[Samtools-devel] Issues with compiling SVN picard

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Hi,

Just trying to reproduce a stack trace causing bug with SVN picard and run into a small issue building the SVN copy.  Something about NoClassDefFoundError relating to bcel.  There is a copy of bcel in lib/ant but it appears to be being ignored.

Anyone know what I'm doing wrong?

Martin

JDK version: jdk1.6.0_21
Ant version: 1.9.0 (earlier versions tried too)
svn revision: 1441

command run: ant

Error message:
<snip>
package-commands:
   [delete] Deleting directory /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [mkdir] Created dir: /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
     [copy] Copying 853 files to /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [unzip] Expanding: /nfs/users/nfs_m/mercury/src/picard-code/lib/apache-ant-1.8.2-bzip2.jar into /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [unzip] Expanding: /nfs/users/nfs_m/mercury/src/picard-code/lib/cofoja-1.0-r139.jar into /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [unzip] Expanding: /nfs/users/nfs_m/mercury/src/picard-code/lib/commons-jexl-2.1.1.jar into /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [unzip] Expanding: /nfs/users/nfs_m/mercury/src/picard-code/lib/commons-logging-1.1.1.jar into /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp
    [unzip] Expanding: /nfs/users/nfs_m/mercury/src/picard-code/lib/snappy-java-1.0.3-rc3.jar into /nfs/users/nfs_m/mercury/src/picard-code/.command_tmp

BUILD FAILED
/nfs/users/nfs_m/mercury/src/picard-code/build.xml:285: The following error occurred while executing this line:
/nfs/users/nfs_m/mercury/src/picard-code/build.xml:434: The following error occurred while executing this line:
/nfs/users/nfs_m/mercury/src/picard-code/build.xml:363: java.lang.NoClassDefFoundError: org/apache/bcel/classfile/Visitor
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:169)
	at org.apache.tools.ant.types.optional.depend.DependScanner.scan(DependScanner.java:110)
	at org.apache.tools.ant.types.optional.depend.ClassfileSet.getDirectoryScanner(ClassfileSet.java:144)
	at org.apache.tools.ant.types.AbstractFileSet.getDirectoryScanner(AbstractFileSet.java:471)
	at org.apache.tools.ant.taskdefs.Zip.grabResources(Zip.java:1555)
	at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1294)
	at org.apache.tools.ant.taskdefs.Zip.getResourcesToAdd(Zip.java:1228)
	at org.apache.tools.ant.taskdefs.Jar.getResourcesToAdd(Jar.java:861)
	at org.apache.tools.ant.taskdefs.Zip.executeMain(Zip.java:616)
	at org.apache.tools.ant.taskdefs.Zip.execute(Zip.java:568)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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.taskdefs.Sequential.execute(Sequential.java:68)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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.taskdefs.MacroInstance.execute(MacroInstance.java:396)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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.taskdefs.Sequential.execute(Sequential.java:68)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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.taskdefs.MacroInstance.execute(MacroInstance.java:396)
	at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)
	at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	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:435)
	at org.apache.tools.ant.Target.performTasks(Target.java:456)
	at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
	at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
	at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
	at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
	at org.apache.tools.ant.Main.runBuild(Main.java:851)
	at org.apache.tools.ant.Main.startAnt(Main.java:235)
	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.ClassNotFoundException: org.apache.bcel.classfile.Visitor
	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 java.lang.ClassLoader.loadClass(ClassLoader.java:248)
	... 55 more

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