error updating the packages

gistfile1.txt

[root@svijayakumar shiva]# pacman -Su
:: Starting full system upgrade...
:: Replace dbus-python with extra/python2-dbus? [Y/n] 
:: Replace libusb with core/libusbx? [Y/n] 
warning: linux: local (3.4-1) is newer than core (3.3.8-1)
warning: linux-headers: local (3.4-1) is newer than core (3.3.8-1)
resolving dependencies...
looking for inter-conflicts...

Targets (51): apache-2.2.22-4  awesome-3.4.12-1  bison-2.5.1-1  cairo-1.12.2-2
              chromium-19.0.1084.56-1  cifs-utils-5.5-1  colord-0.1.21-2
              dbus-python-1.0.0-1 [removal]  dconf-0.12.1-2  desktop-file-utils-0.20-1
              dnsutils-9.9.1.P1-1  elinks-0.13-10  emacs-24.1-2  fakeroot-1.18.4-1
              filesystem-2012.6-2  firefox-13.0-2  git-1.7.10.4-1  glibc-2.15-11  gnutls-3.0.20-1
              icu-49.1.2-1  initscripts-2012.06.1-1  krb5-1.10.2-1  lib32-glibc-2.15-11
              libcups-1.5.3-5  libmysqlclient-5.5.25-1  libusb-1.0.9-1 [removal]  libusbx-1.0.11-2
              libwbclient-3.6.5-3  linux-api-headers-3.3.8-1  mkinitcpio-0.9.2-1  mysql-5.5.25-1
              mysql-clients-5.5.25-1  nginx-1.2.1-2  nodejs-0.6.19-1  pam-1.1.5-4
              pambase-20120602-1  pango-1.30.1-1  psmisc-22.17-1  python-dbus-common-1.1.0-2
              python2-dbus-1.1.0-2  smbclient-3.6.5-3  sqlite-3.7.13-1  sqlite-doc-3.7.13-1
              sqlite-tcl-3.7.13-1  systemd-tools-185-1  unrar-4.2.4-1  vim-7.3.547-1
              vim-runtime-7.3.547-1  wine-1.5.6-1  xf86-input-synaptics-1.6.2-1  xorg-docs-1.7-1

Total Installed Size:   856.35 MiB
Net Upgrade Size:       9.05 MiB

Proceed with installation? [Y/n] 
(49/49) checking package integrity                           [################################] 100%
(49/49) loading package files                                [################################] 100%
(49/49) checking for file conflicts                          [################################] 100%
error: failed to commit transaction (conflicting files)
filesystem: /var/lock exists in filesystem
filesystem: /var/run exists in filesystem
Errors occurred, no packages were upgraded.
[root@svijayakumar shiva]#