When uupd updates my system, only brew update seems to execute but brew upgrade is silently omitted

Hi, I noticed while checking the logs from journalctl -u uupd.service that during the Brew section only the update is applied but not the upgrade of the outdated packages.

I am currently on bluefin:stable 44.20260519. My rebase history is bluefin (in January, briefly) → bazzite-gnome → bazzite-dx-gnome → bluefin

Here is the Brew output of

journalctl -u uupd.service --no-hostname --since today

may 29 07:41:34 uupd[4216]: {"level":"DEBUG","msg":"Brew module","module_name":"Brew","module_configura> 

may 29 07:41:34 uupd[4216]: {"level":"INFO","msg":"Updating","title":"Brew","description":"CLI Apps","p>

may 29 07:41:43 uupd[4216]: {"level":"DEBUG","msg":"==> Updating Homebrew..."} 

may 29 07:41:43 uupd[4216]: {"level":"DEBUG","msg":"Updated 1 tap (homebrew/core)."} 

may 29 07:41:43 uupd[4216]: {"level":"DEBUG","msg":"==> New Formulae"} 

may 29 07:41:43 uupd[4216]: {"level":"DEBUG","msg":"btdu: Sampling disk usage profiler for btrfs"} 

may 29 07:41:43 uupd[4216]: {"level":"DEBUG","msg":"sanity: Command-line interface for Sanity"}

After that, I ran brew outdated and noticed an available upgrade:

✔︎ JSON API cask.jws.json Downloaded 16.9MB/ 16.9MB

✔︎ JSON API formula.jws.json Downloaded 32.8MB/ 32.8MB

capstone (5.0.8) < 5.0.9

Running ujust update, correctly upgrades the package.

✔︎ JSON API cask.jws.json Downloaded 16.9MB/ 16.9MB

✔︎ JSON API formula.jws.json Downloaded 32.8MB/ 32.8MB

==> Downloading bottle manifests

✔︎ Bottle Manifest capstone (5.0.9) Downloaded 9.0KB/ 9.0KB

==> Upgrading 1 outdated package:

capstone 5.0.8 -> 5.0.9

==> Fetching downloads for: capstone

✔︎ Bottle capstone (5.0.9) Downloaded 4.0MB/ 4.0MB

==> Upgrading capstone

5.0.8 -> 5.0.9

I decided to search again, in journalctl, for the word outdated and found the last instance of upgrading brew was in April 29. After that day, only brew update seems to run with uupd. My system was on bazzite-dx-gnome at that time.

abr 29 06:38:48 uupd[4941]: {"level":"DEBUG","msg":"Brew module","module_name":"Brew","module_configuration":{"Title":"Brew","Description":"CLI Apps","Enabled":true,"MultiUser":false,"DryRun":false,"UserDescription":null}}

abr 29 06:38:48 uupd[4941]: {"level":"INFO","msg":"Updating","title":"Brew","description":"CLI Apps","progress":1,"total":3,"step_progress":97.5,"overall":74}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"==> Updating Homebrew..."}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"Updated 1 tap (homebrew/core)."}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"==> New Formulae"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"barman: Backup and Recovery Manager for PostgreSQL"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"libchardet: Mozilla's Universal Charset Detector C/C++ API"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"zfp: Compressed numerical arrays that support high-speed random access"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"==> Outdated Formulae"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"gh"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"htop"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"python@3.14"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":""}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"You have 3 outdated formulae installed."}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"You can upgrade them with brew upgrade"}

abr 29 06:38:57 uupd[4941]: {"level":"DEBUG","msg":"or list them with brew outdated."}

abr 29 06:39:00 uupd[4941]: {"level":"DEBUG","msg":"==> Upgrading 3 outdated packages:"}

abr 29 06:39:00 uupd[4941]: {"level":"DEBUG","msg":"gh 2.91.0 -> 2.92.0"}

abr 29 06:39:00 uupd[4941]: {"level":"DEBUG","msg":"python@3.14 3.14.4 -> 3.14.4_1"}

abr 29 06:39:00 uupd[4941]: {"level":"DEBUG","msg":"htop 3.5.0 -> 3.5.1"}

abr 29 06:39:00 uupd[4941]: {"level":"DEBUG","msg":"==> Fetching downloads for: gh, python@3.14 and htop"}

abr 29 06:39:05 uupd[4941]: {"level":"DEBUG","msg":"==> Upgrading gh"}

abr 29 06:39:05 uupd[4941]: {"level":"DEBUG","msg":" 2.91.0 -> 2.92.0 "}

abr 29 06:39:05 uupd[4941]: {"level":"DEBUG","msg":"==> Pouring gh--2.92.0.x86_64_linux.bottle.tar.gz"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"🍺 /home/linuxbrew/.linuxbrew/Cellar/gh/2.92.0: 229 files, 39.9MB"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"==> Running `brew cleanup gh`..."}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"Disable this behaviour by setting `HOMEBREW_NO_INSTALL_CLEANUP=1`."}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"Hide these hints with `HOMEBREW_NO_ENV_HINTS=1` (see `man brew`)."}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"Removing: /home/linuxbrew/.linuxbrew/Cellar/gh/2.91.0... (229 files, 39.8MB)"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"Removing: /var/home/alejandro/.cache/Homebrew/gh_bottle_manifest--2.91.0... (7.3KB)"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"Removing: /var/home/alejandro/.cache/Homebrew/gh--2.91.0... (14MB)"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":"==> Upgrading python@3.14"}

abr 29 06:39:08 uupd[4941]: {"level":"DEBUG","msg":" 3.14.4 -> 3.14.4_1 "}

abr 29 06:39:13 uupd[4941]: {"level":"DEBUG","msg":"==> Pouring python@3.14--3.14.4_1.x86_64_linux.bottle.tar.gz"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"🍺 /home/linuxbrew/.linuxbrew/Cellar/python@3.14/3.14.4_1: 3,296 files, 80.4MB"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"==> Running `brew cleanup python@3.14`..."}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"Removing: /home/linuxbrew/.linuxbrew/Cellar/python@3.14/3.14.4... (3,361 files, 81.9MB)"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"Removing: /var/home/alejandro/.cache/Homebrew/python@3.14_bottle_manifest--3.14.4... (31.4KB)"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"Removing: /var/home/alejandro/.cache/Homebrew/python@3.14--3.14.4... (21.5MB)"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"==> Upgrading htop"}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":" 3.5.0 -> 3.5.1 "}

abr 29 06:39:17 uupd[4941]: {"level":"DEBUG","msg":"==> Pouring htop--3.5.1.x86_64_linux.bottle.tar.gz"}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"==> Caveats"}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"htop requires root privileges to correctly display all running processes,"}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"so you will need to run `sudo htop`."}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"You should be certain that you trust any software you grant root privileges."}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"==> Summary"}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"🍺 /home/linuxbrew/.linuxbrew/Cellar/htop/3.5.1: 13 files, 586.3KB"}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"==> Running `brew cleanup htop`..."}

abr 29 06:39:18 uupd[4941]: {"level":"DEBUG","msg":"Removing: /home/linuxbrew/.linuxbrew/Cellar/htop/3.5.0... (13 files, 585.5KB)"}


And here is the output of git remote -v in /var/home/linuxbrew/.linuxbrew/Homebrew/

origin	https://github.com/Homebrew/brew (fetch)
origin	https://github.com/Homebrew/brew (push)

I would like to know if there is something I could do so that the brew upgrade process takes places again with uupd and if anyone else is experiencing something similar, thanks in advance!

Just wanted to add the output of running the uupd command for the brew module manually (after the service ran earlier today; same behavior: only brew update happens, but not upgrade).

brew outdated

✔︎ JSON API cask.jws.json Downloaded 16.9MB/ 16.9MB

✔︎ JSON API formula.jws.json Downloaded 33.2MB/ 33.2MB

libdrm (2.4.133) < 2.4.134

libxkbcommon (1.13.1) < 1.13.2

pnpm (11.4.0) < 11.5.0

Then I used the following command sudo uupd --disable-module-system --disable-module-flatpak --disable-module-distrobox --verbose --log-level debug


INFO: Hardware checks passed

DEBUG: Executed update check

module: system

output: |

No changes in: ostree-image-signed:docker://ghcr.io/ublue-os/bluefin:stable

update: false

DEBUG: System Updater module status

enabled: false

DEBUG: Brew module

module_configuration:

Description: CLI Apps

DryRun: false

Enabled: true

MultiUser: false

Title: Brew

UserDescription: null

module_name: Brew

INFO: Updating

description: CLI Apps

overall: 100

progress: 0

step_progress: 0

title: Brew

total: 0

DEBUG: Already up-to-date.

DEBUG: ==> Updating Homebrew...

INFO: Verbose run requested

INFO: Brew Upgrade

output:

Cli:

- /home/linuxbrew/.linuxbrew/bin/brew

- upgrade

Context: Brew Upgrade

Failure: false

Stderr: null

Stdout: ""

INFO: Updates Completed Successfully