More info. Here is what the build slave log has for that job:

Aug 23, 2012 12:38:49 PM hudson.plugins.doxygen.DoxygenDirectoryParser getDoxyge
nGeneratedDir
INFO: Created filepath with the following 
path:/home/builduser/workspace/job/build/html
Failed to load native POSIX impl; falling back on Java impl. Stacktrace follows.
java.lang.UnsatisfiedLinkError: Unable to load library 'libc.so.6': com.sun.jna.
Native.open(Ljava/lang/String;)J
        at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:166)
        at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:239)
        at com.sun.jna.Library$Handler.<init>(Library.java:140)
        at com.sun.jna.Native.loadLibrary(Native.java:366)
        at org.jruby.ext.posix.POSIXFactory.loadLibC(POSIXFactory.java:96)
        at org.jruby.ext.posix.POSIXFactory.loadLinuxPOSIX(POSIXFactory.java:65)
        at org.jruby.ext.posix.POSIXFactory.getPOSIX(POSIXFactory.java:24)
        at hudson.os.PosixAPI.<clinit>(PosixAPI.java:40)
        at hudson.Util.resolveSymlink(Util.java:1067)
        at hudson.Util.resolveSymlink(Util.java:1030)
        at hudson.util.DirScanner$Glob.scan(DirScanner.java:115)
        at hudson.FilePath.writeToTar(FilePath.java:1820)
        at hudson.FilePath.access$1000(FilePath.java:166)
        at hudson.FilePath$36.invoke(FilePath.java:1761)
        at hudson.FilePath$36.invoke(FilePath.java:1758)
        at hudson.FilePath$FileCallableWrapper.call(FilePath.java:2193)
        at hudson.remoting.UserRequest.perform(UserRequest.java:118)
        at hudson.remoting.UserRequest.perform(UserRequest.java:48)
        at hudson.remoting.Request$2.run(Request.java:326)
        at 
hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
        at java.util.concurrent.FutureTask.run(FutureTask.java:166)
        at 
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at 
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)
Aug 23, 2012 1:29:03 PM hudson.plugins.doxygen.DoxygenDirectoryParser 
retrieveDoxygenDirectoryFromDoxyfile
INFO: Using the Doxyfile information.
Aug 23, 2012 1:29:03 PM hudson.plugins.doxygen.DoxygenDirectoryParser 
loadDoxyFile
INFO: The Doxyfile path is 'file:/home/builduser/workspace/job/build/Doxyfile'.


This build job with the failing Doxygen call works fine on the old Jenkins 
server but fails on the new server even with the job actually running on a 
build slave.

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