Mac Users: Setting Java Preferences to Get Around Java 6 Bug

[William Longabaugh]

I reported earlier today that Macs that are running BioTapestry
using Java 6 would run into stability issues due to an unfixed
bug in Apple's Java 6 implementation. Affected Java builds with
known issues include 1.6.0_15-b03-219 and 1.6.0_15-b03-226; there
may be others. Until Apple fixes this, the best bet is to select
Java 5 to run Java applications, though my previous posting
warned that Snow Leopard (Mac OS 10.6) does not provide you with
this option. See that posting if you are in that situation.

To make the switch, you will run the Java Preferences program.
The first attached screen shot shows you how to get to it.
NOTE: If you don't have Java 6 on your Mac, I don't think the
program will be in this location (it should be in the J2SE 5.0
folder instead), but you shouldn't need to do anything anyway
if you only have 5.0.

Double-click to run the program. The first tab should look like
the second attached picture. The important list is the second,
lower one. Drag the J2SE 5.0 option to the top of this list,
above the Java SE6 option. The screenshot shows what it should
look like when you are done dragging. The top "Java Applet
Plugin" list does not affect BioTapestry execution, so any
change there is optional.

Feel free to post follow-up messages if you have any questions.

-- Bill

[M. Faridounnia]

I have mac os x 10.6.8 and I have downloaded Javaformacosx10-6

I need to use Java 1.6 so what is the bug and how can i know my problems can be also because of a bug in this java version?
In java preferences I have only the two options: I have attached the image. Would be great if I find about it!

[Bill Longabaugh]

The problem with Java 1.6 should no longer be an issue. It involved specific builds at patch level 15, and Java 1.6 is now at patch level 43 or higher. So you should be good to go with what you have on your Mac.

Bill

[M. Faridounnia]

so, i don't know what is it that, no matter what i do i receive error 13 :(

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[Bill Longabaugh]

OK, I'll need a little more info to troubleshoot that. When are you receiving an error 13? Is this trying to start BioTapestry, or while you are trying to do some operation? If it is while you are trying to start the program, how are you trying to start it? How is this error being reported, e.g. can you provide a screen shot of the error message? You should be able to run BioTapestry on the Mac using the Java Web Start link on the project page; does that way work OK?

Bill

[M. Faridounnia]

sorry I'm not a BioTapestry user, I am trying to run a program called cmview.sh when the error happens..

[Bill Longabaugh]

Ok, your screen capture shows that you get the error when the cmview.sh wrapper script tries to run /Applications/AppPyMOL.app. You will need to check that the execute permissions set on that file are appropriate for you being able to run it, e.g. r-xr-xr-x. Please Google for topics like "execution permissions", or ask in another forum that is dedicated to AppPyMOL.app. I am sure that forum has dealt with permissions problems like this before.

Bill