[Bug 225361] [pkg] pkg install xxx removes needed and unrelated packages from system

[bugzilla-noreply at freebsd.org]

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=225361

            Bug ID: 225361
           Summary: [pkg] pkg install xxx removes needed and unrelated
                    packages from system
           Product: Base System
           Version: CURRENT
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: bin
          Assignee: freebsd-bugs at FreeBSD.org
          Reporter: pru13allan at telia.com

When installing a Perl-script from package database several packages were
deleted that was not related to it.
One of them were fwknopd that was running at the time of the installation and
that I had to manually install again to not get locked out from the remote
machine.

The pkg job numbers [1/10], [2/10], ... is not logical (to me, anyway).


[root at fbsd4:~]# pkg install mysqltuner
Updating FreeBSD repository catalogue...
Fetching meta.txz: 100%    944 B   0.9kB/s    00:01    
Fetching packagesite.txz: 100%    5 MiB   2.5MB/s    00:02    
Processing entries: 100%
FreeBSD repository update completed. 24599 packages processed.
All repositories are up to date.
New version of pkg detected; it needs to be installed first.
The following 1 package(s) will be affected (of 0 checked):

Installed packages to be UPGRADED:
        pkg: 1.10.1 -> 1.10.3_1

Number of packages to be upgraded: 1

2 MiB to be downloaded.

Proceed with this action? [y/N]: y
[1/1] Fetching pkg-1.10.3_1.txz: 100%    2 MiB   2.3MB/s    00:01    
Checking integrity... done (0 conflicting)
[1/1] Upgrading pkg from 1.10.1 to 1.10.3_1...
Extracting pkg-1.10.3_1: 100%
Updating FreeBSD repository catalogue...
FreeBSD repository is up to date.
All repositories are up to date.
The following 10 package(s) will be affected (of 0 checked):

Installed packages to be REMOVED:
        mesa-libs-17.2.4
        libva-1.8.3
        ffmpeg-3.4,1
        gnupg-2.2.2
        gpgme-1.9.0_1
        fwknop-2.6.9_2
        motion-4.0.1_5

New packages to be INSTALLED:
        mysqltuner: 1.7.2

Installed packages to be REINSTALLED:
        apr-1.6.3.1.6.1
        libidn2-2.0.4

Number of packages to be removed: 7
Number of packages to be installed: 1
Number of packages to be reinstalled: 2

The operation will free 68 MiB.
547 KiB to be downloaded.

Proceed with this action? [y/N]: y
[1/10] Fetching mysqltuner-1.7.2.txz: 100%   54 KiB  55.1kB/s    00:01    
[2/10] Fetching apr-1.6.3.1.6.1.txz: 100%  399 KiB 408.2kB/s    00:01    
[3/10] Fetching libidn2-2.0.4.txz: 100%   95 KiB  96.9kB/s    00:01    
Checking integrity... done (0 conflicting)
[1/10] Deinstalling fwknop-2.6.9_2...
You may need to manually remove /usr/local/etc/fwknop/access.conf if it is no
longer needed.
You may need to manually remove /usr/local/etc/fwknop/fwknopd.conf if it is no
longer needed.
[1/10] Deleting files for fwknop-2.6.9_2: 100%
[2/10] Deinstalling gpgme-1.9.0_1...
[2/10] Deleting files for gpgme-1.9.0_1: 100%
[3/10] Deinstalling gnupg-2.2.2...
Deleting files for gnupg-2.2.2: 100%
[1/10] Deinstalling motion-4.0.1_5...
[1/10] Deleting files for motion-4.0.1_5: 100%
[2/10] Deinstalling ffmpeg-3.4,1...
[2/10] Deleting files for ffmpeg-3.4,1: 100%
[3/10] Deinstalling libva-1.8.3...
Deleting files for libva-1.8.3: 100%
[1/10] Deinstalling mesa-libs-17.2.4...
[1/10] Deleting files for mesa-libs-17.2.4: 100%
[2/10] Installing mysqltuner-1.7.2...
[2/10] Extracting mysqltuner-1.7.2: 100%
[3/10] Reinstalling apr-1.6.3.1.6.1...
Extracting apr-1.6.3.1.6.1: 100%
[1/10] Reinstalling libidn2-2.0.4...
[1/10] Extracting libidn2-2.0.4: 100%
Message from apr-1.6.3.1.6.1:
/!\ ================================================================== /!\

The Apache Portable Runtime project removed support for FreeTDS with
version 1.6. Users requiring MS-SQL connectivity must migrate
configurations to use the added ODBC driver and FreeTDS' ODBC features.

/!\ ================================================================== /!\

My system:
FreeBSD fbsd4 12.0-CURRENT FreeBSD 12.0-CURRENT #0 r320146M: Tue Jun 20
09:59:03
 MDT 2017  raspberry at hive.raspbsd.org:/usr/home/brd/rpi3/crochet/work/obj
 /arm64.aarch64/usr/src/sys/GENERIC  arm64

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