# Help to fix a broken Yunohost system
**URL:** https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396
**Category:** Support
**Tags:** raspberrypi, english
**Created:** [June 3, 2026, 3:55pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396 "2026-06-03T15:55:27Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 3:55pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/1 "2026-06-03T15:55:27Z")
**What type of hardware are you using** : Raspberry Pi 3, 4+
**What YunoHost version are you running** : 12.1.40.1
**How are you able to access your server** : The webadmin
SSH
**Are you in a special context or did you perform specific tweaking on your YunoHost instance ?** : No (t sure)
### Describe your issue
My system is up to date,
The diagnosis starts with a warning:
`Unable to extract mainline kernel version from the kernel info '#1642 SMP PREEMPT Mon Apr 3 17:24:16 BST 2023' ... Therefore YunoHost will be unable to check for security issues related to the kernel. Please try to report this message to the YunoHost team to improve the situation`,
but rusults are green except:
`Network name resolution seems to be working, but it looks like you're using a custom /etc/resolv.conf.` (I don’t remember having twiked resolv.conf).
I need to upgrade Nextcloud from 32.0.5~ynh1 to 33.0.4~ynh1. The first run of the update stops because
`File or folder '/etc/php/8.3/fpm/pool.d/nextcloud.conf' to be backed up does not exist` [https://paste.yunohost.org/raw/ebunakihuv](https://paste.yunohost.org/raw/ebunakihuv)
I figured that if he wants that file, we may as well give it to him, so I entered
`touch /etc/php/8.3/fpm/pool.d/nextcloud.conf`
and run the update again.
This time the issue sounds more serious:
`An error occured inside the script snippet : Unable to install apt dependencies, it might be due to a conflict with another app - or you should check and share the previous log about what are the problematic dependencies` [https://paste.yunohost.org/raw/apoporodit](https://paste.yunohost.org/raw/apoporodit)
Then I switched to Roundcube, which need to be upgraded from 1.6.12~ynh1 to 1.6.15~ynh1 but the update stops because:
`Aborting the upgrade, because a safety backup could not be created (Failed to collect files to be backed up)` [https://paste.yunohost.org/raw/losicisexi](https://paste.yunohost.org/raw/losicisexi)
Meanwhile, neither Nextcloud nor Roundcube work, and I can’t even access the applications from the GUI.
Any help will be sincerely appreciated
Nick
### Share relevant logs or error messages
-
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 4:24pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/2 "2026-06-03T16:24:58Z")
Hi @bionick
Can you run `sudo apt update` and share the output ?
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 4:38pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/3 "2026-06-03T16:38:12Z")
Sure, here is the output:
```auto
root@xxxx:~# sudo apt update
Get:1 https://forge.yunohost.org/debian bookworm InRelease [15.4 kB]
Get:2 http://archive.raspberrypi.org/debian bookworm InRelease [55.0 kB]
Hit:3 http://security.debian.org/debian-security bookworm-security InRelease
Hit:4 http://deb.debian.org/debian bookworm InRelease
Get:5 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]
Hit:6 https://dl.yarnpkg.com/debian stable InRelease
Hit:7 https://packages.sury.org/apache2 bookworm InRelease
Hit:8 https://packages.sury.org/php bookworm InRelease
Get:9 http://archive.raspberrypi.org/debian bookworm/main armhf Packages [570 kB]
Get:10 http://archive.raspberrypi.org/debian bookworm/main arm64 Packages [569 kB]
Fetched 1,265 kB in 7s (178 kB/s)
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
All packages are up to date.
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 4:45pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/4 "2026-06-03T16:45:41Z")
Ok, I guess you already updated the sury repo key, right?
And
```auto
sudo apt-cache policy php8.4-fpm
```
?
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 4:48pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/5 "2026-06-03T16:48:25Z")
Actually I dont remember, but:
```auto
root@xxxx:~# sudo apt-cache policy php8.4-fpm
php8.4-fpm:
Installed: (none)
Candidate: (none)
Version table:
root@xxxx:~#
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 4:51pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/6 "2026-06-03T16:51:32Z")
Let’s try
```auto
sudo apt clean
sudo apt update
sudo apt-cache policy php8.4-fpm
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 4:57pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/7 "2026-06-03T16:57:06Z")
Nothing, unfortunately:
```auto
root@xxxx:~# sudo apt clean
root@xxxx:~# sudo apt update
Hit:1 http://security.debian.org/debian-security bookworm-security InRelease
Hit:2 http://deb.debian.org/debian bookworm InRelease
Hit:3 https://dl.yarnpkg.com/debian stable InRelease
Hit:5 http://deb.debian.org/debian bookworm-updates InRelease
Hit:6 https://packages.sury.org/apache2 bookworm InRelease
Hit:7 https://packages.sury.org/php bookworm InRelease
Hit:4 https://forge.yunohost.org/debian bookworm InRelease
Hit:8 http://archive.raspberrypi.org/debian bookworm InRelease
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
All packages are up to date.
root@xxxx:~# sudo apt-cache policy php8.4-fpm
php8.4-fpm:
Installed: (none)
Candidate: (none)
Version table:
root@xxxx:~#
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 4:59pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/8 "2026-06-03T16:59:30Z")
```auto
sudo cat /etc/apt/sources.list.d/extra_php_version.list
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:00pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/9 "2026-06-03T17:00:47Z")
```auto
root@xxxx:~# sudo cat /etc/apt/sources.list.d/extra_php_version.list
cat: /etc/apt/sources.list.d/extra_php_version.list: No such file or directory
```
I remember having done something because of a conflict …
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:01pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/10 "2026-06-03T17:01:49Z")
Ok…
```auto
ls -la /etc/apt/sources.list.d/
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:02pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/11 "2026-06-03T17:02:34Z")
```auto
root@xxxx:~# ls -la /etc/apt/sources.list.d/
total 28
drwxr-xr-x 2 root root 4096 Mar 17 19:09 .
drwxr-xr-x 9 root root 4096 Nov 8 2024 ..
-rw-r--r-- 1 root root 113 Mar 17 18:56 apache2.list
-rw-r--r-- 1 root root 109 Mar 17 18:56 php.list
-rw-r--r-- 1 root root 191 Nov 8 2024 raspi.list
-rw-r--r-- 1 root root 91 Nov 8 2024 yarn.list
-rw-r--r-- 1 root root 108 Nov 8 2024 yunohost.list
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:03pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/12 "2026-06-03T17:03:18Z")
```auto
sudo cat /etc/apt/sources.list.d/php.list
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:03pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/13 "2026-06-03T17:03:58Z")
```auto
root@xxxx:~# sudo cat /etc/apt/sources.list.d/php.list
deb [arch=amd64 signed-by=/usr/share/keyrings/sury-keyring.gpg] https://packages.sury.org/php/ bookworm main
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:06pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/14 "2026-06-03T17:06:17Z")
> [@bionick](#):
>
> `arch=amd64 `
RPI is arm64 afaik
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:07pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/15 "2026-06-03T17:07:05Z")
> [@otm33](#):
>
> RPI is arm64 afaik
Yes, it is!
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:07pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/16 "2026-06-03T17:07:15Z")
```auto
sudo yunohost tools regen-conf apt --force
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:08pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/17 "2026-06-03T17:08:17Z")
```auto
root@xxxx:~# sudo yunohost tools regen-conf apt --force
Success! Configuration updated for 'apt'
apt:
applied:
/etc/apt/sources.list.d/extra_php_version.list:
status: force-created
pending:
root@xxxx:~#
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:09pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/18 "2026-06-03T17:09:07Z")
```auto
sudo apt update
sudo apt-cache policy php8.4-fpm
```
---
### Author:  [@bionick](https://forum.yunohost.org/u/bionick)
#### Post date: [June 3, 2026, 5:15pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/19 "2026-06-03T17:15:45Z")
ok, that was the issue that made me moving away `extra_php_version.list`
```auto
root@xxxx:~# sudo apt update
E: Conflicting values set for option Signed-By regarding source https://packages.sury.org/php/ bookworm: /etc/apt/trusted.gpg.d/extra_php_version.gpg != /usr/share/keyrings/sury-keyring.gpg
E: The list of sources could not be read.
root@xxxx:~#
```
---
### Author:  [@otm33](https://forum.yunohost.org/u/otm33)
#### Post date: [June 3, 2026, 5:18pm UTC](https://forum.yunohost.org/t/help-to-fix-a-broken-yunohost-system/42396/20 "2026-06-03T17:18:06Z")
For now, just comment out the other source (you should remove it later)
```auto
sudo nano /etc/apt/sources.list.d/php.list
# deb [arch=amd64 signed-by=/usr/share/keyrings/sury-keyring.gpg] https://packages.sury.org/php/ bookworm main
```
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