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Stat
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Q: Repairing permissions after 10.5.8 update extreme oops maybe???

Ok I understand that there is still the issue of Repairing permissions regarding hard code links no big deal. Apple still has not fixed this in this update.

The problem that I have at the moment is understanding why the dbase is not updated properly it appears.

After applying the update to two separate machines both intel based and running Repair permissions through Disk Utility which is what I always do after any os update, there were some very strange oddities that pertains to core files and even after reboots and rechecking seferal times there is no change.

Someone at Apple messed up I think and did not update the permissions dbase during or after the update. I also used the Combo updater versus the smaller regular update as I always do to to avoid some intermittent occasional install problems some tend to see when using the smaller updaters.

Anyone else seeing this and how big of an issue is it to have it show for core files permissiona "should be ?--------- ," ??

Below is an example and is on both an iMac 24" and a MacBook Pro:

Reading permissions database.
Reading the permissions database can take several minutes.
...... I cut out the standard stuff we are used to seeing with the links "l" permisions

Permissions differ on "System/Library/Frameworks/AppKit.framework/Versions/C/_CodeSignature/CodeResou rces", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonC ore.framework/Versions/A/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ CoreGraphics.framework/Versions/A/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/_CodeS ignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/Resour ces/DotMacSyncHelper.app/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/Resour ces/dotmacsyncui.app/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/DotMacLegacy.framework/Versions/A/_CodeSignat ure/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeDirecto ry", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeResourc es", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeSignatu re", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/ Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/ Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/ Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/C ontents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/C ontents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/C ontents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.k ext/Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.k ext/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.k ext/Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/ Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/ Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/ Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMou se.kext/Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMou se.kext/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMou se.kext/Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/ Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/ Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/ Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDriv er.kext/Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDriv er.kext/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDriv er.kext/Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kex t/Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kex t/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kex t/Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBLib.bundle/Co ntents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.ke xt/Contents/_CodeSignature/CodeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.ke xt/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.ke xt/Contents/_CodeSignature/CodeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/C odeDirectory", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/C odeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/C odeSignature", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/CoreServices/CCacheServer.app/Contents/_CodeSignature/CodeResou rces", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/CoreServices/Kerberos.app/Contents/_CodeSignature/CodeResources ", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/CoreServices/KerberosAgent.app/Contents/_CodeSignature/CodeReso urces", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/Frameworks/Kerberos.framework/Versions/A/_CodeSignature/CodeRes ources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/KerberosPlugins/KerberosDatabasePlugins/db2.bundle/Contents/_Co deSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/KerberosPlugins/KerberosDatabasePlugins/kldap.bundle/Contents/_ CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/SystemProfiler/SPDisplaysReporter.spreporter/Contents/_CodeSign ature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/CoreServices/Screen Sharing.app/Contents/_CodeSignature/CodeResources", should be ?--------- , they are -rw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/ScreenSharing.framework/Versions/A/_CodeSigna ture/CodeResources", should be ?--------- , they are -rw-r--r-- .

Permissions repair complete

G5, MBP. MB, and iMac 24", Mac OS X (10.4.11), Also 10.5.8 in some intel machines

Posted on Aug 5, 2009 7:22 PM

by Gerben Wierda,Solvedanswer
Gerben Wierda Gerben Wierda
Level 2 (186 points)
Mac OS X
A:
I think this is what happens:
- For files not installed yet, their permissions (and owner) are taken from nonexisting files during the update process and stored in the package Receipts (Base system). Obviously, the combo drive may affect more files.
- Installing the update twice +without repairing permissions between+ re-reads permissions from the files which at that point are available and the receipts are fixed.

I have tested this and it works. If you install the update twice without repairing permissions in between, the permissions database does not have the permission-000 settings for the files.

Posted on Aug 6, 2009 10:53 PM

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Stat

Q: Repairing permissions after 10.5.8 update extreme oops maybe???

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  • by Sean Coon,

    Sean Coon Sean Coon Aug 6, 2009 9:39 AM in response to Stat
    Level 1 (0 points)
    Aug 6, 2009 9:39 AM in response to Stat
    I don't know if this fixes the problem, but it did for me. I used the combo update and got the same permission issues. I tried using the delta and had the same thing.

    I restarted the computer with the shift key down (safe boot), reinstalled the Combo update. After that was finished, I ran disk utility again to repair disk permissions. It listed the permissions issues. I ran Repair disk permissions again I got this:

    *Repairing permissions for “Macintosh HD”*
    * Reading permissions database.*
    * Reading the permissions database can take several minutes.*


    *Permissions repair complete*


    So far it good for me.

  • by V.K.,

    V.K. V.K. Aug 6, 2009 9:40 AM in response to mert
    Level 9 (56,110 points)
    Aug 6, 2009 9:40 AM in response to mert
    mert wrote:
    mert wrote:
    Idea: has anyone tried doing the 10.5.8 Combo update again (after getting this issue). Does it fix these files up? If yes, then I just won't run Repair Perms after repeating the Combo update.


    I tried re-applying 10.5.8 Combo and it does fix the files.
    If I run "find -x / -perm 000" on the Terminal, nothing comes up.
    Now I just have to remember not to run Repair Permissions until this gets resolved... in 10.5.9??

    you might have to have a long wait for that one. In all likelihood 10.5.8 is the last leopard point update. Snow leopard comes out in September and AFAIK, Apple always freezes the development of older OSes when a new ones comes out. only security updates are issued after that.

    I would suggest you use the method suggested by lobitz above

    http://discussions.apple.com/message.jspa?messageID=9945828#9945828

  • by mert,

    mert mert Aug 6, 2009 10:04 AM in response to Sean Coon
    Level 3 (880 points)
    Aug 6, 2009 10:04 AM in response to Sean Coon
    Thanks Sean. Although, I hope that doesn't mean Disk Utility made all the problem files 000, and is now happy with them that way.

    Could you double check in Terminal...
    You could look over your whole disk: sudo find -x / -perm 000
    (Takes a minute or so to run. If anything shows up, there's still a problem)

    or just check a couple files (here's one):
    ls -l /System/Library/CoreServices/CCacheServer.app/Contents/_CodeSignature/CodeResou rces
    (If the first part of the line is "----------", there's still a problem).

    EDIT: oops, forgot sudo on find command

  • by V.K.,

    V.K. V.K. Aug 6, 2009 9:53 AM in response to Sean Coon
    Level 9 (56,110 points)
    Aug 6, 2009 9:53 AM in response to Sean Coon
    Sean Coon wrote:
    I don't know if this fixes the problem, but it did for me. I used the combo update and got the same permission issues. I tried using the delta and had the same thing.

    I restarted the computer with the shift key down (safe boot), reinstalled the Combo update. After that was finished, I ran disk utility again to repair disk permissions. It listed the permissions issues. I ran Repair disk permissions again I got this:

    *Repairing permissions for “Macintosh HD”*
    * Reading permissions database.*
    * Reading the permissions database can take several minutes.*


    *Permissions repair complete*


    So far it good for me.

    before you start celebrating I suggest you run the following terminal command

    sudo find -x / -perm 000

    you'll have to enter your admin password (which you won't see). that's normal. the command will run a long time and list all (if any exist) files on your startup drive with permissions 000. if it returns any output at all you still have problems and the fact that repair permissions returns no errors is actually misleading.

    Message was edited by: V.K.

  • by mert,

    mert mert Aug 6, 2009 10:16 AM in response to V.K.
    Level 3 (880 points)
    Aug 6, 2009 10:16 AM in response to V.K.
    V.K. wrote:
    lobitz wrote:
    I too experienced this problem after applying the combo update. I then applied the delta update and was left with fewer such anomalies. After also scripting a 'chmod 644' fix to the remaining files I went on to script the following which was executed as root:

    pkgutil --edit-pkg com.apple.pkg.update.os.10.5.8 --volume / --learn "offendingfile_fullpath"

    A subsequent Disk Utility repair permissions showed no remaining problems.


    Thanks. without a fix from Apple this is probably the cleanest way to deal with this. Note that if you used the combo update then in the above command put com.apple.pkg.update.os.10.5.8.combo


    I'm a little nervous about using pkgutil, so, before I use it, could you review for correctness an exact line I should execute? I currently have a fresh Combo-updated 10.5.8 system with nothing reported by "sudo find -x / -perm 000". I did not run Repair Perms yet. I saved the complete list of 000 files from my first update (Combo, followed by Repair Perms). Would I run the following line (all on one line) for each file from my original list of 000 files?

    sudo pkgutil --edit-pkg com.apple.pkg.update.os.10.5.8.combo --volume / --learn "/System/Library/CoreServices/CCacheServer.app/Contents/_CodeSignature/CodeResources"

  • by RonL,

    RonL RonL Aug 6, 2009 10:16 AM in response to Stat
    Level 1 (45 points)
    Aug 6, 2009 10:16 AM in response to Stat
    This began for me with 10.5.7 and persists with 10.5.8.

    I was hoping that it would be corrected in this new update but it hasn't been.

    Stat... as you show... I also have a very long list each time I repair permissions.

    I have been using Macs for over a decade and professionally and am certain I have done nothing to cause this.

    Fortunately it does not appear to cause any problems.

    I remember many versions back when lots of people had long lists of 'corrected' permissions after each repair but I don't recall it involving core services.

  • by V.K.,

    V.K. V.K. Aug 6, 2009 10:21 AM in response to mert
    Level 9 (56,110 points)
    Aug 6, 2009 10:21 AM in response to mert
    Would I run the following line (all on one line) for each file from my original list of 000 files?

    sudo pkgutil --edit-pkg com.apple.pkg.update.os.10.5.8.combo --volume / --learn "/System/Library/CoreServices/CCacheServer.app/Contents/_CodeSignature/CodeResources"

    yes, that's exactly the command to run. you can get the full list of files you need to run it on by running "verify permissions" instead of repair permissions". verify permissions" only report permissions errors but does not fix any of them so it is safe to run at any time.

    Message was edited by: V.K.

  • by mert,

    mert mert Aug 6, 2009 10:23 AM in response to RonL
    Level 3 (880 points)
    Aug 6, 2009 10:23 AM in response to RonL
    Yes. Agreed, I have seen numerous permission problems from time to time across OS X updates, however, I don't recall one so egregious as to set permissions to 000 (no access, well, except by root).

    EDIT: and in this case, Repair Permissions actually breaks the files. Re-Repair doesn't help either.

    Message was edited by: mert

  • by Richard Outerbridge,

    Richard Outerbridge Richard Outerbridge Aug 6, 2009 10:24 AM in response to V.K.
    Level 1 (15 points)
    Aug 6, 2009 10:24 AM in response to V.K.
    The method lobitz suggested (namely, sudo pkgutil --edit-pkg com.apple.pkg.update.os.10.5.8 --volume / --learn "offendingfile_fullpath") works fine, but you must apply it to each and every affected file (remembering to change the name of the package to "com.apple.pkg.update.os.10.5.8.combo" if you need to as pointed out by V.K.). Since there may be package "tainting" happening here (if you have applied the Delta over the Combo or vice-versa) it's hard to know what is going on in the install database, but the --learn method should fix things. You may want to keep the finished script around in case you ever need to use it again.

    That having been said, I don't know if there is actually any harm in running these files with 000 permissions apart from the "?----------" blemishes kicked out by Repair Permissions, even though they seem to have been installed (and thus perhaps intended to be run) "-rw-r--r--".

  • by Sean Coon,

    Sean Coon Sean Coon Aug 6, 2009 10:30 AM in response to V.K.
    Level 1 (0 points)
    Aug 6, 2009 10:30 AM in response to V.K.
    I typed in sudo find -x / -perm 000 in the terminal and got this:


    Last login: Thu Aug 6 13:29:39 on ttys000
    macpro1:~ macpro$ sudo find -x / -perm 000

    WARNING: Improper use of the sudo command could lead to data loss
    or the deletion of important system files. Please double-check your
    typing when using sudo. Type "man sudo" for more information.

    To proceed, enter your password, or type Ctrl-C to abort.

    Password:
    macpro1:~ macpro$


    It didn't take too long. That's all I got from the terminal command.

  • by V.K.,

    V.K. V.K. Aug 6, 2009 10:35 AM in response to Richard Outerbridge
    Level 9 (56,110 points)
    Aug 6, 2009 10:35 AM in response to Richard Outerbridge

    That having been said, I don't know if there is actually any harm in running these files with 000 permissions apart from the "?----------" blemishes kicked out by Repair Permissions, even though they seem to have been installed (and thus perhaps intended to be run) "-rw-r--r--".

    I don't know for sure either but it is mighty suspicious. and I'd as soon not take any chances particularly because on my other computer (that I updated just using the delta update) all these files have 644 permissions and repair permissions reports no errors there. as I said, this can't be right. the same system files should have the same permissions on any system after you run repair permissions.

  • by mert,

    mert mert Aug 6, 2009 10:57 AM in response to Stat
    Level 3 (880 points)
    Aug 6, 2009 10:57 AM in response to Stat
    I submitted a bug report to:
    https://bugreport.apple.com/cgi-bin/WebObjects/RadarWeb.woa

  • by stylr,

    stylr stylr Aug 6, 2009 12:04 PM in response to mert
    Level 3 (630 points)
    Aug 6, 2009 12:04 PM in response to mert
    Has anyone had any issues with this situation? Or all we all worried about something that hasn't and may not affect us in any way?

  • by mert,

    mert mert Aug 6, 2009 12:08 PM in response to stylr
    Level 3 (880 points)
    Aug 6, 2009 12:08 PM in response to stylr
    stylr wrote:
    Has anyone had any issues with this situation? Or all we all worried about something that hasn't and may not affect us in any way?

    I can't say I have yet. But, some of the system files in the list seem pretty important. I need to apply this update to 50-some machines, so hopefully, by making sure Apple is aware of it (via the bug report), they can release a definitive statement (KB article) one way or the other.

  • by William Steinberg,

    William Steinberg William Steinberg Aug 6, 2009 1:07 PM in response to Stat
    Level 1 (0 points)
    Aug 6, 2009 1:07 PM in response to Stat
    Same thing happened to me. MacPro updating from 10.5.7 to 10.5.8 using the manually downloaded combo updater.

    Had to manually shut down when the update was done, after waiting 10 minutes to no avail. Then the usual dual restart after a combo update. Then my usual run of Disk Utility to fix permissions, and like others are reporting, besides the slew of linked files (-l) that show up as permission errors (and don't get fixed, which is OK because they shouldn't be fixed), another slew of files that had normal permissions, but Disk Utility thought "should" have had 000 permissions, according to the receipt files. Unfortunately, due to habit, I had selected repair not verify, so Disk Utility "fixed" all the permissions to 000 (which is wrong).

    Running "sudo find -x / -perm 000" as root turned up this huge list, *+ALL HAVING TO DO WITH _CodeSignatures+*:
    /System/Library/CoreServices/CCacheServer.app/Contents/_CodeSignature/CodeResour ces
    /System/Library/CoreServices/Kerberos.app/Contents/_CodeSignature/CodeResources
    /System/Library/CoreServices/KerberosAgent.app/Contents/_CodeSignature/CodeResou rces
    /System/Library/CoreServices/Screen Sharing.app/Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeDirector y
    /System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeResource s
    /System/Library/Extensions/IOUSBFamily.kext/Contents/_CodeSignature/CodeSignatur e
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/C ontents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/C ontents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBEHCI.kext/C ontents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/Co ntents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/Co ntents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBHub.kext/Co ntents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.ke xt/Contents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.ke xt/Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBMergeNub.ke xt/Contents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/C ontents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/C ontents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOHCI.kext/C ontents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMous e.kext/Contents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMous e.kext/Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBOpticalMous e.kext/Contents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/C ontents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/C ontents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/AppleUSBUHCI.kext/C ontents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDrive r.kext/Contents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDrive r.kext/Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBCompositeDrive r.kext/Contents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kext /Contents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kext /Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBHIDDriver.kext /Contents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBLib.bundle/Con tents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.kex t/Contents/_CodeSignature/CodeDirectory
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.kex t/Contents/_CodeSignature/CodeResources
    /System/Library/Extensions/IOUSBFamily.kext/Contents/PlugIns/IOUSBUserClient.kex t/Contents/_CodeSignature/CodeSignature
    /System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/Co deDirectory
    /System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/Co deResources
    /System/Library/Extensions/IOUSBMassStorageClass.kext/Contents/_CodeSignature/Co deSignature
    /System/Library/Frameworks/AppKit.framework/Versions/C/_CodeSignature/CodeResour ces
    /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/C oreGraphics.framework/Versions/A/_CodeSignature/CodeResources
    /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCo re.framework/Versions/A/_CodeSignature/CodeResources
    /System/Library/Frameworks/Kerberos.framework/Versions/A/_CodeSignature/CodeReso urces
    /System/Library/KerberosPlugins/KerberosDatabasePlugins/db2.bundle/Contents/_Cod eSignature/CodeResources
    /System/Library/KerberosPlugins/KerberosDatabasePlugins/kldap.bundle/Contents/_C odeSignature/CodeResources
    /System/Library/PrivateFrameworks/DotMacLegacy.framework/Versions/A/_CodeSignatu re/CodeResources
    /System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/_CodeSi gnature/CodeResources
    /System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/Resourc es/DotMacSyncHelper.app/Contents/_CodeSignature/CodeResources
    /System/Library/PrivateFrameworks/DotMacSyncManager.framework/Versions/A/Resourc es/dotmacsyncui.app/Contents/_CodeSignature/CodeResources
    /System/Library/PrivateFrameworks/ScreenSharing.framework/Versions/A/_CodeSignat ure/CodeResources
    /System/Library/SystemProfiler/SPDisplaysReporter.spreporter/Contents/_CodeSigna ture/CodeResources

    Everything seemed to work, but I know that permissions for the above files should NOT be 000, so I re-ran the combo updater in Safe Boot mode, loggged in as Root. I also unmounted all the external drives, including the one that holds my normal (non-root) user, which is NOT the boot drive. This 2nd update also hung when it was done and I had clicked the "restart" button, requiring a manual reboot using the power button on the MacPro.

    As expected, a "sudo find -x / -perm 000" turned up nothing (zero files with permissions set to 000), but wonderfully enough, when I then ran Disk Utility in verify mode, no files turned up that Disk Utility wanted to set to permissions 0. (The files with the -l errors still show up, but that's another story, and not a problem). I also manually checked the files in Terminal, and they all have the correct permissions. So it appears that the receipt file(s) are now correct, and a repair run in Disk Utility won't mess them up.

    Just another anecdotal report.

    Billy
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