"pkg upgrade" issue encountered & resolved: "Repository ... has a wrong packagesite, need to re-create database"

[David Wolfskill]

For my "production" machines at home, I build FreeBSD (from sources) and
build packages (from ports) on a dedicated "build machine," then install
onto the production machines, as described in
<http://www.catwhisker.org/~david/FreeBSD/upgrade.html>.

In preparation for the stable/10 -> stable/11 migration, I had restored
backup images from one of the production machines ("albert") to a very
similar machine, then changed /etc/rc.conf to reflect a different IP
address and hostname ("pogo").  I had verified that it worked, then
tried performing a "normal" (stable/10 -> stablbe/10) update to it; when
that worked, I then updated its installed packages; that also worked.

Then I tried updating from stable/10 -> stable/11 -- which worked.  And
I then made a list of the installed packages, blew away all of them,
then installed the lot (from my local repository).  And that worked.

Well, that was about a month ago (05 Sep).  So this morning, I thought
it was time to refresh things a bit.

I first refreshed the stable/11  FreeBSD base, going from:

FreeBSD pogo.catwhisker.org 11.0-PRERELEASE FreeBSD 11.0-PRERELEASE #51  r305404M/305415:1100502: Mon Sep  5 04:22:27 PDT 2016     root at freebeast.catwhisker.org:/common/S3/obj/usr/src/sys/ALBERT  amd64

to

FreeBSD pogo.catwhisker.org 11.0-PRERELEASE FreeBSD 11.0-PRERELEASE #82  r306879M/306902:1100503: Sun Oct  9 06:34:36 PDT 2016     root at freebeast.catwhisker.org:/common/S3/obj/usr/src/sys/ALBERT  amd64

On reboot, things seemed OK, so I started the package update, only to
get a whine:

Repository custom has a wrong packagesite, need to re-create database

after which the machine rebooted.  No messages in /var/log; the
machine doesn't have a console, and I was running it headless.

I tried a couple more times, while running other things to try to
find out what was happening.  (One time, I ran top(1), and it
provided a hint that something was using a lot of CPU just before
the reboot.)

But other than that (CPU usage), I had no clue.

I poked around a bit on the Net, to no avail.

Finally, I checked which version of pkg I had on my more-recently-updated
systems (pkg-1.8.7_3) vs. what was install on pogo (pkg-1.8.7_1)
and figured I'd try updating pkg first.

My first attempt ("pkg upgrade ports-mgmt/pkg") failed the same as the
other "pkg upgrade" attempts did, so then I:

pkg delete -f ports-mgmt/pkg

which worked, then

pkg bootstrap

which also worked (and even picked it up from my local repository, as
desired).

I then verified that pkg claimed to be pkg-1.8.7_3, then tried "pkg
upgrade" again.

Success!  :-)


...
Checking integrity... done (0 conflicting)
The following 103 package(s) will be affected (of 0 checked):

Installed packages to be REMOVED:
        opencv-core-2.4.9_3

New packages to be INSTALLED:
        opencv2-core: 2.4.13.1_1

Installed packages to be UPGRADED:
        xterm: 325 -> 327
        x264: 0.144.2533_3 -> 0.148.2708
...
        bind99: 9.9.9P2_1 -> 9.9.9P3
        bash: 4.3.46_1 -> 4.4

Installed packages to be REINSTALLED:
        webp-0.5.0 (needed shared library changed)
        nspluginwrapper-1.4.4_5 (direct dependency changed: libX11)
        linux-c6-xorg-libs-7.4_5 (direct dependency changed: linux-c6-fontconfig)
...
        linux-c6-dri-11.0.7 (direct dependency changed: linux-c6-xorg-libs)
        linux-c6-cups-libs-1.4.2_5 (direct dependency changed: linux-c6-gnutls)
        linux-c6-alsa-plugins-oss-1.1.0 (direct dependency changed: linux-c6-alsa-lib)

Number of packages to be removed: 1
Number of packages to be installed: 1
Number of packages to be upgraded: 84
Number of packages to be reinstalled: 17

The operation will free 20 MiB.

Proceed with this action? [y/N]: y
....



Anyway, I thought I'd post about it in case anyone else needed hint.

Peace,
david
-- 
David H. Wolfskill				david at catwhisker.org
Those who would murder in the name of God or prophet are blasphemous cowards.

See http://www.catwhisker.org/~david/publickey.gpg for my public key.
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