If you try to update the same drive you boot from, not all files can be updated first time around because the system is still running, its like trying to replace a rug while you are still walking on it. This is because by booting from a different drive, the one you are updating is completely accessible and files can be updated quickly without delay. In my experience, this virtually eliminates the reports you hear about the update taking forever, and or the system taking forever to reboot, or runs slow after the update.
DOWNLOAD MACOS SIERRA 10.13 COMBO UPDATE INSTALL
never boot from and install an update to/from the same boot partition. That's a tip everyone should follow, i.e. I don't know if it would have worked had I gone through MAS I always apply my updates by manually running the installer BECAUSE I always boot from another drive to run update. Then I was able to apply SecUpdate2018-004 (which results in build number 15G22010 btw). I had to first RE-APPLY SecUpdate2018-003 (the newer one and the one you get currently if you download a fresh copy from Apple) to get the build number from 15G21012 to 15G21013. Run it over SecUpdate2018-003 build 15G21013 and no issues.
NOW, if you try manually try to run SecUpdate2018-004 over SecUpdate2018-003 build 15G21012, it will refuse and say the SecUpdate2018-004 update can not be installed. If you installed the initial SecUpdate2018-003 download, the build number shows 15G21012, if you waited and downloaded it after Apple replaced it with the new one, the build is 15G21013 when completed. There were TWO SecUpdate2018-003 updates for El Cap, an initial and a slip stream version that Apple very quietly slipped in to replace the initial one a few days later. When applying SecUpdate2018-004 to previous SecUpdate2018-003 installation on El Capitan, HEADS UP.
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