More help for beast-mcmc needed (Was: Help with java package (beast-mcmc) needed)
Hi,
On Wed, Jan 11, 2012 at 11:03:08AM +0100, Olivier Sallou wrote:
>
> Manifest file in JAR files is used only when program is called like:
> java -jar myfile.jar
> It uses in this case the manifest file and the default class.
>
> If a specific class is used:
> java -cp myfile.jar org.debian.myclass
>
> then classpath in manifest is not used, and all dependencies must be set
> in the java classpath (with -cp or -classpath, or env CLASSPATH).
> In this cas it must contains all jars needed by specific class call
After following these hints and adding CLASSPATH to those wrappers that
obviosely needed it I was able to fire up all those executables and
assumed that I now dealt with the issue. However, it comes harder when
trying beast-mcmc on any of the included example.
I would be more than happy if anybody would download the packages from
http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/
and try for instance
$ beast-mcmc /usr/share/doc/beast-mcmc/examples/calibrations/constrainedTaxaTest1.xm
...
Exception in thread "main" java.lang.NoClassDefFoundError: jebl/evolution/trees/RootedTree
at dr.evomodelxml.tree.TreeMetricStatisticParser.<init>(Unknown Source)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
at java.lang.Class.newInstance0(Class.java:372)
at java.lang.Class.newInstance(Class.java:325)
at dr.app.beast.BeastParser.loadProperties(Unknown Source)
at dr.app.beast.BeastParser.<init>(Unknown Source)
at dr.app.beast.BeastMain.<init>(Unknown Source)
at dr.app.beast.BeastMain.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: jebl.evolution.trees.RootedTree
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 11 more
or any other example. It always fails with the same error. And yes, I
verified that /usr/share/java/jebl.jar contains the class in question
and I even tried the jebl.jar which is shipped with upstream tarball (it
ships with this lib included but an older version). I also tried to
set CLASSPATH explicitely - no success with all trials.
This program is really a beast. :-(
Any help would be highly welcome.
Kind regards
Andreas.
--
http://fam-tille.de
Reply to: