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Generated JAR file - JNI error has occurred

I am using the IntelliJ IDEA to create a jar artifact from a LeanFT project.
The jar artifact was generated, but with the following error message:
JNI error has occurred, please check your installation and try again
when trying to execute the jar file directly.
It is working when I use the IDE for execution. No arguments or parameter values are required. I am getting the same error when I generate a jar file from a simple "Hello World".
Stack trace:
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.SecurityException:
Invalid signature file digest for Manifest main attributes
at sun.security.util.SignatureFileVerifier.processImpl(Unknown Source)
at sun.security.util.SignatureFileVerifier.process(Unknown Source)
at java.util.jar.JarVerifier.processEntry(Unknown Source)
at java.util.jar.JarVerifier.update(Unknown Source)
at java.util.jar.JarFile.initializeVerifier(Unknown Source)
at java.util.jar.JarFile.getInputStream(Unknown Source)
at sun.misc.URLClassPath$JarLoader$2.getInputStream(Unknown Source)
at sun.misc.Resource.cachedInputStream(Unknown Source)
at sun.misc.Resource.getByteBuffer(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassLoader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)

I looked into the exception you got : Invalid signature file digest for Manifest main attributes.
Are you using signed jar files as dependencies of your project? If so, when you generate a jar containing the dependencies, then try to execute it - the JVM detects your generated jar as a manipulation of the signed jars you are using.
Here is a list of questions where this exception was encountered:
Valid JAR signature for JavaFX projects
“Invalid signature file” when attempting to run a .jar
Invalid signature file digest for Manifest main attributes
Re: [iText-questions] Invalid signature file digest for Manifest main attributes
Follow the links above and find the exact solution which will help you. The solution depends on what exactly you are doing, deployment-wise (specifics of how you are creating your jar artifact).

It's likely something to do with the version of java installed on your PC. check that it is the same as the java version being used to compile your code.

Weird ClassNotFoundException

This line of code is working fine when I debug in eclipse.
this.primaryStage.addEventHandler(KeyEvent.KEY_PRESSED, new EventHandler<KeyEvent>() {
#Override
public void handle(KeyEvent keyEvent) {
InputManager.Instance().addEvent(keyEvent);
}
});
When I export it into .jar ussing my own code (not script), it throws a rather long exception.
Exception in Application start method
java.lang.reflect.InvocationTargetException
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 com.sun.javafx.application.LauncherImpl.launchApplicationWithArgs(Unk
nown Source)
at com.sun.javafx.application.LauncherImpl.launchApplication(Unknown Sou
rce)
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.launcher.LauncherHelper$FXHelper.main(Unknown Source)
Caused by: java.lang.RuntimeException: Exception in Application start method
at com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown So
urce)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication$156(
Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NoClassDefFoundError: test/Game$1
at test.Game.start(Game.java:62)
at com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$163
(Unknown Source)
at com.sun.javafx.application.PlatformImpl.lambda$runAndWait$176(Unknown
Source)
at com.sun.javafx.application.PlatformImpl.lambda$null$174(Unknown Sourc
e)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.javafx.application.PlatformImpl.lambda$runLater$175(Unknown S
ource)
at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(Unknown Source)
at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
at com.sun.glass.ui.win.WinApplication.lambda$null$149(Unknown Source)
... 1 more
Caused by: java.lang.ClassNotFoundException: test.Game$1
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 10 more
Exception running application test.Game
Yet when I export it the same way, but with the handler commented out, it works fine.
I have tried root.addEventHandler, root/primaryStage.setOnKeyPressed, declaring the handler separately, ..
Can you spot the ex reason?

export it into .jar using my own code
Your "own code" is not doing it right, because it is not including the test/Game$1.class file in the .jar file.
Your class is called Game in the test package. When the class uses anonymous classes, those classes must be given a name in order for the .class file to be created (also need the name internally). The name of such files can be anything, but the current scheme is to name it after the defining class, adding a sequence number after a $ sign, so the first anonymous class is called Game$1.class, the second would be called Game$2.class, and so on.
That is why, when you compile Game.java, you end up with 2 files: Game.class and Game$1.class. Both of those files must be added to the .jar file.
You shouldn't rely on this naming convention, if at all possible, because it could change in the future, and other compilers might do it differently.

ClassNotFound exception is usually due to your CLASSPATH environment variable not getting set correctly.
The JVM must have transversed everywhere from the CLASSPATH directory but was not able to find your compiled *.class and java jar files. One way to fix this would be to use the -cp option from the java binary. Or you can set your CLASSPATH environment to the directory where your java files are sitting.
Things run fine in Ecplipse because the classPath set to the workspace and the IDE has got this handled for you.
Read here for more information about CLASSPATH.
https://docs.oracle.com/javase/tutorial/essential/environment/paths.html

Java - Apache Commons HttpClient throws a NoClassDefFoundError

I'm using the Apache Commons HTTP Client and I have included all the required jar files (ie commons-httpclient-3.0.1.jar and commons-httpclient-3.1.jar) in the class path.
The purpose of this code is to send files (in this case images) to the content management system when a website user creates and saves a new image article. The exception appears in the File Sender window when the filesender attempts to transfer images from the Tomcat temp folder to the CMS. This causes the process to fail and the images remain stuck in the temp folder.
What could be the cause of this error?
SEVERE: Policy class "uk.co.content.article.MoodboardArticlePolicy" spec
ified by input template MoodboardArticle as top policy has a dependency
on some class where runtime version is incompatible with the version compiled ag
ainst
java.lang.NoClassDefFoundError: org/apache/commons/httpclient/methods/RequestEnt
ity
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Unknown Source)
at com.polopoly.cm.policy.PolicyFactoryDependencyInjecting$DependencyInj
ectionPolicyInstantiator.createInstance(PolicyFactoryDependencyInjecting.java:71
)
at com.polopoly.cm.policy.PolicyFactory.createPolicyInstance(PolicyFacto
ry.java:141)
at com.polopoly.cm.policy.PolicyFactoryDependencyInjecting.createPolicyI
nstance(PolicyFactoryDependencyInjecting.java:49)
at com.polopoly.cm.policy.PolicyFactory.createPolicy(PolicyFactory.java:
103)
at com.polopoly.cm.policy.PolicyCMServerBase.getPolicyFor(PolicyCMServer
Base.java:1046)
at com.polopoly.cm.policy.PolicyCMServerBase.getPolicyFor(PolicyCMServer
Base.java:972)
at com.polopoly.cm.policy.PolicyCMServerBase.createNewVersion(PolicyCMSe
rverBase.java:177)
at com.polopoly.cm.policy.PolicyCMServerBase.createNewVersion(PolicyCMSe
rverBase.java:157)
at com.polopoly.cm.policy.PolicyCMServerBase.createContentVersion(Policy
CMServerBase.java:740)
at com.polopoly.cm.policy.PolicyCMServerBase.createContentVersion(Policy
CMServerBase.java:754)
at uk.co.prestige.ftpclient.FileSender.updatePolopolyContent(Fil
eSender.java:244)
at uk.co.prestige.ftpclient.FileSender.sendFile(FileSender.java:
194)
at uk.co.prestige.ftpclient.HotFolderWorker.notifyFileProcessLis
teners(HotFolderWorker.java:61)
at uk.co.prestige.ftpclient.DirectoryScanner.scanNow(DirectorySc
anner.java:79)
at uk.co.prestige.ftpclient.HotFolderWorker.run(HotFolderWorker.
java:88)
Caused by: java.lang.ClassNotFoundException: org.apache.commons.httpclient.metho
ds.RequestEntity
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 17 more

SSL using RSAL Toolkit not encapsulated by a jar Error

I'm running a 3rd party app which fails with the following stacktrace when trying to create a SSL connection to a server:
The root exception is this:
Caused by: java.lang.SecurityException: Toolkit not encapsulated by a jar.
at com.rsa.jcm.f.hq.a(Unknown Source)
at com.rsa.jcm.f.jg.b(Unknown Source)
at com.rsa.crypto.jcm.ModuleLoader.a(Unknown Source)
at com.rsa.crypto.jcm.ModuleLoader.load(Unknown Source)
... 43 more
Has anyone seen this occur when connecting over SSL that uses RSA? I've worked the google and there isn't anything obvious as to why this would happen.
This particular error happens on a Mac, and I've got a windows version of the same app which works correctly. Main difference being they bundle the JRE in the windows version, so I checked various security policies etc but there are no great differences in the JRE on windows vs the JRE on my mac.
The full stacktrace looks like this:
Caused by: java.lang.Error: Problem loading module.
at com.rsa.cryptoj.o.ju.g(Unknown Source)
at com.rsa.cryptoj.o.ju.c(Unknown Source)
at com.rsa.cryptoj.o.gd.a(Unknown Source)
at com.rsa.cryptoj.o.dm.b(Unknown Source)
at com.rsa.cryptoj.o.dm.<clinit>(Unknown Source)
at com.rsa.cryptoj.o.me.newInstance(Unknown Source)
at javax.crypto.Cipher.chooseProvider(Cipher.java:845)
at javax.crypto.Cipher.init(Cipher.java:1348)
at sun.security.ssl.CipherBox.<init>(CipherBox.java:175)
at sun.security.ssl.CipherBox.newCipherBox(CipherBox.java:208)
at sun.security.ssl.CipherSuite$BulkCipher.newCipher(CipherSuite.java:467)
at sun.security.ssl.CipherSuite$BulkCipher.isAvailable(CipherSuite.java:507)
at sun.security.ssl.CipherSuite$BulkCipher.isAvailable(CipherSuite.java:485)
at sun.security.ssl.CipherSuite.isAvailable(CipherSuite.java:190)
at sun.security.ssl.SSLContextImpl.getApplicableCipherSuiteList(SSLContextImpl.java:342)
at sun.security.ssl.SSLContextImpl.getDefaultCipherSuiteList(SSLContextImpl.java:300)
at sun.security.ssl.SSLSocketImpl.init(SSLSocketImpl.java:576)
at sun.security.ssl.SSLSocketImpl.<init>(SSLSocketImpl.java:512)
at sun.security.ssl.SSLSocketFactoryImpl.createSocket(SSLSocketFactoryImpl.java:73)
at com.somevendor.client.common.spring.remoting.http.e.createSocket(Unknown Source)
at org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
at org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$HttpConnectionAdapter.open(MultiThreadedHttpConnectionManager.java:1361)
at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:346)
at com.somevendor.client.common.spring.remoting.http.SecureHttpInvokerRequestExecutor.executePostMethod(Unknown Source)
at org.springframework.remoting.httpinvoker.CommonsHttpInvokerRequestExecutor.doExecuteRequest(CommonsHttpInvokerRequestExecutor.java:140)
at org.springframework.remoting.httpinvoker.AbstractHttpInvokerRequestExecutor.executeRequest(AbstractHttpInvokerRequestExecutor.java:136)
at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.executeRequest(HttpInvokerClientInterceptor.java:192)
at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.executeRequest(HttpInvokerClientInterceptor.java:174)
at org.springframework.remoting.httpinvoker.HttpInvokerClientInterceptor.invoke(HttpInvokerClientInterceptor.java:142)
... 7 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
... 39 more
Caused by: java.lang.SecurityException: Toolkit not encapsulated by a jar.
at com.rsa.jcm.f.hq.a(Unknown Source)
at com.rsa.jcm.f.jg.b(Unknown Source)
at com.rsa.crypto.jcm.ModuleLoader.a(Unknown Source)
at com.rsa.crypto.jcm.ModuleLoader.load(Unknown Source)
... 43 more

Answering as I worked it out (5 years ago..). This exception happens when there is whitespace in the fully qualified path to the jar file that is been executed.
So this works:
/Users/stringy05/app/app.jar
But if you use a path with a space:
/Volumes/Macintosh HD/Users/stringy05/app/app.jar
Then it fails. When this originally happened I had a soft link in /Users/stringy05 to another hard disk, so either java or the OS was resolving the link path to the real path and it would fail.

Java3D - Some classes not found but classpath is set correctly

I have a class that uses Java3D that successfully compiles, although when I try to run it it says: Exception in thread "main" java.lang.NoClassDefFoundError:
javax/media/j3d/Canvas3D,
With the following stack trace:
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Unknown Source)
at java.lang.Class.getMethod0(Unknown Source)
at java.lang.Class.getMethod(Unknown Source)
at sun.launcher.LauncherHelper.getMainMethod(Unknown Source)
at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)
Caused by: java.lang.ClassNotFoundException: javax.media.j3d.Canvas3D
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
Stuff I have already tried:
I couldn't even get it to compile until I copied the Java3D jars into /jre/lib/ext/.
I have the latest Java, Java3D and I am using Notepad++ and I have tried reinstalling Java3D.
I have set the classpath/path correctly.
There are no errors in the code.
I can run normal Java applications I have created.
I have tried using the classpath thing when running the application (java -classpath blahblah ApplicationName).
I have checked inside the jars and the classes (including Canvas3D) are definitely in there.

Not everything you say is true.
IF the classes are in the jars, and IF you have set the classpath correctly, THEN you would not get this message.
I suspect you have a build path confused with a classpath (which is mostly associated with runtime, where build path is associated with compile time). Without knowing more details of your runtime environment, it's hard to be more specific.
It always puzzles me how someone with a problem they cannot solve asserts so definitely that all these things are set up "correctly": how do you know? Isn't the problem some evidence to the contrary, at least enough for a small doubt?