Based on the information provided, that sounds a bit like the CSS files don’t load properly. That’s something you can easily verify with the ‘Network’ tab of the browser’s developers tools (press F12). You’ll see broken links there for the CSS assets.
If that’s the cause, it typically happens by not setting the baseURL configuration variable in your configuration file properly.
Hugo renders pages based on files in the /content/ folder, which you can optionally also ‘hide’ from rendering by setting their draft variable to true (because Hugo only renders non-draft pages by default).
But based on the information provided I cannot tell why you cannot commit those changes.
For me there’s not information in your post to even guess about what’s going on here.
Now you can either wait until someone with experience of R Markdown and the Creative Portfolio theme visits this thread. But that’s only a small subset of Hugo users, so that might not happen. 
Another option is to look at the requesting help suggestions, which has tips that make it easier for people on the forum to help you.