pkg 2.7.4: pkg clean used with some of my repos enabled reports: "pkg: No package database installed. Nothing to do!"

[markmi]

It does not looks like DEBUG_LEVEL=4 has output that is directly about the package database status at all.

# pkg -v
2.7.4

# env DEBUG_LEVEL=4 pkg clean
DBG(1)[7398]> (config) loading repositories in /etc/pkg/
DBG(1)[7398]> (config) loading /etc/pkg//FreeBSD.conf
DBG(1)[7398]> (config) parsing key 'FreeBSD-ports'
DBG(1)[7398]> (config) parsing repository object FreeBSD-ports
DBG(1)[7398]> (config) parsing key 'FreeBSD-ports-kmods'
DBG(1)[7398]> (config) parsing repository object FreeBSD-ports-kmods
DBG(1)[7398]> (config) parsing key 'FreeBSD-base'
DBG(1)[7398]> (config) parsing repository object FreeBSD-base
DBG(1)[7398]> (config) loading repositories in /usr/local/etc/pkg/repos/
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//FreeBSD.conf
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//main-CA76-default.conf
DBG(1)[7398]> (config) parsing key 'main-CA76-default'
DBG(1)[7398]> (config) parsing repository object main-CA76-default
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//main-aarch64-alt.conf
DBG(1)[7398]> (config) parsing key 'main-aarch64-alt'
DBG(1)[7398]> (config) parsing repository object main-aarch64-alt
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//main-aarch64-default.conf
DBG(1)[7398]> (config) parsing key 'main-aarch64-default'
DBG(1)[7398]> (config) parsing repository object main-aarch64-default
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//main-armv7-alt.conf
DBG(1)[7398]> (config) parsing key 'main-armv7-alt'
DBG(1)[7398]> (config) parsing repository object main-armv7-alt
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//main-armv7-default.conf
DBG(1)[7398]> (config) parsing key 'main-armv7-default'
DBG(1)[7398]> (config) parsing repository object main-armv7-default
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//official14-armv7-default.conf
DBG(1)[7398]> (config) parsing key 'official14-armv7-default'
DBG(1)[7398]> (config) parsing repository object official14-armv7-default
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//rel-aarch64-alt.conf
DBG(1)[7398]> (config) parsing key 'rel-aarch64-alt'
DBG(1)[7398]> (config) parsing repository object rel-aarch64-alt
DBG(1)[7398]> (config) loading /usr/local/etc/pkg/repos//rel-armv7-alt.conf
DBG(1)[7398]> (config) parsing key 'rel-armv7-alt'
DBG(1)[7398]> (config) parsing repository object rel-armv7-alt
pkg: No package database installed.  Nothing to do!

# pkg repos
FreeBSD-ports: { 
    url             : "pkg+https://pkg.FreeBSD.org/FreeBSD:16:aarch64/latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }
FreeBSD-ports-kmods: { 
    url             : "pkg+https://pkg.FreeBSD.org/FreeBSD:16:aarch64/kmods_latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }
FreeBSD-base: { 
    url             : "pkg+https://pkg.FreeBSD.org/FreeBSD:16:aarch64/base_latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }
main-CA76-default: { 
    url             : "file:///usr/local/poudriere/data/packages/main-CA76-default",
    enabled         : no,
    priority        : 0
  }
main-aarch64-alt: { 
    url             : "file:///usr/local/poudriere/data/packages/main-aarch64-alt",
    enabled         : no,
    priority        : 0
  }
main-aarch64-default: { 
    url             : "file:///usr/local/poudriere/data/packages/main-aarch64-default",
    enabled         : yes,
    priority        : 0
  }
main-armv7-alt: { 
    url             : "file:///usr/local/poudriere/data/packages/main-armv7-alt",
    enabled         : no,
    priority        : 0
  }
main-armv7-default: { 
    url             : "file:///usr/local/poudriere/data/packages/main-armv7-default",
    enabled         : no,
    priority        : 0
  }
official14-armv7-default: { 
    url             : "file:///usr/local/poudriere/data/packages/official14-armv7-default",
    enabled         : no,
    priority        : 0
  }
rel-aarch64-alt: { 
    url             : "file:///usr/local/poudriere/data/packages/release-aarch64-alt",
    enabled         : no,
    priority        : 0
  }
rel-armv7-alt: { 
    url             : "file:///usr/local/poudriere/data/packages/release-armv7-alt",
    enabled         : no,
    priority        : 0
  }

[markmi]

In case it helps:

# ls -lodTt  /var/db/pkg/* /var/db/pkg/repos/*/*
-rw-r--r--   1 root wheel -        0 Apr 17 19:52:00 2026 /var/db/pkg/repos/FreeBSD-base/lock
-rw-r--r--   1 root wheel -        0 Apr 17 19:51:58 2026 /var/db/pkg/repos/FreeBSD-base/db-journal
-rw-r--r--   1 root wheel - 77934592 Apr 17 16:57:23 2026 /var/db/pkg/local.sqlite
-rw-r--r--   1 root wheel -  1118208 Apr 17 16:18:16 2026 /var/db/pkg/repos/FreeBSD-base/db
-rw-r--r--   1 root wheel -      173 Apr 17 16:18:16 2026 /var/db/pkg/repos/FreeBSD-base/meta
-r--r--r--   1 root wheel -  9196923 Apr 16 23:45:09 2026 /var/db/pkg/vuln.xml
-rw-r--r--   1 root wheel -        0 Apr 16 12:59:56 2026 /var/db/pkg/repos/main-aarch64-default/lock
-rw-r--r--   1 root wheel -        0 Apr 16 12:59:54 2026 /var/db/pkg/repos/main-aarch64-default/db-journal
-rw-r--r--   1 root wheel -   688128 Apr 16 12:59:06 2026 /var/db/pkg/repos/main-aarch64-default/db
-rw-r--r--   1 root wheel -      173 Apr 16 12:59:06 2026 /var/db/pkg/repos/main-aarch64-default/meta
-rw-r--r--   1 root wheel -        0 Oct 30 13:28:39 2025 /var/db/pkg/repos/FreeBSD-ports/lock
-rw-r--r--   1 root wheel -        0 Oct 30 13:24:42 2025 /var/db/pkg/repos/FreeBSD-ports/db-journal
-rw-r--r--   1 root wheel -      173 Oct 30 13:24:29 2025 /var/db/pkg/repos/FreeBSD-ports/meta
-rw-r--r--   1 root wheel - 67346432 Oct 29 03:47:25 2025 /var/db/pkg/repos/FreeBSD-ports/db
drwxr-xr-x  12 root wheel -      512 Oct  5 13:22:17 2025 /var/db/pkg/repos
-rw-r--r--   1 root wheel -        0 Jul  7 15:06:15 2025 /var/db/pkg/repos/FreeBSD/lock
-rw-r--r--   1 root wheel -        0 Jul  1 10:03:34 2025 /var/db/pkg/repos/FreeBSD/db-journal
-rw-r--r--   1 root wheel - 65814528 Jun 30 02:07:19 2025 /var/db/pkg/repos/FreeBSD/db
-rw-r--r--   1 root wheel -      173 Jun 30 02:07:19 2025 /var/db/pkg/repos/FreeBSD/meta
-rw-r--r--   1 root wheel -        0 Jun 15 13:05:02 2025 /var/db/pkg/repos/FreeBSD-base-release/lock
-rw-r--r--   1 root wheel -        0 Apr 27 10:22:14 2025 /var/db/pkg/repos/base/lock
-rw-r--r--   1 root wheel -        0 Apr 27 10:17:29 2025 /var/db/pkg/repos/rel-alt/db-journal
-rw-r--r--   1 root wheel -      173 Apr 27 10:17:29 2025 /var/db/pkg/repos/rel-alt/meta
-rw-r--r--   1 root wheel -        0 Apr 27 10:17:29 2025 /var/db/pkg/repos/rel-alt/lock
-rw-r--r--   1 root wheel -        0 Apr 27 10:17:29 2025 /var/db/pkg/repos/base/db-journal
-rw-r--r--   1 root wheel -   778240 Apr 27 02:45:28 2025 /var/db/pkg/repos/base/db
-rw-r--r--   1 root wheel -      173 Apr 27 02:45:28 2025 /var/db/pkg/repos/base/meta
-rw-r--r--   1 root wheel -        0 Apr 15 22:45:53 2025 /var/db/pkg/repos/custom-quarterly/lock
-rw-r--r--   1 root wheel -        2 Mar  5 15:34:16 2025 /var/db/pkg/repos/base/expired_packages.ucl
-rw-r--r--   1 root wheel -        2 Mar  5 15:34:16 2025 /var/db/pkg/repos/base/groups.ucl
-rw-r--r--   1 root wheel -        2 Mar  5 15:33:52 2025 /var/db/pkg/repos/FreeBSD/expired_packages.ucl
-rw-r--r--   1 root wheel -        2 Mar  5 15:33:52 2025 /var/db/pkg/repos/FreeBSD/groups.ucl
-rw-r--r--   1 root wheel -        0 Sep  2 20:43:33 2024 /var/db/pkg/repos/custom/db-journal
-rw-r--r--   1 root wheel -        2 Sep  2 20:43:33 2024 /var/db/pkg/repos/custom/groups.ucl
-rw-r--r--   1 root wheel -        0 Sep  2 20:43:33 2024 /var/db/pkg/repos/custom/lock
-rw-r--r--   1 root wheel -   671744 Jul  6 00:45:09 2024 /var/db/pkg/repos/custom/db
-rw-r--r--   1 root wheel -      172 Jul  6 00:45:09 2024 /var/db/pkg/repos/custom/meta
-rw-r--r--   1 root wheel -        0 Jul  6 00:00:08 2024 /var/db/pkg/repo-FreeBSD.sqlite-journal
-rw-r--r--   1 root wheel -      158 Jul  6 00:00:02 2024 /var/db/pkg/FreeBSD.meta
-rw-r--r--   1 root wheel -        0 Jul  5 22:57:03 2024 /var/db/pkg/repo-base.sqlite-journal
-rw-r--r--   1 root wheel -      158 Jul  5 22:56:57 2024 /var/db/pkg/base.meta
-rw-r--r--   1 root wheel -   765952 Jul  5 15:38:01 2024 /var/db/pkg/repo-base.sqlite
-rw-r--r--   1 root wheel - 63107072 Jul  3 06:42:23 2024 /var/db/pkg/repo-FreeBSD.sqlite

[markmi]

Turns out that having enabled:yes for the unused pair of repos shown below leads to the message and lack of any cleanout:

FreeBSD-ports: { 
    url             : "pkg+https://pkg.FreeBSD.org/FreeBSD:16:aarch64/latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }
FreeBSD-ports-kmods: { 
    url             : "pkg+https://pkg.FreeBSD.org/FreeBSD:16:aarch64/kmods_latest",
    enabled         : yes,
    priority        : 0,
    mirror_type     : "SRV",
    signature_type  : "FINGERPRINTS",
    fingerprints    : "/usr/share/keys/pkg"
  }

Replacing the 2 "yes" with "no" got things working.

[markmi]

In this context FreeBSD-base and main-aarch64-default had enable:yes and should have had pkg data base information about installed packages from them. But nothing was installed from FreeBSD-ports or FreeBSD-ports-kmods, despite the enabled:yes for each of them (before I changed them to no).

Treating such as a "-a" operation overall instead of reporting the information about which enable:yes repo(s) had no installs when others do have installs seems rather destructive for such a mix.

But, may be I misinterpreted the code of the fix for #2646 .

[bapt]

it is not dangerous, the way clean has always been work, is: clean -a should remove every thing anyway, clean should remove anything which does not exist in any enabled repo.

[markmi]

clean should remove anything which does not exist in any enabled repo.

Just to be clear: everything that existed was also from one of 2 enabled repos. It is just that there were also 2 enabled repos that did not have anything existing.