Compiling Jalview Source Code

Last login: Wed Aug  1 10:19:38 on ttys000
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$ pwd
/Users/asyavuz/Downloads/jalview
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$ java -version
java version "1.6.0_33"
Java(TM) SE Runtime Environment (build 1.6.0_33-b03-424-11M3720)
Java HotSpot(TM) 64-Bit Server VM (build 20.8-b03-424, mixed mode)
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:Downloads asyavuz$ javac -version
javac 1.6.0_33
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$ ant
Buildfile: /Users/asyavuz/Downloads/jalview/build.xml

usage:
     [echo] ~~~Jalview Ant build.xml Usage~~~~
     [echo] Targets include:
     [echo] usage - default target, displays this message
     [echo] buildindices - generates JavaHelpSearch from the help files
     [echo] build - compiles all necessary files for Application
     [echo] makedist - compiles and places all necessary jar files into directory dist
     [echo] makefulldist - signs all jar files and builds jnlp file for full distribution
     [echo]               this needs a keystore and key. See docs/building.html for more information.
     [echo] compileApplet - compiles all necessary files for Applet
     [echo] makeApplet - compiles, then packages and obfuscates the Applet
     [echo] See docs/building.html and the comments in build file for other targets.
     [echo] note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk.
     [echo] Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation

BUILD SUCCESSFUL
Total time: 0 seconds
dyn1133-232:jalview asyavuz$ ant makeApplet
Buildfile: /Users/asyavuz/Downloads/jalview/build.xml

init:

clean:

compileApplet:
    [mkdir] Created dir: /Users/asyavuz/Downloads/jalview/classes
    [javac] /Users/asyavuz/Downloads/jalview/build.xml:461: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 37 source files to /Users/asyavuz/Downloads/jalview/classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -Xlint:deprecation for details.
    [javac] Note: Some input files use unchecked or unsafe operations.
    [javac] Note: Recompile with -Xlint:unchecked for details.

buildPropertiesFile:
[properties] write property file /Users/asyavuz/Downloads/jalview/classes/.build_properties

packageApplet:
     [copy] Copying 1 file to /Users/asyavuz/Downloads/jalview/classes/images
     [copy] Copying 1 file to /Users/asyavuz/Downloads/jalview/classes/images
      [jar] Building jar: /Users/asyavuz/Downloads/jalview/in.jar

-obfuscatefake:

-obfuscatereally:
 [proguard] ProGuard, version 3.7
 [proguard] Reading program jar [/Users/asyavuz/Downloads/jalview/in.jar]
 [proguard] Reading library jar [/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar]
 [proguard] Reading library jar [/Users/asyavuz/Downloads/jalview/appletlib/JmolApplet-12.1.13.jar]
 [proguard] Preparing output jar [/Users/asyavuz/Downloads/jalview/jalviewApplet.jar]
 [proguard]   Copying resources from program jar [/Users/asyavuz/Downloads/jalview/in.jar]
   [delete] Deleting: /Users/asyavuz/Downloads/jalview/in.jar

obfuscate:

makeApplet:

BUILD SUCCESSFUL
Total time: 13 seconds
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$ java jalview.jar
Exception in thread "main" java.lang.NoClassDefFoundError: jalviewApplet/jar
Caused by: java.lang.ClassNotFoundException: jalviewApplet.jar
    at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$
dyn1133-232:jalview asyavuz$ java -Djava.ext.dirs=~/Downloads/jalview/lib -cp ~/Downloads/jalview/jalview.jar jalview.bin.Jalview
Exception in thread "main" java.lang.NoClassDefFoundError: jalview/bin/Jalview
Caused by: java.lang.ClassNotFoundException: jalview.bin.Jalview
    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)
dyn1133-232:jalview asyavuz$