libgl libraries not found after homebrew install

[kevinwithak]

I'm a little clueless here so not sure if this should be posted here or in homebrew-bio

after installing coot on my M1 mac with homebrew, I get warnings on startup:

(Maccoot:69106): GLib-GIRepository-WARNING **: 11:59:58.538: Failed to load shared library 'libgobject-2.0.0.dylib' referenced by the typelib: dlopen(libgobject-2.0.0.dylib, 0x0009): tried: 'libgobject-2.0.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibgobject-2.0.0.dylib' (no such file), '/usr/lib/libgobject-2.0.0.dylib' (no such file, not in dyld cache), 'libgobject-2.0.0.dylib' (no such file)

(Maccoot:69106): GLib-GIRepository-WARNING **: 11:59:58.538: Failed to load shared library 'libglib-2.0.0.dylib' referenced by the typelib: dlopen(libglib-2.0.0.dylib, 0x0009): tried: 'libglib-2.0.0.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OSlibglib-2.0.0.dylib' (no such file), '/usr/lib/libglib-2.0.0.dylib' (no such file, not in dyld cache), 'libglib-2.0.0.dylib' (no such file)

I fixed it by adding to my .zshrc:
export DYLD_FALLBACK_LIBRARY_PATH="$(brew --prefix)/lib:$DYLD_FALLBACK_LIBRARY_PATH"

But can/should this be included in the homebrew formula?

[huwjenkins]

This is discussed on homebrew-bio here:

brewsci/homebrew-bio#1987

Patching the wrapper script which becomes what$HOMEBREW_PREFIX/bin/coot links to set DYLD_FALLBACK_LIBRARY_PATH is a work-around. If this is done in the formula then homebrew knows what HOMEBREW_PREFIX will be so there'll be no need to determine this at run time.

The underlying issue is that homebrew patches their library path into girepository-1.0 but this has now moved into GLib and become girepository-2.0 and not all the patches were transferred. The failure in Coot was triggered when homebrew updated PyGObject to > 3.50 which was the last version that used girepository-1.0 (https://gitlab.gnome.org/GNOME/pygobject/-/merge_requests/320)