Setting Up a Personal Access Token via R

Last updated on 2024-12-03 | Edit this page

I use SSH, Why should I use HTTPS?

GitHub has announced that passwords will no longer be used for authentication from the command line starting in August 2021. While you may or may not be comfortable with SSH, here a few things that may motivate you:

  1. HTTPS is recommended by both GitHub and RStudio for people starting with R, so switching to HTTPS will help you empathize and demonstrate the ropes to learners in the long run.
  2. HTTPS gives you more fine-grained control over what access each token gives.
  3. RStudio Cloud is a really good platform that can connect to your GitHub account if you need to work on lesson development when you don’t have your computer handy. You cannot use SSH with that service, but it is possible to access it via HTTPS.
  4. You can connect to the GitHub API with a higher rate limit, which means that you can auto-create remote repositories and analyze GitHub data without a web browser.

Verifying Your Git Situation

To confirm that your Git session is correctly configured, open RStudio, and run the following line to check if your HTTPS credentials are set up properly:

R 

library("usethis")
git_sitrep() # git situation report

Pay attention to the GitHub report. What does it look like?

GitHub connected via PAT

OUTPUT 

Git config (global)
● Name: 'Zhian N. Kamvar'
● Email: 'zkamvar@gmail.com'
● Vaccinated: FALSE
ℹ See `?git_vaccinate` to learn more
● Default Git protocol: 'ssh'
GitHub
● Default GitHub host: 'https://github.com'
● Personal access token for 'https://github.com': '<discovered>'
● GitHub user: 'zkamvar'
● Token scopes: 'gist, repo, user, workflow'
● Email(s): 'zkamvar@gmail.com (primary)', ...
Git repo for current project
ℹ No active usethis project

If your output looks like this, then you are properly set up and you are good to go! If not, read on!

Creating a New GitHub Personal Access Token

If you see errors associated with your GitHub token (see below, e.g. ‘Token is invalid’ or ‘Can’t retrieve registered email address(es)’), then you should create a new one. Dr. Jenny Bryan wrote an excellent resource for creating and caching your GitHub credentials on your computer that will walk you through the process of generating a PAT, and storing it in a secure location. Here are the steps briefly via R:

  1. Create a GitHub PAT via R with usethis::create_github_token() (this will open a page in your browser pre-populated with the appropriate scopes. If this does not work, use this link to generate a new token for R.)
  2. Copy and store the token in a password manager (Lastpass, 1Password)
  3. Back in R, use gitcreds::gitcreds_set() to register your token with git.
  4. Check your credentials again with usethis::git_sitrep()

At this point, you should have things set up properly. If you are still having problems, you can try the following two steps (after you have your PAT):

  1. in R, use credentials::git_credential_forget() to clear the cache
  2. use credentials::set_github_pat() and paste your token.

Common Token Errors

There are a few possible errors you might see, but the remedy is always the same: get a new token and register it in your credentials keychain.

Invalid Personal Access Token

Invalid tokens can come from old tokens that were deleted from your GitHub account.

OUTPUT 

Git config (global)
● Name: 'Zhian N. Kamvar'
● Email: 'zkamvar@gmail.com'
● Vaccinated: FALSE
ℹ See `?git_vaccinate` to learn more
● Default Git protocol: 'ssh'
GitHub
● Default GitHub host: 'https://github.com'
● Personal access token for 'https://github.com': '<discovered>'
✖ Token is invalid
✖ Can't retrieve registered email address(es)
  If you are troubleshooting, check GitHub host, token, and token scopes
Git repo for current project
ℹ No active usethis projectw

Password as Token

This error often means that you have your password stored in your keychain instead of your token. This seems like a weird error until you realize that GitHub will stop allowing password authentication from the command line in August 2021.

OUTPUT 

Git config (global)
● Name: 'Zhian N. Kamvar'
● Email: 'zkamvar@gmail.com'
● Vaccinated: FALSE
ℹ See `?git_vaccinate` to learn more
● Default Git protocol: 'ssh'
GitHub
● Default GitHub host: 'https://github.com'
Error: GitHub PAT must have one of these forms:
  * 40 hexadecimal digits (older PATs)
  * A 'ghp_' prefix followed by 36 to 251 more characters (newer PATs)
Type .Last.error.trace to see where the error occured

No Personal Access Token Detected

This means you have not registered a Personal Access Token with git and are good to start fresh!

OUTPUT 

● Name: 'Zhian N. Kamvar'
● Email: 'zkamvar@gmail.com'
● Vaccinated: FALSE
ℹ See `?git_vaccinate` to learn more
● Default Git protocol: 'ssh'
GitHub
● Default GitHub host: 'https://github.com'
● Personal access token for 'https://github.com': <unset>
✖ Call `gh_token_help()` for help configuring a token
Git repo for current project
ℹ No active usethis project