Bug 749 – 'Help > Update Fiji' throws NoSuchMethodError, fall-back to remote updater fails

Bug 749 - 'Help > Update Fiji' throws NoSuchMethodError, fall-back to remote updater fails


Summary:	'Help > Update Fiji' throws NoSuchMethodError, fall-back to remote updater fails

Status:	RESOLVED FIXED

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Duplicates:	750
Depends on:
Blocks:

Reported:	2014-05-19 09:39 CDT by Jan Eglinger
Modified:	2014-05-20 12:33 CDT
CC List:	4 users (show)

See Also:

Attachments
scijava-common.jar intended to fix the XML problems, once and for all (550.93 KB, application/x-java-archive) 2014-05-19 11:59 CDT, Johannes Schindelin

Description Jan Eglinger 2014-05-19 09:39:16 CDT

After updating Fiji today, running Help > Update Fiji results in the file bootstrap.js being opened in a text window, and no updater running.

Starting Fiji from command line and then running Help > Update Fiji results in the terminal output pasted below:

java.lang.NoSuchMethodError: org.apache.xpath.XPathContext.<init>(Z)V
	at org.apache.xpath.jaxp.XPathImpl.eval(XPathImpl.java:207)
	at org.apache.xpath.jaxp.XPathImpl.evaluate(XPathImpl.java:281)
	at org.scijava.util.XML.xpath(XML.java:142)
	at org.scijava.util.XML.cdata(XML.java:133)
	at net.imagej.util.MediaWikiClient.getPageSource(MediaWikiClient.java:83)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:64)
	at net.imagej.updater.util.AvailableSites.initializeSites(AvailableSites.java:136)
	at net.imagej.updater.util.AvailableSites.initializeAndAddSites(AvailableSites.java:185)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:101)
	at fiji.updater.IJ2Updater.run(IJ2Updater.java:63)
	at fiji.updater.Updater.run(Updater.java:30)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)
java.lang.ClassNotFoundException: imagej.updater.gui.ImageJUpdater
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at fiji.updater.Updater.run(Updater.java:35)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)
Falling back to remote updater at http://update.imagej.net/bootstrap.js
java.lang.NoSuchMethodError: org.apache.xpath.XPathContext.<init>(Z)V
	at org.apache.xpath.jaxp.XPathImpl.eval(XPathImpl.java:207)
	at org.apache.xpath.jaxp.XPathImpl.evaluate(XPathImpl.java:281)
	at org.scijava.util.XML.xpath(XML.java:142)
	at org.scijava.util.XML.cdata(XML.java:133)
	at net.imagej.util.MediaWikiClient.getPageSource(MediaWikiClient.java:83)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:64)
	at net.imagej.updater.util.AvailableSites.initializeSites(AvailableSites.java:136)
	at net.imagej.updater.util.AvailableSites.initializeAndAddSites(AvailableSites.java:185)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:101)
	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 sun.reflect.misc.Trampoline.invoke(MethodUtil.java:57)
	at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at sun.reflect.misc.MethodUtil.invoke(MethodUtil.java:260)
	at sun.org.mozilla.javascript.internal.MemberBox.invoke(MemberBox.java:130)
	at sun.org.mozilla.javascript.internal.NativeJavaMethod.call(NativeJavaMethod.java:188)
	at sun.org.mozilla.javascript.internal.Interpreter.interpretLoop(Interpreter.java:3068)
	at sun.org.mozilla.javascript.internal.Interpreter.interpret(Interpreter.java:2234)
	at sun.org.mozilla.javascript.internal.InterpretedFunction.call(InterpretedFunction.java:136)
	at sun.org.mozilla.javascript.internal.ContextFactory.doTopCall(ContextFactory.java:323)
	at com.sun.script.javascript.RhinoScriptEngine$1.superDoTopCall(RhinoScriptEngine.java:92)
	at com.sun.script.javascript.RhinoScriptEngine$1.doTopCall(RhinoScriptEngine.java:85)
	at sun.org.mozilla.javascript.internal.ScriptRuntime.doTopCall(ScriptRuntime.java:2747)
	at sun.org.mozilla.javascript.internal.InterpretedFunction.exec(InterpretedFunction.java:147)
	at sun.org.mozilla.javascript.internal.Context.evaluateReader(Context.java:1169)
	at com.sun.script.javascript.RhinoScriptEngine.eval(RhinoScriptEngine.java:152)
	at javax.script.AbstractScriptEngine.eval(AbstractScriptEngine.java:232)
	at fiji.updater.Updater.runRemote(Updater.java:83)
	at fiji.updater.Updater.run(Updater.java:41)
	at ij.IJ.runUserPlugIn(IJ.java:201)
	at ij.IJ.runPlugIn(IJ.java:165)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.9.3
  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: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140516231031)
Fiji: http://fiji.sc/update/ (last check:20140518040429)
Bio-Formats: http://sites.imagej.net/Bio-Formats/ (last check:20140517194832)
BioVoxxel: http://sites.imagej.net/BioVoxxel/ (last check:20140404153808)
Cookbook: http://sites.imagej.net/Cookbook/ (last check:20131221001857)
IBMP-CNRS: http://www-ibmp.u-strasbg.fr/fijiupdates/ (last check:20131014121029)
ScientiFig: http://sites.imagej.net/Aigouy/ (last check:20140516135525)

Files not up-to-date:
  5cf0711e (LOCAL_ONLY) 20120807002303 jars/akutan-1.0.jar
  01eace7e (LOCAL_ONLY) 20120508221510 jars/antlr-runtime-3.4.jar
  0449e3ec (LOCAL_ONLY) 20120807002304 jars/colt-1.2.0.jar
  c91e55ee (LOCAL_ONLY) 20131022134831 jars/commons-io-1.3.2.jar
  6cd7cd7d (LOCAL_ONLY) 20120807002305 jars/concurrent-1.3.4.jar
  6227c67b (LOCAL_ONLY) 20121120185253 jars/curve-fitter-1.0.0-SNAPSHOT-with-libs.jar
  be9b3c4c (LOCAL_ONLY) 20140307135110 jars/formats-common-5.0.0.jar
  49acf09d (LOCAL_ONLY) 20131021211549 jars/jsr166-1.7.0.jar
  c480d491 (LOCAL_ONLY) 20120807002302 jars/jxlayer.jar
  8523861f (LOCAL_ONLY) 20120807002305 jars/lma-1.3.jar
  04f8e59b (LOCAL_ONLY) 20120807002305 jars/native-library-util-2.0-SNAPSHOT.jar
  9b5581f0 (LOCAL_ONLY) 20130104113738 jars/sqlite-jdbc-3.7.8-20111025.014814-1.jar
  3f82055b (LOCAL_ONLY) 20130128163053 lib/macosx/libffmpeg.dylib
  202e3bea (LOCAL_ONLY) 20140206101241 luts/isolum_cbs.lut
  f2b7e781 (LOCAL_ONLY) 20121123111454 luts/lifetime.lut
  401ec8c7 (LOCAL_ONLY) 20120224160206 macros/BatchMacro.ijm
  7ba86896 (LOCAL_ONLY) 20110906150138 macros/toolsets/AdvancedPlots.txt
  37c78470 (LOCAL_ONLY) 20110419151136 macros/toolsets/Icons.txt
  c74d5c56 (LOCAL_ONLY) 20110915101513 macros/toolsets/Magic Montage.txt
  9ce4aacd (LOCAL_ONLY) 20111018114005 plugins/ActionBar/new_action_bar.txt
  dfa49649 (LOCAL_ONLY) 20110518183240 plugins/Blend_Images.class
  19f37464 (LOCAL_ONLY) 20131022135630 plugins/Blind_Experiment-0.1.0-SNAPSHOT.jar
  b6fe6c30 (LOCAL_ONLY) 20121029120912 plugins/BugTest_Plugin.class
  3082317f (LOCAL_ONLY) 20131015135732 plugins/Combine_ROIs.jar
  e5a6054f (LOCAL_ONLY) 20131102164621 plugins/Example_.class
  aaeffc0c (LOCAL_ONLY) 20130128163044 plugins/FFMPEG_IO.jar
  51fc63d2 (LOCAL_ONLY) 20130529182520 plugins/Fiber_Segmentation.class
  41170d42 (LOCAL_ONLY) 20101208151551 plugins/Frac_Lac.jar
  a7414736 (LOCAL_ONLY) 20101208151731 plugins/Fractal_Generator.class
  4c9d1443 (LOCAL_ONLY) 20101208132146 plugins/Grid_.class
  47e11681 (LOCAL_ONLY) 20140307135109 plugins/HGOME_plugins-1.0.2-SNAPSHOT.jar
  0a96c958 (LOCAL_ONLY) 20040618103702 plugins/Hough_Center/Accumulator.class
  c852d1a0 (LOCAL_ONLY) 20040617122714 plugins/Hough_Center/Analyser.class
  240c49ad (LOCAL_ONLY) 20040618103640 plugins/Hough_Center/BinaryAccumulator.class
  06624be7 (LOCAL_ONLY) 20040618103518 plugins/Hough_Center/BooleanMatrix.class
  87b4a5e9 (LOCAL_ONLY) 20040618103514 plugins/Hough_Center/Canny.class
  ae179215 (LOCAL_ONLY) 20040619100852 plugins/Hough_Center/Hough$DoublePoint.class
  eccb02c0 (LOCAL_ONLY) 20040619100852 plugins/Hough_Center/Hough$PtOut.class
  3ad8ce15 (LOCAL_ONLY) 20040619100852 plugins/Hough_Center/Hough.class
  44a76d03 (LOCAL_ONLY) 20120525133622 plugins/Hough_Center/Hough_.class
  2936b9b9 (LOCAL_ONLY) 20040617115652 plugins/Hough_Center/LinkedListMod$Entry.class
  cdd4d004 (LOCAL_ONLY) 20040617115652 plugins/Hough_Center/LinkedListMod.class
  58846771 (LOCAL_ONLY) 20040617115702 plugins/Hough_Center/RectDouble.class
  9ea322de (LOCAL_ONLY) 20040617161252 plugins/Hough_Center/RectInt.class
  9a6b7db0 (LOCAL_ONLY) 20040617135150 plugins/Hough_Center/VotingPoint.class
  59693620 (LOCAL_ONLY) 20120524110350 plugins/Hough_Circles.class
  20e2cec7 (LOCAL_ONLY) 20140225102153 plugins/ICTN_1_6_.jar
  3c505c2f (LOCAL_ONLY) 20140407201310 plugins/LOCI/misc_plugins-1.0.0-SNAPSHOT.jar
  65b35fcd (LOCAL_ONLY) 20120814144529 plugins/Morphology/BinaryDilateNoMerge8_.class
  583118b2 (LOCAL_ONLY) 20120521173122 plugins/Morphology/Particles8_.class
  f07dd15c (LOCAL_ONLY) 20120116113716 plugins/NeuronJ_.jar
  ec17890b (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20131128094658 plugins/OMERO.insight-ij/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/TableLayout.jar
  ff61a1b4 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ai_path.jar
  c3a86bd0 (LOCAL_ONLY) 20131104145522 plugins/OMERO.insight-ij/libs/assumeng.jar
  364315a9 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/axis.jar
  0af1624e (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/backport-util-concurrent.jar
  6912f440 (LOCAL_ONLY) 20140403210120 plugins/OMERO.insight-ij/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/bufr.jar
  031cc2a6 (LOCAL_ONLY) 20140403205940 plugins/OMERO.insight-ij/libs/common.jar
  940245e0 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-discovery.jar
  c62bea1b (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-httpclient.jar
  d59d3e4c (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-lang.jar
  7018824c (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/commons-validator.jar
  abf211c5 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ehcache-core.jar
  991b5e8a (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/gicentreUtils.jar
  dbcde867 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/gluegen-rt.jar
  e33cecc2 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/grib.jar
  ac0dfbec (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/guava-jdk5.jar
  85c28658 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/hibernate-jpa-2.0-api.jar
  1911c9e1 (LOCAL_ONLY) 20131120120114 plugins/OMERO.insight-ij/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20131120120114 plugins/OMERO.insight-ij/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20131120120114 plugins/OMERO.insight-ij/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20131120120114 plugins/OMERO.insight-ij/libs/ice.jar
  6e7614ee (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/jaxrpc.jar
  4156c7b5 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/jcommon.jar
  c57f20b0 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/jfreechart.jar
  df7a0b63 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20131104145522 plugins/OMERO.insight-ij/libs/joda-time.jar
  9a9b947a (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/jogl.jar
  d2af3ac9 (LOCAL_ONLY) 20131104145522 plugins/OMERO.insight-ij/libs/kryo.jar
  b2911375 (LOCAL_ONLY) 20140403205856 plugins/OMERO.insight-ij/libs/lwf-stubs.jar
  0f7b1b81 (LOCAL_ONLY) 20140403205936 plugins/OMERO.insight-ij/libs/model-psql.jar
  a127d67c (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/nanoxml.jar
  e1a35a80 (LOCAL_ONLY) 20131104145522 plugins/OMERO.insight-ij/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20131128094658 plugins/OMERO.insight-ij/libs/netcdf.jar
  e665d66a (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ols-client.jar
  18382f06 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20131104145522 plugins/OMERO.insight-ij/libs/perf4j.jar
  6340be70 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/physics.jar
  b3056152 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/poi.jar
  af4b3176 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/processing-controlP5.jar
  1cb045e1 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/processing-core.jar
  2e6cf711 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/saaj.jar
  eedc0cd9 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/serializer.jar
  5085d943 (LOCAL_ONLY) 20140401124614 plugins/OMERO.insight-ij/libs/slf4j-api.jar
  1deeabc9 (LOCAL_ONLY) 20140403205852 plugins/OMERO.insight-ij/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/swingx.jar
  7c4005e7 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/wsdl4j.jar
  c8694e76 (LOCAL_ONLY) 20131104145444 plugins/OMERO.insight-ij/libs/xalan.jar
  56926bee (LOCAL_ONLY) 20140403210440 plugins/OMERO.insight-ij/omero_ij.jar
  c22d9e9e (LOCAL_ONLY) 20140226105352 plugins/PHANTAST_-0.2-SNAPSHOT.jar
  33814455 (LOCAL_ONLY) 20130605091713 plugins/PixFRETSettings.txt
  b9701e7b (LOCAL_ONLY) 20060517103802 plugins/PixFRET_.jar
  b87c730c (LOCAL_ONLY) 20130619180156 plugins/Plate_Explorer.jar
  0e56fc96 (LOCAL_ONLY) 20111012174728 plugins/Polar_Transformer.class
  ed1ea5da (LOCAL_ONLY) 20140224160228 plugins/Print_Argument.ijm
  617c3507 (LOCAL_ONLY) 20110815172458 plugins/QuickTime_Plugins.jar
  66e61806 (LOCAL_ONLY) 20131202125257 plugins/Radial_Profile_Angle_Ext.class
  3995f903 (LOCAL_ONLY) 20131202104808 plugins/Radial_Profile_Angle_Ext.jar
  005fba78 (LOCAL_ONLY) 20131202125731 plugins/Radial_Profile_Angle_Ext2.class
  576b0a18 (LOCAL_ONLY) 20100709151138 plugins/Retinex_.class
  9a8e5535 (LOCAL_ONLY) 20130312162050 plugins/SQL_Table_Statistics.jar
  fb75aafd (LOCAL_ONLY) 20140410000354 plugins/ScientiFig/ScientiFigPrefs.txt
  54eb2ba4 (LOCAL_ONLY) 20130321143838 plugins/ScientiFig_FIJI/HowToInstall.txt
  b9057bc8 (LOCAL_ONLY) 20130710171325 plugins/ScientiFig_FIJI/ScientiFigPrefs.txt
  7872d78f (LOCAL_ONLY) 20130321143836 plugins/ScientiFig_FIJI/lib/AbsoluteLayout.jar
  c3cdf2d0 (LOCAL_ONLY) 20130321143836 plugins/ScientiFig_FIJI/lib/REngine.jar
  6ba3fcd5 (LOCAL_ONLY) 20130321143836 plugins/ScientiFig_FIJI/lib/Rserve.jar
  269cc20e (LOCAL_ONLY) 20130321143836 plugins/ScientiFig_FIJI/lib/Rsession.jar
  9333c8a9 (LOCAL_ONLY) 20130321143838 plugins/ScientiFig_FIJI/licence.txt
  410d6fcd (LOCAL_ONLY) 20140407201404 plugins/Sprout_Analysis-0.2.0-SNAPSHOT.jar
  df2b3e75 (LOCAL_ONLY) 20091012120814 plugins/Sprouting/Analyze_Stack12_highres.txt
  8d44b668 (LOCAL_ONLY) 20091107205525 plugins/Sprouting/Analyze_Stack13.txt
  5288228f (LOCAL_ONLY) 20100224144753 plugins/Sprouting/Convert_ZVI_stack_to_2-channel_Maximum_TIF.txt
  034e784d (LOCAL_ONLY) 20110419151242 plugins/Sprouting/Sprout_Analysis_v1.txt
  844452cd (LOCAL_ONLY) 20100302220059 plugins/Sprouting/Sprout_Analysis_v2_triangle.txt
  15a7eddd (LOCAL_ONLY) 20100302224308 plugins/Sprouting/Sprout_Analysis_v3_triangle.ijm
  028b4940 (LOCAL_ONLY) 20100302225326 plugins/Sprouting/Sprout_Analysis_v3_triangle_default.txt
  c17a1903 (LOCAL_ONLY) 20120821191822 plugins/Temp/Dupl_.js
  979b4518 (LOCAL_ONLY) 20111011160809 plugins/Test_.jar
  e23a2d35 (LOCAL_ONLY) 20130308120209 plugins/Tools/Bare_PlugIn.class
  7aad5bf4 (LOCAL_ONLY) 20130314163526 plugins/Triplet_Statistics.jar
  0dfa5070 (LOCAL_ONLY) 20120116113721 plugins/imagescience.jar
  7f0caa5d (LOCAL_ONLY) 20120807002258 plugins/miglayout-3.7.3.1-swing.jar
  1bc5c5f5 (LOCAL_ONLY) 20130313113612 plugins/my_test.jar
  88fcf0b4 (LOCAL_ONLY) 20111012133253 plugins/qr_decoder_1.0.jar
  41cae167 (LOCAL_ONLY) 20130408133640 plugins/slim_plugin-1.0.0-SNAPSHOT.jar
  c2b03914 (LOCAL_ONLY) 20080206113100 plugins/sobel3D/Sobel_Convolution$FloatArray.class
  71ef7c2b (LOCAL_ONLY) 20080206113100 plugins/sobel3D/Sobel_Convolution$FloatArray2D.class
  bdf07ef4 (LOCAL_ONLY) 20080206113102 plugins/sobel3D/Sobel_Convolution$FloatArray3D.class
  fb2a0deb (LOCAL_ONLY) 20080206113102 plugins/sobel3D/Sobel_Convolution.class
  14eaf670 (LOCAL_ONLY) 20120807002301 plugins/visad-lite-2.0.20070828.jar
  574cdfce (LOCAL_ONLY) 20120807002302 plugins/visbio_plugins-1.0-SNAPSHOT.jar
  d3260180 (LOCAL_ONLY) 20100610022426 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20100610022426 scripts/Record_Window.py

Comment 1 Niko Ehrenfeuchter 2014-05-19 09:51:17 CDT

Jan, any chance you're having the update site "Trackmate-dev" enabled?

Comment 2 Johannes Schindelin 2014-05-19 10:03:04 CDT

Niko: thanks to the new updater, we can actually see the list of active update sites in the bug report. So no, TrackMate-dev is not enabled (but others are).

My hunch is that the problem is caused by plugins/OMERO.insight-ij/libs/xalan.jar.

Jan, could you call the "Find Jar For Class" command and figure out which .jar file contains org.apache.xpath.XPathContext (it says "The class org.apache.xpath.XPathContext is contained in /.../Fiji.app/jars/batik.jar" here)? The bug is most likely caused by one of those projects who ship obsolete versions of the XML libraries. If you remove the offending file, the updater should work again.

This is of course only a workaround... If you let me know what caused (and what fixed) it on your side, I can try to fix it properly.

Comment 3 Jan Eglinger 2014-05-19 10:28:29 CDT

Great catch, thanks Johannes!

"
The class org.apache.xpath.XPathContext is contained in /Applications/Fiji/Fiji.app/jars/batik.jar
WARNING! org.apache.xpath.XPathContext is also contained in /Applications/Fiji/Fiji.app/plugins/OMERO.insight-ij/libs/xalan.jar!
"

Deleting xalan.jar fixed things on my side.

NB: I previously noticed that a bunch of redundant files in the OMERO-ij package can safely be deleted [1], but the normal user installation according to OMERO [2] will result in this bug showing up. Anyways, thanks a lot for the quick replies!

[1] http://lists.openmicroscopy.org.uk/pipermail/ome-users/2014-April/004333.html
[2] http://help.openmicroscopy.org/imagej.html#plugins

Comment 4 Johannes Schindelin 2014-05-19 11:59:44 CDT

Created attachment 149
scijava-common.jar intended to fix the XML problems, once and for all

Comment 5 Johannes Schindelin 2014-05-19 12:05:06 CDT

Now the question is: what can we possibly do about the problem? There are plenty of hacky ways we could special-case Insight and work around the problem.

I fear, however, that the only non-hacky way would be to shade xalan for use with scijava-common. Which is, ahem, a suboptimal solution, given that xalan is actually included into Java since version 1.6.

However, I tried a different approach after debugging this further for an hour: try to work around version skews by falling back to Java's own XML libraries. The changes can be found here, for the moment: https://github.com/scijava/scijava-common/compare/6cfca44...b90dd3c

I also attached a compiled version to this ticket.

Jan, may I ask you to put back the offending xalan.jar, verify that it breaks the updater again (filesystems are *really* funny these days, so it might not cause trouble now, which would be bad), and then replace your local jars/scijava-common-0.19.1.jar with the attached version and see whether that works around the issue?

Thanks!

Comment 6 Curtis Rueden 2014-05-19 12:21:38 CDT

*** Bug 750 has been marked as a duplicate of this bug. ***

Comment 7 Johannes Schindelin 2014-05-19 14:45:29 CDT

Graeme, please do not add comments to a closed bug when it has been labeled a duplicate. I almost missed your comments.

Also, did you remove your original scijava-common.jar when you replaced with the attached version?

Comment 8 Graeme Ball 2014-05-19 15:21:32 CDT

Apologies for commenting on the closed bug <:-)

Yes, I moved the old scijava-common out of the way (~/Desktop) before I dropped in the one in your attachment 149. 

If you think it ought to work I can add the OMERO plugin back and try it again more carefully?

g

PS. If it makes life easier, just treat Insight as a special case for now (it *is* a bit of a beast)

Comment 9 Johannes Schindelin 2014-05-19 19:16:39 CDT

Graeme, thanks for testing. It took another hour of debugging to come up with a more complete fix (actually testing myself with a fresh download of OMERO.insight). Could you please replace your local scijava-common.jar with this version: http://jenkins.imagej.net/view/SciJava/job/SciJava-common/lastSuccessfulBuild/artifact/target/scijava-common-2.19.2-SNAPSHOT.jar

For lurkers: my original fix assumed that there is only one place where things can break and need to fall back to an ugly work-around (and I took the location of that place from the stack trace provided by Jan in the initial bug report). But it was not enough, because in my case, the breakage happened only later. So I force the breakage to occur right away now: https://github.com/scijava/scijava-common/compare/7015070...18cf9d9

I plan to release and upload this tomorrow (UTC-6).

Comment 10 Graeme Ball 2014-05-19 19:32:13 CDT

Nice one Johannes -- all seems fine now. 

I am using the new scijava-common jar, with the OMERO Insight plugin installed, and both the Insight plugin and Fiji updater seem to run no problem.

Cheers,

Graeme

Comment 11 Jan Eglinger 2014-05-20 03:24:54 CDT

Thanks a lot, Johannes.

I can confirm that the latest scijava-common-2.19.2-SNAPSHOT.jar from jenkins fixes things on my side, too.

Cheers,
Jan

Comment 12 Johannes Schindelin 2014-05-20 12:33:52 CDT

The respective file has been uploaded.