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Level 1

0 points

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

106 replies

psicekus

Level 1

0 points

Aug 6, 2009 2:24 PM in response to Stat

Ok, I have the same issues. I tried to run combo in safe boot but it didnt help. If I run Disk tool and use "verify permissions" I get only info with links. When I try to repair i get files with 000 😟

What is strange, that before reapplying combo update I got permissions problem with questionmark like ?---------- and now are ----------.

Any advice? System works fine, but I can't afford it to crash unexpectedly and repeatedly 😟

J

Aug 6, 2009 3:03 PM in response to MACundari

1. 10.5.8 server has the same problem
2. commandline "pkgutil --verify com.apple.etc" does not show this problem, so it might be DIsk Utility reading things wrong?

Ugly, ugly

Is it OK to run the pkgutil --edit-pkg --learn solution? I'd rather not have a setup where the next repair permissions damages my system.

Aug 6, 2009 3:10 PM in response to Gerben Wierda

Ai! Ai! Ai!

Now suddenly on the updated server Terminal will not start up a shell. I had not fixed anything yet.

Apple, what have you done with this update?? This could not have come at a worse moment!

Aug 6, 2009 3:40 PM in response to Stat

Interesting find. It turns out this was in my logging (from during update). A lot of

8/6/09 11:03:04 PM pkgutil[49815] Updating receipt 'com.apple.pkg.BaseSystem' path 'System/Library/PrivateFrameworks/SPSupport.framework/Versions/A/_CodeSignature ' on '/' with actual metadata from '/System/Library/PrivateFrameworks/SPSupport.framework/Versions/A/_CodeSignatur e'.

But pkgutil says it is from the combo:

bash-3.2# pkgutil --file-info "/System/Library/CoreServices/Screen Sharing.app/Contents/_CodeSignature/CodeResources"
volume: /
path: System/Library/CoreServices/Screen Sharing.app/Contents/_CodeSignature/CodeResources

pkgid: com.apple.pkg.update.os.10.5.8.combo
pkg-version: 1.0.1.1191932192
install-time: 1249592158
uid: 0
gid: 0
mode: 0

V.K.

Level 9

56,174 points

Aug 6, 2009 3:51 PM in response to Gerben Wierda

Gerben Wierda wrote:
1. 10.5.8 server has the same problem
2. commandline "pkgutil --verify com.apple.etc" does not show this problem, so it might be DIsk Utility reading things wrong?

Ugly, ugly

Is it OK to run the pkgutil --edit-pkg --learn solution?

yes, it's ok to run it. it works just fine. but you might want to rerun the combo update first. I did it on two computers and on one it got rid of ALL such messages (out of about 60) and on the other of all but a few. I guess your mileage can vary. still this is quite ugly as you say.

I'd rather not have a setup where the next repair permissions damages my system.

Aug 6, 2009 4:04 PM in response to V.K.

I also found a probably cause of this.

My guess is that the updater package runs pkgutil --learn -like activities before the files actually have been installed and thus puts faulty data in the database about the then still nonexisting file. The reason I thnk that is because my logging says many lines of

8/6/09 11:03:11 PM pkgutil[49896] Updating receipt 'com.apple.pkg.BaseSystem' path 'System/Library/PrivateFrameworks/ServerKit.framework/Versions/A/CodeResources' on '/' with actual metadata from '/System/Library/PrivateFrameworks/ServerKit.framework/Versions/A/CodeResources '.

before it says:

8/6/09 11:03:23 PM Installer[43588] Starting file extraction

Other problems may come from this too, because not only permissions = 0, also owner and group are.

dsanfili

Level 1

12 points

Aug 6, 2009 5:35 PM in response to Gerben Wierda

I've found that reapplying the 10.5.8 Combo while booted from an external disk solves the permissions problems.

The ?------- permissions problem will totally disappear.

The long list of problems with lrw-r-r permissions will, however, still be there. This one, though, I can live with. I understand it and know it is harmless.

I've done this on three different machines and it has worked like a charm each time!

Aug 6, 2009 6:28 PM in response to dsanfili

dsanfili: So I've already installed the 10.5.8 combo. Can I simply reinstall right over it while operating from a differnet startup disk?

Aug 6, 2009 6:31 PM in response to MACundari

If you are asking if you can install the update to a different volume, yes. You can install updates to any volume as long as OS X recognizes it as a valid OS X Startup volume.

dsanfili

Level 1

12 points

Aug 6, 2009 6:54 PM in response to MACundari

MACundari : Absolutely! Even if you've repaired permissions and things are screwed up, simply reinstall 10.5.8 while booted from a different startup disk. At least it certainly worked for me.

Aug 6, 2009 6:56 PM in response to Community User

That's not what I am asking, macwiz1220. He said: +"reapplying the 10.5.8 Combo while booted from an external disk"+.

I assume the word "reapply" means to reinstall. So can I simply reinstall the combo update directly over the one I just installed? Or must I uninstall or go back to 10.5.6 first?

He also used the phrase +"external disk"+. Is that literal? Must it be an actual external drive, or can I perform the re-installation from a separate internal drive? I have a totally separate internal that has 10.5.5 on it. Will starting up from that drive in order to reinstall 10.5.8 combo on my main drive suffice?

EDIT: Ah! Thank you, dsanfili. Posted the above comment just as you posted your latest response!

Message was edited by: MACundari

Stat Author

Level 1

0 points

Aug 6, 2009 9:42 PM in response to dsanfili

mert I know it is a bit early and I have not had a chance yet to check but please keep us advised to the answers from your bug report.

dsanfili although tis may make the items disappear it is not the best option for fixing this especially for those unfamiliar with separate boot drives partitions etc. My question becomes back to my second post # 3 of this thread and also includes the question about the folder called "_CodeSignature". and other code resource files in the folder just above those.

Considering after reading some of the others posts here including the fact an updated server Terminal will not start up a shell according to Gerben Wierda it makes me wonder more if something actually doesn't get broken in some areas of the core files.

Although you may have seemed to fix the errors that originally started this post ar you 100% sure that things are back to where they should be?

Apple has not addressed these issues or concerns yet and although I feel it is an oops in their update patching, and even if this was originally meant to plug security holes or improve stability maybe, I'm hesitant to fully trust in this method to fix something that got broken by the same installer package.

Not to mention this is no way to apply fixes to hundreds of potential machines at any businesses that may have already applied the updates and are now finding they have a major headache to deal with.

Fortunately I have only applied the updates to two machines that are not critical nor in a production state that may slow me down in a critical situation with such weirdness from an OS update installer.

I don't know and may be too paranoid about such things but it is not shall we say kosher in my book.

grmlaw

Level 1

0 points

Aug 6, 2009 10:02 PM in response to dsanfili

dsanfili - I'm a real neophyte to this stuff. Can you please explain to me, step by step, how I go about rebooting from an external drive and then reinstall the 10.5.8 update from that external drive in order to rid my MacBook Pro (upon which I have already installed 10.5.8) of the dozens upon dozens of permissions problems created with the installation of 10.5.8? I have an external drive with three bootable partitions on it. Do I boot into one of those? If so, how do I then reinstall the 10.5.8 update while still running the bootable partition on the external drive? None of my bootable external drive partitions have the 10.5.8 update on them. How do I get it on one of the bootable partitions on my external drive? Sorry to be so unsophisticated.

Aug 6, 2009 10:16 PM in response to grmlaw

I don't know about this particular problem, but it is perfectly possible to re-run the combo installer on the drive you are booted from. Just launch the installer and follow the instructions. I have done it in the past for permissions problems where the BOM had got out of sync and caused (harmless) permissions problems which were solved this way.

It was not necessary to boot from a separate volume. Possibly for this situation booting from a separate volume is necessary for it to work.

Are your "dozens upon dozens of permissions problems" like the OP's in this thread with ______? or the more common but harmless type without the _____?

Message was edited by: Mike Boreham

RonL

Level 1

52 points

Aug 6, 2009 10:32 PM in response to Stat

According to Apple support if any of the 'error' messages that are listed on the following link are listed... there is nothing to be concerned about...

* http://support.apple.com/kb/TS1448*

Of course it would be nice if they simply did not appear so that we wouldn't have to take the time to post or go through all of them (I happen to have lots of them after the 10.5.8 update).

Repairing permissions after 10.5.8 update extreme oops maybe???