After updating the GitHub pages Jekyll resources useing bundle update, there are quite a few problems. Based on internet resolutions. Below are some tricks should be considered.

1. Download and install Python 2.7 from here, not the latest version but only version 2.7

2. Recall minima gem. You have to first locate your minima gem:

    bundle show minima
   

   Will give you something like /very/long/path/to/2.2.0/gems/minima-1.0.1. You can then copy/paste _includes, _layouts and _sass folders from your gem to your site root from the file explorer. Or you can do it with the command line from your root:

    cd your/root/folder
    cp -R `echo "$(bundle show minima)/_*/"` .
   

   Your site will now work on gh pages. And theme gem is now useless, because overridden by copied files. Please check the answer here.