Ynh system update and/or new app install seems to break other apps

[njiruk]

What type of hardware are you using: Old laptop or computer
What YunoHost version are you running: 12.1.32.1
How are you able to access your server: web access, Direct access via physical keyboard/screen, ssh
Are you in a special context or did you perform specific tweaking on your YunoHost instance ?: I updated Yunohost from version 12.0.17

Describe your issue

I installed a yunohost update on October 25th via the webadmin portal.
It seemed to be fine until I noticed I got an error, something regarding PID in the Grist app.
I tried updating the Grist app, but this resulted in a bigger failure: the installation took a very long time, it was stuck on “building the app”. I patiently waited for a day. But now the app is not accessible anymore. I also noticed a very long install procedure with the Penpot app, but that eventually worked.
Also, restoring the Grist app is not possible anymore.
So I decided to revert the update. There was no yunohost backup made before the update I noticed, but I had a full HD back-up, from Restic (which I installed via the command line). I restored the paths /etc /home/yunohost.app /var /usr via an Ubuntu live system. The restored system booted fine but the LDAP service doesn’t want to start and I cannot ssh - "Permission denied “publickey)”. I still can log in with the original root user though.

I realised a little late that I probably could have tried reverting the yunohost install to an older version in another way! (Using a yunohost command?) This may be still an option, because before doing the Restic restore I also made a full disc backup with the dd command - which probably will be OK to restore! (?)

Or do you think it is worth fixing the LDAP and SSH (and possibly further?) issues? This would bring me directly back to the state before the buggy yunohost update.

Share relevant logs or error messages

Various. See general description.

[njiruk]

Update: while the Restic restore finally seemed to have resolved the main issue (see below) there were other issues, which got worse after some tweaking. Eventually I didn’t seem any way out there, so I decided to go back to the state before the Restic restore! (using the dd backup I made.)

So, back here, it looks like the main problem is the update or installation of Grist (and potentially other apps - I tried a few, but they installed ok, also a Python based app, fastapi).
I tried restoring the old Grist backup (made by yunohost before attempting an upgrade from 1.6.1~ynh1 to 1.7.4~ynh2). While it seems to work, opening the app either results in a 502 Bad gateway, or a blank page.

Trying to re-install Grist, or installing a second copy fails in the installation at “Building the app (this may take some time)”. When it shows this, the server becomes entirely non-responsive. Only when doing this from the command line I’m able to stop it with a control-C. I have waited an entire day on this, so it doesn’t look like it is just a slow and heavy building process. Also, in the partially restored system (see first paragraph) that step did take about 5 minutes.

Here are the last lines of the installation log (/var/log/yunohost/operations/20251030-083806-app_upgrade-grist.log)

2025-10-30 09:40:37,223: INFO - [#########+…] > Building the app (may take a while)
2025-10-30 09:40:37,224: DEBUG - + ynh_hide_warnings ynh_exec_as_app yarn run build:prod
2025-10-30 09:40:37,226: DEBUG - + ynh_exec_as_app yarn run build:prod
2025-10-30 09:40:37,226: DEBUG - + sudo -u grist env PATH=/opt/node_n/n/versions/node/22.21.1/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin COREPACK_ENABLE_DOWNLOAD_PROMPT=0 NPM_CONFIG_UPDATE_NOTIFIER=false yarn run build:prod
2025-10-30 09:40:37,585: DEBUG - yarn run v1.22.22
2025-10-30 09:40:37,665: DEBUG - $ buildtools/build.sh prod
2025-10-30 09:40:37,691: DEBUG - Building for production
2025-10-30 09:40:37,692: DEBUG - + node buildtools/sanitize_translations.js
2025-10-30 09:40:38,774: DEBUG - + tsc --build tsconfig-prod.json
2025-10-30 09:41:53,542: DEBUG - + buildtools/update_type_info.sh app
2025-10-30 09:41:53,635: DEBUG - + webpack --config buildtools/webpack.config.js --mode production

The logs of other install attempts also end there (e.g. followed by “ERROR - Failed to upgrade grist: The operation was manually interrupted?” when I interupted with control-C)

So it looks like that is the operation that takes forever. Not sure what next steps could be now…

[njiruk]

Omg, I got a clue via chatgpt that this is about RAM running out… Didn’t think about that!
I have 6Gb RAM and 1Gb swap, the command
free -h
showed me:
total used free shared buff/cache available
Mem: 5.6Gi 4.0Gi 272Mi 175Mi 1.8Gi 1.6Gi
Swap: 979Mi 837Mi 142Mi
No good!
And
ps -e -o pid,user,%mem,cmd --sort=-%mem
gave me the memory usage of processes in descending order.
Indeed, it was actually not the yunohost update that “broke” things, but the Penpot app I installed right after that (which required the yunohost update). That app took 13% of RAM, and there were already quite a bunch of services running. I stopped some, and stopped + disabled others, until I got 1,8Gb used RAM. Then Grist installed smoothly…

This was a good lesson for me in many perspectives. I hope it can be useful for others. Though the title and problem description may not lead those people here, as the symptoms can probably be very different…