Re: Error in background subtraction plugin after upgrade _NEW ERROR

[Pedro J CamelloDr Pedro J Camello]

I have found again an error using BG_subtraction_form_ROI plugin in another machine with 1.51 imagej installation. The first lines of the console message are below. There are some differences with my previous error (already fixed; thanks again, Curtis).

Although for java experts this is likely a silly question I think I´ll change my macro to avoid using that plugin. I would like to know if there is any tool to determine the speed of a piece of code, since the procedure (subtract the average value of a background ROI from each frame of a 200-1000 frames stack) will be slower using the macro language.


BG_Subtraction_from_ROI not up-to-date because 1 source files are not up-to-date (C:\Users\PC\AppData\Local\Temp\java5969048686117654763\src\main\java\BG_Subtraction_from_ROI.java)
Compiling 1 file in C:\Users\PC\AppData\Local\Temp\java5969048686117654763
No javax.tools.JavaCompiler available. Checking for explicit javac.
No javac.jar found (looked in C:\Users\PC\Desktop\FIJI\Fiji.app\jars)!
java.lang.ClassNotFoundException: com.sun.tools.javac.Main
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:94)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:538)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:463)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:446)
        at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:209)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:136)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:174)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Could not find javac java.lang.ClassNotFoundException: com.sun.tools.javac.Main, falling back to system javac
Executing: 'javac' '-classpath' 'C:\Users\PC\AppData\Local\Temp\java5969048686117654763\target\classes;C:\Users\PC\Desktop\FIJI\Fiji.app\plugins\3D_Blob_Segmentation-
java.lang.RuntimeException: Could not even fall back  to javac in the PATH
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:129)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:538)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:463)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:446)
        at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:209)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:136)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:174)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: java.io.IOException: Cannot run program "javac" (in directory "."): CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:137)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:71)
        at org.scijava.minimaven.JavaCompiler.execute(JavaCompiler.java:169)
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:126)
        ... 15 more
Caused by: java.io.IOException: Cannot run program "javac" (in directory "."): CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
        at java.lang.Runtime.exec(Runtime.java:620)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:98)
        ... 18 more
Caused by: java.io.IOException: CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at java.lang.ProcessImpl.create(Native Method)
        at java.lang.ProcessImpl.<init>(ProcessImpl.java:386)
        at java.lang.ProcessImpl.start(ProcessImpl.java:137)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
        ... 20 more
BG_Subtraction_from_ROI not up-to-date because 1 source files are not up-to-date (C:\Users\PC\AppData\Local\Temp\java2628626558850101460\src\main\java\BG_Subtraction_from_ROI.java)
Compiling 1 file in C:\Users\PC\AppData\Local\Temp\java2628626558850101460

No javax.tools.JavaCompiler available. Checking for explicit javac.
No javac.jar found (looked in C:\Users\PC\Desktop\FIJI\Fiji.app\jars)!
java.lang.ClassNotFoundException: com.sun.tools.javac.Main
        at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:94)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:538)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:463)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:446)
        at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:209)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:136)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:174)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Could not find javac java.lang.ClassNotFoundException: com.sun.tools.javac.Main, falling back to system javac
Executing: 'javac' '-classpath'
java.lang.RuntimeException: Could not even fall back  to javac in the PATH
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:129)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:538)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:463)
        at org.scijava.minimaven.MavenProject.build(MavenProject.java:446)
        at org.scijava.plugins.scripting.java.JavaEngine.compile(JavaEngine.java:209)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:136)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:174)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:177)
        at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
        at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
        at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask.run(FutureTask.java:266)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: java.io.IOException: Cannot run program "javac" (in directory "."): CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:137)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:71)
        at org.scijava.minimaven.JavaCompiler.execute(JavaCompiler.java:169)
        at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:126)
        ... 15 more
Caused by: java.io.IOException: Cannot run program "javac" (in directory "."): CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048)
        at java.lang.Runtime.exec(Runtime.java:620)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:98)
        ... 18 more
Caused by: java.io.IOException: CreateProcess error=2, El sistema no puede encontrar el archivo especificado
        at java.lang.ProcessImpl.create(Native Method)
        at java.lang.ProcessImpl.<init>(ProcessImpl.java:386)
        at java.lang.ProcessImpl.start(ProcessImpl.java:137)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029)
        ... 20 more

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