Problem running AutoCellSeg in MacOS

AngeloTorelli / AutoCellSeg

A Matlab implementation for automatic segmentation with a graphical user interface

MIT License

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Problem running AutoCellSeg in MacOS #2

Open wu-lab-uva opened 4 years ago

wu-lab-uva commented 4 years ago

Dear Angelo, I installed MATLAB_R2016b on my mac and when I tried to run the AutoCellSeg with the following command ./run_AutoCellSeg.sh /Applications/MATLAB/MATLAB_Runtime/v91

I got the following error messages and the program popped up a Download window and stuck at 0%. Do you know what can be problem?

Thanks,

Martin

Setting up environment variables

DYLD_LIBRARY_PATH is .:/Applications/MATLAB/MATLAB_Runtime/v91/runtime/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/bin/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/sys/os/maci64 2019-10-10 14:55:45.713 AutoCellSeg[79553:64753414] Unknown class 'Download', using 'NSObject' instead. Encountered in Interface Builder file at path /Users/martinwu/Downloads/AutoCellSeg-master/Mac/AutoCellSeg.app/Contents/Resources/en.lproj/MainMenu.nib. 2019-10-10 14:55:45.713 AutoCellSeg[79553:64753414] Failed to connect (downloadPercent) outlet from (NSObject) to (NSTextFieldCell): missing setter or instance variable 2019-10-10 14:55:45.713 AutoCellSeg[79553:64753414] Failed to connect (image) outlet from (NSObject) to (NSImageView): missing setter or instance variable 2019-10-10 14:55:45.713 AutoCellSeg[79553:64753414] Failed to connect (progress) outlet from (NSObject) to (NSProgressIndicator): missing setter or instance variable 2019-10-10 14:55:45.713 AutoCellSeg[79553:64753414] Failed to connect (window) outlet from (NSObject) to (NSWindow): missing setter or instance variable d-172-25-48-254:Mac martinwu$ ./run_AutoCellSeg.sh /Applications/MATLAB/MATLAB_Runtime/v91

wu-lab-uva commented 4 years ago

It looks like the issue has been raised before. Hopefully the error messages may help you figure out the issues. I tried executing AutoCellSeg.app directly as you suggested but it froze at the same Download window.

snail123815 commented 3 years ago

If you do this in terminal:

DYLD_LIBRARY_PATH=.:/Applications/MATLAB/MATLAB_Runtime/v91/runtime/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/bin/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/sys/os/maci64
export DYLD_LIBRARY_PATH

And then add execution primision to AutoCellSeg.app/Contents/MacOS/setup:

chmod u+x AutoCellSeg.app/Contents/MacOS/setup

Then run it:

AutoCellSeg.app/Contents/MacOS/setup

The download and installation then will start. Follow the instruction and install a new copy of AutoCellSeg.app.

After finishing the above, I was able to run the newly installed AutoCellSeg.app.

wn835166087 commented 2 years ago

If you do this in terminal:
DYLD_LIBRARY_PATH=.:/Applications/MATLAB/MATLAB_Runtime/v91/runtime/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/bin/maci64:/Applications/MATLAB/MATLAB_Runtime/v91/sys/os/maci64
export DYLD_LIBRARY_PATH
And then add execution primision to AutoCellSeg.app/Contents/MacOS/setup:
chmod u+x AutoCellSeg.app/Contents/MacOS/setup
Then run it:
AutoCellSeg.app/Contents/MacOS/setup
The download and installation then will start. Follow the instruction and install a new copy of AutoCellSeg.app.

After finishing the above, I was able to run the newly installed AutoCellSeg.app.

I tried this method. But it shows "zsh: segmentation fault AutoCellSeg.app/Contents/MacOS/setup" Not sure what happened. This tool sounds very attractive, but it seems to be a bit hard to install. any chance that there is a conda package for rookie user?

snail123815 commented 2 years ago

zsh: segmentation fault AutoCellSeg.app/Contents/MacOS/setup means that you are using the wrong binary file. But I guess you are on ARM Mac right? With M1 chip or higher. Try turn on rosetta for command line and see what you get.

wn835166087 commented 2 years ago

Thank you. I'm using 2017 Mac with intel i5, not with M1. So I guess rosetta is not the problem? what did you mean by "wrong binary file"?

snail123815 commented 2 years ago

Thank you. I'm using 2017 Mac with intel i5, not with M1. So I guess rosetta is not the problem? what did you mean by "wrong binary file"?

I think it means that the program is not compiled using your architecture. But since you are using a 2017 Mac. The problem might be more complicated than that. Which I have no idea about.