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Last week i was having trouble installing homebrew onto a new mac running mountain lion, i tried adding command line tools for xcode and installing X11 aswell as following a load of other things i found online.. all this got me no were and to the point were i didnt know what id done. So i decided seeing as it was a new machine to wipe the HD and do a clean install of mountain lion.

Now that ive done that if i go to disk utility to verify the disk premissions i get a load of xcode and X11 related errors, i run permission repair, but it never seems to fix them.. any ideas what i can do ? Is it best to do another clean install ? (how clean is a clean install as im not sure why its getting these X11 errors as i didnt install it again after i did the first wipe..)

heres the log from disk utility (bellow) note i can run verify, then repair, then verify again and the same problems come up ?

Verifying permissions for “Macintosh HD”
Permissions differ on “usr/X11/bin/freetype-config”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/agvtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/ibtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/instruments”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/opendiff”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/xcode-select”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/xcodebuild”; should be lrwxr-xr-x ; they are -rwxr-xr-x .

Permissions verification complete

Repairing permissions for “Macintosh HD”
Permissions differ on “usr/X11/bin/freetype-config”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/X11/bin/freetype-config”
Permissions differ on “usr/bin/agvtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/agvtool”
Permissions differ on “usr/bin/ibtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/ibtool”
Permissions differ on “usr/bin/instruments”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/instruments”
Permissions differ on “usr/bin/opendiff”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/opendiff”
Permissions differ on “usr/bin/xcode-select”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/xcode-select”
Permissions differ on “usr/bin/xcodebuild”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Repaired “usr/bin/xcodebuild”

Permissions repair complete

Verifying permissions for “Macintosh HD”
Permissions differ on “usr/X11/bin/freetype-config”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/agvtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/ibtool”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/instruments”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/opendiff”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/xcode-select”; should be lrwxr-xr-x ; they are -rwxr-xr-x .
Permissions differ on “usr/bin/xcodebuild”; should be lrwxr-xr-x ; they are -rwxr-xr-x .

Permissions verification complete
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If you know a better title for this question please suggest it as an edit .. –  sam Dec 5 '12 at 11:23
    
Have you tried repairing the disk from the recovery partition? –  ؘؘؘ Dec 5 '12 at 14:50
    
@LauriRanta i havnt, when i reinstalled the system i did it via the internet recovery, is it different via the partition ? –  sam Dec 5 '12 at 15:47

1 Answer 1

Those aren't actually permissions errors -- if you look at the detailed errors, like Permissions differ on “usr/bin/xcodebuild”; should be lrwxr-xr-x ; they are -rwxr-xr-x ., the difference is in the first symbol (l vs. -), which is the item type, not a permissions flag. The "should be" type, l, indicates a symbolic link, while - indicates a plain file. On my computer:

$ ls -l /usr/bin/xcodebuild
lrwxr-xr-x  1 root  wheel  5 Jul 13 16:35 /usr/bin/xcodebuild -> xcrun

I haven't updated Xcode in a while, so it's possible it should be a plain file in the latest version; or it may be that your install of Xcode is somehow garbled. In either case, the permissions themselves are fine. If there is a problem, it's something ... different.

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