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Bug 750 - Updater broken?
Updater broken?
Status: RESOLVED DUPLICATE of bug 749
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2014-05-19 12:16 CDT by Graeme Ball
Modified: 2014-05-19 13:11 CDT
3 users (show)

See Also:


Attachments
stack trace upon Fiji update with replacement scijava-common jar (4.36 KB, text/plain)
2014-05-19 13:04 CDT, Graeme Ball

Description Graeme Ball 2014-05-19 12:16:19 CDT
I ran the Fiji updater, and got a stack trace (pasted below). It directed me to run a script called "bootstrap.js", which I did, but nothing happens. I also tried quitting Fiji and erpeating the process, but no cigar. Presumably there's a bug and/or I have a duff config somehow? (I didn't try downloading a fresh copy of Fiji and starting again yet...)

Here's the trace:-

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.GeneratedMethodAccessor6.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)
Done: Checksummer

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.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20140516221031)
Fiji: http://fiji.sc/update/ (last check:20140518030429)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20140321065917)

Files not up-to-date:
  eb8dccd3 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-app-2.0.0-beta-7.7.jar
  9f31a952 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-commands-2.0.0-beta-7.7.jar
  f7d0e2eb (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-core-2.0.0-beta-7.7.jar
  24e0bde0 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-data-2.0.0-beta-7.7.jar
  00efaa63 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-launcher-2.0.2.jar
  56855167 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-legacy-2.0.0-SNAPSHOT.jar
  6e95217d (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-minimaven-2.0.0-beta-7.7.jar
  7600e777 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-options-2.0.0-beta-7.7.jar
  7e2766e2 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-platforms-2.0.0-beta-7.7.jar
  7a824b7e (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-beanshell-2.0.0-beta-7.7.jar
  433f2bc8 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-clojure-2.0.0-beta-7.7.jar
  0a5d89fe (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-java-2.0.0-beta-7.7.jar
  de00b500 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-javascript-2.0.0-beta-7.7.jar
  8345a4fd (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-jruby-2.0.0-beta-7.7.jar
  598d0fdf (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-scripting-jython-2.0.0-beta-7.7.jar
  351a73ce (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-text-2.0.0-beta-7.7.jar
  3cd39ba0 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-tools-2.0.0-beta-7.7.jar
  d514e8f0 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-2.0.0-beta-7.7.jar
  b6ce787a (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-common-awt-2.0.0-beta-7.7.jar
  05b1de42 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-swing-2.0.0-beta-7.7.jar
  c1ce4424 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-swing-commands-2.0.0-beta-7.7.jar
  31d20704 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-swing-script-editor-2.0.0-beta-7.7.jar
  d4409c26 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-swing-tools-2.0.0-beta-7.7.jar
  59100d0b (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-ui-swing-updater-2.0.0-beta-7.7.jar
  4bcfadc6 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-updater-core-2.0.0-beta-7.7.jar
  61d1660a (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-updater-ssh-2.0.0-beta-7.7.jar
  6f60a5ac (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-updater-webdav-2.0.0-beta-7.7.jar
  27161205 (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-util-awt-2.0.0-beta-7.7.jar
  11b4297f (OBSOLETE_UNINSTALLED) 20140401203606 jars/ij-util-swing-2.0.0-beta-7.7.jar
  eedc0cd9 (OBSOLETE_UNINSTALLED) 20140401203606 jars/serializer-2.7.1.jar
  9ae3dd1b (OBSOLETE_UNINSTALLED) 20140401203606 jars/slf4j-log4j12-1.7.2.jar
  36cdef55 (OBSOLETE_UNINSTALLED) 20140401203606 jars/xalan-2.7.1.jar
  56caeadd (LOCAL_ONLY) 20140410221648 macros/BatchMacro.ijm
  8de72b0a (LOCAL_ONLY) 20140519122352 macros/DisplayRangeMacros.txt
  0d6e4e4a (LOCAL_ONLY) 20140519123218 macros/Gamma.txt
  0a5c1981 (LOCAL_ONLY) 20140509155303 plugins/Color_Profiler.jar
  27dcbe2a (LOCAL_ONLY) 20140519122235 plugins/Macros/DisplayRangeMacros.txt
  ec17890b (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/JHotDraw.jar
  91ece67d (LOCAL_ONLY) 20131128104658 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/JWlz.jar
  36cb5c0a (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/TableLayout.jar
  ff61a1b4 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ai_path.jar
  c3a86bd0 (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/assumeng.jar
  364315a9 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/axis.jar
  0af1624e (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/backport-util-concurrent.jar
  c9d60a9e (LOCAL_ONLY) 20140224162818 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/blitz.jar
  189f61fa (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/bufr.jar
  19c30fe9 (LOCAL_ONLY) 20140224162650 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/common.jar
  940245e0 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-codec.jar
  64d8a654 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-collections.jar
  86ab9004 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-digester.jar
  9e9eb622 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-discovery.jar
  c62bea1b (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-httpclient.jar
  d59d3e4c (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-io.jar
  f6139801 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-lang.jar
  7018824c (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-logging.jar
  60a83b54 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/commons-validator.jar
  abf211c5 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ehcache-core.jar
  991b5e8a (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/gicentreUtils.jar
  dbcde867 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/gluegen-rt.jar
  e33cecc2 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/grib.jar
  ac0dfbec (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/guava-jdk5.jar
  85c28658 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/hibernate-jpa-2.0-api.jar
  1911c9e1 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-glacier2.jar
  b1d709fb (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-grid.jar
  c49b8fa2 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice-storm.jar
  53aa5393 (LOCAL_ONLY) 20131120130114 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ice.jar
  6e7614ee (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ij.jar
  6ce638fb (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ini4j.jar
  f1b65457 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/java-getopt.jar
  c827227f (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/java-image-scaling.jar
  e72f9b2b (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jaxrpc.jar
  4156c7b5 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jcommon.jar
  c57f20b0 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jfreechart.jar
  df7a0b63 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jna.jar
  4c09d41c (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/joda-time.jar
  9a9b947a (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/jogl.jar
  d2af3ac9 (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/kryo.jar
  c6b60cce (LOCAL_ONLY) 20140224162614 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/lwf-stubs.jar
  91c79a92 (LOCAL_ONLY) 20140224162648 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/model-psql.jar
  a127d67c (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/nanoxml.jar
  e1a35a80 (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/native-lib-loader.jar
  a51a31db (LOCAL_ONLY) 20131128104658 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/netcdf.jar
  e665d66a (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ols-client.jar
  18382f06 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/ome-java.jar
  7af6ddeb (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/perf4j.jar
  6340be70 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/physics.jar
  b3056152 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/platform.jar
  4ef2cfd3 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/poi.jar
  af4b3176 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/processing-controlP5.jar
  1cb045e1 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/processing-core.jar
  2e6cf711 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/saaj.jar
  eedc0cd9 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/serializer.jar
  572a727b (LOCAL_ONLY) 20131104155522 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/slf4j-api.jar
  f4d01930 (LOCAL_ONLY) 20140224162610 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/specification.jar
  ba32bfdf (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/swingx.jar
  7c4005e7 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/wsdl4j.jar
  c8694e76 (LOCAL_ONLY) 20131104155444 plugins/OMERO.insight-ij-5.0.0-ice35-b19/libs/xalan.jar
  56a05ff0 (LOCAL_ONLY) 20140224163050 plugins/OMERO.insight-ij-5.0.0-ice35-b19/omero_ij.jar
  b120935d (LOCAL_ONLY) 20140511210303 plugins/SIMcheck_.jar
  71331805 (LOCAL_ONLY) 20140501010801 plugins/jacop_.jar
Comment 1 Curtis Rueden 2014-05-19 12:21:38 CDT
The problem is caused by having the OMERO.insight-ij plugin installed. See bug #749 for details. A proper fix is forthcoming.

*** This bug has been marked as a duplicate of bug 749 ***
Comment 2 Johannes Schindelin 2014-05-19 12:24:15 CDT
Graeme, in particular, I would be thankful if you tried after replacing your local scijava-common with the version attached to 749.
Comment 3 Graeme Ball 2014-05-19 13:04:01 CDT
Created attachment 150
stack trace upon Fiji update with replacement scijava-common jar
Comment 4 Graeme Ball 2014-05-19 13:11:18 CDT
I moved the whole OMERO plugin folder & its libs/ folder out of Fiji.app/plugins and indeed, the updater runs fine in this case (so the problem is duplicate xalan.jar?)

Good luck ;-) will be great to have OMERO/insight playing nicely with Fiji / updater.