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Log4j warning and ClassNotFoundException problem

I am trying to run my javaFX project on the console using the jar file of the project on windows. I am running the program with the following command: java -jar INF202_PROJECT.jar

When I run it in the IDE (I am using intellij) it runs normally and as expected but I get the following output: 

log4j:WARN No appenders could be found for logger (org.apache.pdfbox.pdfparser.PDFObjectStreamParser).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

And when I run the program on the cmd an ClassNotFoundException occurs: 

Exception in thread "JavaFX Application Thread" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
        at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1774)
        at javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(FXMLLoader.java:1657)
        at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
        at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
        at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
        at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
        at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
        at javafx.event.Event.fireEvent(Event.java:198)
        at javafx.scene.Node.fireEvent(Node.java:8411)
        at javafx.scene.control.Button.fire(Button.java:185)
        at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:182)
        at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:96)
        at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:89)
        at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
        at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
        at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
        at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
        at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
        at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
        at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
        at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
        at javafx.event.Event.fireEvent(Event.java:198)
        at javafx.scene.Scene$MouseHandler.process(Scene.java:3757)
        at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
        at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
        at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494)
        at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:394)
        at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
        at java.security.AccessController.doPrivileged(Native Method)
        at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:432)
        at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:410)
        at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:431)
        at com.sun.glass.ui.View.handleMouseEvent(View.java:555)
        at com.sun.glass.ui.View.notifyMouse(View.java:937)
        at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
        at com.sun.glass.ui.win.WinApplication.lambda$null$4(WinApplication.java:186)
        at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.reflect.InvocationTargetException
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at sun.reflect.misc.Trampoline.invoke(Unknown Source)
        at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at sun.reflect.misc.MethodUtil.invoke(Unknown Source)
        at javafx.fxml.FXMLLoader$MethodHandler.invoke(FXMLLoader.java:1769)
        ... 48 more
Caused by: java.lang.NoClassDefFoundError: org/apache/pdfbox/pdmodel/font/PDFont
        at sample.controllers.ReportController.areEquipmentFieldsEmpty(ReportController.java:601)
        at sample.controllers.ReportController.getReport(ReportController.java:455)
        at sample.controllers.ReportController.pdfButtonOnAction(ReportController.java:368)
        ... 58 more
Caused by: java.lang.ClassNotFoundException: org.apache.pdfbox.pdmodel.font.PDFont
        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)
        ... 61 more

log4j-1.2.17.jar is added to the libraries of the project as follows:

enter image description here

I sow multiple answers that I should add log4j.properties to my src folder in my project to configure log4j so I added the following file:

# Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=INFO, A1

# A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender

# A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n

I seem not knowing what I am doing so any help will be appreciated.

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Answer

The problem was sourced from intellij. So if you want your jar’s to be included in the jar file of your program you have to put them in the Modules and not in the libraries!!

like this:

enter image description here

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