Disk repair permissions question

Though the following permissions are repaired, they still show-up under repair list. I did verify and repair twice to re-confirm this. Any inputs on why this happens?
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar", should be lrwxr-xr-x , they are lrw-r--r-- .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/Deploy.bundle/ Contents/Resources/JavaPluginCocoa.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar", should be -rw-r--r-- , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/deploy.jar".
Permissions differ on "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib", should be -rwxr-xr-x , they are lrwxr-xr-x .
Repaired "System/Library/Frameworks/JavaVM.framework/Versions/1.6.0/Resources/JavaPlugin Cocoa.bundle/Contents/Resources/Java/libdeploy.jnilib".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Thanks in advance...

Hi newbie--
They're completely normal.
Not to worry.
This article will explain more.
http://support.apple.com/kb/TS1448

Similar Messages

Disk utility permissions question

Hello,
I am VERY happy with my Mac. However, since installing OS10.5 (upgrade from my 10.4) whenever I used my Disk Utility to repair permissions, I get a HUGE list of repairs. Every time I used the Utility, it comes up with this huge list that, as far as I can tell, is all the same.
So my question is, is it actually repairing the permissions?
I've never had this happen on my previous OS. If something showed up, it repaired it and then, when I run the utility again, it shows that all is well and no repairs are necessary.
Can anyone help me? I have also been having problems with my Toast Titanium 10 and my MOTU Digital Performer 5 since my OS upgrade.
I took a screen shot of my Utility permissions after it's been run. I could send that to you if you would need to see it.
Thank you for all your help!!!!!!!!!!!!

Welcome to Apple Discussions:
It's always good to search first.
Check this thread for starters:
http://discussions.apple.com/thread.jspa?messageID=9422112&#9422112

Our MacbookPro began running very slow a few days ago. I ran disk repair, permissions repair, and restored the OS from the Apple server. Kernal_Task appears to be using excessive CPU.

EtreCheck version: 1.9.11 (43) - report generated June 15, 2014 at 7:45:12 AM CDT
Hardware Information:
          MacBook Pro - model: MacBookPro8,2
          1 2 GHz Intel Core i7 CPU: 4 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
          AMD Radeon HD 6490M - VRAM: 256 MB
System Software:
          OS X 10.9.3 (13D65) - Uptime: 0 days 6:20:35
Disk Information:
          TOSHIBA MK5065GSXF disk0 : (500.11 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 499.25 GB (294.57 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-898
USB Information:
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Computer, Inc. IR Receiver
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Gatekeeper:
          Mac App Store and identified developers
Kernel Extensions:
          [not loaded] com.intego.Family-Protector.safe-boot (10.7.5 - SDK 10.8) Support
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist Support
          [running] com.intego.commonservices.daemon.integod.plist Support
          [running] com.intego.commonservices.daemon.taskmanager.plist Support
          [loaded] com.intego.commonservices.icalserver.plist Support
          [loaded] com.intego.commonservices.metrics.kschecker.plist Support
          [running] com.intego.Family-Protector.daemon.plist Support
          [running] com.intego.netbarrier.daemon.logger.plist Support
          [running] com.intego.netbarrier.daemon.monitor.plist Support
          [running] com.intego.netbarrier.daemon.plist Support
          [running] com.intego.netupdate.daemon.plist Support
          [running] com.intego.PersonalBackup.daemon.plist Support
          [loaded] com.intego.virusbarrier.daemon.emlparser.plist Support
          [running] com.intego.virusbarrier.daemon.logger.plist Support
          [running] com.intego.virusbarrier.daemon.plist Support
          [running] com.intego.virusbarrier.daemon.scanner.plist Support
          [running] com.intego.WashingMachine.service.plist Support
          [loaded] com.microsoft.office.licensing.helper.plist Support
Launch Agents:
          [running] com.intego.commonservices.integomenu.plist Support
          [loaded] com.intego.commonservices.taskmanager.plist Support
          [loaded] com.intego.commonservices.uninstaller.plist Support
          [running] com.intego.Family-Protector.agent.plist Support
          [loaded] com.intego.netbarrier.alert.plist Support
          [running] com.intego.netupdate.agent.plist Support
          [loaded] com.intego.personalbackup.agent.plist Support
          [loaded] com.intego.virusbarrier.alert.plist Support
User Launch Agents:
          [loaded] com.adobe.ARM.[...].plist Support
          [failed] com.apple.CSConfigDotMacCert-[...]@me.com-SharedServices.Agent.plist
User Login Items:
          VirusBarrier X6
          Antispam Engine
          iTunesHelper
          Activity Monitor
          Dropbox 1.40.07 PM
          AdobeResourceSynchronizer
Internet Plug-ins:
          JavaAppletPlugin: Version: Java 7 Update 51 Check version
          FlashPlayer-10.6: Version: 14.0.0.125 - SDK 10.6 Support
          Default Browser: Version: 537 - SDK 10.9
          AdobePDFViewerNPAPI: Version: 11.0.06 - SDK 10.6 Support
          AdobePDFViewer: Version: 11.0.06 - SDK 10.6 Support
          Flash Player: Version: 14.0.0.125 - SDK 10.6 Support
          QuickTime Plugin: Version: 7.7.3
          SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 Support
          iPhotoPhotocast: Version: 7.0 - SDK 10.8
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
User Internet Plug-ins:
          WebEx64: Version: 1.0 - SDK 10.5 Support
3rd Party Preference Panes:
          Flash Player Support
Time Machine:
          Skip System Files: NO
          Mobile backups: OFF
          Auto backup: NO - Auto backup turned off
          Volumes being backed up:
                    Macintosh HD: Disk size: 464.96 GB Disk used: 190.62 GB
          Destinations:
                    My Passport [Local] (Last used)
                    Total size: 464.98 GB
                    Total number of backups: 19
                    Oldest backup: 2012-07-22 00:08:58 +0000
                    Last backup: 2014-06-14 17:10:32 +0000
                    Size of backup disk: Too small
                              Backup size 464.98 GB < (Disk used 190.62 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               3%          WindowServer
               1%          Activity Monitor
               1%          sysmond
               0%          ps
               0%          aosnotifyd
Top Processes by Memory:
          217 MB          mds_stores
          152 MB          com.apple.IconServicesAgent
          111 MB          Safari
          94 MB          softwareupdated
          49 MB          WindowServer
Virtual Memory Information:
          1018 MB          Free RAM
          1.41 GB          Active RAM
          604 MB          Inactive RAM
          1021 MB          Wired RAM
          1.65 GB          Page-ins
          0 B          Page-outs

I uninstalled all of the Intego products. I restarted the laptop, also ran disk repair and permissions repair again. Then allowed the machine to run with no apps active, just in case the OS was perfroming cleanup funtions. Results: No discernible improvement in performance. The kernal_task shows 500+% and the CPU graph shows 70%-80%.
There is one hardware issue: The magsafe battery port stopped charging the battery, so the laptop must be plugged in all the time.
Stan
EtreCheck version: 1.9.12 (48)
Report generated June 16, 2014 at 8:05:11 AM CDT
Hardware Information:
          MacBook Pro (15-inch, Early 2011) (Verified)
          MacBook Pro - model: MacBookPro8,2
          1 2 GHz Intel Core i7 CPU: 4 cores
          4 GB RAM
Video Information:
          Intel HD Graphics 3000 - VRAM: 384 MB
                    Color LCD 1440 x 900
          AMD Radeon HD 6490M - VRAM: 256 MB
System Software:
          OS X 10.9.3 (13D65) - Uptime: 0 days 21:8:4
Disk Information:
          TOSHIBA MK5065GSXF disk0 : (500.11 GB)
                    EFI (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 499.25 GB (293.77 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          MATSHITADVD-R   UJ-898
USB Information:
          Apple Inc. FaceTime HD Camera (Built-in)
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Inc. BRCM2070 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Apple Computer, Inc. IR Receiver
Thunderbolt Information:
          Apple Inc. thunderbolt_bus
Gatekeeper:
          Mac App Store and identified developers
Launch Daemons:
          [loaded] com.adobe.fpsaud.plist Support
          [loaded] com.microsoft.office.licensing.helper.plist Support
User Launch Agents:
          [loaded] com.adobe.ARM.[...].plist Support
          [failed] com.apple.CSConfigDotMacCert-[...]@me.com-SharedServices.Agent.plist
User Login Items:
          VirusBarrier X6
          Antispam Engine
          iTunesHelper
          Activity Monitor
          Dropbox 1.40.07 PM
          AdobeResourceSynchronizer
Internet Plug-ins:
          JavaAppletPlugin: Version: Java 7 Update 51 Check version
          FlashPlayer-10.6: Version: 14.0.0.125 - SDK 10.6 Support
          Default Browser: Version: 537 - SDK 10.9
          AdobePDFViewerNPAPI: Version: 11.0.06 - SDK 10.6 Support
          AdobePDFViewer: Version: 11.0.06 - SDK 10.6 Support
          Flash Player: Version: 14.0.0.125 - SDK 10.6 Support
          QuickTime Plugin: Version: 7.7.3
          SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 Support
          iPhotoPhotocast: Version: 7.0 - SDK 10.8
Audio Plug-ins:
          BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
          AirPlay: Version: 2.0 - SDK 10.9
          AppleAVBAudio: Version: 203.2 - SDK 10.9
          iSightAudio: Version: 7.7.3 - SDK 10.9
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.9
User Internet Plug-ins:
          WebEx64: Version: 1.0 - SDK 10.5 Support
3rd Party Preference Panes:
          Flash Player Support
Time Machine:
          Skip System Files: NO
          Mobile backups: OFF
          Auto backup: NO - Auto backup turned off
          Volumes being backed up:
                    Macintosh HD: Disk size: 464.96 GB Disk used: 191.37 GB
          Destinations:
                    My Passport [Local] (Last used)
                    Total size: 464.98 GB
                    Total number of backups: 19
                    Oldest backup: 2012-07-22 00:08:58 +0000
                    Last backup: 2014-06-14 17:10:32 +0000
                    Size of backup disk: Too small
                              Backup size 464.98 GB < (Disk used 191.37 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               5%          WindowServer
               3%          Activity Monitor
               3%          com.apple.WebKit.WebContent
               1%          hidd
               0%          sysmond
Top Processes by Memory:
          168 MB          softwareupdated
          139 MB          com.apple.IconServicesAgent
          123 MB          Safari
          119 MB          installd
          115 MB          mds_stores
Virtual Memory Information:
          498 MB          Free RAM
          1.62 GB          Active RAM
          927 MB          Inactive RAM
          998 MB          Wired RAM
          1.18 GB          Page-ins
          400 KB          Page-outs

Verify and repair permissions questions from wierdness

Good morning
I'm getting ready to upgrade to the snow cat but !!!!
I went into disk utility with 10.5.8 to verify and repiar perimissions and I now have a list disk utility won't touch, eg, "permissions differ system/library/coreservice/airport base station agent ..... " and others but the ones that really worry me are showing up in history like "Warning SUID file "system/library/filesystems/appleshare/afpload" has been modified and cannot be repaired.
I haven't start up from the OSx disk to repair permissions but from the Hd.
Any advice out there ?
thanks

Worry not!
Permissions you can ignore on 10.5:
http://support.apple.com/kb/TS1448?viewlocale=en_US
using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard changed the location of a number of system components.

Repair Disk / Repair Permissions -- which first

If I want to run repair permissions or repair disk, which should I do first?
Does it matter?

"Repair disk" makes modifications to the structure of data on the disk itself. If there is an error, this really needs to be done first since the errors could manifest themselves as botched permissions, mangled files, etc. If the disk's integrity is actually compromised, the highest priority is to repair it. One thing to keep in mind is that certain repairs cannot be made on a mounted disk (such as the one you boot from), so for the disk repair procedure to work, you should boot of another disk (your OS installation disk, a bootable external hard disk, etc.). Even then, Apple's disk repair is curiously basic -- there's many errors it simply does not detect or fix and for that you need something like DiskWarrior. Mind you, disk errors like that shouldn't occur, and if they do you may have hardware issues to be concerned about.
"Repair permissions" compares file ownership and permissions in a directory to a list stored in the package bundles in /Library/Receipts. If there's a difference between what it finds in the file list stored in the receipt package, and the files on disk, it attempts to set the permissions and ownership of the file to what appears in the list (which should reflect the state of the file when installed). It doesn't do anything at all to preferences, user preferences, user files, logs, file created after and application is installed, etc.
Contrary to popular belief, repairing permissions doesn't generally do much for you. It should be pretty rare that it finds a difference unless you've really been mucking about, and generally when it does find something it's either because you explicitly changed the permissions or because there's some other problem where an application or disk issue is changing the permissions. The one time where it really makes sense, actually, is after you repair a disk issue.
It's common advice that people tell you to repair permissions as a step to address problems, but mostly because it's an easy thing to do. Similarly, zapping your PRAM is frequently advised when trouble-shooting, though the process of a cold-boot (complete power-off, then power back on a few seconds later) is generally the portion of that procedure that actually produces the desired result.

External disk - repair permissions

It seems the permissions on my HD need to be repaired.
Unfortunately I have lost the Repair disk during an international move.
I still have the install disk - so I tried to install OS 10.6 onto an external drive. The intention was to boot from the external drive and repair permisions on the MacBook HD.
The installation kept showing the external disk as having not been ejected correctly, which is not correct. Anyway, I erased all partitions on this external disk, using Disk Utility, did a 7 pass erase, and then also ran the repair disk function too; Disk Utilityshowed that there were no issues with this external disk. However, I still got the same result from the OS installation program, that the external disk had not been ejected correctly. I went around in the circle a number of times before giving up.
Now I am at a loss how to make the external boot disk to repair permisions on the computer HD.
I know in the distant past it was possible to just copy the System folder to an external drive and it would boot; but I was told this no longer works.
Any get around this issue or a solution would be most welcome.
Thank you

It seems that there is a theory that you don't need to repair permissions anymore.
Correct. It is unnecessary and doen't repair your permissions anyway.
About Disk Utility's Repair Disk Permissions feature
When files loose their connection with the program that created them is one example why permisions need to be repaired.
No, that is an indication that Launch Services has got corrupted or confused and maybe it needs rebuilding. Repair permissions does nothing to the launch services data base.
The last time I had issues was 18 months ago and running repair disk permissions solved all the instability problems; I don't think I was dillusional about this; so as I have warnings to repair disk permissions and instability issues I what I want to repair the permissions; that is irrespective of any currrent thought that this isn't necessary.
You believe what you want. Read the link about repairing permissions and what it does.
The repair disk has a minimal system and disk utilities on it that allows you to boot from the DVD and repair the internal HD. In the early days you could just drag a minimal of certain files from the system onto a flopy or latter a CD together with disk repair and it would do the job. I lost my repair disk, so I want to create a system on an external drive which together with Disk Utility so I can repair the permissions. Or even make a DVD with a minimum system and disk utilities.
There is no such thing as a "repair disk". You have installer dvd's that came with your hardware or the recovery partition that is part of Lion. You boot it and run Disk Utility to verify/repair, and yes, if you insist, repair permissions. Or you boot from another bootable disk and use its Disk Utilities to repair/verify your drives from there. That is because you cannot repair the drive you are currently booted from.
You can't repair permissions from the HD that has issues, ("If necessary (which is seldom), permissions should be repaired from the selfsame disk.') well at least up to OS10.6, you need an external system to do this, i.e. external HD or DVD. Apple genius bars use external drives to do this; being in Spain there is only one of those some 3+ hours away; a final option if I can't get success.
I basically just said this immediately above.
As I mentioned when I tried to install OS10.6 onto an external drive I had issues doing this, as covered in my initial email.
First a 7-pass erase it a complete waste of time when a simple erase will do. Second I think the you are getting "disk ejected improperly" because you may have one of those enclosures that has a tendency to go off line on its own, which of course is indeed ejecting the disk incorrectly. I'm guessing on this last point of course but it seems reasonable to me.

Repair Disk & Repair Permissions Using Leopard Install Disk NOT WORKING!!

I start up from my Leopard disk and click the Mac OS Partition in disk utility and two things go wrong...
Firstly, when I click either verify or repair permissions the progress bar stays as the moving angled lines forever (haven't tried leaving it for more than five minutes though).
Secondly, when I verify my disk it says everything appears to be okay, but when I try and repair the disk it says "The disk Macintosh HD cannot be unmounted" so I am unable to repair my disk. Are these fixable issues or is it a Leopard thing?

UPDATE: I let Repair Permissions run for a good twenty minutes and it worked, just took a long time, this in turn fixed my Repair Disk problem, so I'm all set.

Lost Option For Disk Repair Permissions

Hi Gang
I'm using 10.4.11
Unless I'm missing something here, it seems I've lost the option to Repair Disk Permissions for all of my
Non-System Drives? I now only have the option to Repair Disk Permissions for the System Drive only.
I never had this condition before - always ran Repair Disk Permissions for all the external drives on a regular basis. Perhaps this process was never necessary to begin with? But that still doesn't explain why the option is 'Grayed Out'
What have I done differently? The only thing I can think of, is the fact that I added an 800 FW cable internally (to the 3rd internal FW800 Out Port), on one if the PCI Multi Port Cards. That additional Drive is turned off right now.
Screen Shots;
http://www.locationstudio.net/YesRepair.jpg
http://www.locationstudio.net/NoRepair-1.jpg
http://www.locationstudio.net/NoRepair-2.jpg
Yes I realize I have a lot of external drives, but I'd rather not get into a discussion of SATA Controller Cards at this point. I've got tons of Video Files that would ALL need reconnection in FCP. Trust me, it's not an option right now.
I'm just looking for an opinion about the loss of that Option to 'Repair Disk Permissions'
Thanx
Mike

And you mean, therefore, only SYSTEM Disks can have 'Repair Disk Permissions' performed? Correct?
Correct.
If so, then why was I able to see that function before? 'Repair Disk Permissions' was ALWAYS there despite the circumstances. Ummm?
Did you ever clone your internal to these before? It really should not be available unless there is an OSX on it.
How bout 'Disk Repair'? Does it benefit to perform this function on all of these external drives? I've always read this before.
Actually, THE most important one is Disk Repair, and it really should be done before any Permission Repairs... now it's not a problem to Repair Permissions if the Disk is OK, but Repairing Permissions if the Disk Directory is the slightest messed up is like sending envelopes of cash out to addresses, but all the street signs have been changed.
Just to see if it would make a difference, I checked the Box 'Ignor Disk Permissions' Same result - can only perform 'Disk Repair'
Yes, the way it should be, but normally you want Ignore permission set on external drives. You can have or set Permissions on external drives, but it's normally not needed.
BTW, Repair Permissions does not Repair all Permissions on your Boot Drive either, just on System Files/Folders, not any in your Users folder for instance.

Repair Permissions questions

Just did my monthly Repair Permissions. Today, for some reason, it took about 5 minutes. Usually this is a 30 second procedure. I noticed that there are about 10 items that end with "has been modified and will not be repaired." Things that end in "readconfig," "writeconfig," "runner," "DiskManagementTool," "Locum."
They all originate out of System/Library/PrivateFrameworks or System/Library/CoreServices.
What's that all about?????????
I do this monthly Repair Permissions routinely as suggested years ago.
Thanks.
Frank

Those, as has been covered here before, common and harmless. Some people report that most go away if you download the standalone 10.5.1 updater and reinstall, but at least one such message will persist and it is, per Apple, something you can ignore.

10.5.1: Disk Repair Permissions and SUID's

In 10.5.0 I had 3 entries while repairing permissions:
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
and the 2 ACL found lines...
After 10.5.1 was installed...
Warning: SUID file "usr/libexec/load_hdi" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Reso urces/Locum" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
Warning: SUID file "usr/libexec/authopen" has been modified and will not be repaired.
Warning: SUID file "System/Library/CoreServices/Finder.app/Contents/Resources/OwnerGroupTool" has been modified and will not be repaired.
and of course...
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
The ACL lines have disappeared.
Can anybody explain this? And should I be concerned?
Thanks Chuck

Frankly, I think there are few to any warnings that Repair Permissions throws that you should be worried about, EVER.
People think repairing permissions "repairs" things. It really doesn't "repair" anything. It CHECKS permissions against a set of files which indicate what they were when things were installed. If these permissions were changed in some way (sometimes, this was done INTENTIONALLY), repair permissions will throw errors or warnings, which can be benign.

Disk utility - disk repair permissions

I recently upgraded from OSX Tiger to Snow Leopard and also upgraded Firefox to 20.0, but have kept Safari as the default browser. Ever since, it doesn't take long for everything to slow down especially the 'net. I use disk utility to repair disk permissions (almost daily!) which helps. This takes about an hour. The problem seems to be in the System Library Core Services; e.g under Remote Management Resources Library it should be "drwxr-xr-x" but is "-rwxr-xr-x" and so on down the line including System Library Frameworks, Java..... What caused this and what can I do to get back to proper functioning?

I use disk utility to repair disk permissions (almost daily!) which helps.
No it doesn't. That's a complete waste of time.
First, back up all data immediately, as your boot drive might be failing.
There are a few other possible causes of generalized slow performance that you can rule out easily.
Reset the System Management Controller.
If you have many image or video files on the Desktop with preview icons, move them to another folder.
If applicable, uncheck all boxes in the iCloud preference pane.
Disconnect all non-essential wired peripherals and remove aftermarket expansion cards, if any.
Check your keychains in Keychain Access for excessively duplicated items.
Boot into Recovery mode, launch Disk Utility, and run Repair Disk.
Otherwise, take the steps below when you notice the problem.
Step 1
Launch the Activity Monitor application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Activity Monitor in the icon grid.
Select the CPU tab of the Activity Monitor window.
Select All Processes from the menu in the toolbar, if not already selected.
Click the heading of the % CPU column in the process table to sort the entries by CPU usage. You may have to click it twice to get the highest value at the top. What is it, and what is the process? Also post the values for % User, % System, and % Idle at the bottom of the window.
Select the System Memory tab. What values are shown in the bottom part of the window for Page outs and Swap used?
Next, select the Disk Activity tab. Post the approximate values shown for Reads in/sec and Writes out/sec (not Reads in and Writes out.)
Step 2
If you have more than one user account, you must be logged in as an administrator to carry out this step.
Launch the Console application in the same way you launched Activity Monitor. Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left. If you don't see that menu, select
View ▹ Show Log List
from the menu bar.
Select the 50 or so most recent entries in the log. Copy them to the Clipboard (command-C). Paste into a reply to this message (command-V). You're looking for entries at the end of the log, not at the beginning.
When posting a log extract, be selective. Don't post more than is requested.
Please do not indiscriminately dump thousands of lines from the log into this discussion.
Important: Some personal information, such as your name, may appear in the log. Anonymize before posting. That should be easy to do if your extract is not too long.

Disk repair permissions, what's the point??

In the quest to try to do something about the noisy hard disk activity on a new 17-inch macbook pro, i had a go at repairing disk permissions in the hope that this might quieten things some. Well, the machine found gazillions of permissions to repair and did so. Well then I ran it again. Wouldn't you think all the repairs had been done already? But no, gazillions more repairs were made. Can anyone tell me if any of this matters??

It may matter. Here is a list of the errors that you can safely ignore:
http://support.apple.com/kb/TS1448?viewlocale=en_US

Repairing Permissions Question

Now what does this mean:
Warning: SUID file "usr/sbin/pppd" has been modified and will not be repaired.
Thank you,
James

It means either a Mac OS X update or another activity has changed that file so that it's different from the information specified for it in the original installation receipt.
(46608)

10.3.9: G3 iMac won't run 'Repair Permissions' from Panther Disk!

I upgraded the memory to 1024 mb RAM and reinstalled Panther yesterday after leaving it on the shelf for a couple of years due to numerous problems running it on Kihei and Pismo (both with 256 mb RAM). The loading process went well; I ran the following utilities after loading all of the updates:
TechTool 4.0.1
Disk First Aid from Panther disk
Repair Permissions from Panther Disk
Reset NVRAM, PRAM and OF
TechTool showed no problems and Disk First Aid said a repair was made. The first time I attempted to repair 'permissions' the process seemed to be about half way complete when it stopped and displayed the following error:
'Disk Management Tool' has lost contact with Disk Utility, close function and restart Disk Utility' or something to this effect.
Every attempt afterwards results in the same error message coming up almost immediately. iMac seems to be running properly at the moment; is it about to crash again like it did so many times in the past before I reverted to Jaguar? Any insight or advice will be welcome. I will post a copy of this on the 10.3 Panther board too.

Road Hazard: Try the instructions in this article. It is not possible to use the Panther installation disks to repair the permissions on a system which is experiencing this issue.
scapesuiter: A Kihei is one of the models which make up the first slot-loading iMac machines. These came out in October 1999 and were discontinued in July 2000.
(15253)

Repair Permissions with/without Tiger disk?

I was wondering what the best way is to repair permissions. Should one repair them booting off the Tiger disk or can one just open disk utility and repair the permissions while running on their hard drive?
Also, my new iMac came with two disks. I also have a Tiger disk from when I purchased Tiger for my PowerBook. If it is necessary to repair permissions from the disk, which disk should I use? Can I use the Tiger disk or should I use one of the disks that came with my iMac?
Thanks!

Regarding your first question, it makes no difference so there isn't any need to boot from the install disc to repair disk permissions.
Regarding your second question, the same applies but you should use the Tiger install package that shipped with your new iMac to run repair disk via Disk First Aid when booted from the iMac's install disc on your iMac's boot volume which is much more important than repairing disk permissions.
The Tiger retail install package is not Universal - it is for a Mac with a PPC processor only and your new iMac has an Intel processor.
Check this link for system troubleshooting procedures which includes running repair disk, repairing disk permissions and system and user cache cleaning.
http://www.thexlab.com/faqs/repairprocess.html
And this link for recommended maintenance for OS X which isn't much focusing on the Maintenance Myths section.
http://www.thexlab.com/faqs/maintainingmacosx.html
And this link about running repair disk via Disk First Aid.
http://www.thexlab.com/faqs/durepairfns.html

Disk repair permissions question

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