What app is this about, and its version: Grist 1.7.11
What YunoHost version are you running: 12.1.39
What type of hardware are you using: VPS bought online
Clicked to upgrade app through webadmin and the upgrade failed. Restoration from backup failed. The app is currently in an unusable state and Yunohost software has removed it from the dashboard of accessible apps.
Nevermind. I have resolved the issue and consider this request for help as Closed/Resolved.
And what was the resolution?
Deleted the app from webadmin and reinstalled. The data directory was intact so all my files reloaded into the new instance nicely. However, there is a syntax error in the upgrade script that originally caused this error and made the system believe the data directory did not exist. Which is what caused this failure to begin with.
The error is strange:
2026-04-12 17:20:01,018: DEBUG - Reading package lists...
2026-04-12 17:20:01,034: DEBUG - + admin_email=*****@maindomain.tld
2026-04-12 17:20:01,035: DEBUG - ++ get_email_header
2026-04-12 17:20:01,038: DEBUG - +++ jq -r .yunohost.version
2026-04-12 17:20:01,051: WARNING - E: Could not get lock /var/lib/apt/lists/lock. It is held by process 3304738 (apt-get)
2026-04-12 17:20:01,052: WARNING - E: Unable to lock directory /var/lib/apt/lists/
2026-04-12 17:20:01,054: DEBUG - +++ yunohost --version --json
2026-04-12 17:20:01,166: INFO - <strong>Could not complete the operation 'Fetching available system updates and refreshing app catalog'. Please provide the full log of this operation by <a href="#/tools/logs/20260412-211959-tools_update">clicking here</a> to get help</strong>
Sounds like:
apt during the upgrade (by the administrator maybe?)yunohost --version --json checks the lock from apt and fails otherwiseI originally went to to updates>>Upgrade all packages in webadmin when the error occurred. I didn’t do anything else. I was waiting idle for the process to complete, when i got the failure message. Then I mmediate came to the forum and made my post with the server logs. So, maybe the system got ahead of itself?
Oh wow, realizing right now some weird behavior: when I remove verbosity from DEBUG logs and only take the one before the crash:
curl -s https://paste.yunohost.org/raw/obanorugic | grep "INFO" | sed '/Could not complete the operation/,$ d'
I get this result:
curl -s https://paste.yunohost.org/raw/obanorugic | grep "INFO\|WARN\|ERROR" | sed '/Could not complete the operation/,$ d'
2026-04-12 17:18:46,552: INFO - Updating sources...
2026-04-12 17:18:50,642: INFO - Updating system_user...
2026-04-12 17:18:50,809: INFO - Updating install_dir...
2026-04-12 17:18:50,822: INFO - Updating data_dir...
2026-04-12 17:18:50,836: INFO - Updating permissions...
2026-04-12 17:18:50,882: WARNING - This permission is currently granted to all users in addition to other groups. You probably want to either remove the 'all_users' permission or remove the other groups it is currently granted to.
2026-04-12 17:18:51,188: INFO - Updating ports...
2026-04-12 17:18:51,199: INFO - Updating apt...
2026-04-12 17:18:53,301: INFO - Now upgrading grist…
2026-04-12 17:18:53,302: INFO - Creating a safety backup prior to the upgrade
2026-04-12 17:18:53,373: INFO - Collecting files to be backed up for grist…
2026-04-12 17:18:53,585: INFO - Declaring files to be backed up...
2026-04-12 17:18:53,904: INFO - /home/yunohost.app/grist will not be saved, because 'BACKUP_CORE_ONLY' is set.
2026-04-12 17:18:54,440: INFO - Backup script completed for grist. (YunoHost will then actually copy those files to the archive).
2026-04-12 17:18:55,033: INFO - Creating a backup archive from the collected files…
2026-04-12 17:18:55,034: INFO - The archive will contain about 817MB of data.
2026-04-12 17:19:13,983: INFO - Updating nodejs...
2026-04-12 17:19:14,258: INFO - Backup grist-pre-upgrade1 was deleted because it is replaced by a newer backup grist-pre-upgrade2
2026-04-12 17:19:17,051: INFO - Updating sources...
2026-04-12 17:19:36,772: INFO - Now upgrading grist…
2026-04-12 17:19:36,773: INFO - Creating a safety backup prior to the upgrade
2026-04-12 17:19:37,441: INFO - Collecting files to be backed up for grist…
2026-04-12 17:19:37,622: INFO - Declaring files to be backed up...
2026-04-12 17:19:38,148: INFO - /home/yunohost.app/grist will not be saved, because 'BACKUP_CORE_ONLY' is set.
2026-04-12 17:19:38,776: INFO - Backup script completed for grist. (YunoHost will then actually copy those files to the archive).
2026-04-12 17:19:39,090: INFO - Updating system_user...
2026-04-12 17:19:39,551: INFO - Updating install_dir...
2026-04-12 17:19:39,564: INFO - Updating data_dir...
2026-04-12 17:19:39,580: INFO - Updating permissions...
2026-04-12 17:19:39,647: WARNING - This permission is currently granted to all users in addition to other groups. You probably want to either remove the 'all_users' permission or remove the other groups it is currently granted to.
2026-04-12 17:19:39,986: INFO - Updating ports...
2026-04-12 17:19:40,005: INFO - Updating apt...
2026-04-12 17:19:40,080: INFO - Creating a backup archive from the collected files…
2026-04-12 17:19:40,081: INFO - The archive will contain about 817MB of data.
2026-04-12 17:19:59,131: INFO - Fetching available upgrades for system packages…
2026-04-12 17:19:59,155: INFO - Fetching available upgrades for system packages…
2026-04-12 17:19:59,384: INFO - Backup grist-pre-upgrade2 was deleted because it is replaced by a newer backup grist-pre-upgrade1
2026-04-12 17:19:59,737: INFO - Updating nodejs...
2026-04-12 17:20:01,051: WARNING - E: Could not get lock /var/lib/apt/lists/lock. It is held by process 3304738 (apt-get)
2026-04-12 17:20:01,052: WARNING - E: Unable to lock directory /var/lib/apt/lists/
You can see that many logs are printed twice!
For example Updating sources..., Updating system_user..., …
2026-04-12 17:18:46,552: INFO - Updating sources...
...
2026-04-12 17:19:17,051: INFO - Updating sources...
2026-04-12 17:18:50,642: INFO - Updating system_user...
...
2026-04-12 17:19:39,090: INFO - Updating system_user...
It’s very strange…
Given my previous message, is it possible you actually have double-clicked on the Upgrade all packages ? (of course, it would be a bug of Yunohost that the process ran twice anyway)
Related issue (occurred with Immich):
It is not possible, It has to be a bug in the system. When you click on upgrade all packages button it launches a full screen “Server processing action” screen with a Pac-Man icon. During this process nothing is clickable as it is hidden behind this screen and there are no buttons on the screen itself. Just a dialog window that is telling you what actions it is performing and a progress bar at the top that indicates how complete the progress is.
I don’t know if it matters, but a recent update to the Yunohost system was completed just before updating these packages.
Prior to this update there have been no problems with this system and I have been using it for almost a year. I mean occasionally the admin-api will go down and you have to restart the api service. But, no major bugs other than that. Since this update though, I randomly get notified of services being dead and have to go restart them manually using Services>>Restart. When I reboot, certain services don’t initialize by themselves. I have actually had to add entries to crontab to restart those services when the server reboots to ensure active service and accessible applications.
Please consider what I said earlier:
Given my previous message, is it possible you actually have double-clicked on the
Upgrade all packages? (of course, it would be a bug of Yunohost that the process ran twice anyway)
I mean that even if you double-clicked and that it triggered the upgrade process to run twice, it’s a bug of Yunohost. Just for diagnosing and trying to reproduce.
If it’s not the case, we would have to look for other possibilities.
As I have stated previously, it is not possible due to how the system is setup to process. It has to be some sort of script error that caused it, Maybe from the recent system update.
Just for clarification, I did not click the button twice. I clicked Upgrade All once and it started processing by launching the process screen and I waited until it gave me the error screen
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