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0.000 2015-10-28 13:08:14; Factorio 0.12.14 (Build 17183, linux64)
0.070 Operating system: Linux (Ubuntu 14.04)
0.070 Program arguments: "/opt/factorio/bin/x64/factorio" "--apply-update" "/tmp/factorio-update/core-linux64-0.12.14-0.12.15-update.zip"
0.070 Read data path: /opt/factorio/data
0.070 Write data path: /opt/factorio
0.070 Binaries path: /opt/factorio/bin
0.087 Running in headless mode
0.090 Loading mod core 0.0.0 (data.lua)
0.093 Loading mod base 0.12.14 (data.lua)
0.693 Factorio initialised
0.694 Info Updater.cpp:369: Applying update /tmp/factorio-update/core-linux64-0.12.14-0.12.15-update.zip
1.374 Error Util.cpp:49: File /opt/factorio/bin/x64/factorio has unexpected content
1.389 Goodbye
EDIT: It just occured to me that it may be caused by the fact that the server is headless and the update zip file may not be expecting that, but I'm not certain if there is a different update file for the headless version.
EDIT 2: That is exactly the problem. I ran the update_factorio.py script as "python update_factorio.py -u HellUnit -t <token> -x -l" and it lists:
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Available packages:
core-win32
core-linux32
core-mac
core-linux_headless64
core-linux64
core-win64
scenario-pack