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jenkins build 103 fails (Bad type on operand stack) #6

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opened 2021-11-22 15:14:25 +01:00 by graffy · 3 comments
graffy commented 2021-11-22 15:14:25 +01:00
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https://jenkins.ipr.univ-rennes1.fr/job/lipase-build/103/execution/node/26/log/

micro_manager_metadata_file_parent_path = /opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images/res_soleil2018/white/white_24112018_2
warning: replace_outer_frame is not implemented yet
org.bytedeco.javacpp.opencv_core$Mat[width=1024,height=1024,depth=16,channels=1]
org.bytedeco.javacpp.opencv_core$Mat[width=77,height=77,depth=8,channels=1]
before opencv_imgproc.morphologyEx
after opencv_imgproc.morphologyEx
org.bytedeco.javacpp.opencv_core$Mat[width=1024,height=1024,depth=16,channels=1]
org.bytedeco.javacpp.opencv_core$Mat[width=77,height=77,depth=8,channels=1]
before opencv_imgproc.morphologyEx
after opencv_imgproc.morphologyEx
java.lang.VerifyError: Bad type on operand stack
Exception Details:
  Location:
    ij/gui/NonBlockingGenericDialog.dispose()V @5: invokestatic
  Reason:
    Type 'ij/gui/NonBlockingGenericDialog' (current frame, stack[0]) is not assignable to 'java/awt/Window'
  Current Frame:
    bci: @5
    flags: { }
    locals: { 'ij/gui/NonBlockingGenericDialog' }
    stack: { 'ij/gui/NonBlockingGenericDialog' }
  Bytecode:
    0x0000000: 2ab7 001a 2ab8 001b 2ab4 000b c600 1e2a
    0x0000010: b400 0bb6 000c 4c2b c600 122a b400 0fc6
    0x0000020: 000b 2b2a b400 0fb6 001c b1            
  Stackmap Table:
    same_frame(@42)

	at ij.plugin.filter.RankFilters.showDialog(RankFilters.java:109)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:63)
	at ij.IJ.runPlugIn(IJ.java:206)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:68)
	at ij.IJ.run(IJ.java:317)
	at ij.IJ.run(IJ.java:407)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190)
	at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:208)
	at org.python.core.PyObject.__call__(PyObject.java:494)
	at org.python.core.PyObject.__call__(PyObject.java:498)
	at lipase.imagej.ijimageengine$py.mean_filter$50(__pyclasspath__/lipase/imagej/ijimageengine.py:433)
	at lipase.imagej.ijimageengine$py.call_function(__pyclasspath__/lipase/imagej/ijimageengine.py)
	at org.python.core.PyTableCode.call(PyTableCode.java:173)
	at org.python.core.PyBaseCode.call(PyBaseCode.java:306)
	at org.python.core.PyBaseCode.call(PyBaseCode.java:197)
	at org.python.core.PyFunction.__call__(PyFunction.java:485)
	at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:237)
	at org.python.core.PyMethod.__call__(PyMethod.java:228)
	at lipase.telemos$py._remove_particles$3(__pyclasspath__/lipase/telemos.py:114)
...
https://jenkins.ipr.univ-rennes1.fr/job/lipase-build/103/execution/node/26/log/ ``` micro_manager_metadata_file_parent_path = /opt/ipr/cluster/work.global/graffy/jenkins-store/lipase/raw-images/res_soleil2018/white/white_24112018_2 warning: replace_outer_frame is not implemented yet org.bytedeco.javacpp.opencv_core$Mat[width=1024,height=1024,depth=16,channels=1] org.bytedeco.javacpp.opencv_core$Mat[width=77,height=77,depth=8,channels=1] before opencv_imgproc.morphologyEx after opencv_imgproc.morphologyEx org.bytedeco.javacpp.opencv_core$Mat[width=1024,height=1024,depth=16,channels=1] org.bytedeco.javacpp.opencv_core$Mat[width=77,height=77,depth=8,channels=1] before opencv_imgproc.morphologyEx after opencv_imgproc.morphologyEx java.lang.VerifyError: Bad type on operand stack Exception Details: Location: ij/gui/NonBlockingGenericDialog.dispose()V @5: invokestatic Reason: Type 'ij/gui/NonBlockingGenericDialog' (current frame, stack[0]) is not assignable to 'java/awt/Window' Current Frame: bci: @5 flags: { } locals: { 'ij/gui/NonBlockingGenericDialog' } stack: { 'ij/gui/NonBlockingGenericDialog' } Bytecode: 0x0000000: 2ab7 001a 2ab8 001b 2ab4 000b c600 1e2a 0x0000010: b400 0bb6 000c 4c2b c600 122a b400 0fc6 0x0000020: 000b 2b2a b400 0fb6 001c b1 Stackmap Table: same_frame(@42) at ij.plugin.filter.RankFilters.showDialog(RankFilters.java:109) at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:63) at ij.IJ.runPlugIn(IJ.java:206) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:68) at ij.IJ.run(IJ.java:317) at ij.IJ.run(IJ.java:407) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:190) at org.python.core.PyReflectedFunction.__call__(PyReflectedFunction.java:208) at org.python.core.PyObject.__call__(PyObject.java:494) at org.python.core.PyObject.__call__(PyObject.java:498) at lipase.imagej.ijimageengine$py.mean_filter$50(__pyclasspath__/lipase/imagej/ijimageengine.py:433) at lipase.imagej.ijimageengine$py.call_function(__pyclasspath__/lipase/imagej/ijimageengine.py) at org.python.core.PyTableCode.call(PyTableCode.java:173) at org.python.core.PyBaseCode.call(PyBaseCode.java:306) at org.python.core.PyBaseCode.call(PyBaseCode.java:197) at org.python.core.PyFunction.__call__(PyFunction.java:485) at org.python.core.PyMethod.instancemethod___call__(PyMethod.java:237) at org.python.core.PyMethod.__call__(PyMethod.java:228) at lipase.telemos$py._remove_particles$3(__pyclasspath__/lipase/telemos.py:114) ... ```
graffy added the
bug
 label 2021-11-22 15:14:25 +01:00
graffy commented 2021-11-22 18:56:29 +01:00
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https://forum.image.sc/t/processing-filter-headless-in-jython/48055/2 indicates that this was a regression in imagej that is now fixed :

This ImageJ 1.52q regression if fixed in the latest daily build (1.53h55).

This minimal script reproduces the problem:

  imp = IJ.openImage("https://imagej.net/images/blobs.gif");
  IJ.log("blur1: "+imp.getStatistics().stdDev);
  IJ.run(imp, "Gaussian Blur...", "sigma=10");
  IJ.log("blur2: "+imp.getStatistics().stdDev);

Indeed, imagej 1.53c is currently installed on my workstation.

https://forum.image.sc/t/processing-filter-headless-in-jython/48055/2 indicates that this was a regression in imagej that is now fixed : ``` This ImageJ 1.52q regression if fixed in the latest daily build (1.53h55). This minimal script reproduces the problem: imp = IJ.openImage("https://imagej.net/images/blobs.gif"); IJ.log("blur1: "+imp.getStatistics().stdDev); IJ.run(imp, "Gaussian Blur...", "sigma=10"); IJ.log("blur2: "+imp.getStatistics().stdDev); ``` Indeed, imagej 1.53c is currently installed on my workstation.
graffy commented 2021-11-22 19:38:45 +01:00
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unfortunately, the latest version of fiji uses imagej 1.53f, which still has the bug...

It's possiblie to update imagej to 1.53n from fiji's menu but then we have other problems:

Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release
java.lang.IllegalArgumentException: Method void createMacro() in ij.plugin.frame.Recorder does not return on null
        at net.imagej.patcher.CodeHacker.dontReturnOnNull(CodeHacker.java:497)
        at net.imagej.patcher.LegacyExtensions.addEditorExtensionPoints(LegacyExtensions.java:322)
        at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:289)
        at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:306)
        at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:107)
        at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:100)
        at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:494)
        at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:395)
        at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:374)
        at net.imagej.legacy.LegacyService.<clinit>(LegacyService.java:141)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
...
unfortunately, the latest version of fiji uses imagej 1.53f, which still has the bug... It's possiblie to update imagej to 1.53n from fiji's menu but then we have other problems: ``` Java HotSpot(TM) 64-Bit Server VM warning: Using incremental CMS is deprecated and will likely be removed in a future release java.lang.IllegalArgumentException: Method void createMacro() in ij.plugin.frame.Recorder does not return on null at net.imagej.patcher.CodeHacker.dontReturnOnNull(CodeHacker.java:497) at net.imagej.patcher.LegacyExtensions.addEditorExtensionPoints(LegacyExtensions.java:322) at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:289) at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:306) at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:107) at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:100) at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:494) at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:395) at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:374) at net.imagej.legacy.LegacyService.<clinit>(LegacyService.java:141) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ... ```
graffy commented 2022-01-25 15:47:29 +01:00
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note: this bug only affects headless mode, so the user is isn't affected by it.

The bug is not really fixed as it's a bug in imagej but f686d89204 provides a good enough workaround, so I close this ticket (The current release of fiji still has the broken imagej 1.53f, but at some point, a new release of fiji will com with imagej > 1.53n which has this bug fixed).

note: this bug only affects headless mode, so the user is isn't affected by it. The bug is not really fixed as it's a bug in imagej but https://git.ipr.univ-rennes1.fr/graffy/lipase/commit/f686d89204d3b591249e2a38f4f3005c69ad6706 provides a good enough workaround, so I close this ticket (The current release of fiji still has the broken imagej 1.53f, but at some point, a new release of fiji will com with imagej > 1.53n which has this bug fixed).
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