Hello everyone,
While it was running smoothly in Lion, it seems that upon arrival of Mac OSX Mountain Lion, Jalview become unusable - or let's say "not easily usable" - for new Mac OSX users. I have tried installation of both latest version and the development version using Java Web Start, InstallAnywhere and compiling from source code and they both resulted in same errors, detailed below.
Firstly, Java web start (jalview.jnlp) resulted with a security issue, that I couldn't be able to resolve. Even though I added the certificate to trusted list, Java still blocks the web start for jalview. Screenshot 1 ( http://i.imgur.com/WUk9b.png ) and screenshot 2 ( http://i.imgur.com/olefs.png ) may be helpful in understanding the situation.
Second, I have downloaded the InstallAnywhere version (install.zip, Mac OSX version in website), however, this time i have stuck with the "damaged" package error (Screenshot 3: http://i.imgur.com/DiUj2.png ). I have tried unzipping file with bundled "Archive Utility" and UnZip 5.82 separately. The latter one have not provided the same error, though, it didn't run either.
And as a last result, I have downloaded the source code (jalview_2_7.tar.gz). Followed the instructions and make an ant build, and ant makeApplet build. Afterwards, I have tried running the produced applet with and without the instructed parameters. Both give the same "Exception in thread 'main' java.lang.NoClassDefFoundError: jalview/jar" error, and yet I could not be able to solve. Full terminal outputs can be found here: http://pastebin.com/1fWAm3k3
So, I don't know what else can I try to make it work and any suggestions on this matter will be very much appreciated.
Thank you for your time!
Sincerely,
Ahmet Sinan Yavuz
Hi Ahmet - thanks for your comprehensive test ! I was wondering if Mountain Lion would be causing problems, since I'm still on Snow Leopard (for various reasons 
).
Firstly, Java web start (jalview.jnlp) resulted with a security issue, that I couldn't be able to resolve. Even though I added the certificate to trusted list, Java still blocks the web start for jalview. Screenshot 1 ( http://i.imgur.com/WUk9b.png ) and screenshot 2 ( http://i.imgur.com/olefs.png ) may be helpful in understanding the situation.
OK - I think this is due to the fact that the certificate used to sign Jalview's jars is now out of date, and that we have self-signed it. I'll look at this for the next release. [lodged as http://issues.jalview.org/browse/JAL-1134\]
Second, I have downloaded the InstallAnywhere version (install.zip, Mac OSX version in website), however, this time i have stuck with the "damaged" package error (Screenshot 3: http://i.imgur.com/DiUj2.png ). I have tried unzipping file with bundled "Archive Utility" and UnZip 5.82 separately. The latter one have not provided the same error, though, it didn't run either.
Eww - no idea what's going on here. We are due to upgrade the version of InstallAnywhere used to package Jalview for 2.8, so I'll see if that fixes it. One alternative is to try the 'Unix' distribution - which is a simple tarball with a shell script for launching.. but read on..
And as a last result, I have downloaded the source code (jalview_2_7.tar.gz). Followed the instructions and make an ant build, and ant makeApplet build. Afterwards, I have tried running the produced applet with and without the instructed parameters. Both give the same "Exception in thread 'main' java.lang.NoClassDefFoundError: jalview/jar" error, and yet I could not be able to solve. Full terminal outputs can be found here: Compiling Jalview Source Code - Pastebin.com
OK - this I can help you with
1. Build the desktop jars with:
ant makedist
2. Run Jalview with:
java -Djava.ext.dirs=dist jalview.bin.Jalview
That *should* work - since the compilation seemed to run fine judging from your pastebin..
If you'd like to register over at http://issues.jalview.org then you can set a 'watch' on those bugs - when I fix them, you'll be emailed so you can try out the updated installers/webstart packages.
Jim.
ยทยทยท
On Wed Aug 1 12:34:42 2012, Yavuz, Ahmet Sinan wrote:
