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Bug 712 - Update window does not close when pressing 'Close' button
Update window does not close when pressing 'Close' button
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Other
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-03-07 09:15 CST by laurent.holtzer
Modified: 2014-07-25 10:36 CDT
2 users (show)

See Also:
Description laurent.holtzer 2014-03-07 09:15:30 CST 
When I start FIJI update from the menu (probably also when it is automatically started when FIJI is starting) it is not possible to close the 'ImageJ Updater' window using the Close button. Also pressing the red cross in the upper-left corner does not work. The other buttons work fine.

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.2
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-11M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  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: Unexpected end of ZLIB input stream

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  ij.dir => /Applications/Fiji.app

Information about the version of each plugin:

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  aa0fa91d 20120829144824 plugins/Fiji_Updater.jar
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  8b85c6b0 20111117165114 plugins/Image_5D.jar
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  65b42030 20130619163839 plugins/Interactive_3D_Surface_Plot-2.31.1-SNAPSHOT.jar
  b483961e 20130619163848 plugins/IsoData_Classifier-2.0.0-SNAPSHOT.jar
  28582f55 20110303204100 plugins/JRuby/imagej.rb
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  a7edca68 20130906110107 plugins/Jython_Interpreter-2.0.0-SNAPSHOT.jar
  2d8f3e60 20130902145348 plugins/LOCI/misc_plugins-1.0.0-SNAPSHOT.jar
  542ef100 20120523104144 plugins/LSM_Reader.jar
  de0f4b67 20110307151006 plugins/LSM_Toolbox.jar
  5830f8ee 20130619163846 plugins/Lasso_and_Blow_Tool-2.0.0-SNAPSHOT.jar
  c10ee505 20130619163843 plugins/Linear_Kuwahara-2.0.0-SNAPSHOT.jar
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  587c9f4b 20130619163846 plugins/MTrack2_-2.0.0-SNAPSHOT.jar
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  64ccfd05 20130619163847 plugins/M_I_P-2.0.0-SNAPSHOT.jar
  65a2dd78 20110303204100 plugins/Macros/About_Plugin_Macros.txt
  dff5642d 20110303204100 plugins/Macros/Bulls_Eye.txt
  e7ffe8ba 20110303204100 plugins/Macros/Polygon_.txt
  39f7ffcd 20110303204100 plugins/Macros/RGB_Histogram.txt
  3ee0edfa 20110303204100 plugins/Macros/batch_convert_any_to_tif.txt
  55f5b6a0 20130619163845 plugins/Manual_Tracking-2.0.0-SNAPSHOT.jar
  9c541ad9 20130619163843 plugins/MosaicJ_-2.0.0-SNAPSHOT.jar
  94ff9125 20131118135326 plugins/Mosaic_ToolSuite/Mosaic_ToolSuite.jar
  04496884 20110412125422 plugins/OpenSPE_.class
  04a4a5c1 20130619163844 plugins/PIV_analyser-1.1.1-SNAPSHOT.jar
  19181db3 20130619163845 plugins/PointPicker_-2.0.0-SNAPSHOT.jar
  964d054a 20130716105601 plugins/QuickPALM_-1.1.1-SNAPSHOT.jar
  9fb03125 20130619163841 plugins/RATS_-2.0.0-SNAPSHOT.jar
  5c7f3968 20130619163841 plugins/RandomJ_-1.5.1-SNAPSHOT.jar
  7d1ad162 20120507131036 plugins/Reconstruct_Reader.jar
  8bc6c355 20140221182853 plugins/Refresh_Javas-2.0.0-SNAPSHOT.jar
  4ddf620c 20120507131036 plugins/SPIM_Opener.jar
  5b5857d2 20140113173159 plugins/SPIM_Registration-2.0.0-SNAPSHOT.jar
  b9076c0a 20130619163842 plugins/Samples_-2.0.0-SNAPSHOT.jar
  70234ddb 20110412125427 plugins/SaveAsSPE_.class
  6d88799a 20131206101007 plugins/Script_Editor-2.0.0-SNAPSHOT.jar
  578994ca 20130814110432 plugins/Scripts/File/Make_Screencast.bsh
  c70b2e6f 20110303204100 plugins/Scripts/File/Open_Samples/Adelsons_Squares.ijm
  60df5674 20130507095553 plugins/Scripts/File/Open_Samples/Spirals_.ijm
  a3edd6db 20110303204100 plugins/Scripts/Image/Adjust/Scale_to_DPI.js
  209aed52 20110307140923 plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm
  1de6c712 20130709093305 plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm
  af064f17 20130906110108 plugins/Scripts/Plugins/Registration/Correct_3D_drift.py
  a6e496fc 20130226113444 plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh
  b5ee58a2 20130318153719 plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh
  fc46bd40 20120809103709 plugins/Scripts/Plugins/Utilities/Record_Desktop.py
  9d4d012a 20120809103709 plugins/Scripts/Plugins/Utilities/Record_Window.py
  8cb22fe2 20140303165833 plugins/Series_Labeler-2.0.0-SNAPSHOT.jar
  7c62b5c5 20130619163853 plugins/SheppLogan_-2.0.0-SNAPSHOT.jar
  259df97d 20140122110329 plugins/Sholl_Analysis-3.4.0.jar
  95dc5b19 20131206101009 plugins/Simple_Neurite_Tracer-2.0.2-SNAPSHOT.jar
  0bd5f179 20130619163848 plugins/Siox_Segmentation-1.0.1-SNAPSHOT.jar
  52fecf09 20130619163851 plugins/Skeletonize3D_-1.0.1-SNAPSHOT.jar
  b0820703 20130619163850 plugins/Snakuscule_-2.0.0-SNAPSHOT.jar
  1a37539b 20110412125419 plugins/SpeHeader.class
  33b6af85 20131122101024 plugins/SplineDeformationGenerator_-2.0.0-SNAPSHOT.jar
  27de591e 20130619163842 plugins/StackReg_-2.0.0-SNAPSHOT.jar
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  59f36299 20130619163850 plugins/Statistical_Region_Merging-2.0.0-SNAPSHOT.jar
  c6e48864 20140120102753 plugins/Stitching_-2.0.0-SNAPSHOT.jar
  30100de7 20130619163840 plugins/Sync_Win-1.7-fiji2-SNAPSHOT.jar
  685ca9dc 20130619163848 plugins/Thread_Killer-2.0.0-SNAPSHOT.jar
  2cee6c37 20130619163840 plugins/Threshold_Colour-2.0.1-SNAPSHOT.jar
  d822b123 20130125175325 plugins/Time_Stamper-2.0.0-SNAPSHOT.jar
  584cb5b9 20130619163853 plugins/ToAST_-25.0.1-SNAPSHOT.jar
  4cf59217 20130619163850 plugins/TopoJ_-2.0.0-SNAPSHOT.jar
  b7e761fb 20140113173202 plugins/TrackMate_-2.2.0-SNAPSHOT.jar
  279a86b1 20140214155641 plugins/Trainable_Segmentation-2.0.0-SNAPSHOT.jar
  59124982 20131014163226 plugins/TrakEM2_-1.0b-SNAPSHOT.jar
  8e7f3b79 20130619163841 plugins/TransformJ_-2.8.1-SNAPSHOT.jar
  c4e87a76 20130619163849 plugins/TurboReg_-2.0.0-SNAPSHOT.jar
  9558400d 20110307151013 plugins/UnwarpJ_.jar
  a32dfe46 20110303204100 plugins/Utilities/Close_All_Without_Saving.txt
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  baa78901 20130910135819 plugins/Vaa3d_Reader-2.0.0-SNAPSHOT.jar
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  73396eef 20130619163847 plugins/View5D_-1.3.1-SNAPSHOT.jar
  980c0ed9 20130619163853 plugins/Volume_Calculator-1.0.1-SNAPSHOT.jar
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  2079ca32 20130606140642 plugins/bUnwarpJ_-2.6.1-SNAPSHOT.jar
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  659ad6a3 20110307151007 plugins/ij-ImageIO_.jar
  82f900ac 20130619163850 plugins/level_sets-1.0.1-SNAPSHOT.jar
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  e6e0879f 20110303204101 retro/backport-util-concurrent-3.1.jar
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  25be149f 20110908154946 scripts/Matlab3DViewerDemo_2.m
  cb529b6c 20120809103709 scripts/Matlab3DViewerDemo_3.m
  53d2da73 20120809103709 scripts/Matlab3DViewerIntroduction.m
  4bb342fa 20120809103709 scripts/Miji.m
  868cd434 20110908154946 scripts/Miji_Test.m
  d3260180 20110303204101 scripts/Record_Desktop.py
  0ea7f8fc 20110303204101 scripts/Record_Window.py
  dc94c3a3 20110324134114 scripts/bfopen.m
  a77cab39 20130814110434 scripts/importTrackMateTracks.m
Comment 1 laurent.holtzer 2014-03-07 09:26:44 CST 
Just an additional comment. I had this bug a few times (today and yesterday), but now it seems to be fine again. I will add a comment if it happens again.
Comment 2 Johannes Schindelin 2014-03-07 09:31:25 CST 
It would be good if you could ask your MacOSX to put the console output into the Console window (I only have Snow Leopard where this is done automatically but I understand newer MacOSX versions helpfully hide the console output).

This console output would be incredibly useful in debugging such issues.
Comment 3 laurent.holtzer 2014-03-07 09:40:17 CST 
I got it once more and now I get the following Exception every time I start FIJI, not sure if it is related, but it only showed after I was not able to close that window.

(Fiji Is Just) ImageJ 1.48r; Java 1.6.0_65 [64-bit]; Mac OS X 10.9.2; 14MB of 5455MB (<1%)
 
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
	at fiji.updater.Adapter.check(Adapter.java:276)
	at fiji.updater.Adapter.checkOrShowDialog(Adapter.java:78)
	at fiji.updater.Updater.run(Updater.java:14)
	at fiji.updater.UptodateCheck.run(UptodateCheck.java:8)
	at fiji.FijiTools.runPlugInGently(FijiTools.java:391)
	at fiji.FijiTools.runUpdater(FijiTools.java:401)
	at fiji.patches.FijiInitializer$1.run(FijiInitializer.java:44)
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at fiji.updater.Adapter.invokeStatic(Adapter.java:449)
	at fiji.updater.Adapter.check(Adapter.java:274)
	... 6 more
Caused by: java.io.EOFException: Unexpected end of ZLIB input stream
	at java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:223)
	at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:141)
	at java.util.zip.GZIPInputStream.read(GZIPInputStream.java:90)
	at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:105)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityManager$RewindableInputStream.read(XMLEntityManager.java:2993)
	at com.sun.org.apache.xerces.internal.impl.XMLEntityManager.setupCurrentEntity(XMLEntityManager.java:701)
	at com.sun.org.apache.xerces.internal.impl.XMLVersionDetector.determineDocVersion(XMLVersionDetector.java:186)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:779)
	at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:744)
	at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:128)
	at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1208)
	at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:543)
	at imagej.updater.core.XMLFileReader.read(XMLFileReader.java:135)
	at imagej.updater.core.XMLFileReader.read(XMLFileReader.java:111)
	at imagej.updater.core.FilesCollection.read(FilesCollection.java:367)
	at imagej.updater.core.FilesCollection.read(FilesCollection.java:361)
	at imagej.updater.core.FilesCollection.read(FilesCollection.java:355)
	at imagej.updater.core.UpToDate.check(UpToDate.java:108)
	at imagej.updater.core.UpToDate.check(UpToDate.java:84)
	... 12 more
Comment 4 Johannes Schindelin 2014-03-07 10:16:32 CST 
Bummer. That means that a previous attempt to write the local plugin index failed, and now it cannot be read again.

There is a fix in the updater's source code, but I really need to add a few more things before I can test it thoroughly and upload it. Please bear with me there.

To work around it, please delete the db.xml.gz before restarting Fiji and running the updater. Note that by now all the information about your update sites is lost; you need to re-add them.

Sorry!
Comment 5 Johannes Schindelin 2014-07-25 10:36:54 CDT 
This should be solved for some weeks now.