[Taverna-users] Taverna display errors with Mac Java update

Wed, 24 Jun 2009 12:27:53 -0700

Thanks for all the suggestions - I got it working again in about a half hour.
Paul wins with the functional solution, which was literally a 3-click- fix. I tried changing the preferences in the Java Prefs, then modifying info.plist, and finally accessed Time Machine to just replace it with the old version of Java. Using a different operating system would have been a solution of last resort, and fortunately was avoidable. 


In case anyone else has problems with this in the future, the two  
items I replaced are:

System/Library/Frameworks/JavaScriptCore.framework
System/Library/Frameworks/JavaVM.framework

Other notes -


Stian - I tried adding that to info.plist, but I must be doing it  
wrong. There's no <key> value to associate the <string> value with in  
that particular file. I made one up, but that didn't seem to do it -  
and usually I've made the necessary modifications in  
mygrid.properties, where it didn't seem to quite fit the syntax. Also,  
I think R uses Quartz for graph rendering, would that interfere? I  
know Quartz used to show me some lousy behaviors that really screwed  
up workflow performance, but I'm not sure if they went away because  
someone else fixed something or because I started using dev.off() with  
my R graph scripts.



It's also pretty unrealistic to expect any kind of "average" user to  
know that they should ignore warnings from their OS to update  
versions. I only knew it was the Java update to blame because it has  
happened before, and specifically with Taverna. This kind of issue is  
particularly problematic for anyone whose computing tools are  
maintained by an information systems department - they are well- 
meaning, but tantamount to gremlins that come through and  
"improve" (sabotage) your computer while you are not looking.  
Especially anything to do with security. Nothing gets those gremlins  
meddling quicker than the word "security."



Fan & gilleain - Thanks, I knew the Java Preferences existed, but had  
forgotten the location because it really ought to be in the System  
Prefs along with the other cool software. Unfortunately, this did not  
work, although who knows - maybe all it needed was a restart after  
resetting the JM VM order? Sometimes that makes a difference, for no  
knowable reason.




On Jun 24, 2009, at 12:21 PM, [email protected] 
 wrote:



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Today's Topics:

  1. Re: Taverna display errors with Mac Java update
     (Stian Soiland-Reyes)
  2. Re: Taverna display errors with Mac Java update (Paul Fisher)
  3. Re: Taverna display errors with Mac Java update (Wim De Smet)
  4. Re: Taverna display errors with Mac Java update (Fan Dong)
  5. Re: Taverna display errors with Mac Java update
     (gilleain torrance)


----------------------------------------------------------------------

Message: 1
Date: Wed, 24 Jun 2009 15:45:33 +0100
From: Stian Soiland-Reyes <[email protected]>
Subject: Re: [Taverna-users] Taverna display errors with Mac Java
        update
To: [email protected]
Message-ID:
        <[email protected]>
Content-Type: text/plain; charset=UTF-8

So the general advice about Java for OSX 10.5 update 4 from the
java-dev list at apple is simply - don't update..

Could you try to modify Info.plist (I know you know how!) to add
-Dapple.awt.graphics.UseQuartz=false as a system property?



From http://lists.apple.com/archives/Java-dev/2009/Jun// 
msg00291.html:



A potentially relevant change was that we flipped the
default graphics pipeline in J2SE 5.0 back to the Quartz
renderer. You might try explicitly setting the Sun 2D renderer
using -Dapple.awt.graphics.UseQuartz=false if you can
reproduce the issue.




On Wed, Jun 24, 2009 at 15:26, Andrea Wiggins<[email protected]> wrote:

I'm afraid I've found a couple more bugs...


I updated my Java version just the other day as prompted by my  
regular

updater

(http://support.apple.com/downloads/ 
Java_for_Mac_OS_X_10_5_Update_4), all

the while thinking in the back of my head, "This is going to screw up
Taverna. I just know it."

It did.


I can no longer see any details on the workflow diagrams in Taverna  
1.7.1,
just the shapes. In Taverna 2.1 beta, the labels exist, but are  
dissociated

from the shapes. And missing their first characters. ?I've attached
screenshots to demonstrate what I'm seeing.


Also, I noticed a second quirky behavior: when I tried to open a  
workflow
with a JDBC component in T2.1b, I got the predictable error when it  
fails to

open. After dismissing the error, however, the entire menu bar had

disappeared. Fortunately, I could use the icons in the UI for the  
same
operations, and clicking on the open folder icon caused the menu  
bar options

to return. I'm sure it's not intended to work quite that way.


Sorry to bring more errors to the table; unfortunately this makes  
it a
little harder to do my work. I didn't realize how much I depend on  
the
workflow diagram to navigate the structure until I couldn't see the  
labels!
Can anyone point to directions on how to roll back the Java update  
so I can

have everything working again?

Andrea


Andrea Wiggins
PhD Student, School of Information Studies
Syracuse University

337 Hinds Hall
Syracuse, NY 13244
[email protected]
www.andreawiggins.com


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--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester



------------------------------

Message: 2
Date: Wed, 24 Jun 2009 15:46:23 +0100
From: Paul Fisher <[email protected]>
Subject: Re: [Taverna-users] Taverna display errors with Mac Java
        update
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Sorry but I have to...

Mac 0.
Windows 1.

I'm not sure on how to roll back with a mac, unless you have time
machine on.
I'm a PC.

Paul.

Andrea Wiggins wrote:

I'm afraid I've found a couple more bugs...





------------------------------

Message: 3
Date: Wed, 24 Jun 2009 16:52:15 +0200
From: Wim De Smet <[email protected]>
Subject: Re: [Taverna-users] Taverna display errors with Mac Java
        update
To: [email protected]
Message-ID: <[email protected]>
Content-Type: text/plain; charset=UTF-8; format=flowed

Stian Soiland-Reyes wrote:

So the general advice about Java for OSX 10.5 update 4 from the
java-dev list at apple is simply - don't update..



Isn't this the update that fixed the critical security vulnerability

they left open for about a month? In that case, do update. (and run  
java

in a linux or windows vm until apple stops breaking it)

regards,
Wim



------------------------------

Message: 4
Date: Wed, 24 Jun 2009 11:27:10 -0400
From: "Fan Dong" <[email protected]>
Subject: Re: [Taverna-users] Taverna display errors with Mac Java
        update
To: <[email protected]>
Message-ID: <001b01c9f4e0$3fa21bd0$bee653...@[email protected]>
Content-Type: text/plain;       charset="us-ascii"

Hi Andrea,


If you are on Mac, go to Utilities in your application folder, then  
try to
find something similar to "java control panel" -- My Mac isn't with  
me right
now I cannot give you the exact name of that little monster -- from  
where

you can active any previously installed Java version.

Fan


-----Original Message-----
From: Paul Fisher [mailto:[email protected]]
Sent: June 24, 2009 10:46 AM
To: [email protected]

Subject: Re: [Taverna-users] Taverna display errors with Mac Java  
update


Sorry but I have to...

Mac 0.
Windows 1.

I'm not sure on how to roll back with a mac, unless you have time
machine on.
I'm a PC.

Paul.

Andrea Wiggins wrote:

I'm afraid I've found a couple more bugs...




------------------------------

Message: 5
Date: Wed, 24 Jun 2009 17:18:28 +0100
From: gilleain torrance <[email protected]>
Subject: Re: [Taverna-users] Taverna display errors with Mac Java
        update
To: [email protected]
Message-ID:
        <[email protected]>
Content-Type: text/plain; charset="iso-8859-1"

Hi,


The application /Applications/Utilities/Java Preferences lets you  
set the
order in which java applications try different java virtual  
machines, in the

lower box on the 'General' tab.

gilleain

On Wed, Jun 24, 2009 at 4:27 PM, Fan Dong <[email protected]> wrote:


Hi Andrea,


If you are on Mac, go to Utilities in your application folder, then  
try to
find something similar to "java control panel" -- My Mac isn't with  
me

right

now I cannot give you the exact name of that little monster -- from  
where

you can active any previously installed Java version.

Fan


-----Original Message-----
From: Paul Fisher [mailto:[email protected]]
Sent: June 24, 2009 10:46 AM
To: [email protected]

Subject: Re: [Taverna-users] Taverna display errors with Mac Java  
update


Sorry but I have to...

Mac 0.
Windows 1.

I'm not sure on how to roll back with a mac, unless you have time
machine on.
I'm a PC.

Paul.

Andrea Wiggins wrote:

I'm afraid I've found a couple more bugs...



Andrea Wiggins
PhD Student, School of Information Studies
Syracuse University

337 Hinds Hall
Syracuse, NY 13244
[email protected]
www.andreawiggins.com


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