Conflicts during pacman -Syu

[Hypnosis4U2NV]

Well I resorted to copying over the system files with a backup I had and I was able to boot up again.. I could use a little help getting past this when trying to update:

$this->bbcode_second_pass_code('', '
[root@Pogoplug ~]# pacman -Syu --ignore glibc
:: Synchronizing package databases...
core 38.1 KiB 1302K/s 00:00 [######################] 100%
extra 430.7 KiB 2.22M/s 00:00 [######################] 100%
community 420.6 KiB 2.60M/s 00:00 [######################] 100%
alarm 5.0 KiB 6.32M/s 00:00 [######################] 100%
aur 11.0 KiB 11.5M/s 00:00 [######################] 100%
error: duplicated database entry 'ppp'
error: duplicated database entry 'pacman'
error: duplicated database entry 'kmod'
error: duplicated database entry 'avahi'
error: duplicated database entry 'glibc'
error: duplicated database entry 'syslog-ng'
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (30): binutils-2.22-10 coreutils-8.19-1 dhcpcd-5.6.2-1
ffmpeg-1:1.0-1 filesystem-2012.8-1 gnutls-3.1.2-1
hwids-20120922-1 initscripts-2012.08.3-2 kmod-10-1
libarchive-3.0.4-2 libpipeline-1.2.2-1 libtasn1-2.14-1
libwbclient-3.6.8-1 man-db-2.6.3-1 minidlna-1.0.25-2
mkinitcpio-busybox-1.20.2-1 nfsidmap-0.25-1
pacman-mirrorlist-20120916-1 pinentry-0.8.2-1 procps-ng-3.3.3-6
samba-3.6.8-1 sdl-1.2.15-3 smbclient-3.6.8-1 systemd-193-1
sysvinit-2.88-8 sysvinit-tools-2.88-8 tzdata-2012f-1
uboot-env-2009.11-4 util-linux-2.22-6 webmin-1.600-1

Total Download Size: 11.12 MiB
Total Installed Size: 299.45 MiB
Net Upgrade Size: 10.06 MiB

Proceed with installation? [Y/n] y
:: Retrieving packages from core...
kmod-10-1-arm 85.8 KiB 1818K/s 00:00 [######################] 100%
systemd-193-1-arm 1109.8 KiB 2.33M/s 00:00 [######################] 100%
:: Retrieving packages from extra...
webmin-1.600-1-arm 9.9 MiB 2.52M/s 00:04 [######################] 100%
(30/30) checking package integrity [######################] 100%
(30/30) loading package files [######################] 100%
(30/30) checking for file conflicts [######################] 100%
error: failed to commit transaction (conflicting files)
kmod: /usr/lib/libkmod.so.2.2.0 exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/api-index-full.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/ch01.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/home.png exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/index.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/index.sgml exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/left.png exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-3.devhelp2 exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-libkmod-config.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-libkmod-list.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-libkmod-loaded.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-libkmod-module.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/libkmod-libkmod.html exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/right.png exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/style.css exists in filesystem
kmod: /usr/share/gtk-doc/html/libkmod-3/up.png exists in filesystem
Errors occurred, no packages were upgraded.
[root@Pogoplug ~]#
')

[Hypnosis4U2NV]

Is there anyway to clear this from running updates?

error: duplicated database entry 'ppp'
error: duplicated database entry 'pacman'
error: duplicated database entry 'kmod'
error: duplicated database entry 'avahi'
error: duplicated database entry 'glibc'
error: duplicated database entry 'syslog-ng'

[moonman]

$this->bbcode_second_pass_code('', 'pacman -Scc') and answer Y to both questions.

[pepedog]

$this->bbcode_second_pass_quote('moonman', '[')code]pacman -Scc[/code] and answer Y to both questions.

[Hypnosis4U2NV]

Tried the pacman -Scc and -Syy, also reinstalling the duplicate packages with negative results..

$this->bbcode_second_pass_code('', '
[root@Pogoplug ~]# pacman -Scc
Cache directory: /var/cache/pacman/pkg/
Do you want to remove ALL files from cache? [y/N] y
removing all files from cache...

Database directory: /var/lib/pacman/
Do you want to remove unused repositories? [Y/n] y
removing unused sync repositories...
[root@Pogoplug ~]# pacman -Syy
:: Synchronizing package databases...
core 38.1 KiB 141K/s 00:00 [######################] 100%
extra 430.7 KiB 861K/s 00:01 [######################] 100%
community 420.6 KiB 2.06M/s 00:00 [######################] 100%
alarm 5.0 KiB 6.10M/s 00:00 [######################] 100%
aur 11.0 KiB 4.60M/s 00:00 [######################] 100%
warning: pacman-4.0.3-3 is up to date -- reinstalling
resolving dependencies...
looking for inter-conflicts...

Targets (1): pacman-4.0.3-3

Total Download Size: 1.00 MiB
Total Installed Size: 3.39 MiB
Net Upgrade Size: 0.00 MiB

Proceed with installation? [Y/n] y
:: Retrieving packages from core...
pacman-4.0.3-3-arm 1020.8 KiB 608K/s 00:02 [######################] 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%
(1/1) upgrading pacman [######################] 100%
[root@Pogoplug ~]# reboot

Broadcast message from root@Pogoplug (pts/0) (Tue Oct 2 05:46:51 2012):

The system is going down for reboot NOW!
[root@Pogoplug ~]#
login as: root
root@192.168.0.180's password:
Last login: Tue Oct 2 05:44:53 2012 from 192.168.0.199
[root@Pogoplug ~]# pacman -Syu
:: Synchronizing package databases...
core is up to date
extra is up to date
community is up to date
alarm is up to date
aur is up to date
error: duplicated database entry 'pacman'
error: duplicated database entry 'avahi'
error: duplicated database entry 'glibc'
error: duplicated database entry 'syslog-ng'
:: Starting full system upgrade...
resolving dependencies...
looking for inter-conflicts...

Targets (29): binutils-2.22-10 coreutils-8.19-1 dhcpcd-5.6.2-1
ffmpeg-1:1.0-1 filesystem-2012.8-1 gnutls-3.1.2-1
hwids-20120922-1 initscripts-2012.08.3-2 libarchive-3.0.4-2
libpipeline-1.2.2-1 libtasn1-2.14-1 libwbclient-3.6.8-1
man-db-2.6.3-1 minidlna-1.0.25-2 mkinitcpio-busybox-1.20.2-1
nfsidmap-0.25-1 pacman-mirrorlist-20120916-1 pinentry-0.8.2-1
procps-ng-3.3.3-6 samba-3.6.8-1 sdl-1.2.15-3 smbclient-3.6.8-1
systemd-193-1 sysvinit-2.88-8 sysvinit-tools-2.88-8
tzdata-2012f-1 uboot-env-2009.11-4 util-linux-2.22-6
webmin-1.600-1

Total Download Size: 42.84 MiB
Total Installed Size: 298.95 MiB
Net Upgrade Size: 9.83 MiB

Proceed with installation? [Y/n] y

warning: directory permissions differ on sys/
filesystem: 755 package: 555
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.

')

Notice the error at the end after I try a pacman -Syu

[pepedog]

How long since your last upgrade?
http://www.archlinux.org/news/filesystem-upgrade-manual-intervention-required/
I think you might review this after
http://www.archlinux.org/news/

[Hypnosis4U2NV]

Unfortunately, still getting these duplicate package errors:

error: duplicated database entry 'pacman'
error: duplicated database entry 'avahi'
error: duplicated database entry 'glibc'
error: duplicated database entry 'syslog-ng'