Hi Mark.

On 12/06/2014 14:30, Mark A Saper wrote:
> I traced the problem to my jalview.jlnp file that I use to launch jalview. 
> Although Java downloaded the new jalview 2.8.1 I continued to launch jalview 
> with a jalview.jnlp file that I have in my /Applications folder which had 
> reference to the older version of JABAWS.
Well done for working that out !
>    This has happened several times before over the years. How can always 
> launch the program with the most recent jalview?  Use a link?
That's a good question. We could change the way we distribute the code 
so the jnlp file just contains a reference to one (or two) stable jar 
files that contain all the other dependencies.. this would mean that 
once you had configured your favourite JNLP once, it would work for all 
future versions regardless of dependency changes. The downside of that 
is that it is a fairly large single file download.

I'll raise a feature request about this and get back to you - we plan to 
change the way the desktop is launched in the next 6 months or so, which 
should get around all these problems, but if you want to hear about when 
we do something about it sooner, then hit the 'watch' button on the 
issue (http://issues.jalview.org/browse/JAL-1525).

Once again, thanks for taking the time to work out what was going wrong 
!  In principle, Java should actually have prevented Jalview from 
launching because the default security settings do not allow 
applications to be launched from a JNLP that doesn't match the version 
shipped with the application (e.g. one that has different 
dependencies).. but that would have been just as annoying, I guess.

Cheers,
Jim
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