Cannot apt update

Hi, my current problem is as following: I want to install a new app and it says to do that I need to do an update, but the update vie the web interface doesn’t work so I’m trying via the command line and that also fails with return code 100 and with the output as below.

My YunoHost server

Hardware: KVM on intel-CPU
YunoHost version: 4.1.8
I have access to my server : Through SSH and through virt-manager
Are you in a special context or did you perform some particular tweaking on your YunoHost instance ? : yes
If yes, please explain:
had to use the vps install method on debian due to issues with the default installer (because the main “drive” is /dev/vda and not /dev/sda)

Description of my issue

sudo apt update command fails as following:

$ sudo apt update                                                                                                                                                                          
Hit:1 http://download.onlyoffice.com/repo/debian squeeze InRelease                                                                                                                           
Hit:2 http://download.opensuse.org/repositories/devel:/languages:/crystal/Debian_9.0  InRelease                                                                                              
Ign:3 http://packages.erlang-solutions.com/debian buster InRelease                                                                                                                           
Hit:4 http://security.debian.org/debian-security buster/updates InRelease                                                                                                                    
Hit:5 http://deb.debian.org/debian buster-backports InRelease                                                                                                                                
Hit:6 http://debian.inf.tu-dresden.de/debian buster InRelease                                                                                                                                
Hit:7 http://forge.yunohost.org/debian buster InRelease                                                                                                                                      
Hit:8 http://packages.erlang-solutions.com/debian buster Release                                                                                                                             
Hit:9 http://debian.inf.tu-dresden.de/debian buster-updates InRelease                                                                                                                        
Get:10 http://mirrors.ubuntu.com/mirrors.txt Mirrorlist [1,731 B]                                                                                                                            
Ign:11 http://mirror.stw-aachen.de/ubuntu precise InRelease                                                                                                                                  
Ign:13 http://mirror.serverloft.eu/ubuntu/ubuntu precise-backports InRelease                                                                                                                 
Ign:14 http://ftp.uni-kl.de/pub/linux/ubuntu precise-security InRelease                                                                                                                      
Ign:13 https://mirror.de.vangus.co.il/ubuntu precise-backports InRelease                                                                                                                     
Ign:11 http://archive.ubuntu.com/ubuntu precise InRelease                                                                                                                                    
Ign:11 https://mirror.de.vangus.co.il/ubuntu precise InRelease                                                                                                                               
Ign:14 http://ftp-stud.hs-esslingen.de/ubuntu precise-security InRelease                                                                                                                     
Ign:13 http://mirror.23media.com/ubuntu precise-backports InRelease                                                                                                                          
Hit:15 https://repo.jellyfin.org/debian buster InRelease                                                                                                                                     
Ign:14 https://mirror.23m.com/ubuntu precise-security InRelease                                                                                                                              
Ign:11 http://artfiles.org/ubuntu.com precise InRelease                                                                                                                                      
Ign:13 http://archive.ubuntu.com/ubuntu precise-backports InRelease                                                                                                                          
Ign:14 http://suse.uni-leipzig.de/pub/releases.ubuntu.com/ubuntu precise-security InRelease                                                                                                  
Ign:11 http://mirror2.tuxinator.org/ubuntu precise InRelease                                                                                                                                 
Ign:14 http://ftp.rrzn.uni-hannover.de/pub/mirror/linux/ubuntu precise-security InRelease                                                                                                    
Ign:11 http://ftp-stud.hs-esslingen.de/ubuntu precise InRelease                                                                                                                              
Ign:14 http://archive.ubuntu.com/ubuntu precise-security InRelease                                                                                                                           
Ign:11 http://mirror.funkfreundelandshut.de/ubuntu precise InRelease                                                                                                                         
Ign:14 http://packages.oth-regensburg.de/ubuntu precise-security InRelease                                                                                                                   
Ign:14 http://mirror.ipb.de/ubuntu precise-security InRelease                                                                                                                                
Ign:11 https://mirror.scaleuptech.com/ubuntu precise InRelease                                                                                                                               
Ign:11 http://ftp.fau.de/ubuntu precise InRelease                                                                                                                                            
Ign:14 https://mirror.dogado.de/ubuntu precise-security InRelease
Ign:11 http://mirror.ratiokontakt.de/mirror/ubuntu precise InRelease
Ign:14 http://linux.darkpenguin.net/distros/ubuntu-archive precise-security InRelease
Ign:11 http://ftp.halifax.rwth-aachen.de/ubuntu precise InRelease
Ign:14 http://ftp5.gwdg.de/pub/linux/debian/ubuntu precise-security InRelease
Ign:14 https://mirror.de.vangus.co.il/ubuntu precise-security InRelease
Ign:11 http://suse.uni-leipzig.de/pub/releases.ubuntu.com/ubuntu precise InRelease
Get:14 http://mirror.eu-fr.kamatera.com/ubuntu precise-security InRelease [55.7 kB]
Ign:11 https://files.tux-users.net/ubuntu precise InRelease
Ign:11 https://mirror.23m.com/ubuntu precise InRelease                                  
Ign:11 http://mirror.23media.com/ubuntu precise InRelease
Err:14 http://mirror.eu-fr.kamatera.com/ubuntu precise-security InRelease
  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5                                                                         
Ign:11 http://mirror.ipb.de/ubuntu precise InRelease
Ign:11 http://ftp.rrzn.uni-hannover.de/pub/mirror/linux/ubuntu precise InRelease
Ign:12 https://ftp.uni-stuttgart.de/ubuntu precise-updates InRelease
Ign:13 https://ftp.uni-stuttgart.de/ubuntu precise-backports InRelease
Ign:12 http://ftp.rrzn.uni-hannover.de/pub/mirror/linux/ubuntu precise-updates InRelease
Ign:11 https://ftp.uni-stuttgart.de/ubuntu precise InRelease
Ign:13 https://mirror.dogado.de/ubuntu precise-backports InRelease
Get:12 http://mirror.eu-fr.kamatera.com/ubuntu precise-updates InRelease [55.7 kB]
Ign:11 https://mirror.dogado.de/ubuntu precise InRelease
Err:12 http://mirror.eu-fr.kamatera.com/ubuntu precise-updates InRelease
  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5                                                                         
Ign:13 http://ftp5.gwdg.de/pub/linux/debian/ubuntu precise-backports InRelease
Ign:11 http://ftp.hosteurope.de/mirror/archive.ubuntu.com precise InRelease
Ign:13 http://debian.charite.de/ubuntu precise-backports InRelease
Ign:13 http://mirror.kamp.de/ubuntu precise-backports InRelease
Ign:13 http://linux.darkpenguin.net/distros/ubuntu-archive precise-backports InRelease
Ign:13 https://files.tux-users.net/ubuntu precise-backports InRelease
Ign:13 http://mirror.wtnet.de/ubuntu precise-backports InRelease
Get:13 http://mirror.eu-fr.kamatera.com/ubuntu precise-backports InRelease [55.7 kB]
Ign:11 https://de.mirrors.clouvider.net/ubuntu precise InRelease
Ign:11 http://mirror.wtnet.de/ubuntu precise InRelease
Err:13 http://mirror.eu-fr.kamatera.com/ubuntu precise-backports InRelease
  The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5
Ign:11 http://mirror.eu-fr.kamatera.com/ubuntu precise InRelease                                                                                                                            
Ign:11 http://ubuntu.mirror.tudos.de/ubuntu precise InRelease                                                                                                                               
Ign:11 http://ftp.tu-chemnitz.de/pub/linux/ubuntu-ports precise InRelease                                                                                                                   
Ign:11 http://mirror.netcologne.de/ubuntu precise InRelease                                                                                                                                 
Ign:11 https://mirror.de.leaseweb.net/ubuntu precise InRelease                                                                                                                              
Ign:11 http://mirror.serverloft.eu/ubuntu/ubuntu precise InRelease                                                                                                                          
Ign:11 http://packages.oth-regensburg.de/ubuntu precise InRelease                                                                                                                           
Ign:11 http://ubuntu.unitedcolo.de/ubuntu precise InRelease                                                                                                                                 
Ign:11 https://mirror.dogado.de/ubuntu precise InRelease                                                                                                                                    
Ign:17 http://ftp.stw-bonn.de/ubuntu precise Release                                                                                                                                        
Ign:17 http://mirror.ipb.de/ubuntu precise Release                                                                                                                                          
Ign:17 http://artfiles.org/ubuntu.com precise Release                                                                                                                                       
Ign:17 http://ftp.hosteurope.de/mirror/archive.ubuntu.com precise Release                                                                                                                   
Ign:17 http://packages.oth-regensburg.de/ubuntu precise Release                                                                                                                             
Ign:17 http://ftp5.gwdg.de/pub/linux/debian/ubuntu precise Release                                                                                                                          
Ign:17 http://ftp.rz.tu-bs.de/pub/mirror/ubuntu-packages precise Release                                                                                                                    
Ign:17 http://ubuntu.mirror.tudos.de/ubuntu precise Release                                                                                                                                 
Ign:17 http://ftp.rrzn.uni-hannover.de/pub/mirror/linux/ubuntu precise Release                                                                                                              
Ign:17 http://ubuntu.mirror.lrz.de/ubuntu precise Release                                                                                                                                   
Ign:17 http://mirror2.tuxinator.org/ubuntu precise Release                                                                                                                                  
Ign:17 http://mirror.stw-aachen.de/ubuntu precise Release                                                                                                                                   
Ign:17 https://mirror.de.vangus.co.il/ubuntu precise Release                                                                                                                                
Ign:17 https://mirror.23m.com/ubuntu precise Release                                                                                                                                        
Ign:17 https://mirror.dogado.de/ubuntu precise Release                                                                                                                                      
Ign:17 http://mirror.kamp.de/ubuntu precise Release                                                                                                                                         
Ign:17 http://ftp.tu-chemnitz.de/pub/linux/ubuntu precise Release                                                                                                                           
Ign:17 https://ftp.uni-stuttgart.de/ubuntu precise Release                                                                                                                                  
Ign:17 http://ftp.tu-chemnitz.de/pub/linux/ubuntu-ports precise Release                                                                                                                     
Ign:17 http://ftp-stud.hs-esslingen.de/ubuntu precise Release                                                                                                                               
Ign:17 http://suse.uni-leipzig.de/pub/releases.ubuntu.com/ubuntu precise Release                                                                                                            
Ign:17 http://ftp.fau.de/ubuntu precise Release                                                                                                                                             
Ign:17 http://ftp.halifax.rwth-aachen.de/ubuntu precise Release                                                                                                                             
Ign:17 https://files.tux-users.net/ubuntu precise Release                                                                                                                                   
Get:17 http://mirror.funkfreundelandshut.de/ubuntu precise Release [49.6 kB]                                                                                                                
Get:18 http://mirror.funkfreundelandshut.de/ubuntu precise Release.gpg [198 B]                                                                                                              
Ign:18 http://mirror.funkfreundelandshut.de/ubuntu precise Release.gpg                                                                                                                      
Reading package lists... Done                                                                                                                                                               
W: GPG error: http://mirror.eu-fr.kamatera.com/ubuntu precise-security InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5
E: The repository 'mirror://mirrors.ubuntu.com/mirrors.txt precise-security InRelease' is not signed.                                                                                       
N: Updating from such a repository can't be done securely, and is therefore disabled by default.                                                                                            
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://mirror.eu-fr.kamatera.com/ubuntu precise-updates InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5
E: The repository 'mirror://mirrors.ubuntu.com/mirrors.txt precise-updates InRelease' is not signed.                                                                                        
N: Updating from such a repository can't be done securely, and is therefore disabled by default.                                                                                            
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://mirror.eu-fr.kamatera.com/ubuntu precise-backports InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5
E: The repository 'mirror://mirrors.ubuntu.com/mirrors.txt precise-backports InRelease' is not signed.                                                                                      
N: Updating from such a repository can't be done securely, and is therefore disabled by default.                                                                                            
N: See apt-secure(8) manpage for repository creation and user configuration details.
W: GPG error: http://mirror.funkfreundelandshut.de/ubuntu precise Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 40976EAF437D05B5
E: The repository 'mirror://mirrors.ubuntu.com/mirrors.txt precise Release' is not signed.
N: Updating from such a repository can't be done securely, and is therefore disabled by default.                                                                                            
N: See apt-secure(8) manpage for repository creation and user configuration details.
$ sudo yunohost --version
yunohost: 
  repo: stable
  version: 4.1.8
yunohost-admin: 
  repo: stable
  version: 4.1.4
moulinette: 
  repo: stable
  version: 4.1.4
ssowat: 
  repo: stable
  version: 4.1.3

Hi,

You should try yunohost tools update. Yunohost run with some old/outdated package version, and updating the common way (apt update && apt upgrade) could break it.

Anyway, it seems you are not on the last yunohost version (which is 4.2.8.3).

Try yunohost tools update and yunohost tools upgrade system.

Which app are you trying to install ?

Nota :

  • your system seems to be installed on Ubuntu instead of the classical Debian.
  • Some repo are broken, you should fix them (pubkey issue)

Yes I’m nut running the current yunohost version because as you can see I can’t update. Also some repos are broken which might be the issue why I can’t update. Which is why I made this post in the first place.

Well it looks like you have a shitload or repositories in your apt config … among which some ubuntu stuff which should have nothing to do with debian / yunohost …

Could it be that you manually edited some /etc/apt/sources.list* files …?

It looks like it’s running in a container? I guess on a Ubuntu machine?

What’s your OS:

lsb_release -a

Could you list all your apt repo:

cat /etc/apt/sources.list
grep deb /etc/apt/sources.list.d/*
$ lsb_release -a
No LSB modules are available.
Distributor ID: Debian
Description:    Debian GNU/Linux 10 (buster)
Release:        10
Codename:       buster
$ cat /etc/apt/sources.list && grep deb /etc/apt/sources.list.d/*
deb mirror://mirrors.ubuntu.com/mirrors.txt precise main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-updates main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-backports main restricted universe multiverse
deb mirror://mirrors.ubuntu.com/mirrors.txt precise-security main restricted universe multiverse 

# deb cdrom:[Debian GNU/Linux 10.6.0 _Buster_ - Official amd64 NETINST 20200926-10:16]/ buster main

#deb cdrom:[Debian GNU/Linux 10.6.0 _Buster_ - Official amd64 NETINST 20200926-10:16]/ buster main

deb http://debian.inf.tu-dresden.de/debian/ buster main
deb-src http://debian.inf.tu-dresden.de/debian/ buster main

deb http://security.debian.org/debian-security buster/updates main
deb-src http://security.debian.org/debian-security buster/updates main

# buster-updates, previously known as 'volatile'
deb http://debian.inf.tu-dresden.de/debian/ buster-updates main
deb-src http://debian.inf.tu-dresden.de/debian/ buster-updates main

# This system was installed using small removable media
# (e.g. netinst, live or single CD). The matching "deb cdrom"
# entries were disabled at the end of the installation process.
# For information about how to configure apt package sources,
# see the sources.list(5) manual.
/etc/apt/sources.list.d/buster-backports.list:deb http://deb.debian.org/debian buster-backports main contrib non-free
/etc/apt/sources.list.d/crystal.list:#deb https://dl.bintray.com/crystal/deb all stable
/etc/apt/sources.list.d/devel:languages:crystal.list:deb http://download.opensuse.org/repositories/devel:/languages:/crystal/Debian_9.0/ /
/etc/apt/sources.list.d/jellyfin.list:deb https://repo.jellyfin.org/debian buster main
/etc/apt/sources.list.d/mobilizon.list:deb http://packages.erlang-solutions.com/debian buster contrib
/etc/apt/sources.list.d/onlyoffice.list:deb http://download.onlyoffice.com/repo/debian squeeze main
/etc/apt/sources.list.d/yunohost.list:deb http://forge.yunohost.org/debian/ buster stable

Commenting the Ubuntu repos and then updating worked. I tried to find out why these were installed, but according to list all packages from a repository in ubuntu / debian - Server Fault there are no packages installed from those repos. So I’ll just wait and see if something breaks.