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java.lang.NoClassDefFoundError when using weka.jar file in my own java file

I'm having problems executing my java program. The code is placed in the file RunMining.java and contains multiple import weka.[..] lines. The weka library (weka.jar) is placed in the same folder.
I compile it:
$ javac -cp weka.jar RunMining.java
This creates three files: RunMining.class, RunMining$1.class, RunMining$classifierType.class
When i run it: java -cp weka.jar RunMining i get the following error:
Exception in thread "main" java.lang.NoClassDefFoundError: RunMining
Caused by: java.lang.ClassNotFoundException: RunMining
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
My RunMining.java file only contains one class called RunMining, which contains the main method. I would prefer not to add the weka.jar file to my CLASSPATH since this file will be compiled using a makefile and executed using a script, on different machines.
Any suggestions, to how i can run the compiled files?

You need to add the classpath of your compiled files as follows:
java -cp weka.jar;. RunMining
This assumes your files are compiled in the root directory which your javac command suggests.

Getting ClassNotFound Exception while executing shell script

I want to write a shell script, which should call classes inside the jars. I am getting a ClassNotFound Exception when one jar's class file calling another jar's class file.
Here is what I've tried:
cd /home/appteam/encrypt/REPORT/CRYPTO4REPORT/
echo $1
echo $2
pwd
set JAVA_HOME = /App/jdk1.6.0_25/bin;
set path= /App/jdk1.6.0_25/bin;
java -classpath .:jars/log4j-1.2.8.jar:jars/xmlsec-1.4.2.jar:jars/CryptoUtils.jar:jars/bcprov-jdk15-146.jar:jars/commons-logging.jar:jars/Utils.jar:jars/Crypto.jar com.crypto.pki.PkiCrypto 1>> files/log/SuccessLog.log 2>>files/log/ErrorLog.log "ILI_RPT_TRV_07022013_001.enc" "crypto4decrypt.properties" DECRYPT
From the above code, I am calling com.crypto.pki.PkiCrypto class which is inside Crypto.jar. Form the PriCrypto class calling FileUtil class which is inside Utils.jar.
I receive a ClassNotFoundException when PriCrypto class file uses the FileUtil class.
I got following Exception:
Exception in thread "main" java.lang.NoClassDefFoundError: com/common/utils/FileUtil
at com.crypto.pki.PkiCrypto.processFile(PkiCrypto.java:75)
at com.crypto.pki.PkiCrypto.main(PkiCrypto.java:31)
Caused by: java.lang.ClassNotFoundException: com.common.utils.FileUtil
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
... 2 more

check Utils.jar is in the class path while running the program and also verify that utils.jar contains com.common.utils.FileUtil class

Javac compilation and execution of 2 java files

The program is written with 2 files filter.java - in which is the main function and ClasifiedWord.java which is only container class. I wrote that on windows on eclipse but want to compile it on Linux javac compiler.
javac filter.java ClasifiedWord.java
runs without mistakes, but when I try to run the program:
snowy:Filter$ java filter
Exception in thread "main" java.lang.NoClassDefFoundError: filter
Caused by: java.lang.ClassNotFoundException: filter
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: filter. Program will exit.
snowy:Filter$ javac filter.java ClasifiedWord.java
snowy:Filter$ java filter ClasifiedWord
Exception in thread "main" java.lang.NoClassDefFoundError: filter
Caused by: java.lang.ClassNotFoundException: filter
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Could not find the main class: filter. Program will exit.
How can I run the program ? It seems that the compilation is ok. I have doubts that maybe I have made a mistake about the file paths in the program.... but I think that this is not the case?
Thanks for your answers!

Type the following command.
java -classpath . filter
If you want to type just java filter, please following these guides.
Linux http://www.cyberciti.biz/faq/linux-unix-set-java_home-path-variable/
Windows http://ac-support.europe.umuc.edu/~arnoldyl/NetBeansTutorials/Setting-Classpath.html
P.S. The last command java filter ClasifiedWord means to run a program filter and use a string ClasifiedWord as an argument.

Roland is right in the comment, you should be able to run it with java -classpath <folderContainingDotClassFiles> filter. Also, you should change filter.java to Filter.java as the standard Java convention for class names (including the files containing them) is to capitalize the first letter.

This looks like you either have a wrong CLASSPATH setting (usually you don't need this at all, but if you have it, it should include . in the list, for the current directory), or you are using packages (wrongly), or both. For the classpath issue, see the other answers.
If you are using packages, i.e. your files contain a package ...; line at the beginning, you should put your source files in a directory structure according to the package structure. For example, if you have package example;, you should have an example directory in your current directory, and in this the two source files.
Then call compiler and interpreter like this:
javac example/filter.java example/ClasifiedWord.java
java example.filter
(This assumes that filter is the main class, otherwise replace its name.)

Java: Exception in thread "main" java.lang.NoClassDefFoundError

To compile my java app, I use from terminal:
javac -cp commons-digester-2.1/commons-digester-2.1.jar:lucene-core-3.0.3.jar CollectionIndexer.java
To run the app I use:
java -classpath commons-digester-2.1/commons-digester-2.1.jar:lucene-core-3.0.3.jar CollectionIndexer
However I get the following error:
Exception in thread "main" java.lang.NoClassDefFoundError: commons-digester-2/1/commons-digester-2/1/jar:lucene-core-3/0/3/jar
Caused by: java.lang.ClassNotFoundException: commons-digester-2.1.commons-digester-2.1.jar:lucene-core-3.0.3.jar
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
I guess I'm defining correctly the classpath.. or what ?

Try -cp instead of classpath. Also add the current directory to the classpath.
$ java -cp .:commons-digester-2.1/commons-digester-2.1.jar:lucene-core-3.0.3.jar CollectionIndexer
or
$ export CLASSPATH=.:commons-digester-2.1/commons-digester-2.1.jar:lucene-core-3.0.3.jar
$ java CollectionIndexer
If on Windows, use backslashes and a semi-colon separator:
java -cp .;commons-digester-2.1\commons-digester-2.1.jar;lucene-core-3.0.3.jar CollectionIndexer

I would suggest you to set the classpath first with
SET CLASSPATH command and then execute your program as
java CollectionIndexer.

How to invoke groovy with 'java' from command line

I have to ship some groovy code to some users that have only java installed (no grooy, no $groovy_home, etc). I'm trying to invoke groovy from the commandline but I'm having no luck. Here's my bat file:
java -classpath .;lib;bin;bin-groovy introspector.AclCollector
And here's my exception:
Exception in thread "main" java.lang.NoClassDefFoundError: groovy/lang/GroovyObject
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
at java.net.URLClassLoader.access$000(URLClassLoader.java:56)
at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
Caused by: java.lang.ClassNotFoundException: groovy.lang.GroovyObject
at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:252)
at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320)
... 12 more
Could not find the main class: introspector.AclCollector. Program will exit.
Does anyone have a clue? I have 'groovy-all-1.6-beta-1.jar' in \lib dir.

You have here another example of Groovy app called from Java (in this case, from ant, but the general idea is the same).
java -cp [...];%GROOVY_HOME%/embeddable/groovy-all-1.5.4.jar;[..]
As mentioned by frankowyer, you have the exact groovy jar explicitly listed on the classpath arguments of the java.
Since your clients do not have special environment variable, just replace the %GROOVY_HOME%/... with the complete path to:
groovy.jar or
goovy-all-VERSION.jar (to minimize any conflict with other libraries)

I think you need to explicitly list the groovy jar in the classpath

One way to avoid problems with different class paths on different machines would be to bundle all the necessary dependencies into one single jar, this would also make distribution to users easier. This can be done with this 'GroovyWrapper' script. The default jars (embeddable/groovy-all-.jar and lib/commons.jar) are included by default in the script and if you require other JARS they can easily be added.
See http://docs.codehaus.org/display/GROOVY/WrappingGroovyScript for the full script and instructions.
Here's an example of how to use GroovyWrapper:
Say you have groovy script HelloWorld.groovy, use GroovyWrapper for building HelloWorld.jar, as follows:
$ groovy GroovyWrapper -c -m HelloWorld
GroovyWrapper will compile the script HelloWorld.groovy to HelloWorld.class, and creates a self-executable jar HelloWorld.jar.
Now you can use the HelloWorld.jar for launching the HelloWorld script, simply by running:
$ java -jar HelloWorld.jar

GREAT ANSWER by VonC:
....... Since your clients do not have special environment variable,
just replace the %GROOVY_HOME%/... with the complete path to:
groovy.jar or
goovy-all-VERSION.jar (to minimize any conflict with other libraries)........
this is for windows Vista:
In System Properties | Environmental Variables | User variables:
Variable Name GROOVY_HOME set to C:\groovy\Groovy-1.8.5
and the Variable Name CLASSPATH value's set to include .;%GROOVY_HOME%\embeddable\groovy-all-1.8.5.jar
Don't make the mistake I did(spinning my wheels a bit), of not prep-ending the path of the 'groovy-all' with ".;" (dot and semi-colon): as the path needs the base folder you're in for finding the main class(strange as it seems)

Watch out of [~]!
java -cp .:~/path-to-groovy-all.jar YourClassName # does not work
java -cp ~/path-to-groovy-all.jar:. YourClassName # works
java -cp .:/full/path/to/goovy-all.jar YourClassName # works
In first line tilde is not processed by bash, and java can not understand it.
In second line tilde is replaced by bash and everything works fine.