maven-assembly-plugin doesn't add dependencies with system scope

Question

This is my pom file:

<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/maven-v4_0_0.xsd"&gt;
  <modelVersion>4.0.0</modelVersion>
  <groupId>com.sia.g7</groupId>
  <artifactId>sia</artifactId>
  <packaging>jar</packaging>
  <version>1.0-SNAPSHOT</version>
  <name>sia</name>
  <url>http://maven.apache.org&lt;/url&gt;
  <dependencies>
    <dependency>
        <groupId>log4j</groupId>
        <artifactId>log4j</artifactId>
        <version>1.2.12</version>
     </dependency>
<dependency>
    <groupId>commons-math</groupId>
    <artifactId>commons-math</artifactId>
    <version>1.2</version>
</dependency>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.8.1</version>
      <scope>test</scope>
    </dependency>

    <dependency>
      <groupId>jmathplot</groupId>
      <artifactId>jmathplot</artifactId>
      <version>1.0</version>
      <scope>system</scope>
      <systemPath>${project.basedir}/lib/jmathplot.jar</systemPath>
    </dependency>

    <dependency>
      <groupId>jgraphx</groupId>
      <artifactId>jgraphx</artifactId>
      <version>1.0</version>
      <scope>system</scope>
      <systemPath>${project.basedir}/lib/jgraphx.jar</systemPath>
    </dependency>

  </dependencies>
<build>
  <plugins>
    <plugin>
      <groupId>org.apache.maven.plugins</groupId>
      <artifactId>maven-compiler-plugin</artifactId>
      <version>2.0.2</version>
      <configuration>
        <source>1.6</source>
        <target>1.6</target>
      </configuration>
    </plugin>
    <plugin>
      <artifactId>maven-assembly-plugin</artifactId>
      <configuration>
        <descriptorRefs>
          <descriptorRef>jar-with-dependencies</descriptorRef>
        </descriptorRefs>
        <appendAssemblyId>false</appendAssemblyId>
        <archive>
          <manifest>
            <mainClass>com.sia.g7.AbstractSimulation</mainClass>
          </manifest>
        </archive>
      </configuration>

    </plugin>
  </plugins>

</build>
</project>

And when I run the jar I get:

Exception in thread "main" java.lang.NoClassDefFoundError: com/mxgraph/swing/mxGraphComponent

which is part of the jgraphx dependency. What am I missing?

Answer 1

It must not be system scope in the first place. This is the source of your problem. Install/deploy your dependency into the repository and make it a normal compile (or runtime) scope dependency.

Answer 2

Yes, and this is one of the reasons you shouldn't abuse system scope dependencies (which is globally a bad practice) and this problem has already been mentioned several times here on SO (here, here). I'm proposing a solution to deal with project relative dependencies in a "clean" way in this answer.

Answer 3

You should remove the <scope>system</scope> clauses from those dependencies. When the scope is set to system that means the artifact is ALWAYS available, so jar-with-dependencies does not include it.