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Hi, I upgraded one of my systems and it failed at this point:
==> WARNING: Possibly missing firmware for module: smsmdtv
-> Running build hook: [filesystems]
-> Running build hook: [keyboard]
-> Running build hook: [btrfs]
==> Generating module dependencies
==> Creating gzip-compressed initcpio image: /boot/initramfs-linux-lts-fallback.img
==> Image generation successful
( 9/11) Warn about old perl modules
(10/11) Updating the info directory file...
error: command failed to execute correctly
(11/11) Rebuilding certificate stores...
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
/usr/bin/update-ca-trust: line 14: /usr/bin/trust: Input/output error
ln: failed to access '/etc/ssl/certs/*': Input/output error
find: ‘/etc/ssl/certs’: Input/output error
error: command failed to execute correctly
warning: could not remove lock file /var/lib/pacman/db.lck
:: Searching databases for updates...
:: Searching AUR for updates...
-> Flagged Out Of Date AUR Packages: libcurl-openssl-1.0
:: 1 Packages to upgrade.
1 aur/pi-hole-server 5.0-1 -> 5.0-2
==> Packages to exclude: (eg: "1 2 3", "1-3", "^4" or repo name)
==>
:: Checking for conflicts...
:: Checking for inner conflicts...
[Aur: 1] pi-hole-server-5.0-2
1 pi-hole-server (Installed) (Build Files Exist)
==> Packages to cleanBuild?
==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4)
==>
error reading /home/alvaro/.cache/yay/pi-hole-server/.git
[alvaro@wankel ~]$ Connection to 192.168.1.3 closed by remote host.
Connection to 192.168.1.3 closed.The machine failed to boot. I recovered by booting from usb, mounting the file system, installing linux - this system was on linux-lts.
Some packages are now broken. Here is a paccheck output (sudo is broken so I su to root):
[root@wankel alvaro]# paccheck --md5sum --quiet
brother-mfc-9325cw: '/opt/brother/Printers/mfc9325cw/inf/brmfc9325cwrc' md5sum mismatch (expected 6c50ce2c04bab12d4bc968bcffac7650)
linux: '/usr/lib/modules/5.6.14-arch1-1/modules.alias' md5sum mismatch (expected 40a0d3ab0b083595fd86342a115130a3)
linux: '/usr/lib/modules/5.6.14-arch1-1/modules.alias.bin' md5sum mismatch (expected 9da72b17666b43f184eaadb15f374a37)
warning: linux-lts-headers: mtree data not available (Success)
nfs-utils: '/var/lib/nfs/state' md5sum mismatch (expected d41d8cd98f00b204e9800998ecf8427e)
warning: perl-ipc-run3: mtree data not available (Success)
warning: perl-mailtools: mtree data not available (Success)
warning: perl-timedate: mtree data not available (Success)
warning: samba: mtree data not available (Success)
warning: smbclient: mtree data not available (Success)
warning: sudo: mtree data not available (Success)
[root@wankel alvaro]# At this point I am treading lightly, the system is back up and running but I am weary of doing any damage.
reading the pacman wiki I am unclear on how to force re-installation of just these packages without doing further damage.
Any help would be appreciated.
Last edited by avongil (2020-05-24 23:12:05)
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Just reinstall those packages. From all the input/output errors, my first suspicion would be the drive is going bad. Have you run a smart test? Could a connection / cable have been jostled loose?
"UNIX is simple and coherent" - Dennis Ritchie; "GNU's Not Unix" - Richard Stallman
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not able to. The wiki warns about using --force *, so I am a bit stalled at this point.
Example install of sudo package:
[root@wankel .snapshots]# pacman -S sudo
warning: sudo-1.9.0-1 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...
Packages (1) sudo-1.9.0-1
Total Installed Size: 4.06 MiB
:: Proceed with installation? [Y/n] Y
(1/1) checking keys in keyring [########################################] 100%
(1/1) checking package integrity [########################################] 100%
(1/1) loading package files [########################################] 100%
(1/1) checking for file conflicts [########################################] 100%
error: failed to commit transaction (conflicting files)
sudo: /usr/bin/cvtsudoers exists in filesystem
sudo: /usr/bin/sudo exists in filesystem
sudo: /usr/bin/sudo_logsrvd exists in filesystem
sudo: /usr/bin/sudo_sendlog exists in filesystem
sudo: /usr/bin/sudoedit exists in filesystem
sudo: /usr/bin/sudoreplay exists in filesystem
sudo: /usr/bin/visudo exists in filesystem
sudo: /usr/include/sudo_plugin.h exists in filesystem
sudo: /usr/lib/sudo/audit_json.so exists in filesystem
sudo: /usr/lib/sudo/group_file.so exists in filesystem
sudo: /usr/lib/sudo/libsudo_util.so exists in filesystem
sudo: /usr/lib/sudo/libsudo_util.so.0 exists in filesystem
sudo: /usr/lib/sudo/libsudo_util.so.0.0.0 exists in filesystem
sudo: /usr/lib/sudo/sample_approval.so exists in filesystem
sudo: /usr/lib/sudo/sudo_noexec.so exists in filesystem
sudo: /usr/lib/sudo/sudoers.so exists in filesystem
sudo: /usr/lib/sudo/system_group.so exists in filesystem
sudo: /usr/lib/systemd/system/sudo_logsrvd.service exists in filesystem
sudo: /usr/lib/tmpfiles.d/sudo.conf exists in filesystem
sudo: /usr/share/doc/sudo/CONTRIBUTORS exists in filesystem
sudo: /usr/share/doc/sudo/ChangeLog exists in filesystem
sudo: /usr/share/doc/sudo/HISTORY exists in filesystem
sudo: /usr/share/doc/sudo/LICENSE exists in filesystem
sudo: /usr/share/doc/sudo/NEWS exists in filesystem
sudo: /usr/share/doc/sudo/README exists in filesystem
sudo: /usr/share/doc/sudo/README.LDAP exists in filesystem
sudo: /usr/share/doc/sudo/TROUBLESHOOTING exists in filesystem
sudo: /usr/share/doc/sudo/UPGRADE exists in filesystem
sudo: /usr/share/doc/sudo/examples/pam.conf exists in filesystem
sudo: /usr/share/doc/sudo/examples/sudo.conf exists in filesystem
sudo: /usr/share/doc/sudo/examples/sudo_logsrvd.conf exists in filesystem
sudo: /usr/share/doc/sudo/examples/sudoers exists in filesystem
sudo: /usr/share/doc/sudo/examples/syslog.conf exists in filesystem
sudo: /usr/share/doc/sudo/schema.ActiveDirectory exists in filesystem
sudo: /usr/share/doc/sudo/schema.OpenLDAP exists in filesystem
sudo: /usr/share/doc/sudo/schema.iPlanet exists in filesystem
sudo: /usr/share/doc/sudo/schema.olcSudo exists in filesystem
sudo: /usr/share/licenses/sudo/LICENSE exists in filesystem
sudo: /usr/share/locale/ast/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/ast/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/ca/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/ca/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/cs/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/cs/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/da/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/da/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/de/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/de/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/el/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/eo/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/eo/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/es/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/eu/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/eu/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/fi/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/fi/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/fr/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/fr/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/fur/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/fur/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/gl/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/hr/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/hr/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/hu/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/hu/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/it/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/it/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/ja/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/ja/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/ko/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/ko/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/lt/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/nb/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/nb/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/nl/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/nl/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/nn/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/pl/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/pl/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/pt/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/pt/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/pt_BR/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/pt_BR/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/ru/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/ru/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/sk/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/sk/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/sl/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/sl/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/sr/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/sr/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/sv/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/sv/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/tr/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/tr/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/uk/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/uk/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/vi/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/vi/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/zh_CN/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/zh_CN/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/locale/zh_TW/LC_MESSAGES/sudo.mo exists in filesystem
sudo: /usr/share/locale/zh_TW/LC_MESSAGES/sudoers.mo exists in filesystem
sudo: /usr/share/man/man1/cvtsudoers.1.gz exists in filesystem
sudo: /usr/share/man/man5/sudo.conf.5.gz exists in filesystem
sudo: /usr/share/man/man5/sudo_logsrv.proto.5.gz exists in filesystem
sudo: /usr/share/man/man5/sudo_logsrvd.conf.5.gz exists in filesystem
sudo: /usr/share/man/man5/sudoers.5.gz exists in filesystem
sudo: /usr/share/man/man5/sudoers.ldap.5.gz exists in filesystem
sudo: /usr/share/man/man5/sudoers_timestamp.5.gz exists in filesystem
sudo: /usr/share/man/man8/sudo.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudo_logsrvd.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudo_plugin.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudo_plugin_python.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudo_sendlog.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudoedit.8.gz exists in filesystem
sudo: /usr/share/man/man8/sudoreplay.8.gz exists in filesystem
sudo: /usr/share/man/man8/visudo.8.gz exists in filesystem
Errors occurred, no packages were upgraded.Offline
The wiki no longer warns about using --force as that is not a valid pacman flag. In errors such as this, however, the guidance is specifically to use --overwrite:
https://wiki.archlinux.org/index.php/Pa … )%22_error
But again, if you are getting I/O errors on your drive, you should really get to the source of that problem.
Last edited by Trilby (2020-05-24 16:19:58)
"UNIX is simple and coherent" - Dennis Ritchie; "GNU's Not Unix" - Richard Stallman
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Running long test now. short SMART test passed.
The machine is bolted to the basement ceiling. I think my son was having a fit upstairs while it was updating. ![]()
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smart reports errors. btrfs scrub reports 28 uncorrectable errors on / subvolume.
seems like /usr is borked.
Any recourse or should I replace the drive and re-install? It's not a big deal, just hosts my unifi controller, pi-hole and some local unimportant shares.
AG
Last edited by avongil (2020-05-24 17:17:01)
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will replace that drive asap, but I did fix most errors by re-installing package with:
pacman -S sudo samba perl linux nfs-utils --overwrite usr/*I probably should have just fixed sudo only as to not use the drive, but it was a good exercise in package repair.
I am now showing these errors. This is better than not having sudo, so I am going to leave it here and wait for some drives.
[root@wankel alvaro]# paccheck --md5sum --quiet
linux: '/usr/lib/modules/5.6.14-arch1-1/modules.alias' md5sum mismatch (expected 40a0d3ab0b083595fd86342a115130a3)
linux: '/usr/lib/modules/5.6.14-arch1-1/modules.alias.bin' md5sum mismatch (expected 9da72b17666b43f184eaadb15f374a37)
warning: linux-lts-headers: mtree data not available (Success)
warning: perl-ipc-run3: mtree data not available (Success)
warning: perl-mailtools: mtree data not available (Success)
warning: perl-timedate: mtree data not available (Success)
warning: smbclient: mtree data not available (Success)AG
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one last question:
The last know anomaly on this is this string of error messages when running pacman:
[alvaro@wankel ~]$ sudo pacman -S vim
warning: vim-8.2.0814-2 is up to date -- reinstalling
resolving dependencies...
looking for conflicting packages...
Packages (1) vim-8.2.0814-2
Total Installed Size: 3.60 MiB
Net Upgrade Size: 0.00 MiB
:: Proceed with installation? [Y/n] Y
(1/1) checking keys in keyring [########################################] 100%
(1/1) checking package integrity [########################################] 100%
(1/1) loading package files [########################################] 100%
(1/1) checking for file conflicts [########################################] 100%
(1/1) checking available disk space [########################################] 100%
:: Running pre-transaction hooks...
(1/1) Performing snapper pre snapshots for the following configurations...
==> root: 20
:: Processing package changes...
(1/1) reinstalling vim [########################################] 100%
ldconfig: File /usr/lib/libdcerpc-binding.so is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-binding.so.0 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-binding.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-samr.so is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-samr.so.0 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-samr.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server-core.so is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server-core.so.0 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server-core.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server.so is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server.so.0 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc-server.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc.so is empty, not checked.
ldconfig: File /usr/lib/libdcerpc.so.0 is empty, not checked.
ldconfig: File /usr/lib/libdcerpc.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libndr-krb5pac.so is empty, not checked.
ldconfig: File /usr/lib/libndr-krb5pac.so.0 is empty, not checked.
ldconfig: File /usr/lib/libndr-krb5pac.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libndr-nbt.so is empty, not checked.
ldconfig: File /usr/lib/libndr-nbt.so.0 is empty, not checked.
ldconfig: File /usr/lib/libndr-nbt.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libndr-standard.so is empty, not checked.
ldconfig: File /usr/lib/libndr-standard.so.0 is empty, not checked.
ldconfig: File /usr/lib/libndr-standard.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libndr.so is empty, not checked.
ldconfig: File /usr/lib/libndr.so.1 is empty, not checked.
ldconfig: File /usr/lib/libndr.so.1.0.0 is empty, not checked.
ldconfig: File /usr/lib/libnetapi.so is empty, not checked.
ldconfig: File /usr/lib/libnetapi.so.0 is empty, not checked.
ldconfig: File /usr/lib/libnss_winbind.so is empty, not checked.
ldconfig: File /usr/lib/libnss_winbind.so.2 is empty, not checked.
ldconfig: File /usr/lib/libnss_wins.so is empty, not checked.
ldconfig: File /usr/lib/libnss_wins.so.2 is empty, not checked.
ldconfig: File /usr/lib/libsamba-credentials.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-credentials.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-credentials.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libsamba-errors.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-errors.so.1 is empty, not checked.
ldconfig: File /usr/lib/libsamba-hostconfig.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-hostconfig.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-hostconfig.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libsamba-passdb.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-passdb.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-passdb.so.0.28.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-policy.cpython-38-x86-64-linux-gnu.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-policy.cpython-38-x86-64-linux-gnu.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-policy.cpython-38-x86-64-linux-gnu.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libsamba-util.so is empty, not checked.
ldconfig: File /usr/lib/libsamba-util.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamba-util.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libsamdb.so is empty, not checked.
ldconfig: File /usr/lib/libsamdb.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsamdb.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libsmbclient.so is empty, not checked.
ldconfig: File /usr/lib/libsmbclient.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsmbclient.so.0.6.0 is empty, not checked.
ldconfig: File /usr/lib/libsmbconf.so is empty, not checked.
ldconfig: File /usr/lib/libsmbconf.so.0 is empty, not checked.
ldconfig: File /usr/lib/libsmbldap.so is empty, not checked.
ldconfig: File /usr/lib/libsmbldap.so.2 is empty, not checked.
ldconfig: File /usr/lib/libtevent-util.so is empty, not checked.
ldconfig: File /usr/lib/libtevent-util.so.0 is empty, not checked.
ldconfig: File /usr/lib/libtevent-util.so.0.0.1 is empty, not checked.
ldconfig: File /usr/lib/libwbclient.so is empty, not checked.
ldconfig: File /usr/lib/libwbclient.so.0 is empty, not checked.
ldconfig: File /usr/lib/libwbclient.so.0.15 is empty, not checked.
:: Running post-transaction hooks...
(1/3) Arming ConditionNeedsUpdate...
(2/3) Performing snapper post snapshots for the following configurations...
==> root: 21
(3/3) Generate GRUB config to let grub-btrfs detect new snapshotsOffline
It seems like they are all part of samba. What I did was put that list into a text file named toremove, cleaned it up and then used "sudo xargs rm <toremove"
reinstalled samba afterwards.
Looks like everything is working again, or at least mostly.
Thanks!
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