Frontend Structure not working in BigSur MacOS

[Andrea Gloria]

Hello, I am not sure what is going on, but after I upgraded my machine from Mojave to Big Sur, the frontend structure no  longer works.

I even tried using the Linux frontend, but still have the same problem. I have delete and (try to) install from scratch both the Mac and Linux versions, without success.

Seems to be related with permissions?.. below is part of the output after I type ./install within the frontend folder. I even tried installing it in the documents folder rather than the Applications folder, since the path to Applications seems more convoluted now than it used to be, but didn't work either.

Copy files to /usr/local/Structure/ ...
cp: class: unable to copy extended attributes to /usr/local/Structure/class: Permission denied
cp: /usr/local/Structure/class/Structure.jar: Permission denied
cp: bin: unable to copy extended attributes to /usr/local/Structure/bin: Permission denied
cp: /usr/local/Structure/bin/structure: Permission denied
cp: images: unable to copy extended attributes to /usr/local/Structure/images: Permission denied
cp: /usr/local/Structure/images/Run.gif: Permission denied
cp: /usr/local/Structure/images/left.gif: Permission denied
cp: /usr/local/Structure/images/Go.gif: Permission denied

cp: /usr/local/Structure/images/Save_All.gif: Permission denied

Any help will be appreciate it.

[Francisco Pina Martins]

Hi Andrea,

I'm not sure about Big Sur, but on a GNU/Linux based OS, you can likely solve the issue by running the install command with `sudo`:

"sudo ./install"

Best,

Francisco

[Andrea Gloria]

Thank you Francisco,

Your suggestion helps to get the Front end interface going, but the output is not being saved in the Results folder.

Andrea

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[Vikram Chhatre]

If the path to your results folder is buried too deep in the file structure, try to shorten it. Sometimes there is a problem with path length.

/home/username/folder1/folder2/folder3/folder4.............folder12/results/

/home/username/structure_results/

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[Andrea Gloria]

Thanks, 

Unfortunately that didn’t solve the problem. I moved up the folder several directories, but there are still no results being written. There seem to be files generated in the plotData folder (which is at the same directory level) though. Although the content is non-sense:

¨Ì sr Obj.PlotData [ datat [[Dxpur [[D«≠ ˇdgˇE xp ur [D>¶å ´cZ xp x

Any other ideas?

Thank you,

Andrea

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[Vikram Chhatre]

Did you move the folder up manually? If so, that's not what I meant. You will need to provide a new path in the front-end configuration which isn't buried too deep in the filesystem.

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[Arony Martinez]

Hi everyone 

A couple of days ago, I had the same problem on Ubuntu 18 on my first try on structure.

It was solved as Francisco and Vikram already stated. Using the sudo command and shortening the path to results directory.  

In my particular situation, the path was deep buried and located in my disk used for backup, so when I changed it to the Desktop directory, results were written in the correct directory. 

Something that I noted when invoking with and without sudo command, was the frontend aspect, the popup windows to select files/directories, etc were different.

Best Regards.

Dr. Arony Martínez
Investigador en Ciencias Médicas 
Departamento de Ecología de Agentes Patógenos
Subdirección de Investigación Biomédica
Hospital General "Dr. Manuel Gea González"
Teléfono 4000-3000 ext 6100
Correo: ar...@live.com.mx

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[Eric Fuchs]

Hello, 

 have you had any luck running de frontend Structure in Big Sur?

 I have tried everything including giving whole disk permissions to STRUCTURE, but I have not been able to run the front end.  I ended up running a virtual box with windows to run the program within it, with serious performance issues.

hope you have found a solution

Eric,

[Josh Banta]

Dear Eric,

Have you tried this?

https://www.youtube.com/watch?v=r9LNgU-ZiSo

Best,

Josh

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[Andrea Gloria]

Hello, I was never able to getting to run. I gave up and used and old machine I had to do it.

Let me know if you do find a fix please!

Andrea

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[Vikram Chhatre]

You can always use the commandline version - it's not scary.

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[Francisco Pina Martins]

+1 for the command line version (made easier with any of the available wrappers).

It does require learning to use the command line, but chances are the future you will thank you for that investment.

Francisco