Structure not running in Mountain Lion

[Chris B]

Hi, I tried to install the latest front end version of Structure (2.3.4) on my Mac running Mac OSX 10.8.4 and after initially getting the damaged .dmg error message I installed the latest version of Java (version 7 update 25) and disabled the Gatekeeper security settings. Structure will now install. The application will launch ok but none of the menu items respond (New Project, Open Project etc...). Has anyone else had this issue and found a solution?

[René Malenfant]

On Tuesday, June 18, 2013 11:47:13 PM UTC-6, Chris B wrote:
> Hi, I tried to install the latest front end version of Structure (2.3.4) on my Mac running Mac OSX 10.8.4 and after initially getting the damaged .dmg error message I installed the latest version of Java (version 7 update 25) and disabled the Gatekeeper security settings. Structure will now install. The application will launch ok but none of the menu items respond (New Project, Open Project etc...). Has anyone else had this issue and found a solution?

Structure 2.3.4 was working fine on Mountain Lion two days ago. Yesterday, Java 7v25 was released by Oracle, as was Apple's own Java 2013-004 update. At least one of these two updates broke the Structure front-end. It doesn't work on either of my Mountain Lion boxes anymore.

[Vikram Chhatre]

FYI, while you are waiting for these problems to resolve, you can always use the back-end version.  

V

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[Thomas Vignaud]

Same problem here on the 10.7.5
If you want to use structure and haven't done the Java upadet yet : Don't do it !

Any idea when this could be fixed ? if few days I might wait, if not I need to find another solution.

Thanks

[Chris B]

Hi Rene and Vikram, thanks for the quick reply,

yes I have since been using the back-end version, thanks Vikram. I have just moved from Snow Leopard to Mountain Lion which does not come with Java from Apple as far as I know so I assume the Oracle update is to blame.
thanks
Chris

[Sascha Rösner]

Same with me.

Can`t load projects or files. Folder or files are neither selectable via mouse nor keyboard.

I downscaled the MB Retina resolution as here, some apps have problems, but that helped me out either.

Would like to see it up and running ... revision deadline is calling :-)

[Pall Melsted]

Apple stopped including java with the newest versions. Additionally they moved the default location of some java files. So the Structure mac application, which is just a bundle around the frontend code doesn't work anymore.

If you are in a bind you can run the frontend directly from the command line.

Open terminal and type

java -cp /Applications/Structure.app/Contents/Resources/Java/Structure.jar RunStructure

this is assuming you've installed java and it is in your path. Also this is assuming the Structure application has been moved to the Applications folder, otherwise change the path.

You can also download the Structure.jar file from the linux frontend distribution ( http://pritch.bsd.uchicago.edu/structure_software/release_versions/v2.3.4/release/structure_linux_frontend.tar.gz ) it will be in the frontend class folder. You can then run it manually via

java -cp class/Structure.jar RunStructure

assuming you are in the frontend folder.

Future versions for the mac will bundle the java runtime directly, as we can't rely on java being on mac os x anymore.

- Pall Melsted

[Pall Melsted]

There was an extra directory missing in the java command line, it should be

java -cp /Applications/Structure.app/Contents/Resources/Java/class/Structure.jar RunStructure

The icons in the app will be missing, which is somewhat normal.

- Pall

[clemence...@gmail.com]

[René Malenfant]

Hi Pall.  I don't think the unbundling of Java is the problem.

Apple stopped including Java with OS X a long time ago, but there were no problems running Structure until the Java update two days ago.  Structure worked fine under Java 7v21 / Java 2013-003 on Mountain Lion.  Java 7v25 / Java 2013-004 will not run it.  FYI, as far as I can tell, neither of your proposed solutions for the frontend work on Mountain Lion.  They both result in the exact same ultra-slow drawing, non-responsive interface that we complained about above.

Looks like it's the command line for now.


-Rene

[Thomas Vignaud]

I tried to downgrade to java 7u21 -> Structure still didn't work (checked version on testjava)
Then to Java 6. -> structure still didn't work.

Any idea why ?

[Thomas Vignaud]

update : I reinstalled structure AFTER downgrading to 7u21. it works but it's slow answering.
If anyone knows how to improve this, please share : )

7u21 version : http://uni-smr.ac.ru/archive/dev/java/JRE/oracle/7/
search javaapple and delete it before installing this.

[Thomas Vignaud]

update 2 : (sorry for the spam)
You need to clic on what you want to do (i.e. open project)
and then to resize the windows. The action will appear.
For every single action you want to do (i.e. select 'simulation summary') you will need to do it blindly and then resize windows for it to appear.

It's a lot of pain but it seems to work that way. Apply to subwindows too. Have been able to run a job, running fine right now.

Hope it helps,

Thomas

[Pall Melsted]

I've updated my java on the mac to the latest version, 1.6.0_51 from 1.6.0_45 and I see the issue now. 

The workaround is to use the following

java -Dswing.systemlaf=javax.swing.plaf.nimbus.NimusLookAndFeel -cp /Applications/Structure.app/Contents/Resources/Java/class/Structure.jar RunStructure

The reason this happens is because Structure wants to make the java application look like a normal system application, and so it asks for the Look&Feel of the system, which as of a couple of days ago no longer exists on the newest mac os x. Nitty gritty details can be found here http://stackoverflow.com/questions/17204465/how-does-java-for-os-x-2013-004-affect-break-swing-applications/17226346#17226346

We'll fix this permanently in the next version.

- Pall

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[Chris B]

Thanks for your help Paul!

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[René Malenfant]

Apple has fixed their Java installation to address this problem.  Apparently it affected a number of other programs as well (e.g. BEAST, Tracer, FigTree).

See comments and fix here:
http://bioguid.info/services/evoldir/get.php?id=642ff9228a6467c78d9cbff38db96d15

On Tuesday, June 18, 2013 11:47:13 PM UTC-6, Chris B wrote:

[Sascha Rösner]

I installed this apple update: http://support.apple.com/kb/DL1572?viewlocale=en_US&locale=en_US for Mountain Lion ...

Tschaka: Structure up an running like it should do !

p.s. this update wa not diplayed on the app store / software update, yet