lmod/lau issue after Tahoe install and brew upgrade

[unixwizard107]

Output of brew config

brew config
HOMEBREW_VERSION: 5.0.16
ORIGIN: https://github.com/Homebrew/brew
HEAD: a0bd077aafa7dcdf3562fa39afd0eb70f36af08c
Last commit: 4 days ago
Branch: stable
Core tap JSON: 05 Mar 20:47 UTC
Core cask tap JSON: 05 Mar 20:47 UTC
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.Yc1UWqqYdQ/org.xquartz:0
HOMEBREW_DOWNLOAD_CONCURRENCY: 20
HOMEBREW_EDITOR: /opt/homebrew/bin/mvim
HOMEBREW_FORBID_PACKAGES_FROM_PATHS: set
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 3.4.8 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/3.4.8/bin/ruby
CPU: deca-core 64-bit arm_firestorm_icestorm
Clang: 17.0.0 build 1700
Git: 2.53.0 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.3-arm64
CLT: 26.3.0.0.1.1771626560
Xcode: 26.3
Metal Toolchain: N/A
Rosetta 2: false

Output of brew doctor

brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed casks are deprecated or disabled.
You should find replacements for the following casks:
  aria2d
  coolterm
  flameshot
  fpc-laz
  hugin
  lazarus
  librecad
  qlmarkdown

Warning: Some installed kegs have no formulae!
This means they were either deleted or installed manually.
You should find replacements for the following formulae:
  tea-cli
  term
  geoip
  burl
  pyyaml
  openssl@1.1
  lua@5.3

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  crash
  espeak
  freeimage
  glade
  gollum
  gssh
  icu4c@76
  icu4c@77
  libcroco
  neofetch
  openssl@1.1
  python-tk@3.9
  python@3.9
  six
  tcptrace
  tldr

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libpas2jslib.dylib

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  tlrc
  httpie
  tldr

Description of issue

lua: version mismatch: app. needs 504.0, Lua core provides 505.0

After I did a an upgrade to Tahoe, I ran:

brew update --verbose && brew outdated --verbose && brew upgrade --greedy --verbose && mas upgrade && brew cleanup --verbose ; brew doctor; tea --sync -n

But when I then tried to run a couple of programs that were using TACC's lmod to set up an environment, which in turn called lua(1). I started to see the failure listed above. I did some internet searching and discovered that in 2020, there was a similar issue between 5.03 and 5.04.

The strange part for me is that I had all three of 5.3, 5.4 and 5.5 installed:

clemc@xorn ~ % ls -ld /opt/homebrew/Cellar/lua*/*
drwxr-xr-x@  9 clemc  admin  288 Dec  3  2022 /opt/homebrew/Cellar/lua@5.3/5.3.6/
drwxr-xr-x  10 clemc  admin  320 Mar  5 15:50 /opt/homebrew/Cellar/lua@5.4/5.4.8/
drwxr-xr-x  10 clemc  admin  320 Mar  5 13:12 /opt/homebrew/Cellar/lua/5.5.0/
drwxr-xr-x  12 clemc  admin  384 Mar  5 13:11 /opt/homebrew/Cellar/luajit-openresty/2.1-20260227/
drwxr-xr-x  11 clemc  admin  352 Mar  5 13:14 /opt/homebrew/Cellar/luajit/2.1.1772619647/
drwxr-xr-x  12 clemc  admin  384 Mar  5 13:13 /opt/homebrew/Cellar/luarocks/3.13.0_1/

"carlocab: suggested running this command to fix the issue at that time: HOMEBREW_NO_AUTO_UPDATE=1 brew install -s lmod
which resulted in:

clemc@xorn ~ % HOMEBREW_NO_AUTO_UPDATE=1 brew install -s lmod
lmod 9.1.2 is already installed but outdated (so it will be upgraded).
==> Fetching downloads for: lmod
✔︎ API Source lmod.rb                                                         Verified      3.6KB/  3.6KB
✔︎ Resource lmod--lua-term                                                    Verified      4.8KB/  4.8KB
✔︎ Resource lmod--luafilesystem                                               Verified     29.3KB/ 29.3KB
✔︎ Resource lmod--luaposix                                                    Verified    189.3KB/189.3KB
✔︎ Formula lmod (9.1.2)                                                       Verified     33.8MB/ 33.8MB
==> Upgrading lmod
  9.1.2 -> 9.1.2_1
==> luarocks make --tree=/opt/homebrew/Cellar/lmod/9.1.2_1/libexec/vendor --lua-dir=/opt/homebrew/opt/lu
==> luarocks make --tree=/opt/homebrew/Cellar/lmod/9.1.2_1/libexec/vendor --lua-dir=/opt/homebrew/opt/lu
==> luarocks make --tree=/opt/homebrew/Cellar/lmod/9.1.2_1/libexec/vendor --lua-dir=/opt/homebrew/opt/lu
==> ./configure --with-siteControlPrefix=yes
==> make install
==> Caveats
To use Lmod, you should add the init script to the shell you are using.

For example, the bash setup script is here: /opt/homebrew/opt/lmod/init/profile
and you can source it in your bash setup or link to it.

If you use fish, use /opt/homebrew/opt/lmod/init/fish, such as:
  ln -s /opt/homebrew/opt/lmod/init/fish ~/.config/fish/conf.d/00_lmod.fish
==> Summary
🍺  /opt/homebrew/Cellar/lmod/9.1.2_1: 303 files, 3.9MB, built in 26 seconds
==> Running `brew cleanup lmod`...
Disable this behaviour by setting `HOMEBREW_NO_INSTALL_CLEANUP=1`.
Hide these hints with `HOMEBREW_NO_ENV_HINTS=1` (see `man brew`).
Removing: /opt/homebrew/Cellar/lmod/9.1.2... (303 files, 3.9MB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod_bottle_manifest--9.1.2... (19.3KB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod--9.1.2... (520.9KB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod--9.1.2.tar.gz... (33.8MB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod--lua-term--0.8.tar.gz... (4.8KB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod--luafilesystem--1.9.0.tar.gz... (29.3KB)
Removing: /Volumes/usrcs/clemc/Library/Caches/Homebrew/lmod--luaposix--36.3.tar.gz... (189.3KB)

This seems to have fixed the issue. But I wanted to at least document it, as I suspect that something in the update/upgrade logic is not working quite as intended, and to note it for the maintainers.

Or, if I did something wrong and will amd headed for a different issue, please let me know what the correct way to repair this.

Thanks,

[cho-m]

I'm guessing you hit the 15 hour interval where lmod wasn't rebuilt after shipping Lua 5.5.0 given the line:

lmod 9.1.2 is already installed but outdated (so it will be upgraded).

For anyone else who sees this, a brew upgrade or brew upgrade lmod should fix it by downloading:

• lmod: revision bump for lua@5.4 homebrew-core#270779

The issue happened due to a bug in detecting dependent formulae where lmod was accidentally skipped in CI runner. The following may fix this in future pull requests:

• test_bot: avoid deferring when only running dependent tests brew#21672

[qianbinbin]

Hi, I would like to ask a question about Lua 5.5 here if you don't mind.

I noticed that after upgrading vim to Lua 5.5, the catppuccin theme cannot be used, but other plugins work fine.

After reverting vim to 9.2.0100, everything works normally.

I have reported an issue to the developers, but it seems that this is not a problem with the catppuccin theme: catppuccin/nvim#974 It seems I'm not the only one who has encountered this problem, based on the likes.

Thanks in advance.

[unixwizard107]

Glad to hear it's all set. Thank you.