[SOLVED] Pacman broken by partial upgrade. How to fix and update?

Question

Pacman partially upgraded a system during pacman -Syu and, as a result, pacman itself is broken.
So I'm facing two issues, the one which caused the upgrade to fail and the fact that pacman no longer works.
I answered yes to all of the below:
:: Starting full system upgrade...
:: Replace kactivities with extra/kactivities4? [Y/n] y
:: Replace lzo2 with core/lzo? [Y/n] y
:: Replace phonon-gstreamer with extra/phonon-qt4-gstreamer? [Y/n] y
:: Replace phonon-gstreamer with extra/phonon-qt5-gstreamer? [Y/n] y
:: Replace polkit-qt with extra/polkit-qt4? [Y/n] y
:: Replace shared-color-profiles with extra/colord? [Y/n] y
:: Replace twisted with extra/python2-twisted? [Y/n] y
All seemed well until all the downloads and verifications were finished.
(646/646) checking for file conflicts [######################] 100%
(1/6) removing lzo2 [######################] 100%
(2/6) removing shared-color-profiles [######################] 100%
(3/6) removing polkit-qt [######################] 100%
(4/6) removing phonon-gstreamer [######################] 100%
(5/6) removing kactivities [######################] 100%
(6/6) removing twisted [######################] 100%
( 1/646) upgrading linux-api-headers [######################] 100%
( 2/646) upgrading tzdata [######################] 100%
( 3/646) upgrading filesystem [######################] 100%
warning: /etc/group installed as /etc/group.pacnew
warning: /etc/passwd installed as /etc/passwd.pacnew
warning: /etc/gshadow installed as /etc/gshadow.pacnew
warning: /etc/shadow installed as /etc/shadow.pacnew
error: extract: not overwriting dir with file /var/run
error: problem occurred while upgrading filesystem
error: could not commit transaction
error: failed to commit transaction (transaction aborted)
Errors occurred, no packages were upgraded.
The upgrade failed because of "extract: not overwriting dir with file /var/run".
The last line is not entirely true because I don't think the removals were rolled back.
Since pacman depends on lzo2 I now get the error below whenever I try to launch it.
pacman: error while loading shared libraries: liblzo2.so.2: cannot open shared object file: No such file or directory
So I need to figure out a way to fix pacman and correct the issue that is causing the update to fail without causing even bigger problems.
I'd appreciate any suggestions!
Thanks.
Last edited by authentec (2014-08-26 07:02:00)

Answer 1

headkase wrote:
Your filesystem package was upgraded, you had 646 packages to upgrade.  You haven't run "pacman -Syu" in years.  Your system will be near impossible to upgrade.  Reinstall, and update regularly.
Am I wrong?
According to pacman.log my last successful upgrade was in April May 2014 (hardly anything upgraded so I missed it in the logs at first).
Strangely enough, pacman -Qe reports the same filesystem version (filesystem 2014.07-1) both before and after the upgrade today.
Unless I'm mistaken that would mean it wasn't upgraded (or it was upgraded and not rolled back when the transaction failed which wouldn't be my first guess).
So it would appear you are wrong on both counts, headkase.
After I forced installation of the replacement lzo the upgrade went ahead without a hitch.
So no, the system wasn't impossible to upgrade either. Wrong there too.
I'm not sure exactly what went wrong though. It might have all been due to lzo2 not being automatically replaced successfully. Yet I'm not sure why it would have attempted to upgrade filesystem when it failed then report the same version after the full system upgrade completed successfully.
Last edited by authentec (2014-08-26 16:16:46)