Make sure the the user the process is running under has permissions to delete files that the update process is targeting under that home directory. I had the issue with Minera once on Ubuntu.
in some cases just using sudo to start the process i question will get it the correct permission for file manipulations.
It was the typical permissions issue. The included permissionsfix script as it says is for "most" linux distro's, just not on my CentOS. Stupid me for not even viewing the two liner. Just in case the auto-updater runs that, I changed it to reflect my settings. Once did that, good.