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PDFBox with Maven - java.lang.NoClassDefFoundError

When installing PDFBox with Maven, it places the libraries in the ~/.m2/repository directory.
My program complies fine with mvn package.
When I try to run it with
java -cp target/java-project-1.0-SNAPSHOT.jar com.example.sub.App
then I get
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/pdfbox/pdmodel/PDDocument
Should I also be specifying the libraries in ~/.m2/repository as part of the classpath? This seems a bit too tedious to do it this way. What is the recommended way to specify the classpath of my PDFBox library while using the library location(s) of Maven?

I wasn't able to find a nice solution with leaving the JAR files in ~/.m2, so the answer below is a workaround based on some other answers. I will be including more clarification though for those who are new to both PDFBox and maven as I am.
1) Add the following to your pom.xml file. If you already have a <build> and <plugins> section, just add the <plugin> section below to that. Otherwise you may need to add the whole code below within the <project> element:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>**REPLACE THIS WITH THE FULL URI OF YOUR MAIN CLASS**</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-my-jar-with-dependencies</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
2) Make sure that you replace the text in the <mainClass> element to match the situation. For example, if your main() method is located in an App class in App.js, and your package name is com.example.sub. Then the above element should read:
<mainClass>com.example.sub.App</mainClass>
3) To compile your app, run mvn package
Note: I have seen some references online using mvn clean compile assembly:single instead of mvn package. I am not sure what the purpose of this is when mvn package seems to run just fine for me.
This will take your project and all of your dependencies and create a single JAR file in the target directory called something like this:
java-project-1.0-SNAPSHOT-jar-with-dependencies.jar
4) To run the project you can do this:
java -cp target/java-project-1.0-SNAPSHOT-jar-with-dependencies.jar com.example.sub.App
Make sure that you modify the above line to it your situation. In other words you may need to change both the name of the jar file and the name of the URI for your main class.

The maven dependencies are not added to the jar in eclipse

I'm coding a maven project with eclipse 2018.09 under java 11 and I've a problem with the maven jar creation. When I clean package the project, it delivers me a jar but no dependencies are added into and i sometimes have warning in eclipse like:
classpath entry junit(for example) will not be exported it may result a ClassNotFoundException.
Which is in fact what's happening when i launch my jar project.
Thanks.

it delivers me a jar but no dependencies are added into [it]
it is totally normal. By default, when Maven builds a jar, it does not add any dependencies in it, but only the .class and resources of your current project.
When you run your programm you want it to find your dependencies otherwise you will face ClassNotFoundException. So you must configure your classpath to reference the dependencies.
1- if you want to run you programm from your local computer with Maven, use the exec Maven plugin with the <java> goal defined in your pom like explained here: https://www.mojohaus.org/exec-maven-plugin/usage.html#Java_goal
alternatively you can run it from a launcher in your IDE. The IDE will build the classpath for you and the classpath will corectly contain your dependencies.
2- if you want to run from the command line on any computer, you have to copy all of you dependencies in one directory (using Maven's dependency plugin mvn dependency:copy) and run you jar like this:
java -cp myProgram.jar:dependencyDirectory/* com.blabla.MainClass
(beware the use of ';' or ':' and '/' or '\' depending on Linux/Windows)
3- as an alternative you can run your jar with java -jar myprogram.jar but only if it contains a correct MANIFEST.MF where the location of all the dependencies are hardcoded.
My advice is to target solution 1 or 2 first.
PS: you can also create "fat jars" or "uber jars" containing your dependencies but I would advise you do not target this solution at first.

You can simply add this to your pom.xml (under the < plugins > tag):
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<archive>
<manifest>
<mainClass>App</mainClass>
</manifest>
</archive>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
<executions>
<execution>
<id>make-assembly</id>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
Remember to change the mainclass to your entrypoint (which class the static void main(string[args]) is).
Now when you run the command mvn clean install there will be a jar in the targets folder with name yourproject-version-SNAPSHOT-jar-with-dependencies.jar

Building and executing JAR file error: could not find main class and unsupported major.minor version 52.0

After building the Java program in NetBeans, I compressed the dist folder, placed the program in a USB. In another computer, after extracting all the files, I tried running the JAR file but a Window prompt said:
"Could not find the main class: logic.Main. Program will exit."
After researching and tried the solutions of similar problems (i.e. creating Manifest file, creating .bat file) but nothing works.
Then I ran it in command prompt and these were the results:
Are there 2 problems: could not find main class and that in the other computer, the Java is not updated? How to solve this?

It was actually able to find a logic.Main, but it wasnt able to load it because it was compiled with Java 8 and the user's machine is running an earlier version of Java. Compiling the file on an earlier version of Java or updating Java on the target machine will fix the issue.

There are multiple ways of creating executable jar.
In netbeans there is a option
Project Properties -> Build -> Packaging -> Build JAR after compiling
Maven Build can also be used for creating executable jar. Define main class in below maven plugin. Also you can select the compiler version to avoid major minor issue.
<plugin>
<!-- Build an executable JAR -->
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.6</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>com.kulhade.elasticsearch.Indexer</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.dstovall</groupId>
<artifactId>onejar-maven-plugin</artifactId>
<version>1.4.4</version>
<executions>
<execution>
<goals>
<goal>one-jar</goal>
</goals>
</execution>
</executions>
</plugin>

NoClassDefFoundError on Maven dependency

My first use of Maven and I'm stuck with dependencies.
I created a Maven project with Eclipse and added dependencies, and it was working without problems.
But when I try to run it via command line:
$ mvn package # successfully completes
$ java -cp target/bil138_4-0.0.1-SNAPSHOT.jar tr.edu.hacettepe.cs.b21127113.bil138_4.App # NoClassDefFoundError for dependencies
It downloads dependencies, successfully builds, but when I try to run it, I get NoClassDefFoundError:
Exception in thread "main" java.lang.NoClassDefFoundError: org/codehaus/jackson/JsonParseException
at tr.edu.hacettepe.cs.b21127113.bil138_4.db.DatabaseManager.<init>(DatabaseManager.java:16)
at tr.edu.hacettepe.cs.b21127113.bil138_4.db.DatabaseManager.<init>(DatabaseManager.java:22)
at tr.edu.hacettepe.cs.b21127113.bil138_4.App.main(App.java:10)
Caused by: java.lang.ClassNotFoundException: org.codehaus.jackson.JsonParseException
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 3 more
My pom.xml is like this:
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>tr.edu.hacettepe.cs.b21127113</groupId>
<artifactId>bil138_4</artifactId>
<version>0.0.1-SNAPSHOT</version>
<packaging>jar</packaging>
<name>bil138_4</name>
<url>http://maven.apache.org</url>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<dependencies>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
</dependency>
</dependencies>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-core-asl</artifactId>
<version>1.9.6</version>
</dependency>
<dependency>
<groupId>org.codehaus.jackson</groupId>
<artifactId>jackson-mapper-asl</artifactId>
<version>1.9.6</version>
</dependency>
</dependencies>
</dependencyManagement>
</project>
Can anyone help me?

By default, Maven doesn't bundle dependencies in the JAR file it builds, and you're not providing them on the classpath when you're trying to execute your JAR file at the command-line. This is why the Java VM can't find the library class files when trying to execute your code.
You could manually specify the libraries on the classpath with the -cp parameter, but that quickly becomes tiresome.
A better solution is to "shade" the library code into your output JAR file. There is a Maven plugin called the maven-shade-plugin to do this. You need to register it in your POM, and it will automatically build an "uber-JAR" containing your classes and the classes for your library code too when you run mvn package.
To simply bundle all required libraries, add the following to your POM:
<project>
...
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>3.4.1</version>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
...
</project>
Once this is done, you can rerun the commands you used above:
$ mvn package
$ java -cp target/bil138_4-0.0.1-SNAPSHOT.jar tr.edu.hacettepe.cs.b21127113.bil138_4.App
If you want to do further configuration of the shade plugin in terms of what JARs should be included, specifying a Main-Class for an executable JAR file, and so on, see the "Examples" section on the maven-shade-plugin site.

when I try to run it, I get NoClassDefFoundError
Run it how? You're probably trying to run it with eclipse without having correctly imported your maven classpath. See the m2eclipse plugin for integrating maven with eclipse for that.
To verify that your maven config is correct, you could run your app with the exec plugin using:
mvn exec:java -D exec.mainClass=<your main class>
Update: First, regarding your error when running exec:java, your main class is tr.edu.hacettepe.cs.b21127113.bil138_4.App. When talking about class names, they're (almost) always dot-separated. The simple class name is just the last part: App in your case. The fully-qualified name is the full package plus the simple class name, and that's what you give to maven or java when you want to run something. What you were trying to use was a file system path to a source file. That's an entirely different beast. A class name generally translates directly to a class file that's found in the class path, as compared to a source file in the file system. In your specific case, the class file in question would probably be at target/classes/tr/edu/hacettepe/cs/b21127113/bil138_4/App.class because maven compiles to target/classes, and java traditionally creates a directory for each level of packaging.
Your original problem is simply that you haven't put the Jackson jars on your class path. When you run a java program from the command line, you have to set the class path to let it know where it can load classes from. You've added your own jar, but not the other required ones. Your comment makes me think you don't understand how to manually build a class path. In short, the class path can have two things: directories containing class files and jars containing class files. Directories containing jars won't work. For more details on building a class path, see "Setting the class path" and the java and javac tool documentation.
Your class path would need to be at least, and without the line feeds:
target/bil138_4-0.0.1-SNAPSHOT.jar:
/home/utdemir/.m2/repository/org/codehaus/jackson/jackson-core-asl/1.9.6/jackson-core-asl-1.9.6.jar:
/home/utdemir/.m2/repository/org/codehaus/jackson/jackson-mapper-asl/1.9.6/jackson-mapper-asl-1.9.6.jar
Note that the separator on Windows is a semicolon (;).
I apologize for not noticing it sooner. The problem was sitting there in your original post, but I missed it.

You have to make classpath in pom file for your dependency. Therefore you have to copy all the dependencies into one place.
Check my blog.
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.1</version>
<executions>
<execution>
<id>copy-dependencies</id>
<phase>package</phase>
<goals>
<goal>copy-dependencies</goal>
</goals>
<configuration>
<outputDirectory>${project.build.directory}/lib</outputDirectory>
<overWriteReleases>false</overWriteReleases>
<overWriteSnapshots>false</overWriteSnapshots>
<overWriteIfNewer>true</overWriteIfNewer>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
<classpathPrefix>lib/</classpathPrefix>
<mainClass>$fullqualified path to your main Class</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>

This is due to Morphia jar not being part of your output war/jar. Eclipse or local build includes them as part of classpath, but remote builds or auto/scheduled build don't consider them part of classpath.
You can include dependent jars using plugin.
Add below snippet into your pom's plugins section
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.0.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
</configuration>
</plugin>

For some reason, the lib is present while compiling, but missing while running.
My situation is, two versions of one lib conflict.
For example, A depends on B and C, while B depends on D:1.0, C depends on D:1.1, maven may
just import D:1.0. If A uses one class which is in D:1.1 but not in D:1.0, a NoClassDefFoundError will be throwed.
If you are in this situation too, you need to resolve the dependency conflict.

I was able to work around it by running mvn install:install-file with -Dpackaging=class. Then adding entry to POM as described here:

Choosing to Project -> Clean should resolve this

Running jar, setting classpath

I've got a project I've made with Maven. I compile a JAR, with "mvn package", and now I want to run it, preferably without setting some insane classpath, as it depends on Spring and half the internet or something. Is there any way I can run it easily? Something like "mvn run" would be great, or an option to throw in all dependencies into the jar so I can do "java -jar" would also be splendid.
How do you deal with this, and what do you recommend doing? Because exporting a CLASSPATH based on ~/.m2 would probably just be hurtful ;-)

Setting CLASSPATH and calling java -jar myjar.jar wouldn't work anyway. Because the java -jar command ignores the CLASSPATH environment variable as well as the -cp flag.
In this case you had to add the classpath entries to the jar's MANIFEST at the Class-Path key, like:
Class-Path: jar1-name jar2-name directory-name/jar3-name

Use the Maven Assembly Plugin - it will automatically build your JAR with all included dependencies, and you can set the main class parameter to make the JAR executable.
The documentation can be confusing, so here is an example of what your POM will look like:
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>2.1</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>package.of.my.MainClass</mainClass>
<packageName>package.of.my</packageName>
</manifest>
</archive>
</configuration>
</plugin>
</plugins>
</build>
And then you can run as:
mvn assembly:assembly

You will want to look into the Maven Assembly Plugin. And then once you have created the XML file required by the plugin and have modified your POM file to work with the plugin, you can run it with:
mvn assembly:assembly
This will create the JAR with all of its dependencies.