It contains six executable files in /usr/bin. Three of them are
starting nicely. These are beast-mcmc, beauti and loganalyser.
However, the other three executables are failing for a reason I do
not understand:
$ logcombiner
Exception in thread "main" java.lang.NoClassDefFoundError: jam/console/ConsoleApplication
at dr.app.tools.LogCombiner.main(Unknown Source)
Caused by: java.lang.ClassNotFoundException: jam.console.ConsoleApplication
at java.net.URLClassLoader$1.run(URLClassLoader.java: 217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.j ava:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:3 21)
at sun.misc.Launcher$AppClassLoader.loadClass(Launche r.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:2 66)
... 1 more
The executable treeannotator fails with the very same error message
and for treestat I get:
$ treestat
Exception in thread "main" java.lang.NoClassDefFoundError: jam/framework/SingleDocApplication
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java :634)
...
I checked that /usr/share/java/jam.jar is installed and contains the
relevant classes. Any idea what might went wrong here?
Kind regards
Andreas.
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01-10-2012, 04:09 AM
Sylvestre Ledru
Help with java package (beast-mcmc) needed
Hi Andreas,
Le dimanche 08 janvier 2012 à 21:42 +0100, Andreas Tille a écrit :
> Hi,
> $ logcombiner
> Exception in thread "main" java.lang.NoClassDefFoundError: jam/console/ConsoleApplication
Usually, this kind of problem is due to the CLASSPATH not containing
jam.jar
Cheers,
Sylvestre
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01-10-2012, 08:59 AM
Andreas Tille
Help with java package (beast-mcmc) needed
Hi Sylvestre,
On Tue, Jan 10, 2012 at 06:09:53AM +0100, Sylvestre Ledru wrote:
> > Exception in thread "main" java.lang.NoClassDefFoundError: jam/console/ConsoleApplication
> Usually, this kind of problem is due to the CLASSPATH not containing
> jam.jar
$ grep jam debian/rules
export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar
As far as I understood you do not need to explicitely set CLASSPATH at
runtime (and it would not explain why the other executables are
perfectly finding the needed jars.
Any further hints?
Kind regards and thanks anyway
Andreas.
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01-10-2012, 10:01 AM
Olivier Sallou
Help with java package (beast-mcmc) needed
Le 1/10/12 10:59 AM, Andreas Tille a écrit :
> Hi Sylvestre,
>
> On Tue, Jan 10, 2012 at 06:09:53AM +0100, Sylvestre Ledru wrote:
>>> Exception in thread "main" java.lang.NoClassDefFoundError: jam/console/ConsoleApplication
>> Usually, this kind of problem is due to the CLASSPATH not containing
>> jam.jar
> $ grep jam debian/rules
> export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar
>
> As far as I understood you do not need to explicitely set CLASSPATH at
> runtime (and it would not explain why the other executables are
> perfectly finding the needed jars.
For classpath, at runtime, all depends on how jar is generated. If it
contains a MANIFEST file with the classpath defined, it will be able to
find the JARS (supposing that libraries path are the same). If it dies
not contains the classpath in the MANIFEST file, classpath must be set
explicitly to each jar file in the command line (usually via a wrapper
shell)
Olivier
> Any further hints?
>
> Kind regards and thanks anyway
>
> Andreas.
>
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IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
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01-10-2012, 12:11 PM
Andreas Tille
Help with java package (beast-mcmc) needed
On Tue, Jan 10, 2012 at 12:01:57PM +0100, Olivier Sallou wrote:
> >> Usually, this kind of problem is due to the CLASSPATH not containing
> >> jam.jar
> > $ grep jam debian/rules
> > export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar
> >
> > As far as I understood you do not need to explicitely set CLASSPATH at
> > runtime (and it would not explain why the other executables are
> > perfectly finding the needed jars.
>
> For classpath, at runtime, all depends on how jar is generated. If it
> contains a MANIFEST file with the classpath defined, it will be able to
> find the JARS (supposing that libraries path are the same). If it dies
> not contains the classpath in the MANIFEST file, classpath must be set
> explicitly to each jar file in the command line (usually via a wrapper
> shell)
Apropos MANIFEST: I formerly fiddled around with packaging using jh_manifest
and there is also some alternative packaging method at
featuring a debian/beast-mcmc.manifest file. Believe it or not it shows
the very same behaviour. The most strange fact for me is that the two
executables loganalyser and logcombiner are very similar but only one of
them runs and the other fails.
Do you think I should simply add a CLASSPATH variable to those scripts that
are failing without understanding why the others are working?
Kind regards
Andreas.
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Help with java package (beast-mcmc) needed
