Remove deleted/corrupt package(s) from pkgutil index?

Question

Hi,
I'm running ML on a system, and I get complains about an old installation of XQuartz, but this version, or actually any version of XQuartz doesn't exist on the system. I get this message from brew:
$ brew doctor
Warning: Your XQuartz (2.6.4) is outdated
Please install XQuartz 2.7.7:
  https://xquartz.macosforge.org
However there are some traces of an old X11 package, digging a little with pkgutil etc. shows traces of a old package:
$ pkgutil --pkgs | egrep -i "x11|XQuartz"
org.x.x11.pkg
$ pkgutil --pkg-info org.x.x11.pkg
package-id: org.x.x11.pkg
version: (null)
volume: /
location: (null)
install-time: 1221163667
…but only "general" directories are left on the system, no files AFAICT:
$ for i in `pkgutil --files org.x.x11.pkg`;do ls -ld /$i 2>/dev/null; done
drwxrwxr-x+ 217 root  admin  7378 Jan 10 01:47 /Applications
drwxrwxr-x+ 35 root  admin  1190 Jan 14 11:13 /Applications/Utilities
drwxr-xr-x+ 4 root  wheel  136 Jun 26  2014 /System
drwxr-xr-x  75 root  wheel  2550 Jun 26  2014 /System/Library
drwxr-xr-x  148 root  wheel  5032 Jan  5 19:10 /System/Library/LaunchAgents
drwxr-xr-x  239 root  wheel  8126 Jan  6 23:17 /System/Library/LaunchDaemons
drwxr-xr-x@ 8 root  wheel  272 Dec 19 14:35 /private
drwxr-xr-x  118 root  wheel  4012 Jan 14 10:47 /private/etc
drwxr-xr-x  3 root  wheel  102 Jan 14 11:13 /private/etc/manpaths.d
drwxr-xr-x  3 root  wheel  102 Jan 14 11:13 /private/etc/paths.d
drwxr-xr-x@ 10 root  wheel  340 Jan 14 11:22 /usr
drwxr-xr-x  1070 root  wheel  36380 Jan  6 23:17 /usr/bin
drwxr-xr-x  281 root  wheel  9554 Jan 14 11:33 /usr/include
drwxr-xr-x  314 root  wheel  10676 Jan 14 11:33 /usr/lib
drwxr-xr-x  53 root  wheel  1802 Dec 19 13:20 /usr/share
drwxr-xr-x  13 root  wheel  442 Jan 10 03:15 /usr/share/man
drwxr-xr-x  1853 root  wheel  63002 Jan  5 19:10 /usr/share/man/man1
And trying to delete it using pkgutil with force doesn't work:
$ pkgutil -vf --forget org.x.x11.pkg
Unknown error Error Domain=NSCocoaErrorDomain Code=4 "“org.x.x11.pkg.bom” couldn’t be removed." UserInfo=0x7fde1bd981f0 {NSFilePath=/var/db/receipts/org.x.x11.pkg.bom, NSUserStringVariant=(
    Remove
), NSUnderlyingError=0x7fde1bdbb380 "The operation couldn’t be completed. No such file or directory"}.
Forgot package 'org.x.x11.pkg' on '/'.
$ ls /var/db/receipts/org.x.x11.pkg
ls: /var/db/receipts/org.x.x11.pkg: No such file or directory
Even thought that I applied -f (force), it's still not removed from pkgutil's db/index:
$ pkgutil --pkgs | egrep -i "x11|XQuartz"
org.x.x11.pkg
So, is there a way I fix/rebuild pkgutil's db/index?

Answer 1

No, the bill of materials file for org.x.x11.pkg perhaps wasn't corrupt (since listing the content worked), I'll grant you that,
It was rather an error in the way pkgutil handled the (at least deletion of) old package, ref. my first post:
$ pkgutil -vf --forget org.x.x11.pkg
Unknown error Error Domain=NSCocoaErrorDomain Code=4 "“org.x.x11.pkg.bom” couldn’t be removed." UserInfo=0x7fde1bd981f0 {NSFilePath=/var/db/receipts/org.x.x11.pkg.bom, NSUserStringVariant=(
    Remove
), NSUnderlyingError=0x7fde1bdbb380 "The operation couldn’t be completed. No such file or directory"}.
Forgot package 'org.x.x11.pkg' on '/'.
$ pkgutil --pkgs | egrep -i "x11|XQuartz"
org.x.x11.pkg
So I'd say the above is a separate pkgutil problem too.
I'll see if I can look into how homebrew searches for XQuartz installations later.
Thanks,