I had the same issue (on Windows). The rebase shortcut did not seem to work, thus I just re-installed the runtime from the download page on the official site.
However, now I get another error:
OpenPLC Runtime was not installed correctly. Please run Rebase OpenPLC program.
If I run the rebase, I get:
fatal: unable to access 'http://github.com/thiagoralves/OpenPLC_v3.git/': Could not resolve host: github.com
I googled and tried a couple of fixes I found online, but none seem to work.
Has it ever happened to you? (or anyone else willing to help?)