[Bug] v.extract fails on macOS 15.4.1 with libgfortran.5.dylib error

[rdzur]

Describe the bug

v.extract fails to execute on macOS 15.4.1 with GRASS 8.4.1 and 8.5.0dev due to libgfortran.5.dylib error. This issue also occurs when attempting to execute r.in.pdal, where the same libgfortran.5.dylib error message appears.

To reproduce

1. Type v.extract at the GRASS GIS terminal.

2. When running v.extract at the GRASS terminal, the following error is encountered:

dyld[49302]: Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <C435405B-BFF1-399F-A1EC-BD43418F546A> /Applications/GRASS-8.5.app/Contents/Resources/lib/libopenblas.0.dylib
  Reason: tried: '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/runner/work/grass/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/runner/work/grass/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/runner/work/grass/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/runner/work/grass/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

Expected behavior

The v.extract help content should appear printed in the terminal.

Screenshots

System description

This error is produced when using both GRASS 8.4.1 (Code revision: 45ca317) and development preview version 8.5.0dev (Code revision: 0095480) on macOS 15.4.1 (24E263). In testing these GRASS GIS builds on macOS 14.3.1 we have not encountered any issue with v.extract.

GRASS version: 8.5.0dev
Code revision: 0095480
Build date: 2025-03-13
Build platform: aarch64-apple-darwin23.6.0
GDAL: 3.10.1
PROJ: 9.5.1
GEOS: 3.13.0
SQLite: 3.48.0
Python: 3.12.8
wxPython: 4.2.2
Platform: macOS-15.4.1-arm64-arm-64bit

GRASS version: 8.4.1
Code revision: 45ca317
Build date: 2025-02-25
Build platform: aarch64-apple-darwin23.6.0
GDAL: 3.10.1
PROJ: 9.5.1
GEOS: 3.13.0
SQLite: 3.48.0
Python: 3.12.8
wxPython: 4.2.2
Platform: macOS-15.4.1-arm64-arm-64bit

Additional context

[joneir]

As this issue is quite urgent, I copy my session here:

Last login: Tue May  6 09:32:52 on ttys000
'/Applications/GRASS-8.5.app/Contents/MacOS/Grass.sh'; exit
(base) joneiriksson@Jons-MacBook-Air ~ % '/Applications/GRASS-8.5.app/Contents/MacOS/Grass.sh'; exit
Default locale settings are missing. GRASS running with C locale.
Starting GRASS GIS...

          __________  ___   __________    _______________
         / ____/ __ \/   | / ___/ ___/   / ____/  _/ ___/
        / / __/ /_/ / /| | \__ \\_  \   / / __ / / \__ \
       / /_/ / _, _/ ___ |___/ /__/ /  / /_/ // / ___/ /
       \____/_/ |_/_/  |_/____/____/   \____/___//____/

Welcome to GRASS GIS 8.5.0dev (44d678df57)
GRASS GIS homepage:                      https://grass.osgeo.org
This version running through:            Z Shell (/bin/zsh)
Help is available with the command:      g.manual -i
See the licence terms with:              g.version -c
See citation options with:               g.version -x
If required, restart the GUI with:       g.gui wxpython
When ready to quit enter:                exit

Launching <wxpython> GUI in the background, please wait...
GRASS : ~ > v.extract input=roadsmajor output=rds_major where="Id = 235)"
dyld[3836]: Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <C435405B-BFF1-399F-A1EC-BD43418F546A> /Applications/GRASS-8.5.app/Contents/Resources/lib/libopenblas.0.dylib
  Reason: tried: '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)
zsh: abort      v.extract input=roadsmajor output=rds_major where="Id = 235)"
GRASS : ~ > v.extract input=roadsmajor output=rds_major where="(Id = 235)"
dyld[3872]: Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <C435405B-BFF1-399F-A1EC-BD43418F546A> /Applications/GRASS-8.5.app/Contents/Resources/lib/libopenblas.0.dylib
  Reason: tried: '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/lib/libgfortran.5.dylib' (no such file), '/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Applications/GRASS-8.5.app/Contents/Resources/grass85/lib/libgfortran.5.dylib' (no such file), '/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)
zsh: abort      v.extract input=roadsmajor output=rds_major where="(Id = 235)"
GRASS : ~ >   

[echoix]

On macOS, now, isn't the non-Fortran compiler LLVM-based? Packaging is now conda-based.

Is gfortran and its runtime libraries playing well with all this?

[echoix]

Also, I find it surprising that the paths of "nicklas" leak through the trace shown, like

'/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib'

[nilason]

On macOS, now, isn't the non-Fortran compiler LLVM-based? Packaging is now conda-based.

Is gfortran and its runtime libraries playing well with all this?

It looks like it is openblas that bring in dependency of gfortran, which is not unexpected. I'll look into that ASAP.

Also, I find it surprising that the paths of "nicklas" leak through the trace shown, like

'/Users/nicklas/dev/grass/dist.aarch64-apple-darwin23.6.0/lib/libgfortran.5.dylib'

That have been stripped on latest releases, but shouldn't be a problem in itself (that is the build path, the install path is included too, both are searched).