running the .jar file of jalview - java

I am trying to get Jalview [1] running on my windows 7 system. The standard installation works without error but when starting (the .exe file) it I get "Windows error 2 occured while loading the Java VM". As this error is quite general I tried then
C:\Program Files (x86)\Jalview>java -jar jalview.jar
which leads to:
Java version: 1.8.0_121
x86 Windows 7 6.1
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/log4j/Layo
ut
at jalview.bin.Jalview.doMain(Jalview.java:210)
at jalview.bin.Jalview.main(Jalview.java:180)
Caused by: java.lang.ClassNotFoundException: org.apache.log4j.Layout
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)
... 2 more
any ideas what is going wrong?
Thx
Morpheus
[1] http://www.jalview.org/Download

This error "java.lang.NoClassDefFoundError" occurs when there is a class missing in your respective packages.
I suggest please check if the class "Layout" is present at path : org/apache/log4j
If not then its correct that you have some missing files/libraries of log4j in the classpath.
Please vote and mark the solution if useful.
Thanks!

First check that in C:\Program Files (x86)\Jalview\lib the library min-jabaws-client-*.jar exists.
To run it from command line
cd C:\Program Files (x86)\Jalview
java -cp jalview.jar;lib/* jalview.bin.Jalview

Related

javamail class not found while trying to run on RHEL

I was asked to configure and use javamail on a RHEL 7 server.
I untar'ed a javamail directory they had here which contains the following files:
activation.jar
cacerts
config.properties
InstallCert.class
InstallCert$SavingTrustManager.class
mail.jar
SimpleSSLMail.class
Also, I have created a /etc/profile.d/java.sh where I have the following:
JAVA_HOME=/usr/java/jre1.6.0_45
export PATH=$JAVA_HOME/bin:/usr/bin:/bin:/usr/sbin:$PATH
export CLASSPATH=$CLASSPATH:/usr/share/javamail/activation.jar:/usr/share/mail.jar:.
cacerts is a keystore which holds gmail's cert to sendmail. When I try to send mail using the following:
java -Djavax.net.ssl.trustStore="cacerts" -Djavax.net.ssl.trustStorePassword="somepassword" SimpleSSLMail "SomeHeader" "Testing..." "some#mail.com"
It fails with message:
Exception in thread "main" java.lang.NoClassDefFoundError:
SimpleSSLMail Caused by: java.lang.ClassNotFoundException:
SimpleSSLMail
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source) Could not find the main class: SimpleSSLMail. Program will exit
I have reviewed many posts saying the problem is java not finding mail and activation jars, but I can't handle correctly the CLASSPATH to work with those files. I also tried using -cp flag like this: java -cp mail.jar -cp activation.jar -Djavax.net.ssl.trustStore="cacerts" .....
It was useless, I get the same error.
What am I missing or how do I get it to work?
I have java jre only; do I need to compile it using javac?
My goal is to make it work in order to create an alias where the user can type only sendmail "Message" "mail.com" or similar
UPDATE
I was having a typo in classpath where instead of using /usr/share/javamail/mail.jar I was using /usr/share/mail.jar.
Now, when creating the alias it works fine in javamail directory but if I try to run it outside the directoy, java complains that it doesn't find config.properties. I believe it is searching for it as ./config_properties.
I don't have the source code, so, is there a way to override the config.properties location with the command line?

NoClassDefFoundError using bluetooth in java

I asked a question earlier here: NoClassDefFoundError with bluecove's javax.microedition
but got no responses.
I am trying to run some java code (Server.java) that requires bluetooth, so I installed the bluecove-2.1.0.jar file in C:\Program Files\Java.
I compile my code with javac -cp "C:\Program Files\Java\bluecove-2.1.0.jar";. Server.java and run it with java Server -cp "C:\Program Files\Java\bluecove-2.1.0.jar"
It compiles successfully, but when I run it, I get the error:
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.NoClassDefFoundError: javax/microedition/io/Connection
at java.lang.Class.getDeclaredMethods0(Native Method)
at java.lang.Class.privateGetDeclaredMethods(Unknown Source)
at java.lang.Class.privateGetMethodRecursive(Unknown Source)
at java.lang.Class.getMethod0(Unknown Source)
at java.lang.Class.getMethod(Unknown Source)
at sun.launcher.LauncherHelper.validateMainClass(Unknown Source)
at sun.launcher.LauncherHelper.checkAndLoadMain(Unknown Source)
Caused by: java.lang.ClassNotFoundException: javax.microedition.io.Connection
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)
... 7 more
Any ideas where i've gone wrong?
EDIT: Following Minus' answer, to fix the error that followed, I also needed to use a different .jar file which I downloaded from http://snapshot.bluecove.org/distribution/download/2.1.1-SNAPSHOT/2.1.1-SNAPSHOT.63/
The problem is that the .dll is not loaded correctly.
The library should contain a .dll that will be saved on disk and loaded, maybe the program cannot save the .dll to disk or cannot read it.
Extract the .dll and follow bluecove installation instructions on Native Library location.
For example:
Create a directory c:\blue, and a directory blue\lib.
Put the files like this:
C:\blue\Sever.java
C:\blue\Sever.class
C:\blue\[bluecove_native_library].dll
C:\blue\lib\bluecove-2.1.0.jar
Open a cmd (Command Prompt) on c:\blue
Try to run the app like this:
java -cp .;lib\bluecove-2.1.0.jar -Dbluecove.native.resource=false Server
This way you will have both Server.class and bluecove-2.1.0.jar in classpath and the DLL in path (since on Windows the current dir is in path).
Add a current folder to a classpath (.;) and make sure that your code is in a package-name folder.
So if your server has a package name :
mypackage
make sure that your class code is in a /mypackage directory
than go to a parent folder to /mypackage and call:
java -cp ".;C:\Program Files\Java\bluecove-2.1.0.jar" mypackage.Server

Specifying Maven Directory when Running Java.exe

I'm a newbie to Java (just two days) and am trying to get an HTTP server running using Spark. I created a new Maven project in IntelliJ and have a Hello World response coming back from Spark when running it in IntelliJ. As a learning exercise, I would like to get the app running from the command line using Java.exe. When I run java Main, I get the following error:
Exception in thread "main" java.lang.BootstrapMethodError:
java.lang.NoClassDef oundError: spark/Request
at Main.main(Main.java:5) Caused by: java.lang.NoClassDefFoundError: spark/Request
... 1 more Caused by: java.lang.ClassNotFoundException: spark.Request
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)
... 1 more
Looks like it can't find the Spark .jar files. There's a command line option -cp to specify paths to dependencies. After looking up where Maven keeps these files, I tried running:
java -cp .;C:\Users\jbuschmann.m2\repository Main
Still same error. How do I specify the path to the Maven dependencies?
Instead of giving the repository in the -classpath, try adding the location of your spark.jar.
java -cp \path\to\spark.jar Main

java.lang.NoClassDefFoundError with LWJGL

So, I am afraid that I have to join the crowds flocking here and asking: "What's wrong with my code?"
I've recently started coding in Java and I've had none of this error until I tried using lwjgl in a project. So, the question is: What is wrong with my JAR when I get the following:
java -cp \lib\win32\lwjgl.jar -jar Valor.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/lwjgl/opengl/Display
at bin.Disp.createWindow(Disp.java:18)
at bin.Thread.gameLoop(Thread.java:13)
at Main.main(Main.java:4)
Caused by: java.lang.ClassNotFoundException: org.lwjgl.opengl.Display
at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 3 more
As is, I am extremely confused about this. I've gone through seven or eight posts here about this very problem, and another five or six on other web sites, yet none of the methods those people used seem to work for me.
Currently, my file structure is:
Valor
-Valor.jar
lib
win32
-lwjgl.jar
-lwjgl.dll
Manifest:
Manifest-Version: 1.0
Main-Class: Main
I did try defining a classpath here... Didn't work. So, I'm pretty much as confused as I can possibly get. Thank you for your help.
Edit: This error doesn't occur while running in Eclipse, only when I export and try to run it myself.
Try to run it like this:
java -cp lib\win32\lwjgl.jar;Valor.jar Main
The problem is that the -cp option is ignored when -jar is used.
Alternativelly you could extend the class path by adding a Class-Path: entry in your manifest and puting lib\win32\lwjgl.jar in it.
Class-Path: lib\win32\lwjgl.jar
use this link to install ljgl and define your classPath : http://www.lwjgl.org/wiki/index.php?title=Setting_Up_LWJGL_with_Eclipse
By running java -cp \lib\win32\lwjgl.jar -jar Valor.jar you're telling Java to look for LWJGL classpath near the root of your filesystem. Seeing your directory structure, use:
java -cp .\lib\win32\lwjgl.jar -jar Valor.jar
Notice the . at the beginning.

NoClassDefFoundError hibernate criterion exporting jar

I'm trying to export a java stand-alone class that uses hibernate. It's a really simple read/insert procedure. I'm stuck with this error
C:\Users\Admin\Desktop>java -jar ImportDatiMeteo2.jar
Exception in thread "main" java.lang.NoClassDefFoundError: org/hibernate/criteri
on/Criterion
at openplan.openergy.standalone.ImportDati.main(ImportDati.java:24)
Caused by: java.lang.ClassNotFoundException: org.hibernate.criterion.Criterion
at java.net.URLClassLoader$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
... 1 more
I was thinking it could be a manifest file problem so i checked. It seem ok to me.
Manifest-Version: 1.0
Class-Path: lib/antlr-2.7.6rc1.jar lib/asm-attrs.jar lib/asm.jar
lib/c3p0-0.8.5.2.jar lib/cglib-2.1.3.jar lib/cleanimports.jar
lib/commons-collections-2.1.1.jar lib/commons-logging-1.0.4.jar lib/concurrent-1.3.2.jar
lib/connector.jar lib/dom4j-1.6.1.jar lib/ehcache-1.1.jar lib/hibernate3.jar
lib/jaas.jar lib/jacc-1_0-fr.jar lib/jaxen-1.1-beta-7.jar
lib/jdbc2_0-stdext.jar lib/jgroups-2.2.7.jar lib/jta.jar lib/log4j-1.2.11.jar
lib/log4j-1.2.9.jar lib/oscache-2.1.jar lib/proxool-0.8.3.jar
lib/swarmcache-1.0rc2.jar lib/xerces-2.6.2.jar lib/xml-apis.jar
Created-By: 1.6.0_21 (Sun Microsystems Inc.)
Main-Class: openplan.openergy.standalone.ImportDati
In my Eclipse all the project work properly, does anyone know where the problem is?
You need to add those libraries in classpath as you are running it from command line :
C:\> java -classpath <referenced-jars> -jar ImportDatiMeteo2.jar
in myEclipse all the project work properly, does anyone know where the problem is ?
--> Because Eclipse will take care of your classpath and adding libraries in your classpath.
Please check Library handling option in your Eclipse export dialog. On my side it works fine with hibernate with Extract required libraries into generated JAR selected.

Categories