Flatpak does not update its apps when run via cron

This simple script runs correctly when launched manually:

#!/bin/sh

flatpak -y update 2>&1 >> ~/cron/cron-flatpak.log

When run with 00 07 * * * sh ~/cron/cron-flatpak.sh (same regular user, not root crontab), it produces the following:

Looking for updates…


 1.     org.chromium.Chromium.Codecs    stable  u   flathub < 1.1 MB
 2.     org.chromium.Chromium.Locale    stable  u   flathub < 112.8 kB (partial)
 3.     org.qbittorrent.qBittorrent stable  u   flathub < 8.3 MB



Updating 1/3…                                                                 
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user

Updating 1/3… ██▌                   13%  41.1 kB/s
Updating 1/3… ████████████████████ 100%  674.8 kB/s
Updating 1/3… ████████████████████ 100%  674.8 kB/s
Updating 2/3…                                                                 
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user

Updating 2/3… ████████████████████ 100%  592 bytes/s
Updating 3/3…                                                                 
Warning: Failed to get revokefs-fuse socket from system-helper: Flatpak system operation GetRevokefsFd not allowed for user

Updating 3/3… ████████████████████ 100%  0 bytes/s
Updates complete.

Afterwards, the versions seem to match what's listed on flathub.io, but the script tries to update everything over and over again on each run. Any suggestions?

ETA: Okay people, I'll be testing the approaches you suggested and I will accept one answer or the other after I manage to make the thing work. Going to take a while since every single iteration requires a new app version rolled out on flathub.

It's not so much a solution as a workaround, or possible clue, but installing Chromium with the --user flag (flatpak uses --system by default) and updating works fine in cron.

flatpak install flathub org.chromium.Chromium # default, has cron issues
flatpak install --user flathub org.chromium.Chromium # no cron issues

Unfortunately, I'm unsure why the ability to update system flatpaks is dropped in cron—at least for the Chromium flatpak since it looks like the third flatpak was able to update just. Maybe the issue is with that particular flatpak.

Edit: I missed the third error in the output, it was not unique to Chromium.

Edit 2: Just some further clarification/steps for using flatpak's --user flag. Since system and user packages are managed separately, this means adding/removing remotes, installing, and updating must also be done separately. A user package cannot pull from a system remote and vice versa.

# add a user remote
flatpak remote-add --if-not-exists --user REMOTE_NAME REMOTE_ADDRESS

# updates just user packages
flatpak update --user

Jobs run through cron, or at, or batch, aren't run in the same runtime environment that you have on your desktop. None of your PATH changes, or other environment variable settings are automatically propagated to your cron job. For example, there's no $DISPLAY, so GUI programs need special treatment (read man xhost).

One can set environment variables for all one's cron jobs in the crontab file Read man 5 crontab.

Look at the results of echo "=== set ===";set;echo "=== env ===";env | sort;echo "=== alias ===";alias in each of your environments.

Since the command part of the crontab line is, by default, interpreted by /bin/sh, which has a simpler syntax than /bin/bash, I recommend having command be a call to a bash script (executable, mounted, starts with #!/bin/bash) which sets up the environment, then calls the desired program.