OnyX for El Capitan report...

[Dreambird]

Report from OnyX on my El Capitan SSD internal HD.... I should note that this restoration of my system was from a Time Machine back up that should not have had these errors but anyway:

volume_arg = /
Starting argv pass #2...
Processing files from package com.apple.update.firmwareupdate...
Processing files from package com.apple.pkg.update.os.SecUpd2017-004ElCapitan.15G17023...
Processing files from package com.apple.pkg.update.os.10.11.6.appstore.15G1076...
Processing files from package com.apple.pkg.update.os.SecUpd2017-002ElCapitan.15G1510...
Processing files from package com.apple.pkg.update.os.SecUpd2016-003ElCapitan.15G1217...
Processing files from package com.apple.update.fullbundleupdate.15G1108...
   Permissions differ on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html", should be lrwxr-xr-x , they are -rw-r--r-- .
   Unable to set owner & group on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html". Error 1: Operation not permitted
   Unable to set permissions on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html". Error 1: Operation not permitted
Processing files from package com.apple.pkg.update.os.SecUpd2016-002ElCapitan.15G1108...
Processing files from package com.apple.update.fullbundleupdate.15G1004...
Processing files from package com.apple.pkg.update.os.SecUpd2016-001ElCapitan.15G1004...
Processing files from package com.apple.pkg.X11redirect...
Processing files from package com.apple.pkg.Essentials...
   Warning: SUID file 'System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent' has been modified and will not be repaired.
Processing files from package com.apple.pkg.BaseSystemResources...
Processing files from package com.apple.update.firmwareupdate...
Processed 424288 paths from 13 packages.

There was an irreparable permissions on an iTunes file but I have 12.6.2 stored so I reran it and it fixed that. I don't know about Safari or ARDAgent.... I don't make a habit of messing with CoreServices, so not sure what to do about these.

Any opinions, shots in the dark... like maybe running the 10.11.6 combo updater... or the whole El Capitan installation... I have that stored too. I haven't noticed anything happening... I don't use Safari, but I'll check it out anyway. It's handy now and then.

Thanks again... 

Actually should be able to reset permissions via Terminal... anyone know the command.... 

[Dreambird]

OK... so "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html" appears to be the help file for Safari which seems to be working fine.

and....

"SUID file 'System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent' has been modified a is Unix Executable.... terminal icon. I would gues the "super user id" has been modified... by what I haven't a clue. All I've done with Terminal were clearly defined commands. Perhaps it's a "hissy fit" because my Machine is called "Diane.lastname's Computer" and my user name or the name of my home directory is d****y. It's always been so, never been an issue. I don't like that home directory name being posted so I'll remove it in awhile... please ask me for it. It's not the name attached to where I am reachable in any case. Rapport always states I'm "really unreachable" on Console. I run the Firewall and Stealth ports.
Found this: https://www.macworld.com/article/1134165/security/ardagent.html
Maybe I've been "had"... ?
Uuuh... it says in that article I can't open it as I don't have permission however I can open it in TextEdit. I'm going to follow the instructions in there.

Uh-huh! supposed to be patched by a security update which I can't install. That article goes back to older OS's though... it's supposed to plug the hole temporarily... follow the instructions before installing security update. That "agent" allows others access to your machine which might be useful in an honest application but.... not here!
AAAhhhkkkk! It won't let me delete it because it's an OSX file and it needed... so much for that! Guess I'll just keep the machine locked down best I can unless someone knows how to put the SUID right.

OK Rapport's Console file has some suspicious stuff not there before. Think I'll roll back to a bit older backup and hope for the best... I'm sick of starting over! Blaaa... T

[Dreambird]

Duh.... this shows how to disable it... which it was already but I disabled Internet Sharing too. Console has com.apple.revisiond but greyed out...
https://www.google.com/search?q=how+to+delete+ARDAgent&ie=utf-8&oe=utf-8&client=firefox-b#kpvalbx=1

[Dreambird]

https://apple.stackexchange.com/questions/111156/warning-suid-file-has-been-modified-and-will-not-be-repaired-after-repairing

says you can ignore it... 

Just installed the new Safari and that went OK... no Kernel Panics! However OnyX still says the same thing:
Permissions differ on "Applications/Safari.app/Contents/Resources/Safari.help/Contents/Resources/index.html", should be lrwxr-xr-x , they are -rw-r--r-- .

OK... gonna go with the line that with El Capitan "permissions are now set automatically and don't need to be checked anymore." Rrrright!

[jchuzi]

I used to get that SUID notice in previous OSs and did, indeed, ignore it. Nothing bad ever happened so I guess that it was safe. As to Time Machine, I have found that it becomes corrupt after awhile. A couple of times, Checkmate has reported issues and neither Disk Utility nor Disk Warrior could repair them. My solution is to erase the TM drive and start from scratch. This seems to happen when the TM volume gets to be almost full.

[Dreambird]

Thanks for that... I probably will erase that drive... and we'll see what it does. I don't care for the fact that it's a FW drive hooked up to Thunderbolt via an adapter... I've gotten 6 years out of that set up. However it might be fine for just stashing stuff... not sure it would boot for a clone, I've got SuperDuper.

Checkmate looks interesting... I used to have TechTools, I think it was Pro. Some time ago. A decent diagnostic piece of software would be good... OnyX is OK and I love DiskWarrior but 2 good ones might be an idea.

[Dreambird]

I went a little too far with trying to weed out iLife crap from my HD... it started to bite into things. Sooo... had to restore a backup from my new Seagate external HD.

WOW!!! It took a whole half hour...  Compared to 2.25 hours on my old external... love it!