FAQ Search Today's Posts Mark Forums Read
» Video Reviews

» Linux Archive

Linux-archive is a website aiming to archive linux email lists and to make them easily accessible for linux users/developers.


» Sponsor

» Partners

» Sponsor

Go Back   Linux Archive > Debian > Debian Java

 
 
LinkBack Thread Tools
 
Old 01-08-2012, 07:42 PM
Andreas Tille
 
Default Help with java package (beast-mcmc) needed

Hi,

I tried building a package from beast and uploaded for simlicity this
stuff to

http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/

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.

--
http://fam-tille.de


--
To UNSUBSCRIBE, email to debian-java-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: 20120108204258.GA18278@an3as.eu">http://lists.debian.org/20120108204258.GA18278@an3as.eu
 
Old 01-10-2012, 04:09 AM
Sylvestre Ledru
 
Default 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




--
To UNSUBSCRIBE, email to debian-java-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: 1326172193.9917.28.camel@pomegues.inria.fr">http://lists.debian.org/1326172193.9917.28.camel@pomegues.inria.fr
 
Old 01-10-2012, 08:59 AM
Andreas Tille
 
Default 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.

--
http://fam-tille.de


--
To UNSUBSCRIBE, email to debian-java-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: 20120110095920.GE28931@an3as.eu">http://lists.debian.org/20120110095920.GE28931@an3as.eu
 
Old 01-10-2012, 10:01 AM
Olivier Sallou
 
Default 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.
>

--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438 (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438



--
To UNSUBSCRIBE, email to debian-java-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: 4F0C1AA5.5090701@irisa.fr">http://lists.debian.org/4F0C1AA5.5090701@irisa.fr
 
Old 01-10-2012, 12:11 PM
Andreas Tille
 
Default 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

http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/manifest/

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.

--
http://fam-tille.de


--
To UNSUBSCRIBE, email to debian-java-REQUEST@lists.debian.org
with a subject of "unsubscribe". Trouble? Contact listmaster@lists.debian.org
Archive: 20120110131155.GA1938@an3as.eu">http://lists.debian.org/20120110131155.GA1938@an3as.eu
 

Thread Tools




All times are GMT. The time now is 07:25 AM.

VBulletin, Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.
Content Relevant URLs by vBSEO ©2007, Crawlability, Inc.
Copyright ©2007 - 2008, www.linux-archive.org