Daniel Higginbotham's adventures in making stuff

How Clojure Babies Are Made: Compiling and Running a Java Program

13 March 2013

If you're at all like me, the moment you got your first Clojure program running you belted out, "SOOO MUUUUUUUCH POOOOOOOWEEEEEEEER!" and thrust one or both fists into the air. Then, fifteen minutes later, you found yourself muttering things like "What's a maven?" and "Classpath what now?" and "What is Leiningen actually doing, anyway? Sure, those are the most handsome mustaches I ever laid eyes on, but can I really trust them?"

This post is here to help you out. In it, I will describe how Java compiles and runs programs, and how this relates to Clojure. In an upcoming post, I will also describe how Leiningen makes this process way easier. Here's an outline of what's to come:

  • Java
    • Compilation
      • javac
      • Class lookup rules & classpath
      • imports
      • packages
      • JAR files
    • Running
      • Class file
      • classpath
      • Executable JAR
  • Leiningen
    • Running an app without Leiningen
    • classpath management
    • Incorporating Clojure automatically
    • Dependency managemenet

(Update: Part 2 of this series is now available!)


Java is going to rule the universe. The sooner you accept that, the better. If you don't have the JDK installed installed, you might want to do that now. To check, just try running java and javac in your terminal. By the way - this post assumes you're somewhat familiar with the terminal. It also assumes you're familiar with object-oriented programming.

Compiling and Running a Basic Program

This section will lay a foundation for your understanding of Java. It doesn't address Clojure directly, but the knowledge you gain will be useful in your Clojuring.

Let's put our game faces on and start with a basic program. Visit the github repo for the examples in this post and clone that baby for all you're worth.

In the folder ShiverMeTimbers, you should find an article named ShiverMeTimbers.java. Here are its contents:

public class ShiverMeTimbers
    public static void main(String[] args)
        System.out.println("Shiver me timbers!!!");

Once you've recovered from your swoon, cd to ShiverMeTimbers and run javac ShiverMeTimbers.java. If you typed everything correctly and you're pure of heart, you should now see a file named ShiverMeTimbers.class.

$ ls
ShiverMeTimbers.class ShiverMeTimbers.java

You've just compiled your first Java program, son! Now run it with java ShiverMeTimbers. You should see:

Shiver me timbers!!!

Which I'm pretty sure is like the Lord's prayer, but for pirates. Anyway, what's happening here is you used the Java compiler, javac, to create a Java class file, ShiverMeTimbers.class. This file is packed with oodles of Java bytecode which the Java Virtual Machine executes when running a program.

When you ran java ShiverMeTimbers, the JVM first looked on your classpath for a class named ShiverMeTimbers. In Java, you're only allowed to have one public class per file and the filename and class name must be the same. This is how java knows to try looking in ShiverMeTimbers.class for the ShiverMeTimbers class's bytecode.

Also, by default, the classpath includes the directory ., or the current directory. Try running java -classpath /tmp ShiverMeTimbers and you will get an error, even though ShiverMeTimbers.class is right there in the same directory.

After java found the bytecode for the ShiverMeTimbers class, it executed that class's main method. Java's kind of like C that way, in that whenever you say "run something, and use this class as your entry point", it always will run that class's main method. Which means that that method has to be public, as you can see above. (Here's more info on Java's access modifiers if you're curious.)

Key Ideas

  • javac compiles java source code to bytecode which the JVM can execute
  • java searches the classpath for the class you specified and executes its main method. That method must be public.

In the next section you'll learn about handling program code that's spread over more than one file. If you don't remove your socks now, they're liable to get knocked off!

Packages and Imports

In this section, you'll learn about how Java handles programs which are spread over more than one file. You'll also learn how to use Java libraries. Once again, we'll look at both compiling and running a program. This section has direct implications for Clojure programming, so pay attention!

Let's start with a couple definitions:

  • package: Similar to Clojure's namespaces, packages serve two purposes. They provide code organization, just like clojure namespaces. They also enforce access rules, which we don't really care about. The directory that a Java file lives in must mirror the package it belongs to. If a file has the line package com.shapemaster in it, then it must be located at com/shapemaster somewhere on your classpath. More about classpath later.
  • import: Java allows you to import classes, which basically means that you can refer to them without using their namespace prefix. So, if you have a class in com.shapemaster named Square, you could write import com.shapemaster.Square; or import com.shapemaster.*; at the top of a .java file so that you can use Square in your code instead of com.shapemaster.Square. Code example below.

Now let's see package and import in action. Here they are as used by the files in make-a-clojure-baby/ContrivedPackageExample. Pay attention to the comments, as they explain a lot of what's going on

Contents of make-a-clojure-baby/ContrivedPackageExample/Conversation.java:

public class Conversation
    public static void main(String[] args)
        // The "ns1" prefix is necessary because ShyGhost belongs to
        // the "ns1" package, and we haven't imported the classes in
        // that package
        ns1.ShyGhost shyGhost = new ns1.ShyGhost();

Contents of make-a-clojure-baby/ContrivedPackageExample/ns1/ShyGhost.java:

// The classes defined in this file belong to the "ns1" package.
// Notice that this file is in the "ns1" directory.
package ns1;

// This basically means, "I hate typing the namespace prefix all the
// time so please allow me to not do that"
import ns2.*;

public class ShyGhost
    public void talk() {
        // the shy ghost can't speak for himself and has to get
        // someone else to do it for him

        // Notice that even though SuperManlyIguana belongs to the ns2
        // namespace, we don't have to use the ns2 prefix
        SuperManlyIguana smi = new SuperManlyIguana();

Contents of make-a-clojure-baby/ContrivedPackageExample/ns2/SuperManlyIguana.java:

// The classes defined in this file belong to the "ns2" package
package ns2;

public class SuperManlyIguana
    public void talk()
        System.out.println("Why hello there");

You can run all the above code with the following:

cd make-a-clojure-baby/ContrivedPackageExample
javac Conversation.java
java Conversation

Can you guess what this outputs? I bet you can!

Anyway, so far we've established the relationship between importing, packages, and directory structure: Packages organize code and require a matching directory structure. Importing classes allows you to "de-namespace" them.

One piece that's missing, which I alluded to above, is the role of the classpath. Try the following:

cd make-a-clojure-baby/ContrivedPackageExample/ns1
javac ../Conversation.java

Boom! The Java compiler just told you to hang your head in shame, and maybe weep a little:

../Conversation.java:13: error: package ns1 does not exist
        ns1.ShyGhost shyGhost = new ns1.ShyGhost();
../Conversation.java:13: error: package ns1 does not exist
        ns1.ShyGhost shyGhost = new ns1.ShyGhost();

It thinks that the ns1 package doesn't exist. But that's stupid, right? I mean, you're in the ns1 directory and everything!

What's happening here is that the java compiler is looking for ./ns1/ShyGhost which it can't find because you're already in the ns1 directory. This is because the default classpath includes '.'. Without changing directories, try running javac -classpath ../ ../Conversation.java

Et voila! It works! So let's amend our understanding of the relationship between importing, packages, and the directory structures: when you're compiling a Java program, Java searches your classpath for packages.

Guess what: the same things happens when you're running a Java program, too. Run the following:

cd make-a-clojure-baby/ContrivedPackageExample
mkdir hide
mv ns1 hide
java Conversation

Another explosion! Now try:

java -classpath .:hide Converstaion


I hope this clarifies the relationship between your directory structure, the classpath, packages, and importing.

Key Ideas

  • Packages provide a way for you to organize classes. Your directory structure must reflect your package names
  • Imports allow you to be lazy and not prefix a class name with its package
  • javac and java search the classpath for packages

JAR Files

JAR, or Java ARchive, files allow you to bundle all your .class files into one single file. Run the following:

cd make-a-clojure-baby/ContrivedPackageExample
jar cvfe contrived.jar Conversation *.class ns*/*.class
java -jar contrived.jar

It works, just like before. You bundled all the class files into contrived.jar with the file patterns *.class and ns*/*.class. You also indicated that the Conversation class is the "entry point" with the e flag. The "entry point" is the class which contains the main method which should be executed when the JAR as a whole is run.

Behind the scenes, java knows which class is the entry point because when you create a jar, the file META-INF/MANIFEST.MF automaticaally gets generated and added. When you add the e flag, the following line gets added:

Main-Class: Conversation

By the way, you might be wondering why Java isn't throwing any exceptions like "can't find package". The reason is that the JAR file maintains the directory structure. You can see its contents with:

jar tf contrived.jar

You'll see that the directory structure is maintained.

One final point: a JAR file is really just a Zip file with a ".jar" extension. You can treat it just the same as any other zip file.

Pulling it All Together: clojure.jar

Let's pull all of this together with some Clojure! Download the 1.5.1 stable release and unzip it. Then cd to the directory that gets created and run

java -jar clojure-1.5.1.jar

You should get that most soothing of sights, the Clojure REPL. So, how did it actually start up? Let's have a look at META-INF/MANIFEST.MF in the jar file:

Manifest-Version: 1.0
Archiver-Version: Plexus Archiver
Created-By: Apache Maven
Built-By: hudson
Build-Jdk: 1.6.0_20
Main-Class: clojure.main

It looks like clojure.main is specified as the entry point. Where does this class come from? Well, have a look at clojure/main.java on github:

 *   Copyright (c) Rich Hickey. All rights reserved.
 *   The use and distribution terms for this software are covered by the
 *   Eclipse Public License 1.0 (http://opensource.org/licenses/eclipse-1.0.php)
 *   which can be found in the file epl-v10.html at the root of this distribution.
 *   By using this software in any fashion, you are agreeing to be bound by
 *   the terms of this license.
 *   You must not remove this notice, or any other, from this software.

package clojure;

import clojure.lang.Symbol;
import clojure.lang.Var;
import clojure.lang.RT;

public class main{

final static private Symbol CLOJURE_MAIN = Symbol.intern("clojure.main");
final static private Var REQUIRE = RT.var("clojure.core", "require");
final static private Var LEGACY_REPL = RT.var("clojure.main", "legacy-repl");
final static private Var LEGACY_SCRIPT = RT.var("clojure.main", "legacy-script");
final static private Var MAIN = RT.var("clojure.main", "main");

public static void legacy_repl(String[] args) {

public static void legacy_script(String[] args) {

public static void main(String[] args) {

As you can see, the class main is defined. It belongs to the package clojure and defines a public static main method. This is all Java needs to run a program.

I hope this has helped clarify Java and how it relates to Clojure! In my next post, I'll dig in to Leiningen. Fun for everybody!!!