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When upgrading from ArcGIS 10.5 and 10.5.1 to ArcGIS Enterprise 10.6 GeoAnalytics Server, the following error message is returned:
Error: A previous uninstall has not completed; the machine must be restarted. After restarting, files may remain on disk that will conflict with the installation. Please rename the folder <ArcGIS GeoAnalytics Server install location>\ArcGIS\Server\ before running the ArcGIS Server 10.6 setup again.
During an upgrade from ArcGIS GeoAnalytics Server 10.5 or 10.5.1 to 10.6, there is a known issue caused by orphaned ArcGIS Server processes which may impede the upgrade process. When these ArcGIS Server processes are still running during an ArcGIS GeoAnalytics Server upgrade, the upgrade may be impeded and server settings may be lost.
If prompted by this error message, rename the folder, restart the machine, and rerun the Server 10.6 setup.exe file. Any preset server settings will be lost.
It is advised to follow the best practices for upgrading ArcGIS GeoAnalytics Server to avoid this error and successfully upgrade ArcGIS GeoAnalytics Server to 10.6.
Prior to upgrading, complete the steps to Back up and restore your ArcGIS Server site configuration and roll back the ArcGIS GeoAnalytics Server site to its backup configuration. After this, follow the steps outlined in the ArcGIS Server help section, Upgrade using the setup program (Windows) or Upgrade ArcGIS Server (Linux) to upgrade the server(s) to ArcGIS GeoAnalytics Server 10.6 without error.