Written by Topher Kessler
As described in this Apple Discussion thread, in some instances the 10.5.8 update seems to not be properly linked to the permissions database, which is resulting in permissions output warnings such as the following:
Permissions differ on "System/Library/CoreServices/KerberosAgent.app/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
This output (should be ?---------) is claiming there should be no permissions for the given file, and if you repair permissions at this point Disk Utility will remove all permissions for the files, which may effectively prevent all but root access to the file.
There are a few ways to address this problem.
As long as the computer is working, a permissions fix is not needed. Granted it would be nice to know that everything is functioning and not run into a problem in the future, but since for the most part these permissions problems are showing otherwise healthy permissions it is more than likely safe to let things be. Still, run a permissions verification and check the files to ensure the current permissions at least give some user/group read access. For the most part you can safely disregard default group changes.
Reapply the update (delta/combo)
Try reapplying the update, which seems to have at least helped the problem for some people, if not fixed it completely. To do this, download and reapply the updater, optionally rolling back to a previous installation from a backup (Time Machine or boot drive clone) beforehand. We recommend if you do this to get the combo updater and then apply it when booted into Safe Mode.
Change permissions manually
If the problem is with only a few files, you can use the Terminal to change the permissions manually, or at least ensure the files are accessible and reporting the proper permissions. We will not go into details on how to change the permissions for files using the Terminal, since each file type may have different permissions and we would need to address each specifically; however, if you are familiar with the terminal you can manually ensure the files are properly accessible.
Teach the database new file permissions.
After you have checked permissions manually, and ensured the files are properly accessible (for the most part, allowing the owner to read and write, and having the group and other users be read only), you can teach teach the updater receipt file the new permissions by running the following command in the Terminal:
sudo pkgutil --edit-pkg com.apple.pkg.update.os.10.5.8 --volume / --learn FILEPATH
In this command, the FILEPATH is the full path to either the parent folder of files that share these permissions problems, or to the individual files themselves. This should only be done if you are certain the current permissions are correct for the files in the "FILEPATH".
After this command is run, the permissions check should not observe permissions changes the files targeted by FILEPATH anymore.
Topher has been an avid Mac user for the past 10-15 years, and has been a contributing author to MacFixIt for just over a year now. One of his diehard passions has been troubleshooting Mac problems and making the best use of Macs and Apple hardware both for family and friends, as well as in the workplace. He and the newly formed MacFixIt team are hoping to bring enhanced and more personable content to our readers, and keep the MacFixIt community going here at CNET. If you have questions or comments for Topher or the other MacFixIt editors, feel free to contact us at http://www.macfixit.com/contactResources