Yunohost Servers Failing on Update

Hardware: Dell R720
YunoHost version: Powered by YunoHost 4.2.6.1 (stable).
I have access to my server : SSH, direct access
Are you in a special context or did you perform some particular tweaking on your YunoHost instance ? : not really. I have a RAID server.

Description of my issue

Trying to update and I get these issues

Fetching available upgrades for system packages...
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://packages.sury.org/php buster InRelease: Splitting up /var/lib/apt/lists/packages.sury.org_php_dists_buster_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://forge.yunohost.org/debian buster InRelease: Splitting up /var/lib/apt/lists/forge.yunohost.org_debian_dists_buster_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://repo.mongodb.org/apt/debian buster/mongodb-org/4.4 Release: At least one invalid signature was encountered.
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://ftp.us.debian.org/debian buster InRelease: Splitting up /var/lib/apt/lists/ftp.us.debian.org_debian_dists_buster_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://security.debian.org/debian-security buster/updates InRelease: Splitting up /var/lib/apt/lists/security.debian.org_debian-security_dists_buster_updates_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://ftp.us.debian.org/debian buster-updates InRelease: Splitting up /var/lib/apt/lists/ftp.us.debian.org_debian_dists_buster-updates_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://deb.nodesource.com/node_14.x buster InRelease: Splitting up /var/lib/apt/lists/deb.nodesource.com_node%5f14.x_dists_buster_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://download.docker.com/linux/debian buster InRelease: Splitting up /var/lib/apt/lists/download.docker.com_linux_debian_dists_buster_InRelease into data and signature failed
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://repo.delellis.com.ar buster InRelease: Splitting up /var/lib/apt/lists/repo.delellis.com.ar_dists_buster_InRelease into data and signature failed
W: Failed to fetch http://ftp.us.debian.org/debian/dists/buster/InRelease Splitting up /var/lib/apt/lists/ftp.us.debian.org_debian_dists_buster_InRelease into data and signature failed
W: Failed to fetch http://security.debian.org/debian-security/dists/buster/updates/InRelease Splitting up /var/lib/apt/lists/security.debian.org_debian-security_dists_buster_updates_InRelease into data and signature failed
W: Failed to fetch http://ftp.us.debian.org/debian/dists/buster-updates/InRelease Splitting up /var/lib/apt/lists/ftp.us.debian.org_debian_dists_buster-updates_InRelease into data and signature failed
W: Failed to fetch https://repo.delellis.com.ar/dists/buster/InRelease Splitting up /var/lib/apt/lists/repo.delellis.com.ar_dists_buster_InRelease into data and signature failed
W: Failed to fetch https://download.docker.com/linux/debian/dists/buster/InRelease Splitting up /var/lib/apt/lists/download.docker.com_linux_debian_dists_buster_InRelease into data and signature failed
W: Failed to fetch https://packages.sury.org/php/dists/buster/InRelease Splitting up /var/lib/apt/lists/packages.sury.org_php_dists_buster_InRelease into data and signature failed
W: Failed to fetch https://deb.nodesource.com/node_14.x/dists/buster/InRelease Splitting up /var/lib/apt/lists/deb.nodesource.com_node%5f14.x_dists_buster_InRelease into data and signature failed
W: Failed to fetch http://forge.yunohost.org/debian/dists/buster/InRelease Splitting up /var/lib/apt/lists/forge.yunohost.org_debian_dists_buster_InRelease into data and signature failed
W: Failed to fetch http://repo.mongodb.org/apt/debian/dists/buster/mongodb-org/4.4/Release.gpg At least one invalid signature was encountered.
W: Some index files failed to download. They have been ignored, or old ones used instead.
Something went wrong while updating the cache of APT (Debian's package manager). Here is a dump of the sources.list lines, which might help identify problematic lines:
sources.list:deb http://ftp.us.debian.org/debian/ buster main non-free contrib sources.list:deb-src http://ftp.us.debian.org/debian/ buster main non-free contrib sources.list:deb http://security.debian.org/debian-security buster/updates main contrib non-free sources.list:deb-src http://security.debian.org/debian-security buster/updates main contrib non-free sources.list:deb http://ftp.us.debian.org/debian/ buster-updates main contrib non-free sources.list:deb-src http://ftp.us.debian.org/debian/ buster-updates main contrib non-free sources.list.d/nodesource.list:deb https://deb.nodesource.com/node_14.x buster main sources.list.d/nodesource.list:deb-src https://deb.nodesource.com/node_14.x buster main sources.list.d/docker.list:deb [arch=amd64] https://download.docker.com/linux/debian buster stable sources.list.d/yunohost.list.save:deb http://forge.yunohost.org/debian/ buster stable sources.list.d/mongodb-org-4.4.list:deb http://repo.mongodb.org/apt/debian buster/mongodb-org/4.4 main sources.list.d/extra_php_version.list.save:deb https://packages.sury.org/php/ buster main sources.list.d/20-pdlib.list.save:deb https://repo.delellis.com.ar buster buster sources.list.d/yunohost.list:deb http://forge.yunohost.org/debian/ buster stable sources.list.d/docker.list.save:deb [arch=amd64] https://download.docker.com/linux/debian buster stable sources.list.d/20-pdlib.list:deb https://repo.delellis.com.ar buster buster sources.list.d/extra_php_version.list:deb https://packages.sury.org/php/ buster main

I also tried to add language tool because it somehow deleted from my server when I last tried to update(??)

Error: "500"

Action: "POST" /yunohost/api/apps

Error message:
Unexpected server error

Traceback

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/moulinette/interfaces/api.py", line 484, in process
    ret = self.actionsmap.process(arguments, timeout=30, route=_route)
  File "/usr/lib/python3/dist-packages/moulinette/actionsmap.py", line 600, in process
    return func(**arguments)
  File "/usr/lib/moulinette/yunohost/log.py", line 380, in func_wrapper
    result = func(*args, **kwargs)
  File "/usr/lib/moulinette/yunohost/app.py", line 888, in app_install
    _assert_system_is_sane_for_app(manifest, "pre")
  File "/usr/lib/moulinette/yunohost/app.py", line 3436, in _assert_system_is_sane_for_app
    if not any(s for s in services if service_status(s)["status"] == "reloading"):
  File "/usr/lib/moulinette/yunohost/app.py", line 3436, in <genexpr>
    if not any(s for s in services if service_status(s)["status"] == "reloading"):
  File "/usr/lib/moulinette/yunohost/service.py", line 317, in service_status
    services = _get_services()
  File "/usr/lib/moulinette/yunohost/service.py", line 688, in _get_services
    services["ssh"]["needs_exposed_ports"] = [int(ssh_port_line[0])]
KeyError: 'ssh'

Running a diagnosis I get

Diagnosis failed for category 'ports':
Traceback (most recent call last): File "/usr/lib/moulinette/yunohost/diagnosis.py", line 198, in diagnosis_run code, report = hook_exec(path, args={"force": force}, env=None) File "/usr/lib/moulinette/yunohost/hook.py", line 372, in hook_exec returncode, returndata = _hook_exec_python(path, args, env, loggers) File "/usr/lib/moulinette/yunohost/hook.py", line 477, in _hook_exec_python ret = module.main(args, env, loggers) File "/usr/share/yunohost/hooks/diagnosis/14-ports.py", line 152, in main return PortsDiagnoser(args, env, loggers).diagnose() File "/usr/lib/moulinette/yunohost/diagnosis.py", line 459, in diagnose items = list(self.run()) File "/usr/share/yunohost/hooks/diagnosis/14-ports.py", line 25, in run services = _get_services() File "/usr/lib/moulinette/yunohost/service.py", line 688, in _get_services services["ssh"]["needs_exposed_ports"] = [int(ssh_port_line[0])] KeyError: 'ssh'

Can you elaborate what you mean by that ?

Does the command cat /etc/yunohost/services.yml displays anything ?

Can you elaborate what you mean by that ?

This problem started when I had a LT update. I clicked update application and then it failed. The LT instance itself, which was at lang.domain.tld stopped responding & the LT tile disappeared from my YNH instance. When I did sudo ncdu there were still all of the LT files on /home, which i deleted.

cat /etc/yunohost/services.yml

Nothing. I ran nano and looked at it too and it’s empty. here’s the directory

root@DOMAIN:/etc/yunohost# ls
apps              current_host   firewall.yml.old  letsencrypt_account.pem  regenconf.yml
apps_catalog.yml  diagnosis.yml  hooks.d           migrations.yaml          services.yml
certs             firewall.yml   installed         psql                     services.yml-old

services.yml-old looks normal-ish except it does include LT which is no longer on the YNH instance that I can tell

But what’s “LT” …?

LanguageTool

Hmokay

Well, it could be interesting to share and read the log of the failed upgrade of the app then …

But apart from this, the issue you describe in the original post seem to be symptomatic of stuff that randomly(?) disappeared, such as maybe signature keys for all the installed repos … And also /etc/yunohost/services.yml which is not supposed to be empty … I guess it could be due, maybe, to a temporary out-of-disk-space situation where the file was to be rewritten, idk

temporary out-of-disk-space situation

this was the case after further investigation. I made a mistake in inital server setup where I ended up giving swap way more space than it needed to be. I think I need to boot from live CD and shrink the swap space (if you had any good guides on that, it would be great).

For now, can I just change /etc/yunohost/services.yml-old to /etc/yunohost/services.yml?

I guess yes, but I wouldn’t be suprised that there may be other collateral damages around

So is there another solution?

I tried that and it seems to have fixed most things except the LT issue. Here are the logs from when I tried to reinstall it: https://paste.yunohost.org/raw/emibefapec

Apparently there’s already a folder named /opt/yunohost/languagetool, probably a residue from a previous install … If you’re confident about it, you can try to delete it with : rm -rf /opt/yunohost/languagetool

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