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Frequent problems with pkgin upgrade or pkgin full-upgrade and a few packages, especially sqlite3 #363
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Here's a longer log extract for a machine that's currently exhibiting the sqlite3 issue.
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on Sep 25, 2023 I have several machines today that are having trouble upgrading openssl. It's an easy workaround -- pkg_delete -f, pkg_add. Log from one:
---Oct 18 14:33:05: [3/4] upgrading openssl-1.1.1w... pkg_add: Conflicting PLIST with openssl-1.1.1pnb1: bin/c_rehash pkg_add: 1 package addition failedThere's further weirdness - some packages claim to install, but another full-upgrade will do it over and over. And I've seen e.g. mozilla-rootcerts listed twice in the upgrade list.
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on Feb 23, 2024 Seeing this today on routine
pkgin full-upgrade:---Mar 05 14:52:07: [1/1] upgrading pkg_install-20240126... pkg_add: Conflicting PLIST with pkg_install-20210410: man/man1/pkg_add.1.gz pkg_add: 1 package addition failedUgh, yeh, lemme see if I can carve out time tomorrow to try and nail this down once and for all.
If it'd help to have ssh access to an affected machine, I can arrange.
The corrupted database warning you mentioned in IRC the other day has appeared on several of our systems:
beautiful 5 $ pkg_admin rebuild pkg_admin: corrupt pkgdb, duplicate PKGBASE entries: pkgsrc-gnupg-keys-20190423 pkgsrc-gnupg-keys-20201014So what's the proper cleanup process here? I'm pretty sure I've removed specific package version in the past, possibly using pkg_add to get key packages back.
Digging deeper, I'll add that the most recent gz where I've had
pkgin full-upgradeproblems does not exhibit thecorrupt pkgdberrors, but does still have conflicting file problems this morning:---Apr 04 12:13:29: [1/19] refreshing ncurses-6.4... ---Apr 04 12:13:29: [2/19] refreshing readline-8.2nb2... ---Apr 04 12:13:29: [3/19] refreshing sqlite3-3.45.2... ---Apr 04 12:13:29: [4/19] refreshing xz-5.4.6... ---Apr 04 12:13:30: [5/19] refreshing ncursesw-6.4... ---Apr 04 12:13:30: [6/19] upgrading pkg_install-20240307... pkg_add: Conflicting PLIST with pkg_install-20211115: man/man1/pkg_add.1.gz pkg_add: 1 package addition failed ---Apr 04 12:13:30: [7/19] refreshing python311-3.11.8... ---Apr 04 12:13:32: [8/19] refreshing python312-3.12.2... ---Apr 04 12:13:35: [9/19] upgrading pkg_install-20240307... pkg_add: Conflicting PLIST with pkg_install-20211115: man/man1/pkg_add.1.gz pkg_add: 1 package addition failed ---Apr 04 12:13:35: [10/19] refreshing libarchive-3.7.2... ---Apr 04 12:13:35: [11/19] refreshing pkgsrc-gnupg-keys-20231210... pkg_add: Conflicting PLIST with pkgsrc-gnupg-keys-20201014: share/gnupg/pkgsrc-security.gpg pkg_add: 1 package addition failed ---Apr 04 12:13:35: [12/19] upgrading pkgin-23.8.1nb3... ---Apr 04 12:13:35: [13/19] refreshing pkgin-23.8.1nb3... ---Apr 04 12:13:36: [14/19] refreshing py312-pip-24.0... ---Apr 04 12:13:36: [15/19] upgrading bsdinstall-20160108nb1... ---Apr 04 12:13:36: [16/19] refreshing py312-wheel-0.43.0... ---Apr 04 12:13:36: [17/19] refreshing py312-setuptools-69.2.0... ---Apr 04 12:13:36: [18/19] refreshing py311-pip-24.0... ---Apr 04 12:13:37: [19/19] refreshing py311-wheel-0.43.0...This is a machine I'm quite convinced has never had an improper tools or bootstrap kit applied -- it got the tools during the new-machine install, and hasn't been messed with.
Another round of this, still with no errors from
pkg_admin rebuild:---May 13 12:14:09: [1/5] upgrading pkg_install-20240307... pkg_add: Conflicting PLIST with pkg_install-20211115: man/man1/pkg_add.1.gz pkg_add: 1 package addition failed ---May 13 12:14:10: [2/5] upgrading pkg_install-20240307... pkg_add: Conflicting PLIST with pkg_install-20211115: man/man1/pkg_add.1.gz pkg_add: 1 package addition failed ---May 13 12:14:10: [3/5] refreshing pkgsrc-gnupg-keys-20231210... pkg_add: Conflicting PLIST with pkgsrc-gnupg-keys-20201014: share/gnupg/pkgsrc-security.gpg pkg_add: 1 package addition failed ---May 13 12:14:10: [4/5] upgrading pkgin-23.8.1nb3... ---May 13 12:14:10: [5/5] upgrading bsdinstall-20160108nb1... avenueq 6 $ pkg_admin rebuild Stored 27252 files and 1 explicit directory from 45 packages in /opt/tools/var/db/pkg/pkgdb.byfile.db. Done.22 remaining items
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on Sep 24, 2026
Per brief IRC discussion:
raising this issue about conflicts of a package with itself in the hope that I have data that might help track down the problem.
Extracts related to sqlite3 from pkg_install-err.log:
pkgdb.byfile.db is attached, gzipped because %^&*( github.
pkgdb.byfile.db.gz