MacOS Compilation error -- "foundatio​n::storage​:vfs::Exce​ption", current threads fail to resolve issue.

I'm trying to compile a complex MATLAB app using the application compiler on MacOS. This works fine unless I try to include any third party toolbox, in which case an error pops during packaging. The contents of the log file are as such:

Preparing Runtime...
mcc -C -a '/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb' -o NeuroPAL_ID -W 'main:NeuroPAL_ID,version=2.0' -T link:exe -d /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/mac_visualize/for_testing -R '-logfile,NeuroPAL_ID_log.txt' -v /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/visualize_light.mlapp -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Documents/About.png -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Models/atlas_xo_rgb.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Models/atlas_xo_rgbw.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Models/atlas_xx_rgb.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Models/atlas_xx_rgbw.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfCheckJavaMemory.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfCheckJavaPath.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfGetFileExtensions.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfGetPlane.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfGetReader.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfInitLogging.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfopen.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfOpen3DVolume.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfsave.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bfUpgradeCheck.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/bioformats_package.jar -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/createMinimalOMEXMLMetadata.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/mlapptools-develop/functionSignatures.json -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Documents/Instructions.png -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/bfmatlab/private/is_octave.m -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/External_Dependencies/mlapptools-develop/ISSUE_TEMPLATE.md -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Documents/Keyboard.png -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/NeuroPAL/male_data.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/NeuroPAL/NeuroPAL_male_data.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/Data/Models/NN_model.mat -a /Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/+DataHandling/PNGViewer.m 
Compiler version: 23.2 (R2023b)

Analyzing file dependencies. 

foundation::storage::vfs::Exception

mcc failed.

While there are other threads that describe this issue (namely this one and this one), the suggested solutions do not resolve the issue when applied. I've ensured that I'm an administrator on the system in question, that all folders involved (i.e. both the app folder and the third party folder) are exist, are accessible, and are set to read & write, and I've tried reinstalling both the package in question and my version of MATLAB. The program functions perfectly fine when not deployed.

Update:

I've tried removing the direct mcc argument (-a '/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb') and including the toolbox's files within my app's folder before compiling, but this results in the same error.

Answer 1

[Abhishek Chakram]

Hi Kevin Rusch,

The error you are encountering during the compilation of the MATLAB app with third-party toolboxes included suggests there is an issue with how the MATLAB Compiler is handling the file dependencies, particularly with the third-party toolbox you are trying to include. The “foundation::storage::vfs::Exception” indicates a problem at a lower level, possibly related to file system access or the way MATLAB Compiler is trying to package these dependencies. Here are a few suggestions to resolve the issue:

• Try copying the third-party toolbox and any other dependencies directly into a simpler path that does not contain spaces or special characters. Sometimes, paths with spaces or special characters can cause issues during compilation.
• If any of the files or directories involved are symbolic links, “symlinks”, try replacing them with the actual files or directories. The MATLAB Compiler might have trouble resolving or packaging “symlinks” correctly.
• Although you have checked file permissions, ensure that there are no hidden or system files within the third-party toolbox directory that might have different permissions. Sometimes, hidden files like “.DS_Store” on macOS can cause issues.
• Given the complexity of the issue and the fact that you are dealing with a lower-level exception, consider reaching out to MathWorks Support directly.

Best Regards,

Abhishek Chakram