> Is there another way of telling the Mac to use java6 for Cytoscape or
> is this behaviour caused by the installer or dmg file.

> Michael

> Gary

> Michi wrote:
> > On a colleagues Mac we a have set up java like you wrote above but
> > when we start Cytoscape by clicking on its icon it seems to start in
> > java5.
> > My plugin uses java6 and I suppose therefore I get the error "
> > java.lang.UnsupportedVersionError: Bad version number in .class
> > file...." when loading my plugin.
> > To get around this error we start Cyptoscape from by skript (or in the
> > console) with the command in the cytoscape.sh file:
> > java -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar
> > cytoscape.CyMain -p plugins "$@"
> > Then Cytoscape doesn't come up with the error and all seems to work
> > fine.

> > Is there another way of telling the Mac to use java6 for Cytoscape or
> > is this behaviour caused by the installer or dmg file.

> > Michael

> --http://baderlab.org
> Terrence Donnelly Centre for Cellular and Biomolecular Research
> University of Toronto

> In my case, I have a Mac Pro with Mac OS 10.5.7 installed, and even
> after the last java update, a "java -version" at the command line kept
> returning version 1.5, and even after changing the order with the Java
> Preferences app.

> The fix for this Java home problem selection, from Apple's Java
> discussion list (see http://discussions.apple.com/thread.jspa?messageID=9657716
> ), is to use the new java_home utility to assign the good value in the
> JAVA_HOME environment variable.

> To do that, edit your .profile file (in your home directory), and
> change the JAVA_HOME line from:
> export JAVA_HOME=/Library/Java/Home

> to (notice the backquotes):
> export JAVA_HOME=`/usr/libexec/java_home`

> I don't know why I had that hard-coded JAVA_HOME assignment in my
> profile, maybe from some old installations or maybe it's just normal.

> Cytoscape worked well afterwards.

> Paul-Henri

> On 20 juin, 17:41, Gary Bader <gary.ba...@utoronto.ca> wrote:
>> Hi Michael - you can tell the Mac to use Java 6 (or any supported
>> version) by default using the "Java Preferences" application, which is
>> in /Applications/Utilities/Java/.

>> Gary

>> Michi wrote:
>> > On a colleagues Mac we a have set up java like you wrote above but
>> > when we start Cytoscape by clicking on its icon it seems to start in
>> > java5.
>> > My plugin uses java6 and I suppose therefore I get the error "
>> > java.lang.UnsupportedVersionError: Bad version number in .class
>> > file...." when loading my plugin.
>> > To get around this error we start Cyptoscape from by skript (or in the
>> > console) with the command in the cytoscape.sh file:
>> > java -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar
>> > cytoscape.CyMain -p plugins "$@"
>> > Then Cytoscape doesn't come up with the error and all seems to work
>> > fine.

>> > Is there another way of telling the Mac to use java6 for Cytoscape or
>> > is this behaviour caused by the installer or dmg file.

>> > Michael

>> --http://baderlab.org
>> Terrence Donnelly Centre for Cellular and Biomolecular Research
>> University of Toronto

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

> I hope Apple releases a new patch soon...

> Kei

> 2009/6/24 phlampe <paulhenri.la...@gmail.com>:

> > In my case, I have a Mac Pro with Mac OS 10.5.7 installed, and even
> > after the last java update, a "java -version" at the command line kept
> > returning version 1.5, and even after changing the order with the Java
> > Preferences app.

> > The fix for this Java home problem selection, from Apple's Java
> > discussion list (seehttp://discussions.apple.com/thread.jspa?messageID=9657716
> > ), is to use the new java_home utility to assign the good value in the
> > JAVA_HOME environment variable.

> > To do that, edit your .profile file (in your home directory), and
> > change the JAVA_HOME line from:
> > export JAVA_HOME=/Library/Java/Home

> > to (notice the backquotes):
> > export JAVA_HOME=`/usr/libexec/java_home`

> > I don't know why I had that hard-coded JAVA_HOME assignment in my
> > profile, maybe from some old installations or maybe it's just normal.

> > Cytoscape worked well afterwards.

> > Paul-Henri

> > On 20 juin, 17:41, Gary Bader <gary.ba...@utoronto.ca> wrote:
> >> Hi Michael - you can tell the Mac to use Java 6 (or any supported
> >> version) by default using the "Java Preferences" application, which is
> >> in /Applications/Utilities/Java/.

> >> Gary

> >> Michi wrote:
> >> > On a colleagues Mac we a have set up java like you wrote above but
> >> > when we start Cytoscape by clicking on its icon it seems to start in
> >> > java5.
> >> > My plugin uses java6 and I suppose therefore I get the error "
> >> > java.lang.UnsupportedVersionError: Bad version number in .class
> >> > file...." when loading my plugin.
> >> > To get around this error we start Cyptoscape from by skript (or in the
> >> > console) with the command in the cytoscape.sh file:
> >> > java -Dswing.aatext=true -Xss5M -Xmx512M -jar cytoscape.jar
> >> > cytoscape.CyMain -p plugins "$@"
> >> > Then Cytoscape doesn't come up with the error and all seems to work
> >> > fine.

> >> > Is there another way of telling the Mac to use java6 for Cytoscape or
> >> > is this behaviour caused by the installer or dmg file.

> >> > Michael

> >> --http://baderlab.org
> >> Terrence Donnelly Centre for Cellular and Biomolecular Research
> >> University of Toronto

> --
> Keiichiro Ono    k...@ucsd.edu

> Cytoscape Core Developer Team:http://www.cytoscape.org/
> UCSD Bioengineering Ideker Lab:http://chianti.ucsd.edu/idekerlab/