rpm -Va

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Good system:
[root@browser520 ~]# rpm -Va
.M....G..    /var/log/gdm
.M.......    /var/lib/nfs/rpc_pipefs
S.5....T.  c /etc/xdg/menus/applications.menu
.......T.  c /etc/kdump.conf
....L....  c /etc/pam.d/fingerprint-auth
....L....  c /etc/pam.d/password-auth
....L....  c /etc/pam.d/postlogin
....L....  c /etc/pam.d/smartcard-auth
....L....  c /etc/pam.d/system-auth
S.5....T.  c /etc/sysctl.conf
.M.......    /var/log/journal
S.5....T.    /usr/lib64/vlc/plugins/plugins.dat
.M.......    /usr/sbin/mount.cifs
S.5....T.  c /etc/cups/cups-browsed.conf
.M.......    /run/libgpod
S.5....T.  c /var/lib/unbound/root.key
.......T.  c /etc/selinux/targeted/contexts/files/file_contexts.local
..5....T.    /var/lib/selinux/targeted/active/commit_num
.......T.    /var/lib/selinux/targeted/active/homedir_template
.......T.    /var/lib/selinux/targeted/active/users_extra
....L....    /usr/lib/os-release
S.5....T.  c /etc/hba.conf
....L....  c /etc/pam.d/fingerprint-auth
....L....  c /etc/pam.d/password-auth
....L....  c /etc/pam.d/postlogin
....L....  c /etc/pam.d/smartcard-auth
....L....  c /etc/pam.d/system-auth
.M.......    /opt/ibm/notes/data/shared/help
.M.......    /opt/ibm/notes/data/shared/help/help9_client.nsf
.M.......    /opt/ibm/notes/data/shared/help/readme.html
missing     /opt/ibm/notes/framework/rcp/deploy/.keystore.JCEKS.IBM_J9_VM.install
S.5....T.    /opt/ibm/notes/framework/rcp/deploy/install.xml
.......T.    /opt/ibm/notes/framework/rcp/eclipse/links/rcp.link
.......T.    /opt/ibm/notes/framework/rcp/eclipse/links/shared.link
S.5....T.    /opt/ibm/notes/framework/rcp/eclipse/plugins/com.ibm.portal_9.0.1.20131002-1404/cai.schemas
SM5....T.    /opt/ibm/notes/framework/rcp/plugin_customization.ini
missing     /opt/ibm/notes/framework/rcp/plugin_customization.ini.orig
.......T.    /opt/ibm/notes/framework/rcp/rcplauncher
S.5....T.    /opt/ibm/notes/framework/rcp/rcplauncher.properties
....L....    /opt/ibm/notes/jvm/bin/ControlPanel
missing     /opt/ibm/notes/notes.schemas
.M.......    /opt/ibm/notes/smsu
missing     /var/run/wpa_supplicant
S.5....T.  c /etc/plymouth/plymouthd.conf
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Questionable system:
[root@alderaan ~]# rpm -Va
.M.......    /run/libgpod
..5....T.    /var/lib/selinux/targeted/active/commit_num
.......T.    /var/lib/selinux/targeted/active/file_contexts
.......T.    /var/lib/selinux/targeted/active/homedir_template
S.5....T.    /var/lib/selinux/targeted/active/policy.kern
.......T.    /var/lib/selinux/targeted/active/seusers
.......T.    /var/lib/selinux/targeted/active/users_extra
missing     /var/run/pulse
S.5....T.  c /etc/hba.conf
....L....  c /etc/pam.d/fingerprint-auth
....L....  c /etc/pam.d/password-auth
....L....  c /etc/pam.d/postlogin
....L....  c /etc/pam.d/smartcard-auth
....L....  c /etc/pam.d/system-auth
.......T.  c /etc/kdump.conf
.M.......    /usr/sbin/mount.cifs
.M.......    /var/log/audit
.M....G..    /var/log/gdm
S.5....T.  c /etc/cups/cups-browsed.conf
.M.......    /var/lib/nfs/rpc_pipefs
S.5....T.  c /etc/plymouth/plymouthd.conf