_ONLY) 20140611122238 jars/bio-formats/ome-xml-5.0.2.jar
  8eb3709e (LOCAL_ONLY) 20140611122236 jars/commons-logging-1.1.1.jar
  f9509b47 (LOCAL_ONLY) 20140611122236 jars/commons-math3-3.2.jar
  3537b250 (LOCAL_ONLY) 20140611122236 jars/fake-2.0.0-SNAPSHOT.jar
  5f4f0bcc (LOCAL_ONLY) 20140611122236 jars/fiji-compat-2.0.0-SNAPSHOT.jar
  3bce0a2d (LOCAL_ONLY) 20140611122236 jars/fiji-scripting-2.0.0-SNAPSHOT.jar
  0fb912b4 (LOCAL_ONLY) 20140611122236 jars/imagescience-2.4.2-SNAPSHOT.jar
  29a106c2 (LOCAL_ONLY) 20140611122236 jars/imageware-2.0.0-SNAPSHOT.jar
  ce6460d3 (LOCAL_ONLY) 20140611122236 jars/imglib2-algorithms-gpl-2.0.0-beta-26.jar
  673fae25 (LOCAL_ONLY) 20140611122236 jars/imglib2-algorithms-legacy-2.0.0-beta-26.jar
  480b3c14 (LOCAL_ONLY) 20140611122236 jars/itextpdf-5.1.1.jar
  a6c1d188 (LOCAL_ONLY) 20140611122236 jars/j3d-core-1.5.2.jar
  053035a0 (LOCAL_ONLY) 20140611122236 jars/j3d-core-utils-1.5.2.jar
  3d81473f (LOCAL_ONLY) 20140611122236 jars/jai-codec-1.1.3.jar
  5f7f32e2 (LOCAL_ONLY) 20140611122236 jars/jai-core-1.1.3.jar
  e4ac596e (LOCAL_ONLY) 20140611122236 jars/java-cup-0.11a.jar
  74e47f13 (LOCAL_ONLY) 20140611122219 jars/javac-1.6.0.24-ubuntu-fiji1.jar
  f3074e37 (LOCAL_ONLY) 20140611122237 jars/jdom2-2.0.5.jar
  88e007cd (LOCAL_ONLY) 20140611122237 jars/jep-2.4.2.jar
  b5efe893 (LOCAL_ONLY) 20140611122237 jars/jgoodies-common-1.7.0.jar
  5198aba1 (LOCAL_ONLY) 20140611122237 jars/jgoodies-forms-1.7.2.jar
  0e15c072 (LOCAL_ONLY) 20140611122237 jars/jgrapht-0.8.3.jar
  0b768690 (LOCAL_ONLY) 20140611122237 jars/jgraphx-1.10.4.1.jar
  90915f54 (LOCAL_ONLY) 20140611122237 jars/jna-3.2.7.jar
  1ad3be0d (LOCAL_ONLY) 20140611122237 jars/jpedalSTD-2.80b11.jar
  324422ad (LOCAL_ONLY) 20140611122237 jars/js-1.7R2.jar
  c335989b (LOCAL_ONLY) 20140611122237 jars/jzlib-1.0.7.jar
  6c859938 (LOCAL_ONLY) 20140611122237 jars/legacy-imglib1-2.0.0-SNAPSHOT.jar
  35c256ae (OBSOLETE_MODIFIED) 20140611122237 jars/log4j-1.2.17.jar
  7e731ab3 (LOCAL_ONLY) 20140611122237 jars/logback-classic-1.1.1.jar
  b1892343 (LOCAL_ONLY) 20140611122237 jars/logback-core-1.1.1.jar
  231d26b8 (LOCAL_ONLY) 20140611122239 jars/meta-fiji-external-plugins-2.0.0-SNAPSHOT.jar
  4a1974eb (LOCAL_ONLY) 20140611122238 jars/mij-1.3.6-fiji2-SNAPSHOT.jar
  d23fbd8f (LOCAL_ONLY) 20140611122238 jars/mpicbg-20111128.jar
  a51a31db (LOCAL_ONLY) 20140611122238 jars/netcdf-4.3.19.jar
  4660a416 (LOCAL_ONLY) 20140611122238 jars/pal-optimization-2.0.0-SNAPSHOT.jar
  82577709 (LOCAL_ONLY) 20140611122238 jars/pentaho-package-manager-1.0.0.jar
  29f840ae (LOCAL_ONLY) 20140611122238 jars/postgresql-8.2-507.jdbc3.jar
  0ed5f9bf (LOCAL_ONLY) 20140611122238 jars/scala-compiler-2.10.0.jar
  b3d3ad92 (LOCAL_ONLY) 20140611122238 jars/scala-library-2.10.0.jar
  fc039139 (LOCAL_ONLY) 20140611122238 jars/scala-reflect-2.10.0.jar
  e6380596 (LOCAL_ONLY) 20140611122238 jars/scifio-bf-compat-1.7.3.jar
  c544d657 (LOCAL_ONLY) 20140611122238 jars/scifio-lifesci-0.5.0.jar
  e5e6a28d (LOCAL_ONLY) 20140611122238 jars/scifio-ome-xml-0.9.0.jar
  543da7dc (LOCAL_ONLY) 20140611122238 jars/scifio-tools-0.15.0.jar
  5085d943 (OBSOLETE_MODIFIED) 20140611122239 jars/slf4j-api-1.7.6.jar
  9ae3dd1b (OBSOLETE_MODIFIED) 20140611122239 jars/slf4j-log4j12-1.7.2.jar
  6f32205f (LOCAL_ONLY) 20140611122239 jars/vecmath-1.5.2.jar
  d8a4cad8 (LOCAL_ONLY) 20140611122239 jars/wavelets-2.0.0-SNAPSHOT.jar
  b94bc93f (LOCAL_ONLY) 20140611122239 jars/weave_jy2java-2.0.0-SNAPSHOT.jar
  9a71e194 (LOCAL_ONLY) 20140611122239 jars/weka-dev-3.7.6.jar
  c432f64b (LOCAL_ONLY) 20140611122144 luts/16_colors.lut
  89419f99 (LOCAL_ONLY) 20140611122144 luts/5_ramps.lut
  dc3a1bdd (LOCAL_ONLY) 20140611122144 luts/6_shades.lut
  0b3bbb6c (LOCAL_ONLY) 20140611122144 luts/Cyan Hot.lut
  655b55e6 (LOCAL_ONLY) 20140611122144 luts/Green Fire Blue.lut
  2918f6d3 (LOCAL_ONLY) 20140611122144 luts/HiLo.lut
  a3312d3f (LOCAL_ONLY) 20140611122144 luts/ICA.lut
  db5bf8a4 (LOCAL_ONLY) 20140611122144 luts/ICA2.lut
  9f7dd167 (LOCAL_ONLY) 20140611122144 luts/ICA3.lut
  697dd3a4 (LOCAL_ONLY) 20140611122144 luts/Magenta Hot.lut
  524604de (LOCAL_ONLY) 20140611122144 luts/Orange Hot.lut
  9c9a56c2 (LOCAL_ONLY) 20140611122144 luts/Rainbow RGB.lut
  4e686ec6 (LOCAL_ONLY) 20140611122144 luts/Red Hot.lut
  2fdb7c96 (LOCAL_ONLY) 20140611122144 luts/Thermal.lut
  32157491 (LOCAL_ONLY) 20140611122144 luts/Yellow Hot.lut
  a4cec22b (LOCAL_ONLY) 20140611122144 luts/blue_orange_icb.lut
  c9e396a3 (LOCAL_ONLY) 20140611122144 luts/brgbcmyw.lut
  60f85e63 (LOCAL_ONLY) 20140611122144 luts/cool.lut
  ba88e5f3 (LOCAL_ONLY) 20140611122144 luts/edges.lut
  0a4dce83 (LOCAL_ONLY) 20140611122144 luts/gem.lut
  c616e765 (LOCAL_ONLY) 20140611122144 luts/glasbey.lut
  325c01f3 (LOCAL_ONLY) 20140611122144 luts/glow.lut
  1f99f07e (LOCAL_ONLY) 20140611122144 luts/phase.lut
  52a3c399 (LOCAL_ONLY) 20140611122144 luts/physics.lut
  49f5e48a (LOCAL_ONLY) 20140611122144 luts/royal.lut
  898954dd (LOCAL_ONLY) 20140611122144 luts/sepia.lut
  ebd4ed6b (LOCAL_ONLY) 20140611122144 luts/smart.lut
  36e7ca9e (LOCAL_ONLY) 20140611122144 luts/thal.lut
  940b38f9 (LOCAL_ONLY) 20140611122144 luts/thallium.lut
  17243681 (LOCAL_ONLY) 20140611122144 luts/unionjack.lut
  a15ba1d0 (LOCAL_ONLY) 20140611122144 macros/ImportResultsTable.txt
  25abcd0c (LOCAL_ONLY) 20140611122144 macros/StartupMacros.fiji.ijm
  a97e1da9 (LOCAL_ONLY) 20140611122144 macros/listManagement.txt
  1785bbbf (LOCAL_ONLY) 20140611122144 macros/toolsets/Clear Custom Tools.txt
  54200f47 (LOCAL_ONLY) 20140611122144 macros/toolsets/Drawing Tools.txt
  9bd39ac4 (LOCAL_ONLY) 20140611122144 macros/toolsets/Lookup Tables.txt
  f1c9843f (LOCAL_ONLY) 20140611122235 plugins/3D_Blob_Segmentation-2.0.0-SNAPSHOT.jar
  4728cb88 (LOCAL_ONLY) 20140611122235 plugins/3D_Objects_Counter-2.0.0-SNAPSHOT.jar
  00fc4b11 (LOCAL_ONLY) 20140611122235 plugins/3D_Viewer-2.0.0-SNAPSHOT.jar
  9274f337 (LOCAL_ONLY) 20140611122144 plugins/Analyze/Dynamic_ROI_Profiler.clj
  7acae667 (LOCAL_ONLY) 20140611122144 plugins/Analyze/Measure_RGB.txt
  f43ca307 (LOCAL_ONLY) 20140611122235 plugins/AnalyzeSkeleton_-2.0.0-SNAPSHOT.jar
  886fda7c (LOCAL_ONLY) 20140611122235 plugins/Analyze_Reader_Writer-2.0.0-SNAPSHOT.jar
  39e505d0 (LOCAL_ONLY) 20140611122235 plugins/Anisotropic_Diffusion_2D-2.0.0-SNAPSHOT.jar
  435feb1d (LOCAL_ONLY) 20140611122235 plugins/Archipelago_Plugins-0.5.0-SNAPSHOT.jar
  5a2c7cca (LOCAL_ONLY) 20140611122235 plugins/Arrow_-2.0.0-SNAPSHOT.jar
  e54e959e (LOCAL_ONLY) 20140611122235 plugins/Auto_Threshold-1.16-SNAPSHOT.jar
  f692b7f2 (LOCAL_ONLY) 20140611122235 plugins/BalloonSegmentation_-2.0.0-SNAPSHOT.jar
  857ca103 (LOCAL_ONLY) 20140611122235 plugins/BeanShell_Interpreter-2.0.0-SNAPSHOT.jar
  bfe3811a (LOCAL_ONLY) 20140611122235 plugins/Bug_Submitter-2.0.0-SNAPSHOT.jar
  601ae229 (LOCAL_ONLY) 20140611122235 plugins/CLI_-2.0.0-SNAPSHOT.jar
  dd366a81 (LOCAL_ONLY) 20140611122235 plugins/CPU_Meter-2.0.0-SNAPSHOT.jar
  924f3739 (LOCAL_ONLY) 20140611122235 plugins/Calculator_Plus-2.0.0-SNAPSHOT.jar
  24c0ac12 (LOCAL_ONLY) 20140611122235 plugins/Clojure_Interpreter-2.0.0-SNAPSHOT.jar
  433b5484 (LOCAL_ONLY) 20140611122235 plugins/Colocalisation_Analysis-2.0.0-SNAPSHOT.jar
  b877eaaa (LOCAL_ONLY) 20140611122235 plugins/Color_Histogram-2.0.6-SNAPSHOT.jar
  4f108f07 (LOCAL_ONLY) 20140611122235 plugins/Color_Inspector_3D-2.4-SNAPSHOT.jar
  2a1debd5 (LOCAL_ONLY) 20140611122235 plugins/Colour_Deconvolution-2.0.0-SNAPSHOT.jar
  87b80665 (LOCAL_ONLY) 20140611122235 plugins/CorrectBleach_-2.0.0-SNAPSHOT.jar
  5650c474 (LOCAL_ONLY) 20140611122235 plugins/Descriptor_based_registration-2.0.0-SNAPSHOT.jar
  49567c7d (LOCAL_ONLY) 20140611122235 plugins/Dichromacy_-2.0.0-SNAPSHOT.jar
  d8adb1ef (LOCAL_ONLY) 20140611122235 plugins/Differentials_-2.0.0-SNAPSHOT.jar
  1ea3d564 (LOCAL_ONLY) 20140611122235 plugins/Directionality_-2.0.1-SNAPSHOT.jar
  83caa3df (LOCAL_ONLY) 20140611122144 plugins/Examples/Add_Popup_Split_Channels.bsh
  f6fcfac7 (LOCAL_ONLY) 20140611122144 plugins/Examples/Anaglyph_for_Red_Cyan_glasses.rb
  5dcd79ab (LOCAL_ONLY) 20140611122144 plugins/Examples/Blobs_Demo_in_Ruby.rb
  73eff736 (LOCAL_ONLY) 20140611122144 plugins/Examples/Command_Launchers/Command_Launcher_BeanShell.bsh
  95549b2f (LOCAL_ONLY) 20140611122144 plugins/Examples/Command_Launchers/Command_Launcher_Clojure.clj
  dceba709 (LOCAL_ONLY) 20140611122144 plugins/Examples/Command_Launchers/Command_Launcher_Javascript.js
  e4954eac (LOCAL_ONLY) 20140611122144 plugins/Examples/Command_Launchers/Command_Launcher_Python.py
  f5111212 (LOCAL_ONLY) 20140611122144 plugins/Examples/Command_Launchers/Command_Launcher_Ruby.rb
  6076ad74 (LOCAL_ONLY) 20140611122144 plugins/Examples/CoverMaker/Cover_Maker.py
  eabbed47 (LOCAL_ONLY) 20140611122144 plugins/Examples/CoverMaker/Prepare_Cover_Maker_Database.py
  77c7bef5 (LOCAL_ONLY) 20140611122144 plugins/Examples/Delayed_Snapshot.py
  5536e038 (LOCAL_ONLY) 20140611122144 plugins/Examples/Delayed_Snapshot_Window.bsh
  4164c08c (LOCAL_ONLY) 20140611122144 plugins/Examples/Edit_LUT_As_Text.py
  780e948e (LOCAL_ONLY) 20140611122144 plugins/Examples/Extended_Profile_Plot.bsh
  b8881af2 (LOCAL_ONLY) 20140611122144 plugins/Examples/Fiji_Cube.ijm
  3687a018 (LOCAL_ONLY) 20140611122144 plugins/Examples/Fiji_Logo_3D.js
  998cb717 (LOCAL_ONLY) 20140611122144 plugins/Examples/Find_Dimension_of_Raw_Image.py
  66cf50fd (LOCAL_ONLY) 20140611122144 plugins/Examples/Image_To_Tool_Icon.bsh
  ccccc81e (LOCAL_ONLY) 20140611122144 plugins/Examples/Multithreaded_Image_Processing.clj
  720c237b (LOCAL_ONLY) 20140611122144 plugins/Examples/Multithreaded_Image_Processing_in_Javascript.js
  92ce736d (LOCAL_ONLY) 20140611122144 plugins/Examples/Plasma_Cloud.rb
  9efb2292 (LOCAL_ONLY) 20140611122144 plugins/Examples/Same_Slice_in_Multiple_Images.rb
  206a0bbd (LOCAL_ONLY) 20140611122144 plugins/Examples/The_Hue_Game.bsh
  1b6eee3a (LOCAL_ONLY) 20140611122144 plugins/Examples/TrakEM2_Example_Scripts/Homogenize_Ball_Radius.py
  940f6500 (LOCAL_ONLY) 20140611122144 plugins/Examples/TrakEM2_Example_Scripts/Measure_AreaLists.py
  3f4bba61 (LOCAL_ONLY) 20140611122144 plugins/Examples/TrakEM2_Example_Scripts/T2_Select_All.py
  72f00949 (LOCAL_ONLY) 20140611122144 plugins/Examples/TrakEM2_Example_Scripts/T2_set_all_transforms_to_identity.py
  89ef0307 (LOCAL_ONLY) 20140611122144 plugins/Examples/TrakEM2_Example_Scripts/extract_stack_under_arealist.py
  f8479f84 (LOCAL_ONLY) 20140611122144 plugins/Examples/blend_two_images.clj
  0989cf74 (LOCAL_ONLY) 20140611122144 plugins/Examples/celsius_to_fahrenheit.clj
  ff3b9902 (LOCAL_ONLY) 20140611122144 plugins/Examples/chess_.py
  69838e21 (LOCAL_ONLY) 20140611122144 plugins/Examples/compose_rgb-stacks.bsh
  4193ae7c (LOCAL_ONLY) 20140611122144 plugins/Examples/downsample_.js
  66a204d6 (LOCAL_ONLY) 20140611122144 plugins/Examples/list_all_threads.py
  ff4099b9 (LOCAL_ONLY) 20140611122144 plugins/Examples/random_noise_example.clj
  528c239e (LOCAL_ONLY) 20140611122235 plugins/Extended_Depth_Field-2.0.0-SNAPSHOT.jar
  923dbe9c (LOCAL_ONLY) 20140611122235 plugins/FS_Align_TrakEM2-2.0.0-SNAPSHOT.jar
  d1b17a3d (LOCAL_ONLY) 20140611122235 plugins/FeatureJ_-1.6.1-SNAPSHOT.jar
  cdb8ed1c (LOCAL_ONLY) 20140611122235 plugins/Feature_Detection-2.0.0-SNAPSHOT.jar
  e0ff5456 (LOCAL_ONLY) 20140611122235 plugins/Fiji_Archipelago-2.0.0-SNAPSHOT.jar
  c02a1e2c (LOCAL_ONLY) 20140611122235 plugins/Fiji_Developer-2.0.0-SNAPSHOT.jar
  815a1db4 (LOCAL_ONLY) 20140611122235 plugins/Fiji_Package_Maker-2.0.0-SNAPSHOT.jar
  e19c9416 (LOCAL_ONLY) 20140611122235 plugins/Fiji_Plugins-2.0.0-SNAPSHOT.jar
  eb9d4fb7 (LOCAL_ONLY) 20140611122235 plugins/Fiji_Updater.jar
  0bd032ee (LOCAL_ONLY) 20140611122235 plugins/FlowJ_-1.29.1-SNAPSHOT.jar
  ab8007d7 (LOCAL_ONLY) 20140611122235 plugins/Graph_Cut-0.2.0.jar
  ce54aeea (LOCAL_ONLY) 20140611122235 plugins/Gray_Morphology-2.3.2-SNAPSHOT.jar
  1b6d6b3b (LOCAL_ONLY) 20140611122235 plugins/Helmholtz_Analysis-2.0.1-SNAPSHOT.jar
  216f3328 (LOCAL_ONLY) 20140611122235 plugins/IJ_Robot-1.0.0.jar
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  e6b88239 (LOCAL_ONLY) 20140611122235 plugins/Image_5D-1.2.5.jar
  27912ed1 (LOCAL_ONLY) 20140611122235 plugins/Image_Expression_Parser-2.0.0-SNAPSHOT.jar
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  845f8555 (LOCAL_ONLY) 20140611122235 plugins/IsoData_Classifier-2.0.0-SNAPSHOT.jar
  28582f55 (LOCAL_ONLY) 20140611122144 plugins/JRuby/imagej.rb
  9d482c55 (LOCAL_ONLY) 20140611122235 plugins/JRuby_Interpreter-2.0.0-SNAPSHOT.jar
  86347e9a (LOCAL_ONLY) 20140611122235 plugins/Javascript_-2.0.0-SNAPSHOT.jar
  96dd5801 (LOCAL_ONLY) 20140611122235 plugins/Jython_Interpreter-2.0.0-SNAPSHOT.jar
  f6d2d6e9 (LOCAL_ONLY) 20140611122235 plugins/Kuwahara_Filter-2.0.0-SNAPSHOT.jar
  3c7037ca (LOCAL_ONLY) 20140611122235 plugins/Lasso_and_Blow_Tool-2.0.0-SNAPSHOT.jar
  6f5873d2 (LOCAL_ONLY) 20140611122235 plugins/Linear_Kuwahara-2.0.0-SNAPSHOT.jar
  686876ba (LOCAL_ONLY) 20140611122235 plugins/LocalThickness_-3.1.1-SNAPSHOT.jar
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  dd55d7ff (LOCAL_ONLY) 20140611122235 plugins/MTrackJ_-1.5.1-SNAPSHOT.jar
  4dc10833 (LOCAL_ONLY) 20140611122235 plugins/M_I_P-2.0.0-SNAPSHOT.jar
  65a2dd78 (LOCAL_ONLY) 20140611122144 plugins/Macros/About_Plugin_Macros.txt
  dff5642d (LOCAL_ONLY) 20140611122144 plugins/Macros/Bulls_Eye.txt
  e7ffe8ba (LOCAL_ONLY) 20140611122144 plugins/Macros/Polygon_.txt
  39f7ffcd (LOCAL_ONLY) 20140611122144 plugins/Macros/RGB_Histogram.txt
  3ee0edfa (LOCAL_ONLY) 20140611122144 plugins/Macros/batch_convert_any_to_tif.txt
  6b03bc82 (LOCAL_ONLY) 20140611122235 plugins/Manual_Tracking-2.0.0-SNAPSHOT.jar
  61c19f0a (LOCAL_ONLY) 20140611122235 plugins/MosaicJ_-2.0.0-SNAPSHOT.jar
  ed85ef71 (LOCAL_ONLY) 20140611122235 plugins/Multi_Kymograph-2.0.0-SNAPSHOT.jar
  b80e2dcb (LOCAL_ONLY) 20140611122235 plugins/PIV_analyser-1.1.1-SNAPSHOT.jar
  483fc65c (LOCAL_ONLY) 20140611122235 plugins/PointPicker_-2.0.0-SNAPSHOT.jar
  e75a66e3 (LOCAL_ONLY) 20140611122235 plugins/QuickPALM_-1.1.1-SNAPSHOT.jar
  ffe58c64 (LOCAL_ONLY) 20140611122235 plugins/RATS_-2.0.0-SNAPSHOT.jar
  c7c4c1d6 (LOCAL_ONLY) 20140611122235 plugins/RandomJ_-1.5.1-SNAPSHOT.jar
  c6e020d3 (LOCAL_ONLY) 20140611122235 plugins/Reconstruct_Reader-2.0.0-SNAPSHOT.jar
  e82b5bf0 (LOCAL_ONLY) 20140611122235 plugins/Refresh_Javas-2.0.0-SNAPSHOT.jar
  05fbfed0 (LOCAL_ONLY) 20140611122235 plugins/SPIM_Opener-2.0.0-SNAPSHOT.jar
  412d7708 (LOCAL_ONLY) 20140611122235 plugins/SPIM_Registration-2.0.0-SNAPSHOT.jar
  fbb87e51 (LOCAL_ONLY) 20140611122235 plugins/Samples_-2.0.0-SNAPSHOT.jar
  d5977d8a (LOCAL_ONLY) 20140611122235 plugins/Scala_Interpreter-1.0.2-SNAPSHOT.jar
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Comment 1 Mark Hiner 2014-06-12 06:42:39 CDT 
Hello,

> This was done on a freshly compiled and updated distribution.

When you say "compiled" do you mean built from source, e.g. https://github.com/fiji/Fiji ? If so, please be aware that this version of Fiji is intended for developers of Fiji source, and not users. It is our aspiration to keep the Fiji source in synch with the user distribution (that is, the Fiji and ImageJ update sites) but the reality is that they are out of synch and the developer version needs some TLC, but with the publicization of ImageJ2 we have been prioritizing what users see.

Next, how are you using Bio-Formats that you got this error? Were you running the Bio-Formats importer? Just wanted to be clear, to attempt to reproduce. Locally I can not reproduce this, with an up-to-date Fiji... my Bio-Formats importer works perfectly.

Regardless if this was from source or not, it looks like you do not have the Fiji update site enabled. The Fiji update site is what provides and manages the Bio-Formats dependencies (they are not part of core ImageJ2).. this is why you have so many "local_only" dependencies in your bug report. Take a look at http://fiji.sc/Frequently_Asked_Questions#How_can_I_verify_that_my_Fiji_is_really_100.25_up_to_date.3F

Anyway, please enable the Fiji update site and update your installation again. Then your Fiji will be truly up-to-date and if you continue to have problems with Bio-Formats, we can go from there.

It looks like you have all the appropriate Bio-Formats 5.0.2 jars installed, but without knowing exactly what your local state is relative to the Fiji update site, and not knowing how you were invoking Bio-Formats, I can't investigate your problem.

Thanks!
- Mark
Comment 2 brotkastennation 2014-06-12 07:14:38 CDT 
Hi, thanks a lot for your detailed explanation.
I tried before to add the bioformats update-site, and this didn't work, but adding the fiji update-site resolved the problem.
And yes,  I used https://github.com/fiji/Fiji for the source code as I thought this would be the place where problems would be first fixed, but I was not aware that it is for developers only.
I was also not clear, the problem arose when running bioformats-importer/-exporter.
Thanks and sorry for the trouble :-)
Comment 3 Mark Hiner 2014-06-12 07:43:08 CDT 
It's no trouble! We're here to answer questions and solve problems, and we absolutely depend on community members who are willing to try things and let us know when they don't work :)

And your intuition was perfectly reasonable to look to the source code for the latest bug fixes. In time we would like the behavior of the source checkout to reflect what's on the update site, so that people can do exactly what you tried.

In the mean time, I added a warning to the Fiji repository to clarify its intended function.. so hopefully that will mitigate future confusion.