pkg upgrade removed pluma and pluma now requires samba to reinstall?

I went to upgrade my packages today and entered a loop where libsoup conflicts with libsoup-rest and both are apparently required by different packages. There were numerous other anomalies present all of which I finally resolved. However, one remaining artifact of this was introduced by removing samba412 also removed the pluma editor. Reinstalling pluma says that samba412 is a dependency.

Code:
]# pkg install pluma
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
The following 3 package(s) will be affected (of 0 checked):

New packages to be INSTALLED:
    gvfs: 1.46.1_2 [FreeBSD]
    pluma: 1.24.1 [FreeBSD]
    samba412: 4.12.9_1 [FreeBSD]

Number of packages to be installed: 3

The process will require 110 MiB more space.
2 MiB to be downloaded.

Proceed with this action? [y/N]: y
[1/1] Fetching pluma-1.24.1.txz: 100%    2 MiB   2.5MB/s    00:01   
Checking integrity... done (0 conflicting)
[1/3] Installing samba412-4.12.9_1...
[1/3] Extracting samba412-4.12.9_1: 100%
[2/3] Installing gvfs-1.46.1_2...
[2/3] Extracting gvfs-1.46.1_2: 100%
[3/3] Installing pluma-1.24.1...
[3/3] Extracting pluma-1.24.1: 100%
=====
Message from samba412-4.12.9_1:

--
How to start: http://wiki.samba.org/index.php/Samba4/HOWTO

* Your configuration is: /usr/local/etc/smb4.conf

* All the relevant databases are under: /var/db/samba4

* All the logs are under: /var/log/samba4

* Provisioning script is: /usr/local/bin/samba-tool

For additional documentation check: http://wiki.samba.org/index.php/Samba4

Bug reports should go to the: https://bugzilla.samba.org
.so.0"

Removing Samba also removes Pluma:

Code:
# pkg remove samba412
Checking integrity... done (0 conflicting)
Deinstallation has been requested for the following 3 packages (of 0 packages in the universe):

Installed packages to be REMOVED:
    gvfs: 1.46.1_2
    pluma: 1.24.1
    samba412: 4.12.9_1

Number of packages to be removed: 3

The operation will free 110 MiB.

Is there a sensible explanation for this behaviour?
 
Just from mind: did you at any time mix packages (' pkg install') with ports? So, the # make install clean method?

Also important: what FreeBSD version are you using?
 
FreeBSD-12.1p12

I built several versions of Samba on this system using Poudriere sometime last year. However, I cannot see any record of having installed anything directly from ports. The packages that I built were installed in jails using pkg. I cannot recall, and I cannot find in history, any indication that samba was installed at all, although clearly it was at some point. I just cannot find how.

In any case, let us assume that this is the problem. How is it fixed?
 
There was one occasion last year where I ran make install:

Code:
43618  2020-08-17 09:52:39: cd /root/Downloads/NVIDIA-FreeBSD-x86_64-450.57
43619  2020-08-17 09:53:07: pkg info -x nvidia
43620  2020-08-17 09:53:40: pkg remove nvidia-driver-304
43621  2020-08-17 09:53:54: pkg remove nvidia-settings
43622  2020-08-17 09:54:10: pkg info -x nvidia
43623  2020-08-17 09:54:23: pkg remove nvidia-xconfig

43624  2020-08-17 09:54:29: make install

43625  2020-08-17 09:55:11: ll /usr/share/mk
43626  2020-08-17 09:55:34: ll /usr/share/mk/bsd.kmod/mk
43627  2020-08-17 09:56:46: pkg info -x drm
43628  2020-08-17 09:57:05: pkg remove drm-legacy-kmod
43629  2020-08-17 09:57:20: pkg remove drm-info
43630  2020-08-17 09:57:30: pkg remove drm_info
43631  2020-08-17 09:57:40: pkh autoremove -n
43632  2020-08-17 09:57:44: pkg autoremove -n
43633  2020-08-17 09:57:52: pkg autoremove
43634  2020-08-17 09:58:18: pkg search nvidia
43635  2020-08-17 09:58:56: pkg install nvidia-driver-390
43636  2020-08-17 10:00:43: more /usr/local/share/doc/NVIDIA_GLX-1.0/README

But that had nothing to do with Samba.
 
Samba is a dependency of gvfs, which in turn is a dependency of pluma. If you remove Samba it will remove gvfs, which in turn removes pluma.
 
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