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Error in background subtraction plugin after upgrade

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Pedro J CamelloDr Pedro J Camello
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Error in background subtraction plugin after upgrade

Pedro J CamelloDr Pedro J Camello
Hi all,

yesterday I upgraded mi Fii installation to ImageJ 1.51j (Java is 1.6.0_24). Immediately after the upgrade a plugin I use frequently (BG_subtraction_from_ROI) fails and the code shown below is displayed in the console. I would appreciate a solution:

Compiling 1 file in C:\Users\p\AppData\Local\Temp\java8674721637468925155
No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
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:211)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
        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$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
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)
        ... 16 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:460)
        at java.lang.Runtime.exec(Runtime.java:593)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
        ... 19 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:81)
        at java.lang.ProcessImpl.start(ProcessImpl.java:30)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
        ... 21 more
Compiling 1 file in C:\Users\p\AppData\Local\Temp\java5157103361452361330
No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
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:211)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
        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$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
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)
        ... 16 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:460)
        at java.lang.Runtime.exec(Runtime.java:593)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
        ... 19 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:81)
        at java.lang.ProcessImpl.start(ProcessImpl.java:30)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
        ... 21 more
Compiling 1 file in C:\Users\p\AppData\Local\Temp\java4618854486569775336
No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
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:211)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:135)
        at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:173)
        at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
        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$2.call(DefaultThreadService.java:191)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
        at java.util.concurrent.FutureTask.run(FutureTask.java:138)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
        at java.lang.Thread.run(Thread.java:662)
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)
        ... 16 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:460)
        at java.lang.Runtime.exec(Runtime.java:593)
        at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
        ... 19 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:81)
        at java.lang.ProcessImpl.start(ProcessImpl.java:30)
        at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
        ... 21 more

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ctrueden
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Re: Error in background subtraction plugin after upgrade

ctrueden
Hi Pedro,

Do you have a file BG_subtraction_from_ROI.java in your plugins folder? And
also one called BG_subtraction_from_ROI.class? If so, move the .java file
out of there, keeping only the .class. Then this error should disappear.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Mar 8, 2017 at 8:51 AM, Pedro J Camello <[hidden email]> wrote:

> Hi all,
>
> yesterday I upgraded mi Fii installation to ImageJ 1.51j (Java is
> 1.6.0_24). Immediately after the upgrade a plugin I use frequently
> (BG_subtraction_from_ROI) fails and the code shown below is displayed in
> the console. I would appreciate a solution:
>
> Compiling 1 file in C:\Users\p\AppData\Local\Temp\java8674721637468925155
> No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
> 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:211)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:135)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:173)
>         at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
>         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$2.call(
> DefaultThreadService.java:191)
>         at java.util.concurrent.FutureTask$Sync.innerRun(
> FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.
> runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 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)
>         ... 16 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:460)
>         at java.lang.Runtime.exec(Runtime.java:593)
>         at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
>         ... 19 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:81)
>         at java.lang.ProcessImpl.start(ProcessImpl.java:30)
>         at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
>         ... 21 more
> Compiling 1 file in C:\Users\p\AppData\Local\Temp\java5157103361452361330
> No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
> 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:211)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:135)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:173)
>         at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
>         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$2.call(
> DefaultThreadService.java:191)
>         at java.util.concurrent.FutureTask$Sync.innerRun(
> FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.
> runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 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)
>         ... 16 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:460)
>         at java.lang.Runtime.exec(Runtime.java:593)
>         at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
>         ... 19 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:81)
>         at java.lang.ProcessImpl.start(ProcessImpl.java:30)
>         at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
>         ... 21 more
> Compiling 1 file in C:\Users\p\AppData\Local\Temp\java4618854486569775336
> No javac.jar found (looked in D:\fiji-win64\Fiji.app\jars)!
> 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:211)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:135)
>         at org.scijava.plugins.scripting.java.JavaEngine.eval(
> JavaEngine.java:173)
>         at org.scijava.script.ScriptModule.run(ScriptModule.java:173)
>         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$2.call(
> DefaultThreadService.java:191)
>         at java.util.concurrent.FutureTask$Sync.innerRun(
> FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.
> runTask(ThreadPoolExecutor.java:886)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(
> ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
> 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)
>         ... 16 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:460)
>         at java.lang.Runtime.exec(Runtime.java:593)
>         at org.scijava.util.ProcessUtils.exec(ProcessUtils.java:97)
>         ... 19 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:81)
>         at java.lang.ProcessImpl.start(ProcessImpl.java:30)
>         at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
>         ... 21 more
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Pedro J CamelloDr Pedro J Camello
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Re: Error in background subtraction plugin after upgrade

Pedro J CamelloDr Pedro J Camello
In reply to this post by Pedro J CamelloDr Pedro J Camello
Many thanks, Curtis, it worked.

Regards

Pedro

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