Often a pull request cannot be merged online due to conflicts. If there's no conflict, it is easy for you to do merging, even from the web client, with one click.
Confirm the merge
If the pull request cannot be merged online or you wish to test things locally before sending the merge to the repo on Github, you can perform the merge locally instead.
This post will explain subject using GitHub project for this task under windows with tool tortoisegit
1. Open your local repo (make pull the repo from git.)
2. Check out the branch you wish to merge to
git checkout master
3. Pull the desired branch from the other user's repo
git pull https://github.com/otheruser/repo.git branchname
4. Resolve any conflicts and commit the merge and review the changes and ensure they are satisfactory
5. Push the merge to your GitHub repo
git push origin master