Error message in Java Console

When I open a page containing the latest MarvinSketch 5.2.02, this is the message in Java Console.

May 28, 2009 3:33:20 PM chemaxon.marvin.uif.resource.BackgroundLoader run
WARNING: Failed to run task: chemaxon.marvin.sketch.swing.SketchModuleLoaderTask@3e3c83
java.lang.RuntimeException: sun.misc.InvalidJarIndexException: Invalid index
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 at chemaxon.marvin.sketch.swing.SketchModuleLoaderTask.run(Unknown Source)
 at chemaxon.marvin.uif.resource.BackgroundLoader.run(Unknown Source)
Caused by: sun.misc.InvalidJarIndexException: Invalid index
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath.getResource(Unknown Source)
 at java.net.URLClassLoader$1.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at java.net.URLClassLoader.findClass(Unknown Source)
 at sun.applet.AppletClassLoader.findClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at sun.applet.AppletClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClassInternal(Unknown Source)
 at java.lang.Class.forName0(Native Method)
 at java.lang.Class.forName(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.loadClass(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 ... 3 more

Hi,

 

We have seen this error message during the tests, but we cannot reproduce it in the final version. Please try to clear the java cache.

Is there any problem in the MarvinSketch, or everythings works fine, just this message appears on the console?

 

Best Regards,

Peter

Cache had been cleaned. It does not seems to affect the functionality of the program, will report if it does.

Not sure what triggers this. Clearing cache did not help. Just in case someone else experience the same.

Java Plug-in 1.6.0_17
Using JRE version 1.6.0_17-b04 Java HotSpot(TM) Client VM
User home directory = C:\Users\yzhou

Reading certificates from 5742 http://ldweb.gnf.org/jchem_5_2_02/marvin/sjars/common/swing/help.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\27\34c48f9b-20d34624.idx
May 20, 2010 4:01:57 PM chemaxon.marvin.uif.resource.BackgroundLoader run
WARNING: Failed to run task: chemaxon.marvin.sketch.swing.SketchModuleLoaderTask@17ad30a
java.lang.RuntimeException: sun.misc.InvalidJarIndexException: Invalid index
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 at chemaxon.marvin.sketch.swing.SketchModuleLoaderTask.run(Unknown Source)
 at chemaxon.marvin.uif.resource.BackgroundLoader.run(Unknown Source)
Caused by: sun.misc.InvalidJarIndexException: Invalid index
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath.getResource(Unknown Source)
 at sun.plugin2.applet.Plugin2ClassLoader$2.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at sun.plugin2.applet.Plugin2ClassLoader.findClassHelper(Unknown Source)
 at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClassInternal(Unknown Source)
 at java.lang.Class.forName0(Native Method)
 at java.lang.Class.forName(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.loadClass(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 ... 3 more
Reading certificates from 22735

Hello,

We have a long weekend due to our national holiday here, but my colleagues will answer you soon.

Regards,
Erika.

I could not manage to reproduce this issue on our site with the latest Java version.

MarvinSketch 5.2.2 applet have been loaded properly.

http://www.chemaxon.com/marvin-archive/5_2_02/marvin/examples/applets/sketch/embed.html

Please check applet on the above URL. Does it work for you?

Yes, I can see the error in the Java Console, with your URL

Java Plug-in 1.6.0_14
Using JRE version 1.6.0_14-b08 Java HotSpot(TM) Client VM
User home directory = C:\Users\yzhou
----------------------------------------------------
c:   clear console window

...

Reading certificates from 5476 http://www.chemaxon.com/marvin-archive/5_2_02/marvin/sjars/spacefill.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\13\2aa40bcd-29182004.idx
Reading certificates from 5744 http://www.chemaxon.com/marvin-archive/5_2_02/marvin/sjars/common/swing/preferences.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\40\7a29bde8-30af13f1.idx
Reading certificates from 5742 http://www.chemaxon.com/marvin-archive/5_2_02/marvin/sjars/common/swing/help.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\29\a38241d-274e8b34.idx
May 27, 2010 9:32:16 AM chemaxon.marvin.uif.resource.BackgroundLoader run
WARNING: Failed to run task: chemaxon.marvin.sketch.swing.SketchModuleLoaderTask@9e0c79
java.lang.RuntimeException: sun.misc.InvalidJarIndexException: Invalid index
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 at chemaxon.marvin.sketch.swing.SketchModuleLoaderTask.run(Unknown Source)
 at chemaxon.marvin.uif.resource.BackgroundLoader.run(Unknown Source)
Caused by: sun.misc.InvalidJarIndexException: Invalid index
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath$JarLoader.getResource(Unknown Source)
 at sun.misc.URLClassPath.getResource(Unknown Source)
 at sun.plugin2.applet.Plugin2ClassLoader$2.run(Unknown Source)
 at java.security.AccessController.doPrivileged(Native Method)
 at sun.plugin2.applet.Plugin2ClassLoader.findClassHelper(Unknown Source)
 at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClass(Unknown Source)
 at java.lang.ClassLoader.loadClassInternal(Unknown Source)
 at java.lang.Class.forName0(Native Method)
 at java.lang.Class.forName(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.loadClass(Unknown Source)
 at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
 ... 3 more
Reading certificates from 22735 http://www.chemaxon.com/marvin-archive/5_2_02/marvin/sjars/sketch/swing/guiconfigurationdialog.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\61\377660bd-3cc0b126.idx
Reading certificates from 5570 http://www.chemaxon.com/marvin-archive/5_2_02/marvin/sjars/view/swing/imageviewframe.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\41\5da6f8e9-1c13a3f4.idx

Please try out also the latest Marvin.

http://www.chemaxon.com/marvin/examples/applets/

Can you reproduce the issue with it?

The new version load jars on demand, which looks better. I don't know which jar triggers the error. there is only one warning.

Reading certificates from 33049 http://www.chemaxon.com/marvin/jmarvin.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\8\66fec588-42d7510c.idx
Reading certificates from 7022 http://www.chemaxon.com/marvin/sjars/sketchstart.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\34\65bbf622-38dbbe15.idx
Reading certificates from 33049 http://www.chemaxon.com/marvin/jmarvin.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\8\66fec588-42d7510c.idx
Reading certificates from 67631 http://www.chemaxon.com/marvin/sjars/sketch.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\18\2af752-7bf08dc7.idx
May 27, 2010 11:05:56 AM chemaxon.marvin.sketch.swing.ClassLoaderTask run
WARNING: Class not found:
Reading certificates from 8346 http://www.chemaxon.com/marvin/sjars/util.jar | C:\Users\yzhou\AppData\LocalLow\Sun\Java\Deployment\cache\6.0\6\44b0c486-4ce65b33.idx

I am seeing the same error (the one in pink) in the java console on a Mac (10.6.3  marvin 5.3.3) though it does not prevent the applet from loading and working.  However, it will not run in Friefox on a windows machine that is using an earlier version of java (pre 1.6).   How do I address that?

 

Can you set the -verbose JVM parameter temporary for your Java-Plugin? If it is active, Java log all class loading (print tons of log to a separate console). It can be very useful for detect which class could not be loaded dynamically in your configuration. If you send (in attachment) the result of verbose output, we would be very appreciate.

Here is what I think you want.

 

Here is what I think you want.

Thanks for the output log but it is not that I expected.
Anyway, I can find the answer for your previous comment.

I am seeing the same error (the one in pink) in

the java console on a Mac (10.6.3  marvin 5.3.3) though it does not

prevent the applet from loading and working.  However, it will not run

in Friefox on a windows machine that is using an earlier version of

java (pre 1.6).   How do I address that?

We know about the warning issue that you have highlighted with pink in your earlier console log (Class not found:). We have fixed this issue and the bugfix will be available in next release.

Firefox 3.6 and later versions can not incorporate with Java 1.5. It is a general Java Plugin issue (independent from Marvin). If you generate applet code with marvin.js (msketch_begin(...); ... msketch_end(...) ), this bugy platform is detected by marvin.js and it prints some warning to the screen.

Our notes crossed in the mail.  Is there a workaround for the Firefox issue -- avoiding the marvin.js?

The marvin.js includes a couple of code hacking to avoid various Java - browser compatibility issues.It pass various parameters to Java-Plugin. These settings can be different under different platform (since certain features are not well supported under all platforms).

If you would not like generate applet code with marvin.js, investigate the code of marvin.js and implement your own solution.

By the Firefox 3.6 - Java 1.5 bug, there is no real workaround. Firefox can not launch Java-Plugin 1.5. To avoid the problem, the Java version should be detected in advance and prevent loading of Marvin applet by the buggy configuration.