Re: [GeneX-dev] Rcluster issues..

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

Hi Greg,

Harry sent me an "old" version, and it works fine now with no
special security settings in IE5.5.

I think the best course of action is to recode this in Java. It would
be best to completely remove Python from the system as it becomes
one more thing to consider. For now, it might be best to take the 
"jar" file that works, and check it into the cvs tree in the proper spot, and
don't rebuild dendo.

Regards,

Michael Pear

----- Original Message ----- 
From: "Greg D. Colello" <gd...@nc...>
To: <gen...@li...>
Sent: Friday, February 02, 2001 7:56 AM
Subject: Re: [GeneX-dev] Rcluster issues..


> Michael:
> 
> I think the answer to your problems with Rcluster might lie in the fact you have 
> a NEW version of it. At PAG we had the same problems. Harry and I explored the 
> OLD versions of Rcluster and found the only one that worked was the one last 
> created by our consultant Andrew Dalke many moons ago. Actually, the new 
> versions of Rcluster do not contain any new functionality. They were just 
> recompiled. Apparently the Python/Java compiler isn't working the same way it 
> did when Andrew was here. Another problem we have to look into. (It may be 
> easier to simply recode the applet in regular Java, since most of the code is 
> Java AWT syntax anyway.)
> 
> Michael, the correct OLD version of Rcluster should be on the PAG demo computer 
> (now genebox.ncgr.org), but it is behind our firewall at the moment. Harry, can 
> you find that jar file for Rcluster on genebox and send it to Michael? I can't 
> log into genebox. I don't seem to have an account or its password is not what I 
> expect. Could you make sure I can log into genebox while you're at it?
> 
> Michael, you also may have to turn off all Java security. I know this works on 
> IE5. Sometimes it doesn't seem to be required, other times it does. I haven't 
> had time to figure out what casues this difference in behavior. If you need help 
> navigating through the IE5 Java options, give me a call and I'll walk you 
> through it.
> 
> Meanwhile, as far as I can tell, there is no Java console for any version of 
> Netscape I have. Java security options are under the menu option 
> Edit/Preferences/Advanced.
> 
> Obviously, this later problem with avoiding applet security errors by opening up 
> security holes in the browser is really serious. We can't have users truning off 
> their Java security. We just haven't had time to address the problem. It 
> probably requires digitally signing the app to fix the problem, but why bother 
> now with that in the Python version, if we are just going to recode it in Java 
> anyway?
> 
> Greg
> 
> 
> >From: "Michael Pear" <mic...@ho...>
> >To: <gen...@li...>
> >MIME-Version: 1.0
> >Content-Transfer-Encoding: 7bit
> >X-Priority: 3
> >X-MSMail-Priority: Normal
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> >Subject: [GeneX-dev] Rcluster issues..
> >Date: Thu, 1 Feb 2001 16:17:04 -0800
> >
> >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
> >
> >
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> >Gen...@li...
> >http://lists.sourceforge.net/lists/listinfo/genex-dev
> 
> 
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