[GeneX-dev] Rcluster issues..

[Michael P. <mic...@ho...>]

I got some of our data to the point of trying Rcluster on the latest install
(pre6).

The most important problem for me right now is the last I encountered.I'm
running into the several exceptions on a windows system using internet
explorer shown below when the dendogram applet tries to run
Any ideas on how to address this?....I know I saw it working at the pag
workshop here in san diego a couple of weeks ago.vI guess this is where
having one thing in the system written in Python comes back to bite (or
strangle,vor whatever snakes like this do).

I tried the applet on netscape on linux, and had zero success there as
well...where do you find
the java console on netscape anyways? I can't see what messages are coming
up.
Any tips on getting this to work on linux and/or sun would be appreciated.

Any alternative display programs for the results would be appreciated. The
files generated seem
fairly useless unless I can display something.

---exceptions on IE under windows---
IOException Loading Archive:
http://be-sf225-2.ucsd.edu/genex/genex/rcluster/dendro.jar
java.io.EOFException: Unexpected end of ZLIB input stream
 at java/util/zip/InflaterInputStream.fill
 .... more in the stack....

com.ms.security.SecurityExceptionEx[org/python/core/Py.initProperties]:
Unable to access system properties.
 at com/ms/security/permissions/PropertyPermission.check
 ...more in the stack...

java.lang.InstantiationException: dendro
 at com/ms/applet/BrowserAppletFrame.newInstance
 at com/ms/applet/AppletPanel.processSentEvent
----end exceptions------

Before this point, I ran into a couple of things in getting Rcluster to run.

I got the error:

Cannot make job directory
/var/genex/local/rcluster/var/poqs/jobs/job4442.3993127: Permission denied
at /var/genex/local/perl5/RCluster/JobControl.pm line 38

which (I think) I corrected by setting permissions on this special
directory. Like other things,
this directory would be better placed in the genex tmp directory which is
already set up with
proper permissions.

Also, I remembered there was a queue_master question in the install about
starting that. Through
various system restarts, that was no longer running so I started it
manually. I still don't know
what this is really needed for and whether it had anything to do with
eventual success.

Regards,

Michael Pear