[solved] pfSense + 25.07.1 check_upgrade: "Updating repositories metadata" returned error code 1 @ 2025-12-10 07:23:47

[luckman212]

Well, in my case:

• I do use IPv6 (but via an HENET GIF tunnel, since my ISP does not provide native v6)
• I do have "Prefer to use IPv4 even if IPv6 is available" checked
• I do have System Patches installed, and all recommended patches applied
• I don't use Service Watchdog
• I do get this error message on every boot

edit: I've been poking around in /usr/local/libexec/pfSense-upgrade and I think I know what's going on now. Will post back shortly.

[luckman212]

Well,
After messing around a bit thinking this was an IPv6 problem (it wasn't) I'm still puzzled.

Still getting this on each boot:

This is on a fully patched 25.11 with System Patches 2.2.26 + all patches applied:

I note that after a reboot, the config.xml has this earlyshellcmd removed:

<earlyshellcmd>/usr/local/bin/php-cgi -f /usr/local/bin/apply_patches.php</earlyshellcmd>

Is that normal/expected?

[stephenw10]

Yes that's generated by the system patches package if you have any applied patches to auto-reapply any that are set to do so.

[luckman212]

@stephenw10 Ok, so it's normal for that shellcmd to be removed even though I have System Patches installed and in use?

[Gertjan]

@luckman212
You mean you haven't

right now ?
That's doesn't seem normal to me.
If the System patcher package is installed, in put this in (the GUI part of the config file shown above) place :

[stephenw10]

Hmm, yeah, I wouldn't expect it to be removed.

Are you seeing it added and removed repeatedly?

[luckman212]

@stephenw10 Yes, correct. If I go to Packages and click reinstall on System Patches, I can see that the apply_patches.php earlyshellcmd gets (re)added. BUT, on my next reboot, it gets removed again.

[Gertjan]

@luckman212

Euh .... you have a patch that does this ? ;)

The only place where the "earlyshellcmd" gets removed is ( see /usr/local/pkg/systempatches.xml )

I image, if for some reason the current "config.xml" gets discarded by pfSense because it found an issue with it, it takes the previous config.xml - the one where "Patches" packages wasn't installed (yet), so it uninstall's it ? (?!) ( I know, a wild shot).
pfSense uninstalling packages without user GUI interaction, that's wild.

[luckman212]

Looking at my config.xml backups, I noticed that around 2025-07-20 the following node "disappeared" and is no longer found in any subsequent backups:

<shellcmdsettings>
	<config>
		<cmd>/usr/local/bin/php-cgi -f /usr/local/bin/apply_patches.php</cmd>
		<cmdtype>earlyshellcmd</cmdtype>
		<description><![CDATA[System Patches default earlyshellcmd. DO NOT EDIT/DELETE!]]></description>
	</config>
</shellcmdsettings>

Comparing the XML, it seems to be when the base pfSense on this unit was upgraded from config ver 22.7 (pfSense 22.05.1) to 24.0 (25.07 probably beta/rc at that time). Not sure if that's a clue or not.

[luckman212]

This appears to be a rare bug. What I did to "fix" it:

1. hand edit config.xml to remove references to the apply_patches.php earlyshellcmd
2. rm /tmp/config.cache
3. manually added back the following shellcmd definition:

After that, everything seems to be kosher and is surviving reboots.

Now back to the original bug reported in this thread which is still occurring...