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August 6, 2009 9:59 AM PDT

Permissions Problems with 10.5.8.

by CNET staff
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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.

  1. Do nothing.
    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.

  2. 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.

  3. 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.

  4. 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.

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Be sure to check us out on Twitter and the CNET Mac forums.


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/contact

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    by GBTrevor August 6, 2009 12:36 PM PDT
    Updated via Apple Software Update, downloaded and installed with no problems, restarted with no problems, Wireless Connected. Done a permissions check, few QT preference panel errors, which I repaired.
    Shut down and restarted.
    Wireless OK, Parallels OK, QuickTime OK, MS Office, Printing OK.
    I do not have any 3rd party utilities installed apart from DiskWarrior.

    New MacBook Pro 2.8GHz Intel Core 2 Duo. 4GB RAM
    (never had issues updating with my old G4 iBook!)
    Reply to this comment
    by tvillarreal August 6, 2009 12:51 PM PDT
    I can verify that by starting up in Safe Mode (shift key at startup), and applying the combo update fixes the permission problems.
    Reply to this comment
    by Ron L August 6, 2009 12:51 PM PDT
    >
    This is a reply to a previous comment by tvillarreal


    I took all precautions in updating (combo update ran during Safe Boot after DU verify and permissions repair) but it still resulted in irreparable permissions (i.e. DU continues to 'repair' the same 'incorrect' permissions over-and-over again).

    Suggest readers refer to the link provided by MU regarding this issue on the Apple forums. Lots of people are having the problem.
    Reply to this comment
    by John Sawyer August 6, 2009 12:51 PM PDT
    >>
    This is a reply to a previous comment by Ron L


    Are you getting the same permissions error described in this article? If not, you may be seeing the "normal" permissions errors that often occur with some files. Then again, you may be seeing some other type of permissions errors altogether. When citing permissions problems, it's best to list the filenames and the specific permissions messages you're getting.
    Reply to this comment
    by tvillarreal August 6, 2009 12:51 PM PDT
    >
    This is a reply to a previous comment by tvillarreal


    I ran the combo updater once and then checked permissions and had the above problems, I then ran it a second time to see if it would fix the problems to no avail, I then booted into safe mode and once again installed the combo updater and again ran permissions and it fixed the problem????
    Reply to this comment
    by kgb2 August 6, 2009 2:41 PM PDT
    Just to clarify the above comment. (because I had the same issue)

    Restarting in safe mode and applying a combo update does set the permissions back to normal, BUT it does not fix the underlying problem. I then did "verify permissions" and the same messages came up, but it didn't change my permissions to ----------

    So, once you do the fix, DO NOT REPAIR PERMISSIONS... unless you want to restart in safe and reinstall from combo (over and over and over...)
    Reply to this comment
    by Edwin-schemer August 6, 2009 3:09 PM PDT
    I booted from another disk and then reapplied the 10.5.8 combo stored on that disk.
    The crazy ?------- permissions problem disappeared.
    However the old, innocuous, problem with |rw-r-r permissions on some files persists.
    The nice thing about installing from an external disk is that the double or triple reboots, which seem long, even you you boot in verbose mode, do not happen.
    The system boots once and quickly.
    Reply to this comment
    by Ackerman August 6, 2009 8:36 PM PDT
    I had no problems with the 10.5.8 upgrade from 10.5.7. However, I did not do the suggested permissions fix before and after. After reading this, I'm glad that I didn't. I did do the other things MacFixIt recommends -- combo updater and Safe Boot.
    Reply to this comment
    by gctwnl2 August 6, 2009 11:05 PM PDT
    This is what happens. I found this out by investigating the system log.

    During the update process, the updater actually tries to take the existing permissions from certain files and makes sure the permissions database reflects the actual permissions of those files on disk. After having changed the permissions database this way, the files in the update are extracted and written.

    When the files do not exist yet (new files in the update), they are still added to the permissions database. But as they do not exist yet, they are added with permissions 0, user 0 and group 0. This happens with the _CodeDirectory/CodeResources etc files. The problem comes from faulty entries that pkgutil creates from (at that point) nonexisting files. I think this could be considered unwanted behaviour by pkgutil.

    If you run repair permissions immediately after installing the updater, the faulty permissions are then used.

    However, there is a simple fix. If you run the updater twice <i>without running repair permissions in between</i>, the repair permissions database is updated the second time from actual files (as they have been installed by the first run of the updater).

    The standard install instructions of Mac Fixit (repair, update, repair) trigger the bug. The safe install in this case is done with repair, update, update, repair.

    I have checked this on my OS X Server (10.5.7 to 10.5.8 with combo updater)
    Reply to this comment
    by tkessler August 6, 2009 11:05 PM PDT
    >
    This is a reply to a previous comment by gctwnl2


    The permissions fix steps are generally a good thing to do; however, in this situation the permissions error can cause problems so I updated the article with a warning to reflect this.
    Reply to this comment
    by outer August 6, 2009 11:05 PM PDT
    >
    This is a reply to a previous comment by gctwnl2


    While this is the emerging consensus (repair permissions; apply combo update; apply combo update again; repair permissions) on how to avoid the problem if it afflicts you, it doesn't explain why some systems aren't affected to begin with.
    Reply to this comment
    by mark4flies August 6, 2009 11:05 PM PDT
    >
    This is a reply to a previous comment by gctwnl2


    Why does this permissions problem occur with this update? Is the process described above new, different from the way it was done before?
    Reply to this comment
    by Born Yesterday August 7, 2009 10:18 AM PDT
    I didn't initially notice this problem on both my Mac's, but it was easy to fix.

    Running the combo update again on both Mac's fixed the strange ? permissions.

    I did try and repair permissions the first time I installed 10.5.8 but the second time I installed it the permissions were fine or fixed.

    For my own experience it didn't matter that the permissions were skewed and just running the update a second solved it unlike reports that your not supposed to fix them before running the update a second time.
    Reply to this comment
    by jamesn20012001 August 8, 2009 7:35 AM PDT
    I usually don't experience any of the problems that usually plague other users after updates.

    I have a Mac Pro 2.67MHZ original model


    I have 2 installations of the Mac OS on this machine.

    1. the main system with all the programs etc.
    2. a 48 GB partition on the 3rd hard drive with just the Mac OS 10.5.7 and installed Diskwarrior and DXO 5.3 photo software. Used only to occasionally run Diskwarrior and DXO .

    I upgraded both 10.5.7 systems to 10.5.8 using the combo updater.

    1. fixed permissions in each system before upgrading
    2. re-started in SAFE mode for each
    3. ran the updates and restarted
    4. ran "verify permissions"

    Results:

    1. On main system software everything OK no permission problems. Good deal

    2. On 48 GB second system I got the dreaded laundry list of permissions problems when verifying permissions. After re-booting into SAFE mode and rerunning 10.5.8 Combo updater verify permissions reported no errors.

    I had recently run Diskwarrior on the main system 10.5.7 a day before the upgrade.
    I have never run Diskwarrior on the 48 GB secondary system.

    I wonder if running Diskwarrior could have had any effect in preventing the Permissions problems that I experienced with the 48 GB secondary system?
    Reply to this comment
    by Steve Ross August 17, 2009 6:53 PM PDT
    After I updated to 10.5.8, I read this article , so I ran the combo updater again in Safe Mode. I then Verified the permissions-the "?" is gone, but the items are still listed, such as:
    Permissions differ on "System/Library/PrivateFrameworks/ScreenSharing.framework/Versions/A/_CodeSignature/CodeResources", should be ---------- , they are -rw-r--r-- .
    Do I now Repair, or Leave alone? I usually repair before cloning the drive, but I am now concerned that I will be back with the "?" again.
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