Help to fix a broken Yunohost system

Support
,
1

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
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

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

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

2

Hi @bionick
Can you run sudo apt update and share the output ?

3

Sure, here is the output:

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.
4

Ok, I guess you already updated the sury repo key, right?

And

sudo apt-cache policy php8.4-fpm

?

5

Actually I dont remember, but:

root@xxxx:~# sudo apt-cache policy php8.4-fpm
php8.4-fpm:
  Installed: (none)
  Candidate: (none)
  Version table:
root@xxxx:~#
6

Let’s try

sudo apt clean
sudo apt update
sudo apt-cache policy php8.4-fpm
7

Nothing, unfortunately:

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:~#
8 
sudo cat /etc/apt/sources.list.d/extra_php_version.list
9 
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 …

10

Ok…

ls -la /etc/apt/sources.list.d/
11 
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
12 
sudo cat /etc/apt/sources.list.d/php.list
13 
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
14

RPI is arm64 afaik

15

Yes, it is!

16 
sudo yunohost tools regen-conf apt --force
1 Like
17 
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:~#
18 
sudo apt update
sudo apt-cache policy php8.4-fpm
1 Like
19

ok, that was the issue that made me moving away extra_php_version.list

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:~#
20

For now, just comment out the other source (you should remove it later)

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