2017 MacOS 10.11 CellProfiler 220 crash on launch

Hi
I have downloaded the latest version of CellProfiler and It crashes upon launch as described in previous issues such as this one

Following the instructions found in the issue above, I have done what is described below.

In short I have verified I have the correct JDK installed, pointed JAVA_HOME to the correct location and attempted to launch CellProfiler from Terminal.

After all of this I still gets tons of errors.

Could you please help me out?

Thanks

Caterina

PS It appears I have four versions of JDK installed:
MacBook-Pro:JavaVirtualMachines strambc$ ls
1.6.0.jdk jdk1.7.0_71.jdk jdk1.8.0_121.jdk jdk1.8.0_131.jdk


Can you please screenshot the “tons of errors” so we can help you better?

Minh

It will not let me paste it it in.
I was already trying and it is saying I am not allowed more than two links because I am a new user.
is there anyway I can attach a text file instead?

Last login: Thu Apr 27 13:34:40 on ttys000
MacBook-Pro:~ strambc$ java -version
java version "1.8.0_131"
Java™ SE Runtime Environment (build 1.8.0_131-b11)
Java HotSpot™ 64-Bit Server VM (build 25.131-b11, mixed mode)
MacBook-Pro:~ strambc$ which java
/usr/bin/java
MacBook-Pro:~ strambc$ echo $JAVA_HOME

MacBook-Pro:~ strambc$ MacBook-Pro:~ strambc$ export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home
-bash: MacBook-Pro:~: command not found
MacBook-Pro:~ strambc$ export JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home
MacBook-Pro:~ strambc$ echo JAVA_HOME /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home MacBook-Pro:~ strambc arch -x86_64 /Applications/CellProfiler.app/Contents/MacOS/CellProfiler

This is what happened

4/27/17 13:43:43.497 CellProfiler: Plugin directory doesn’t point to valid folder: /Applications/CellProfiler.app/Contents/Resources/plugins
4/27/17 13:43:44.206 CellProfiler: objc: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/jli/libjli.dylib and /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
4/27/17 13:43:44.206 CellProfiler: objc: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/jli/libjli.dylib and /Library/Java/JavaVirtualMachines/jdk1.8.0_131.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined.
4/27/17 13:43:46.877 CellProfiler: java.lang.IllegalArgumentException: Cannot handle replace call to list in ij.Menus’s public static synchronized java.lang.String[] getPlugins()
4/27/17 13:43:46.877 CellProfiler: at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725)
4/27/17 13:43:46.877 CellProfiler: at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650)
4/27/17 13:43:46.877 CellProfiler: at net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.java:477)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:175)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
4/27/17 13:43:46.878 CellProfiler: at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
4/27/17 13:43:46.879 CellProfiler: at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
4/27/17 13:43:46.879 CellProfiler: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
4/27/17 13:43:46.879 CellProfiler: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
4/27/17 13:43:46.879 CellProfiler: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
4/27/17 13:43:46.879 CellProfiler: at java.lang.reflect.Method.invoke(Method.java:498)
4/27/17 13:43:46.879 CellProfiler: at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(InstrumentationImpl.java:386)
4/27/17 13:43:46.879 CellProfiler: at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(InstrumentationImpl.java:401)
4/27/17 13:43:46.879 CellProfiler: Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant type: 18
4/27/17 13:43:46.879 CellProfiler: at javassist.CtClassType.getClassFile2(CtClassType.java:203)
4/27/17 13:43:46.879 CellProfiler: at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:110)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:156)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.CodeGen.atIfStmnt(CodeGen.java:390)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.CodeGen.atStmnt(CodeGen.java:354)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
4/27/17 13:43:46.880 CellProfiler: at javassist.compiler.Javac.compileStmnt(Javac.java:568)
4/27/17 13:43:46.880 CellProfiler: at javassist.expr.MethodCall.replace(MethodCall.java:234)
4/27/17 13:43:46.881 CellProfiler: at net.imagej.patcher.CodeHacker$7.edit(CodeHacker.java:686)
4/27/17 13:43:46.881 CellProfiler: at javassist.expr.ExprEditor.loopBody(ExprEditor.java:191)
4/27/17 13:43:46.881 CellProfiler: at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
4/27/17 13:43:46.881 CellProfiler: at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
4/27/17 13:43:46.881 CellProfiler: at javassist.CtBehavior.instrument(CtBehavior.java:618)
4/27/17 13:43:46.881 CellProfiler: at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1278)
4/27/17 13:43:46.881 CellProfiler: at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:670)
4/27/17 13:43:46.881 CellProfiler: … 17 more
4/27/17 13:43:46.881 CellProfiler: Caused by: java.io.IOException: invalid constant type: 18
4/27/17 13:43:46.881 CellProfiler: Caused by: java.io.IOException: invalid constant type: 18
4/27/17 13:43:46.881 CellProfiler: at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
4/27/17 13:43:46.881 CellProfiler: at javassist.bytecode.ConstPool.read(ConstPool.java:970)
4/27/17 13:43:46.881 CellProfiler: at javassist.bytecode.ConstPool.(ConstPool.java:127)
4/27/17 13:43:46.882 CellProfiler: at javassist.bytecode.ClassFile.read(ClassFile.java:693)
4/27/17 13:43:46.882 CellProfiler: at javassist.bytecode.ClassFile.(ClassFile.java:85)
4/27/17 13:43:46.882 CellProfiler: at javassist.CtClassType.getClassFile2(CtClassType.java:190)
4/27/17 13:43:46.882 CellProfiler: … 37 more
4/27/17 13:43:46.882 CellProfiler: … 37 more
4/27/17 13:43:47.158 CellProfiler: java.lang.IllegalArgumentException: Cannot handle app name in ij.ImageJ’s public (java.applet.Applet applet, int mode)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:446)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyExtensions.insertAppNameHooks(LegacyExtensions.java:406)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:291)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
4/27/17 13:43:47.158 CellProfiler: at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
4/27/17 13:43:47.159 CellProfiler: at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
4/27/17 13:43:47.159 CellProfiler: at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
4/27/17 13:43:47.159 CellProfiler: at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
4/27/17 13:43:47.159 CellProfiler: at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
4/27/17 13:43:47.159 CellProfiler: at java.lang.reflect.Method.invoke(Method.java:498)
4/27/17 13:43:47.159 CellProfiler: at java.lang.reflect.Method.invoke(Method.java:498)
4/27/17 13:43:47.159 CellProfiler: at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(InstrumentationImpl.java:386)
4/27/17 13:43:47.159 CellProfiler: at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(InstrumentationImpl.java:386)
4/27/17 13:43:47.159 CellProfiler: Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant type: 18
4/27/17 13:43:47.160 CellProfiler: Caused by: java.lang.RuntimeException: java.io.IOException: invalid constant type: 18
4/27/17 13:43:47.160 CellProfiler: at javassist.CtClassType.getClassFile2(CtClassType.java:203)
4/27/17 13:43:47.160 CellProfiler: at javassist.CtClassType.subtypeOf(CtClassType.java:303)
4/27/17 13:43:47.160 CellProfiler: at javassist.CtClassType.subtypeOf(CtClassType.java:318)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.MemberResolver.compareSignature(MemberResolver.java:247)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:119)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.MemberResolver.lookupMethod(MemberResolver.java:96)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.TypeChecker.atMethodCallCore(TypeChecker.java:704)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.TypeChecker.atCallExpr(TypeChecker.java:681)
4/27/17 13:43:47.160 CellProfiler: at javassist.compiler.JvstTypeChecker.atCallExpr(JvstTypeChecker.java:156)
4/27/17 13:43:47.161 CellProfiler: at javassist.compiler.ast.CallExpr.accept(CallExpr.java:45)
4/27/17 13:43:47.161 CellProfiler: at javassist.compiler.CodeGen.doTypeCheck(CodeGen.java:241)
4/27/17 13:43:47.161 CellProfiler: at javassist.compiler.CodeGen.atStmnt(CodeGen.java:329)
4/27/17 13:43:47.161 CellProfiler: at javassist.compiler.ast.Stmnt.accept(Stmnt.java:49)
4/27/17 13:43:47.161 CellProfiler: at javassist.compiler.Javac.compileStmnt(Javac.java:568)
4/27/17 13:43:47.161 CellProfiler: at javassist.expr.MethodCall.replace(MethodCall.java:234)
4/27/17 13:43:47.161 CellProfiler: at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:427)
4/27/17 13:43:47.161 CellProfiler: at net.imagej.patcher.CodeHacker$4.edit(CodeHacker.java:441)
4/27/17 13:43:47.161 CellProfiler: at javassist.expr.ExprEditor.loopBody(ExprEditor.java:219)
4/27/17 13:43:47.161 CellProfiler: at javassist.expr.ExprEditor.doit(ExprEditor.java:90)
4/27/17 13:43:47.161 CellProfiler: at javassist.CtBehavior.instrument(CtBehavior.java:618)
4/27/17 13:43:47.161 CellProfiler: at net.imagej.patcher.CodeHacker$EagerExprEditor.instrument(CodeHacker.java:1278)
4/27/17 13:43:47.161 CellProfiler: at net.imagej.patcher.CodeHacker.replaceAppNameInCall(CodeHacker.java:402)
4/27/17 13:43:47.161 CellProfiler: … 16 more
4/27/17 13:43:47.162 CellProfiler: Caused by: java.io.IOException: invalid constant type: 18
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ConstPool.read(ConstPool.java:970)
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ConstPool.(ConstPool.java:127)
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ClassFile.read(ClassFile.java:693)
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ClassFile.read(ClassFile.java:693)
4/27/17 13:43:47.162 CellProfiler: at javassist.bytecode.ClassFile.(ClassFile.java:85)
4/27/17 13:43:47.162 CellProfiler: at javassist.CtClassType.getClassFile2(CtClassType.java:190)
4/27/17 13:43:47.162 CellProfiler: … 37 more
4/27/17 13:44:00.518 CellProfiler: vigra import: failed to import the vigra library. Please follow the instructions on
4/27/17 13:44:00.518 CellProfiler: “http://hci.iwr.uni-heidelberg.de/vigra/” to install vigra
4/27/17 13:44:00.519 CellProfiler: Traceback (most recent call last):
4/27/17 13:44:00.519 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/classifypixels.py”, line 50, in
4/27/17 13:44:00.519 CellProfiler: ImportError: No module named vigra
4/27/17 13:44:00.581 CellProfiler: vigra import: failed to import the vigra library. Please follow the instructions on
4/27/17 13:44:00.581 CellProfiler: “http://hci.iwr.uni-heidelberg.de/vigra/” to install vigra
4/27/17 13:44:00.581 CellProfiler: Traceback (most recent call last):
4/27/17 13:44:00.581 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/ilastik_pixel_classification.py”, line 47, in
4/27/17 13:44:00.581 CellProfiler: ImportError: No module named vigra
4/27/17 13:44:09.360 CellProfiler: /Applications/CellProfiler.app/Contents/Resources/lib/python2.7/site-packages.zip/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
4/27/17 13:44:12.890 Papers[77129]: Downloading patches:
4/27/17 13:44:13.215 Papers[77129]: Finished sync: 4/27/17, 13:44
4/27/17 13:44:14.187 CellProfiler: Could not load cellprofiler.modules.exporttocellh5
4/27/17 13:44:14.187 CellProfiler: Traceback (most recent call last):
4/27/17 13:44:14.187 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/init.py”, line 294, in add_module
4/27/17 13:44:14.188 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/modules/exporttocellh5.py”, line 29, in
4/27/17 13:44:14.188 CellProfiler: File “cellh5/init.pyc”, line 12, in
4/27/17 13:44:14.188 CellProfiler: File “cellh5/cellh5.pyc”, line 18, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/pyplot.pyc”, line 29, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/colorbar.pyc”, line 34, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/collections.pyc”, line 27, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/backend_bases.pyc”, line 62, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/textpath.pyc”, line 15, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/font_manager.pyc”, line 1421, in
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/font_manager.pyc”, line 1406, in _rebuild
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/font_manager.pyc”, line 1059, in init
4/27/17 13:44:14.188 CellProfiler: File “matplotlib/font_manager.pyc”, line 581, in createFontList
4/27/17 13:44:14.188 CellProfiler: IOError: [Errno 13] Permission denied: u’/Library/Fonts/WarnockPro-LightDisp.otf’
4/27/17 13:44:14.714 Papers[77129]: SYNCING: We will sync again in 120 seconds
4/27/17 13:44:19.112 CellProfiler: could not load these modules: cellprofiler.modules.exporttocellh5
4/27/17 13:44:19.593 CellProfiler: /Applications/CellProfiler.app/Contents/Resources/lib/python2.7/site-packages.zip/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
4/27/17 13:44:20.414 CellProfiler: Uncaught exception in CellProfiler.py
4/27/17 13:44:20.414 CellProfiler: Traceback (most recent call last):
4/27/17 13:44:20.414 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 226, in main
4/27/17 13:44:20.414 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/cellprofilerapp.py”, line 24, in init
4/27/17 13:44:20.414 CellProfiler: File “wx/_core.pyc”, line 8628, in init
4/27/17 13:44:20.414 CellProfiler: File “wx/_core.pyc”, line 8196, in _BootstrapApp
4/27/17 13:44:20.414 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/cellprofilerapp.py”, line 34, in OnInit
4/27/17 13:44:20.414 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/cpframe.py”, line 19, in
4/27/17 13:44:20.415 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/pipelinelistview.py”, line 27, in
4/27/17 13:44:20.415 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/cpfigure.py”, line 17, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/colorbar.pyc”, line 34, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/collections.pyc”, line 27, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/backend_bases.pyc”, line 62, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/textpath.pyc”, line 15, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/font_manager.pyc”, line 1421, in
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/font_manager.pyc”, line 1406, in _rebuild
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/font_manager.pyc”, line 1059, in init
4/27/17 13:44:20.415 CellProfiler: File “matplotlib/font_manager.pyc”, line 581, in createFontList
4/27/17 13:44:20.415 CellProfiler: IOError: [Errno 13] Permission denied: u’/Library/Fonts/WarnockPro-LightDisp.otf’
4/27/17 13:44:20.415 CellProfiler: Failed to stop Ilastik
4/27/17 13:44:20.601 CellProfiler: Traceback (most recent call last):
4/27/17 13:44:20.602 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 355, in
4/27/17 13:44:20.611 CellProfiler: _run()
4/27/17 13:44:20.611 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/boot.py”, line 336, in _run
4/27/17 13:44:20.612 CellProfiler: exec(compile(source, path, ‘exec’), globals(), globals())
4/27/17 13:44:20.612 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/CellProfiler.py”, line 4, in
4/27/17 13:44:20.618 CellProfiler: cellprofiler.main.main()
4/27/17 13:44:20.618 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/main.py”, line 226, in main
4/27/17 13:44:20.619 CellProfiler: pipeline_path = pipeline_path)
4/27/17 13:44:20.619 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/cellprofilerapp.py”, line 24, in init
4/27/17 13:44:20.620 CellProfiler: super(CellProfilerApp, self).init(*args, **kwargs)
4/27/17 13:44:20.620 CellProfiler: File “wx/_core.pyc”, line 8628, in init
4/27/17 13:44:20.620 CellProfiler: File “wx/_core.pyc”, line 8196, in _BootstrapApp
4/27/17 13:44:20.620 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/cellprofilerapp.py”, line 34, in OnInit
4/27/17 13:44:20.620 CellProfiler: from cellprofiler.gui.cpframe import CPFrame
4/27/17 13:44:20.620 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/cpframe.py”, line 19, in
4/27/17 13:44:20.626 CellProfiler: from cellprofiler.gui.pipelinelistview import PipelineListView
4/27/17 13:44:20.626 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/pipelinelistview.py”, line 27, in
4/27/17 13:44:20.626 CellProfiler: from cellprofiler.gui.cpfigure import window_name, find_fig
4/27/17 13:44:20.626 CellProfiler: File “/Applications/CellProfiler.app/Contents/Resources/lib/python2.7/cellprofiler/gui/cpfigure.py”, line 17, in
4/27/17 13:44:20.626 CellProfiler: import matplotlib.colorbar
4/27/17 13:44:20.626 CellProfiler: File “matplotlib/colorbar.pyc”, line 34, in
4/27/17 13:44:20.626 CellProfiler: File “matplotlib/collections.pyc”, line 27, in
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/backend_bases.pyc”, line 62, in
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/textpath.pyc”, line 15, in
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/font_manager.pyc”, line 1421, in
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/font_manager.pyc”, line 1406, in _rebuild
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/font_manager.pyc”, line 1059, in init
4/27/17 13:44:20.627 CellProfiler: File “matplotlib/font_manager.pyc”, line 581, in createFontList
4/27/17 13:44:20.627 CellProfiler: IOError: [Errno 13] Permission denied: u’/Library/Fonts/WarnockPro-LightDisp.otf’
4/27/17 13:44:20.673 CellProfiler: CellProfiler Error
4/27/17 13:44:20.673 CellProfiler: 2017-04-27 13:44:20.673 CellProfiler[79113:2533038] CellProfiler Error

OK got it. here it is

Ah,

You can also try to zip them together, so it’s gonna be 1 link with .zip file
Other than that, you can go to the command window, select and copy the text.

Hope that helps

THANK YOU for your patience.
Let me know what you can find out.
I am at a loss

Hi again,

OK, let’s slowly solve it.

To get to the same page, can you follow this instruction to install “brew” (if not already)

After brew is installed, please do this in your terminal:

brew install vigra

Then re-launch CellProfiler.
Let’s see if it helps.