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Re: debian biomaj package error

Hi,
I did not get this error on my computer.
COmmons-cli2 is a dependency on Biomaj, not packaged, so I had to get source and compile it with Biomaj. Certainly a missing dependency in control file that was already installed on my system.... 
I gonna have a look and let you know

Olivier

Le 2/17/11 2:10 AM, Scott Christley a écrit :

Hello,

I get the following error when trying to build the biomaj debian package from SVN.  Anybody know what the error is?  I'm guessing a missing dependency.

thanks
Scott


compile:
    [mkdir] Created
dir: /home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr/share/biomaj/lib/vendor/commons-cli2-build/build/classes
    [mkdir] Created
dir: /home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr/share/biomaj/lib/vendor/commons-cli2-build/dist

[javac] /home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr/share/biomaj/lib/vendor/commons-cli2.xml:75: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 43 source files
to /home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr/share/biomaj/lib/vendor/commons-cli2-build/build/classes
    [javac] failed to read ecj.jar (reconfigure with
--with-ecj-jar): /usr/share/java/eclipse-ecj.jar
    [javac] failed to load org.eclipse.jdt.internal.compiler.batch.Main
from ecj.jar: /usr/share/java/eclipse-ecj.jar
    [javac] java.lang.ClassNotFoundException:
org.eclipse.jdt.internal.compiler.batch.Main not found in
java.net.URLClassLoader{urls=[file:/usr/share/java/eclipse-ecj.jar],
parent=gnu.gcj.runtime.SystemClassLoader{urls=[file:/usr/share/ant/lib/ant-launcher.jar,file:/usr/share/java/xmlParserAPIs.jar,file:/usr/share/java/xercesImpl.jar], parent=gnu.gcj.runtime.ExtensionClassLoader{urls=[], parent=null}}}
    [javac]    at java.net.URLClassLoader.findClass(libgcj.so.10)
    [javac]    at java.lang.ClassLoader.loadClass(libgcj.so.10)
    [javac]    at java.lang.ClassLoader.loadClass(libgcj.so.10)
    [javac]    at com.sun.tools.javac.Main.<clinit>(Main.java:91)
    [javac]    at java.lang.Class.initializeClass(libgcj.so.10)
    [javac]    at java.lang.Class.forName(libgcj.so.10)
    [javac]    at java.lang.Class.forName(libgcj.so.10)
    [javac]    at
org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.doesModernCompilerExist(CompilerAdapterFactory.java:165)
    [javac]    at
org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.getCompiler(CompilerAdapterFactory.java:124)
    [javac]    at
org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1088)
    [javac]    at
org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:906)
    [javac]    at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
    [javac]    at java.lang.reflect.Method.invoke(libgcj.so.10)
    [javac]    at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
    [javac]    at org.apache.tools.ant.Task.perform(Task.java:348)
    [javac]    at org.apache.tools.ant.Target.execute(Target.java:390)
    [javac]    at
org.apache.tools.ant.Target.performTasks(Target.java:411)
    [javac]    at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
    [javac]    at
org.apache.tools.ant.Project.executeTarget(Project.java:1329)
    [javac]    at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
    [javac]    at
org.apache.tools.ant.Project.executeTargets(Project.java:1212)
    [javac]    at org.apache.tools.ant.Main.runBuild(Main.java:801)
    [javac]    at org.apache.tools.ant.Main.startAnt(Main.java:218)
    [javac]    at
org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
    [javac]    at
org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

BUILD FAILED
/home/scottc/Projects/tools/debian-med/trunk/packages/biomaj/build-area/biomaj-1.1.0/usr/share/biomaj/lib/vendor/commons-cli2.xml:75: java.lang.ExceptionInInitializerError
   at java.lang.Class.initializeClass(libgcj.so.10)
   at java.lang.Class.forName(libgcj.so.10)
   at java.lang.Class.forName(libgcj.so.10)
   at
org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.doesModernCompilerExist(CompilerAdapterFactory.java:165)
   at
org.apache.tools.ant.taskdefs.compilers.CompilerAdapterFactory.getCompiler(CompilerAdapterFactory.java:124)
   at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1088)
   at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:906)
   at
org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
   at java.lang.reflect.Method.invoke(libgcj.so.10)
   at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
   at org.apache.tools.ant.Task.perform(Task.java:348)
   at org.apache.tools.ant.Target.execute(Target.java:390)
   at org.apache.tools.ant.Target.performTasks(Target.java:411)
   at
org.apache.tools.ant.Project.executeSortedTargets(Project.java:1360)
   at org.apache.tools.ant.Project.executeTarget(Project.java:1329)
   at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
   at org.apache.tools.ant.Project.executeTargets(Project.java:1212)
   at org.apache.tools.ant.Main.runBuild(Main.java:801)
   at org.apache.tools.ant.Main.startAnt(Main.java:218)
   at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
   at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: java.lang.NullPointerException
   at com.sun.tools.javac.Main.<clinit>(Main.java:106)
   at java.lang.Class.initializeClass(libgcj.so.10)
   ...20 more




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