Applauncher does not launch apps.

[J-Moravec]

Applauncher cannot find BEASTInterface class and thus cannot launch apps.

Error:
[java, -Xms8g, -Xms256m, -Djava.library.path=/home/jmoravec/Work/CancerEvolution/MethylationPhylogeny/beast/lib, -cp, "::/home/jmoravec/.beast/2.5/Babel/lib/itextpdf-5.5.9.jar:/home/jmoravec/.beast/2.5/Babel/lib/Babel.addon.jar:/home/jmoravec/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/jmoravec/.beast/2.5/FLC/lib/flc.v1.1.0.jar:/home/jmoravec/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/jmoravec/.beast/2.5/NS/lib/NS.addon.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.src.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.jar", beast.app.tools.PathSampleAnalyser] Error: Unable to initialize main class beast.app.tools.PathSampleAnalyser Caused by: java.lang.NoClassDefFoundError: beast/core/BEASTInterface

[rbouckaert]

Hi Jiri, The class path looks good, and /home/jmoravec/.beast/2.5/BEAST/lib/beast.jar should contain beast.core.BEASTInterface, so I am wondering, which version of Java are you using?

[J-Moravec]

Yes, path look good and from what I can check (with archive manager), it does contain beast interface.

I am am on Ubuntu 18.04 and installed default openJDK version, which is:

openjdk 11.0.2 2019-01-15
OpenJDK Runtime Environment (build 11.0.2+9-Ubuntu-3ubuntu118.04.3)
OpenJDK 64-Bit Server VM (build 11.0.2+9-Ubuntu-3ubuntu118.04.3, mixed mode, sharing)

[rbouckaert]

Thanks for the info -- it should work, so I hope you can help with the following: would you mind trying this directly from a terminal:

java -Xms8g -Xms256m -Djava.library.path=/home/jmoravec/Work/CancerEvolution/MethylationPhylogeny/beast/lib -cp "::/home/jmoravec/.beast/2.5/Babel/lib/itextpdf-5.5.9.jar:/home/jmoravec/.beast/2.5/Babel/lib/Babel.addon.jar:/home/jmoravec/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/jmoravec/.beast/2.5/FLC/lib/flc.v1.1.0.jar:/home/jmoravec/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/jmoravec/.beast/2.5/NS/lib/NS.addon.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.src.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.jar" beast.app.tools.PathSampleAnalyser

Can you try using the version of BEAST with JRE included (available from http://www.beast2.org/download-linux-with-jre/)?

[J-Moravec]

Running from terminal launch specific application without a hitch.

The BEAST with JRE produce the same results as the BEAST without JRE.

Additionally, is it supposed to be stand-alone version (i.e., not using .beast folder), as it still loads everything from .beast:

Running applauncher from console, I get:

 . applauncher 
[./../jre1.8.0_161/bin/java, -Xms8g, -Xms256m, -Djava.library.path=/home/jmoravec/Work/BeastDev/BeastWithJRE/lib, -cp, ::/home/jmoravec/.beast/2.5/Babel/lib/itextpdf-5.5.9.jar:/home/jmoravec/.beast/2.5/Babel/lib/Babel.addon.jar:/home/jmoravec/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/jmoravec/.beast/2.5/FLC/lib/flc.v1.1.0.jar:/home/jmoravec/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/jmoravec/.beast/2.5/NS/lib/NS.addon.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.src.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.jar, beast.app.tools.AppLauncher]

but all the environment variables still point to BeastWithJRE and not to .beast

echo $BEAST_LIB 
/home/jmoravec/Work/BeastDev/BeastWithJRE/lib

Is this intended behaviour?

[rbouckaert]

Thanks for that! The intended behaviour is for beast.jar to be picked up from .beast/2.5/BEAST/lib/beast.jar, so that upgrades of BEAST can be done just like any other package upgrade.

Perhaps some BEAST files became corrupted for some reason. Can you delete the folder /home/jmoravec/.beast/2.5/BEAST/ (or better, move it out of the way, so we can find out what it in there if this is indeed the culprit) and try again? BEAST should restore the folder after starting.

[J-Moravec]

Moved the whole .beast folder:
mv .beast .beastBak
started beauti and installed random package to get some apps and then run applauncher to run apps. Got the same error (although now I got traceback)

bin/applauncher 
[bin/../jre1.8.0_161/bin/java, -Xms8g, -Xms256m, -Djava.library.path=/home/jmoravec/Work/BeastDev/BeastWithJRE/lib, -cp, ::/home/jmoravec/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/jmoravec/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.src.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.jar, beast.app.tools.AppLauncher]
[bin/../jre1.8.0_161/bin/java, -Xms8g, -Xms256m, -Djava.library.path=/home/jmoravec/Work/BeastDev/BeastWithJRE/lib, -cp, "::/home/jmoravec/.beast/2.5/MODEL_SELECTION/lib/MODEL_SELECTION.addon.jar:/home/jmoravec/.beast/2.5/BEASTLabs/lib/BEASTlabs.addon.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.src.jar:/home/jmoravec/.beast/2.5/BEAST/lib/beast.jar", beast.app.tools.PathSampler]
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.NoClassDefFoundError: beast/core/BEASTInterface
	at java.lang.Class.getDeclaredMethods0(Native Method)
	at java.lang.Class.privateGetDeclaredMethods(Class.java:2701)
	at java.lang.Class.privateGetMethodRecursive(Class.java:3048)
	at java.lang.Class.getMethod0(Class.java:3018)
	at java.lang.Class.getMethod(Class.java:1784)
	at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:544)
	at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:526)
Caused by: java.lang.ClassNotFoundException: beast.core.BEASTInterface
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:338)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 7 more

[rbouckaert]

This issue appears to be solved on the issue834 branch -- tested on Jirka's machine with BEAST v2.5.3pre.