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Bug 262 - Error message when creating a new macro from Plugin>New>Macro command
Error message when creating a new macro from Plugin>New>Macro command
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-12-17 01:08 CST by Christophe Leterrier
Modified: 2011-03-23 15:41 CDT
1 user (show)

See Also:
Description Christophe Leterrier 2010-12-17 01:08:41 CST 
[Enter details of the problem or bug and how to reproduce it here.]

Problem when creating a new macro
Plugin>New>Macro displays this error (the scipt editor opens fine afterwards):

java.util.zip.ZipException: error in opening zip file
	at java.util.zip.ZipFile.open(Native Method)
	at java.util.zip.ZipFile.<init>(ZipFile.java:114)
	at java.util.jar.JarFile.<init>(JarFile.java:135)
	at java.util.jar.JarFile.<init>(JarFile.java:72)
	at fiji.scripting.FileFunctions.getResourceList(FileFunctions.java:473)
	at fiji.scripting.TextEditor.addTemplates(TextEditor.java:523)
	at fiji.scripting.TextEditor.<init>(TextEditor.java:253)
	at fiji.scripting.TextEditor.<init>(TextEditor.java:414)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at ij.IJ.runFijiEditor(IJ.java:1767)
	at ij.plugin.NewPlugin.createMacro(NewPlugin.java:85)
	at ij.plugin.NewPlugin.run(NewPlugin.java:70)
	at ij.IJ.runPlugInUnchecked(IJ.java:175)
	at ij.IJ.runPlugIn(IJ.java:157)
	at ij.Executer.runCommand(Executer.java:147)
	at ij.Executer.run(Executer.java:78)
	at java.lang.Thread.run(Thread.java:680)



Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.5
  java.version => 1.6.0_22
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_22-b04-307-10M3261
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 17.1-b03-307
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: You wanted to be reminded later.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  fiji.dir => /Users/christo/Desktop/Fiji new/Fiji.app

Information about the version of each plugin:

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  c9e396a3f83ee8cebf1ed28d3e2d53296cc908e7 20100610022423 luts/brgbcmyw.lut
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  42556198e68860b4135544fe9e4687c9fbffbfe2 20100614020252 plugins/Gray_Morphology.jar
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  72106d6178a646a997ac2344e42432b24d03643e 20101216180933 plugins/IO_.jar
  f372670cec289607ac065298e38cd59ed9b278f7 20101216180401 plugins/Image_5D.jar
  cd8ce4a950d74c5aa88adf357877efff8087b374 20101216181031 plugins/Image_Expression_Parser.jar
  43bb3a7b79d1fc23958a7775f407fa9567c6f67f 20100614020246 plugins/Interactive_3D_Surface_Plot.jar
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  28582f554fdbc4905b5ca4eb192a516202b2f334 20100610022424 plugins/JRuby/imagej.rb
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  00b30a4e1985b2637a4e48ee422d0eee02dfd51a 20100614020243 plugins/Javascript_.jar
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  65a2dd7816efceb28030dc0ea7cb4ad51c42e9a0 20100610022424 plugins/Macros/About_Plugin_Macros.txt
  dff5642dcb662c06fd8cd7dfce73f60a4b8b8244 20100610022424 plugins/Macros/Bulls_Eye.txt
  e7ffe8ba782ce90d3b80ad882c474ab1836b58a4 20100610022424 plugins/Macros/Polygon_.txt
  39f7ffcd9b21888b618524a811eb39c93625578d 20100610022424 plugins/Macros/RGB_Histogram.txt
  3ee0edfae7b40189254e38a6ed8108c52859bc33 20100610022424 plugins/Macros/batch_convert_any_to_tif.txt
  d0cd293b359b7bcdf390e560dc28f68fa8033677 20100614020254 plugins/Manual_Tracking.jar
  de3a020be174270600534345eb47fd76267d8080 20101216180628 plugins/MosaicJ_.jar
  a349b390595c90be2924a20a372aac99bad438e7 20101216180940 plugins/PIV_analyser.jar
  c0e6e54ff0ec7c62350f232af75c85ca7006b51f 20101216180628 plugins/PointPicker_.jar
  32d24a273fef021b079fc64f151c2436af700b30 20101216181031 plugins/QuickPALM_.jar
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  21649af3b91a9d7b49daaa370f13570802b1b78e 20101216180941 plugins/Refresh_Javas.jar
  f520a9e24b1903d3aceba72aa3bfab12dfc8d515 20101216181029 plugins/SPIM_Registration.jar
  6e155e63de9510ee2fb990d9cc6ddf0c5f209cb5 20101216180650 plugins/Samples_.jar
  54b884c9df57a692b25b415fddec8de4fddaf18b 20101216181008 plugins/Script_Editor.jar
  0b422ad448d52a4a3f799b29b2e9d1ec954fb20d 20101216180652 plugins/Series_Labeler.jar
  50ee8cf26b2e4bf1b9774a83d227fae873158ef8 20101216180630 plugins/SheppLogan_.jar
  bf0d28714aff10252a96ef652c5a08f935c12e64 20101216181025 plugins/Simple_Neurite_Tracer.jar
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  1a5f4c622997d1d23f1d08c81c46b80b4da05d47 20100614020248 plugins/Skeletonize3D_.jar
  e71b5942e5343cbc3d591f249cc9f3dfc73c7e29 20101216180630 plugins/Snakuscule_.jar
  41d82921719c38520d5472a3608b79394db1b7b0 20100614020244 plugins/SplineDeformationGenerator_.jar
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  5e20cc0a6c833ebfdcd5fc6517eed89a44ae35dc 20101216180622 plugins/TopoJ_.jar
  963f0b325919991a8c31ef06a1c84ad499d52232 20101216181017 plugins/Trainable_Segmentation.jar
  23acd25af012cdb42209e22d2da02ed7cfa8739d 20101216180959 plugins/TrakEM2_.jar
  39d4aaafb0c6bea4ef6cdf95bcaf2c4665d9bdc2 20101216181000 plugins/TransformJ_.jar
  09868b512410628e06c7dc25a6999c7dda8cf078 20100614020249 plugins/TurboReg_.jar
  9558400db089262849c33428a77645c323390145 20101216180630 plugins/UnwarpJ_.jar
  a32dfe463fa2c8814cb0caf9079478ff4e1c44bf 20100610022424 plugins/Utilities/Close_All_Without_Saving.txt
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  a43c9ad3f07dbfa56be075a9ebdcfa115f6675c8 20100614020246 plugins/View5D_.jar
  b8c3af50365b12b0beb010f1c35134cbd310341a 20100614020247 plugins/Volume_Viewer.jar
  e9a7358277abe3a90df974fc81d96be9c9a71a9e 20100614020236 plugins/bUnwarpJ_.jar
  659ad6a335b4947eef8758b1b0cf050779430b78 20100614020238 plugins/ij-ImageIO_.jar
  f3989138cbab5258cd8d6d682f93454637060d10 20101216181004 plugins/level_sets.jar
  d0fc09ac8b73b60d76627e6f7a10e97a166aa27e 20101216180500 plugins/loci_tools.jar
  902cc98f006103c1b7a46051ebf86d489aec9579 20101216180502 plugins/mpicbg_.jar
  91bf372e9c531a68d08cb158239df303c0a37fb1 20101216181005 plugins/register_virtual_stack_slices.jar
  4d7eaf239c033d305a464a06c3e64c68d096c7e1 20100614020242 plugins/registration_3d.jar
  e6e0879f5d50afa8d0dd213b4b66e396a39a47b7 20100610022426 retro/backport-util-concurrent-3.1.jar
  e250f0c40b768e90ed7d3910d9869075f3e438cd 20100610022426 retro/retrotranslator-runtime-1.2.7.jar
  eea1390da8fac38763ed4c03f1acb3342b942717 20100610022426 retro/retrotranslator-transformer-1.2.7.jar
  d326018044a582f5106efc6fc90ad09f98a6a822 20100610022426 scripts/Record_Desktop.py
  0ea7f8fc6683e74065ae7fd82c1b92676e069526 20100610022426 scripts/Record_Window.py
Comment 1 Christophe Leterrier 2010-12-17 02:07:33 CST 
Similar error happens when drag and dropping a .ijm file on Fiji toolbar:

java.util.zip.ZipException: error in opening zip file
	at java.util.zip.ZipFile.open(Native Method)
	at java.util.zip.ZipFile.<init>(ZipFile.java:114)
	at java.util.jar.JarFile.<init>(JarFile.java:135)
	at java.util.jar.JarFile.<init>(JarFile.java:72)
	at fiji.scripting.FileFunctions.getResourceList(FileFunctions.java:473)
	at fiji.scripting.TextEditor.addTemplates(TextEditor.java:523)
	at fiji.scripting.TextEditor.<init>(TextEditor.java:253)
	at fiji.scripting.Script_Editor.run(Script_Editor.java:41)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at ij.io.Opener.open(Opener.java:165)
	at ij.io.Opener.openAndAddToRecent(Opener.java:228)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:182)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:158)
	at java.lang.Thread.run(Thread.java:680)
Comment 2 Christophe Leterrier 2011-01-13 09:45:39 CST 
and similar error when double clicking on a .ijm macro in the Finder, error displayed before the Script Editor window appear :


java.util.zip.ZipException: error in opening zip file
	at java.util.zip.ZipFile.open(Native Method)
	at java.util.zip.ZipFile.<init>(ZipFile.java:114)
	at java.util.jar.JarFile.<init>(JarFile.java:135)
	at java.util.jar.JarFile.<init>(JarFile.java:72)
	at fiji.scripting.FileFunctions.getResourceList(FileFunctions.java:473)
	at fiji.scripting.TextEditor.addTemplates(TextEditor.java:523)
	at fiji.scripting.TextEditor.<init>(TextEditor.java:253)
	at fiji.scripting.Script_Editor.run(Script_Editor.java:41)
	at ij.IJ.runUserPlugIn(IJ.java:193)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.IJ.runPlugIn(IJ.java:143)
	at ij.io.Opener.open(Opener.java:165)
	at ij.io.Opener.openAndAddToRecent(Opener.java:228)
	at MacAdapter.run(MacAdapter.java:41)
	at java.lang.Thread.run(Thread.java:680)
Comment 3 Christophe Leterrier 2011-01-13 09:49:20 CST 
I want to add that when using Plugins>New>Macro, the new macro is created despite the appearance of the errors in the log windows, but it appears in a new Script Editor window, even if there is already a Script Editor window opened. Should'nt the new macro appear as a tab in the existing Script Editor window ?
Comment 4 Johannes Schindelin 2011-03-23 15:41:34 CDT 
These messages are purely informing you that one of your .jar files are not valid .zip files. Which might make them dysfunctional in the first place.

Maybe it would be better to show these messages in a nicer form, but I lack the time to make them nicer.