Thank you for your reply. I've tried to follow along but not succeed.
I ticked all the files (pic below) and clicked commit
Then, there is fatal-empty-indent-name message popped up. So, I closed and hit push. Unfortunately, it didn't update my repo.
Then, I found terminal tab (normally, I don't use it from inside RStudio). So, I issued
git status
git add .
git status
git commit -m "<COMMIT-MESSAGE>"
and hit push. Now, my repo is up-to-date.
Thank you for your help. 