Win64 CP 2.2.0rc2 rev 1b13225 console errors


#1

Hi all,
I just wanted to report the console errors seen on starting CP 2.2.0rc2 rev 1b13225 on Win64. The software seems to run ok but thought I’d let you know all the same.
Thanks
Neil

java.lang.IllegalArgumentException: Cannot handle replace call to list in ij.Men
us’s public static synchronized java.lang.String[] getPlugins()
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725
)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650
)
at net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.
java:477)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java
:175)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109
)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.jav
a:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.j
ava:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(Unknown Sou
rce)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(Unknown So
urce)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant typ
e: 15
at javassist.CtClassType.getClassFile2(CtClassType.java:203)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:11
0)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96
)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)

    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:15
  1.  at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
     at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.CodeGen.atIfStmnt(CodeGen.java:390)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:354)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.Javac.compileStmnt(Javac.java:568)
     at javassist.expr.MethodCall.replace(MethodCall.java:234)
     at net.imagej.patcher.CodeHacker$7.edit(CodeHacker.java:686)
     at javassist.expr.ExprEditor.loopBody(ExprEditor.java:191)
     at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
     at javassist.CtBehavior.instrument(CtBehavior.java:618)
     at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.j
    

ava:1278)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:670
)
… 17 more
Caused by: java.io.IOException: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
at javassist.bytecode.ConstPool.read(ConstPool.java:970)
at javassist.bytecode.ConstPool.(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.(ClassFile.java:85)
at javassist.CtClassType.getClassFile2(CtClassType.java:190)
… 37 more
java.lang.IllegalArgumentException: Cannot handle app name in ij.ImageJ’s public
(java.applet.Applet applet, int mode)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:44
6)
at net.imagej.patcher.LegacyExtensions.insertAppNameHooks(LegacyExtensio
ns.java:406)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java
:291)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109
)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.jav
a:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.j
ava:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(Unknown Sou
rce)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(Unknown So
urce)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant typ
e: 15
at javassist.CtClassType.getClassFile2(CtClassType.java:203)
at javassist.CtClassType.subtypeOf(CtClassType.java:303)
at javassist.CtClassType.subtypeOf(CtClassType.java:318)
at javassist.compiler.MemberResolver.compareSignature(MemberResolver.jav
a:247)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:11
9)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96
)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)

    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:15
  1.  at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
     at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.Javac.compileStmnt(Javac.java:568)
     at javassist.expr.MethodCall.replace(MethodCall.java:234)
     at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:427)
     at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:441)
     at javassist.expr.ExprEditor.loopBody(ExprEditor.java:219)
     at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
     at javassist.CtBehavior.instrument(CtBehavior.java:618)
     at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.j
    

ava:1278)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:40
2)
… 16 more
Caused by: java.io.IOException: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
at javassist.bytecode.ConstPool.read(ConstPool.java:970)
at javassist.bytecode.ConstPool.(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.(ClassFile.java:85)
at javassist.CtClassType.getClassFile2(CtClassType.java:190)
… 37 more
WARNING: Unable to load module 'vigra.fourier’
ilastik import: failed to import the ilastik. Please follow the instructions on

                      "http://www.ilastik.org" to install ilastik

Traceback (most recent call last):
File “cellprofiler\modules\ilastik_pixel_classification.pyc”, line 70, in
ImportError: No module named ilastik_main
Version: 2016-03-02T21:08:37 1b13225 / 20160302210837


Measure Object Neighbors Error
#2

@nranthony Thanks for posting this information. The errors you are seeing are known to the CP team. They are specific to the ImageJ and ClassifyPixels modules. If you are not using these modules in your pipeline then CP will run correctly and without error.


#3

Hi Kyle, thanks for the speedy reply.

Alas, I am using the classify objects module. I was just about to post regarding the output, as I’m confused on what I’m seeing. I also see errors with the measure neighbors module too*, but I see that on CP2.1.1 also. I’ve pasted the error at the bottom. I always see the out of bounds error, except when I give the same object to measure it’s own neighbors.

I’m relating two primary objects, nuclei and small sections of stained macrophages, and I need to identify the nuclei with the most little chunks of macrophage stain nearby. As I got errors with the neighbors module I moved to trying to relate objects instead but got confused by the output.

Thanks
Neil

  • I have seen previously that the same project file and the same data set on two different machines, both running CP 2.1.1, give different results. I see an error for measure neighbors on one, but not the other…?

MeasureObjectNeighbors Error:

Traceback (most recent call last):
File “cellprofiler\gui\pipelinecontroller.pyc”, line 2826, in do_step
File “cellprofiler\pipeline.pyc”, line 2067, in run_module
File “cellprofiler\modules\measureobjectneighbors.pyc”, line 431, in run
IndexError: index 152 is out of bounds for axis 1 with size 152


MeasureObjectNeighbors Error
#4

Is this still not a resolved problem then?

I just got a new computer and redownloaded CellProfiler, and now see the same println messages as described above when I run CellProfiler. However, on my last computer I didn’t see those messages, but I don’t know what the version of CP was that I was running…I could check though.


#5

Hi guys, I still have this issue with Cellprofiler 2.2.0 (revac0529e)

java.lang.IllegalArgumentException: Cannot handle replace call to list in ij.Men
us’s public static synchronized java.lang.String[] getPlugins()
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725
)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650
)
at net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.
java:477)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java
:175)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109
)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.jav
a:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.j
ava:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(Unknown Sou
rce)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(Unknown So
urce)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant typ
e: 15
at javassist.CtClassType.getClassFile2(CtClassType.java:203)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:11
0)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96
)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)

    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:15
  1.  at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
     at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.CodeGen.atIfStmnt(CodeGen.java:390)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:354)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.Javac.compileStmnt(Javac.java:568)
     at javassist.expr.MethodCall.replace(MethodCall.java:234)
     at net.imagej.patcher.CodeHacker$7.edit(CodeHacker.java:686)
     at javassist.expr.ExprEditor.loopBody(ExprEditor.java:191)
     at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
     at javassist.CtBehavior.instrument(CtBehavior.java:618)
     at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.j
    

ava:1278)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:670
)
… 17 more
Caused by: java.io.IOException: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
at javassist.bytecode.ConstPool.read(ConstPool.java:970)
at javassist.bytecode.ConstPool.(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.(ClassFile.java:85)
at javassist.CtClassType.getClassFile2(CtClassType.java:190)
… 37 more
java.lang.IllegalArgumentException: Cannot handle app name in ij.ImageJ’s public
(java.applet.Applet applet, int mode)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:44
6)
at net.imagej.patcher.LegacyExtensions.insertAppNameHooks(LegacyExtensio
ns.java:406)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java
:291)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109
)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.jav
a:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.j
ava:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(Unknown Sou
rce)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(Unknown So
urce)
Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant typ
e: 15
at javassist.CtClassType.getClassFile2(CtClassType.java:203)
at javassist.CtClassType.subtypeOf(CtClassType.java:303)
at javassist.CtClassType.subtypeOf(CtClassType.java:318)
at javassist.compiler.MemberResolver.compareSignature(MemberResolver.jav
a:247)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:11
9)
at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96
)
at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)

    at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
    at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:15
  1.  at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
     at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
     at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
     at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
     at javassist.compiler.Javac.compileStmnt(Javac.java:568)
     at javassist.expr.MethodCall.replace(MethodCall.java:234)
     at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:427)
     at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:441)
     at javassist.expr.ExprEditor.loopBody(ExprEditor.java:219)
     at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
     at javassist.CtBehavior.instrument(CtBehavior.java:618)
     at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.j
    

ava:1278)
at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:40
2)
… 16 more
Caused by: java.io.IOException: invalid constant type: 15
at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
at javassist.bytecode.ConstPool.read(ConstPool.java:970)
at javassist.bytecode.ConstPool.(ConstPool.java:127)
at javassist.bytecode.ClassFile.read(ClassFile.java:693)
at javassist.bytecode.ClassFile.(ClassFile.java:85)
at javassist.CtClassType.getClassFile2(CtClassType.java:190)
… 37 more
WARNING: Unable to load module 'vigra.fourier’
ilastik import: failed to import the ilastik. Please follow the instructions on
"http://www.ilastik.org" to install ilastik
Traceback (most recent call last):
File “cellprofiler\modules\ilastik_pixel_classification.pyc”, line 70, in
ImportError: No module named ilastik_main