GitHub personal access token

[DavidRach]

Re-posting a question from the old discussion page, in case anyone encounters a similar error. This error would likely be encountered towards the end of the Git walk-through

This was one of the cases of the GitHub and Positron connection not setting correctly on the first attempt. To fix, repeat the following step from Workstation Setup.

Generally this is enough to get the connection working. What you would look for to know whether this worked would be when returning to the GitHub tab you can see your username:

Hope this helps!

Best-
David

[almadtenorio]

Thanks so much for posting this! I did encounter this error. Sadly, the re-do of the GitHub and Positron connection didn't fix this error for me. I am able to view my Username in the GitHub tab as you described. Is there anything else I can try? Thanks in advance!

[DavidRach]

Thanks for reaching out @almadtenorio. Let's see if we can figure out what is going on. What operating system are you using?

One initial thing you could try is shutting down and reopening positron, make sure that you are still within your new Project folder, and then repeat setup:

library(usethis)

use_github(private=TRUE)

If still not working, can you run the following and attach the screenshot:

sessionInfo()

Best-
David

[almadtenorio]

Hi David, I have a macOS. I repeated again and still get the same outcome. Like others, I tried the token and unfortunately, it didn't work for me. I am attaching the screenshot requested. The only other thing I can think of that is different is I get a message when opening Positron saying it needs to be updated because it won't work with ifuture versions of macOS. Thank you in advance for your help!

[almadtenorio]

screenshot continued..

[DavidRach]

Hi @almadtenorio, let's try a different approach. Can you create a new project folder via "New Folder from Template" but leave the "Initialize Git Repository" option left unchecked. Create a couple basic files within the project (something like this).

Once this is done, try the steps in this workflow. After staging and commiting, follow the Positron Publish to GitHub button options. If you encounter another GitHub token error in the process, please screenshot and post it.

My hope is this approach on a new project folder fixes the communication issue between GitHub and Positron. Fingers crossed!

Best Wishes-
David

[almadtenorio]

Hi @DavidRach ,

Thank you for providing the alternative work-around. It worked! I followed all your steps and continued on using positron's interface and clicked on "Publish". I received the "successful" message.

Just wanted to update you, thanks so much, I am enjoying the course!

Alma

[vinced8928]

Hello!
I have the same problem here. I tried to create a token by using the "gh_token_help()" function, but still not working. I am in the right folder, R session is opended and GitHub is linked to Positron.

[drnkcampbell]

I got this error too before this question was posted in the Discussion board and I followed the help prompts to set up an access token linked to my GitHub profile, which seemed to work because I was able to proceed with the rest of the instructions after this. Should I have not set up this token/is it going to cause problems later on in the course? 🙈

[DavidRach]

I believe you should be okay. It was the older version of the connection setup. I will try to replicate tomorrow on one of the core's laptops that hasn't had R on it previously whether this was a step I missed in the documentation.

[vinced8928]

Hi everyone,
Just a follow up for my token problem. Yesterday I followed the instructions to create a token and it didn't seems to work. Today, I clicked on "Publish Branch" in the source control. At first, it didn't seems to work, but when I closed Positron and opened it again, a GitHub window appeard and asked me to connect. Now, everything seems to be backed up on GitHub when I commit.

I hope it help !

[DavidRach]

Hi @vinced8928, glad that it is working for you. Can you check this walk-through and tell me if any of the GitHub pop-ups I screened shot look familiar for what you did. Thanks! Best Wishes -David

[DavidRach]

@vinced8928 , @drnkcampbell , @almadtenorio: We had a similar issue for one of the in-person participants today.

We messed around by clicking up through the Publish branch options, and were able to create the private repository that could be seen on GitHub, but no data was pushed upstream. We then separately noticed that the following install_github function was also not working, meaning both the remotes or usethis packages were active.

We ultimately fixed the issue by reinstalling the curl package, and then reinstalling remotes/usethis to get both of the above to work properly. use_github() was then enough to send the repo to GitHub, with no Github Token being required at anypoint beyond the initial code during Positron setup.

Not quite sure which step in the sequence fixed the issue, but hope to find out and update the documentation later this week. Let me know if it starts working on your end.

Best Wishes-
David

[MjApo123]

Here's my error screenshot:

and here's the output after quarto check:

Thanks David!

[UMGCCCFCSR]

@MjApo123 So it looks like git is working (I can see the options) but we are having issues with the process of moving things from Git to GitHub. Can you open this short walk-through and starting at the staging commit steps see if you can see the publish button option? If yes, follow the walkthrough as far as it will let you. Take screenshots of any additional errors or pop-ups you may encounter. Thanks! David

[MjApo123]

Sorry but when I select source control in the activity bar, the primary side bar disappears. I don't know how to open source control to initialize repository. I'm using Mac Sequoia 15.7.2

[UMGCCCFCSR]

Hi @MjApo123, sorry your reply comment last week got missed. The primary side bar is the area within your screenshot in light gray. The little tabs in the blue bar dictate what contents are shown in the gray area. In the second second screenshot you are seeing the source control view. In the screenshot, you had one file staged (being tracked before the next commit). If after writing a commit message, you saw a publish option, follow it.

If however, there is no publish option, you likely already clicked it/set it up. One way to check would be to open your GitHub account, check under repositories, and see if your Git Practice folder is there.

If it is, return to Positron, hover over the section below in the screenshot below until the ... appears

Then click "pull" to bring in any new changes from GitHub, and then "push" to send your changes to GitHub. If you return to GitHub and you can see the new changes you just uploaded, the connection is set, and you are done.

Hope this helps! You could also try via a new Project Folder as was done this week if the issue persist (several in-person attendees had success this way).

Best Wishes-
David

[MjApo123]

Thanks David! I got this to work.

[FranziskaMarquard]

Hello :)
I have the same problem. I am using macOS Ventura 13.7.8, got the error telling me to generate a token. After generating the token I still got an error. I tried to reinstall remotes, curl and usethis and I restarted the program several times but I am still getting the same error.

[UMGCCCFCSR]

Hi @FranziskaMarquard, so your GitHub connection is present and partly working, as it was able to create the repository. It just wasn't able to pass the files up to the account, which is where it is error-ing out. Let me check and see if I can replicate the issue and get back with a solution. Best- David

[FranziskaMarquard]

Thank you David!

[UMGCCCFCSR]

Hi @FranziskaMarquardl, circling back, there have been several other users that got it to work after trying again in a new project folder (don't have an explanation why their initial attempts didn't work). Can you attempt the following walkthrough and see if that approach works at sending local data to GitHub? Thanks! David

[FranziskaMarquard]

Hi David,
thank you for your reply. I tried again, but I’m still getting the error: ‘Git: remote: Write access to repository not granted. I suspect the issue might be that Git is installed only for my user account, not system-wide. I’ve reached out to our IT department to have it installed with admin rights.
In the meantime I could still follow the course and find it very helpful. Thanks again for all your support!
Franziska

[UMGCCCFCSR]

Hi @FranziskaMarquard, thanks for the update! It could be you are within a folder (OneDrive, DropBox, or something local IT manages) where you don't have the proper permissions to write (create) objects. Generally your Documents folder is okay permission wise, but this is something your IT department should verify. Best- David

[bmottemann]

Ya, I am stuck at the tutorial at this step. I generated a personal access token on github but it doesn't seem to help. from your image I tytped in install_github("hally166/flowSpectrum") and im not sure what it did

[bmottemann]

https://usethis.r-lib.org/articles/git-credentials.html

Following the instructions starting at "Get a personal access token (PAT)" solved the issue for me! I set my PAT to have all the scopes with a 90 day exp.

[DavidRach]

Hi @bmottemann, looks like you went the older route for linking with GitHub (this was the way we used to need to do it for Rstudio). If it is your own personal computer, you can set your token to last longer than 90 days if you wish.

Positron is supposed to cut out this step in the new connecting approach. Still trying to figure out why it is working for some people as the current walk-through is written, but not all.

Out of curiosity, can I get the screenshot of your operating system setup? To get this information, you would type and enter in your terminal tab (to the right of the console tab) the following code

quarto check

And repost a screenshot. Thanks! Best Wishes- David

[bmottemann]

[BethDibnah]

Hello! I also seem to be stuck on this step, tried the suggested steps by David and my github seems to be connected as I can see my username, but still comes up with the error about the personal access token. Not sure what to try as I honestly don't understand the help options, apologies I am very new to this! Any help would be great, thanks so much.

[DavidRach]

Hi @BethDibnah, thanks for trying! Let's try a different approach. Can you create a new project folder via "New Folder from Template" but leave the "Initialize Git Repository" option left unchecked.

Create a couple basic files within the project (something like this).

Once this is done, try the steps in this workflow. After staging and comitting, follow the Positron Publish to GitHub button options. If you encounter another GitHub token error in the process, please screenshot and post it.

My hope is this approach on a new project folder fixes the communication issue between GitHub and Positron. Fingers crossed!

Best Wishes-
David

[BethDibnah]

Thank you David, this fixed the problem! Completed the steps you suggested then went back to my practice folder and ran the use_github(private=TRUE) and everything worked 😊 Thanks again!

[T-Wittenborn]

This fix worked for me too 👍

[liabuffa97]

Hi @DavidRach I'm stuck at this step as well.

I’ve already tried creating a new project folder while leaving the “Initialize Git Repository” option unchecked. I also followed the instructions to create and store a personal access token:
To create a personal access token: usethis::create_github_token()
To store the token for current and future use: gitcreds::gitcreds_set()

However, I’m still encountering the same error.
Is there anything else I could try?

Thanks in advance!

[DavidRach]

Hey @liabuffa97, please don't use the edit_r_environ route, from a password security perspective, it's way less than ideal compared to either of the other two options. Got to love Gemini suggestions some days 😐 Let's try troubleshooting one of the other options first 😃

Overall summary from all the various attempts in this thread

The ideal way for set up is entirely through Positron with the initial GitHub account link from Workstation Setup (most secure of the options). This approach is working for most people setting up. Generally, after providing your GitHub user.email and user.name to the terminal and making your first commit, you will see a Publish button that should manage to setup the connection. The alternate is via "use_github()" from the usethis package.

The GitHub token approach is the older approach (since it was the only way to do it in Rstudio, which is why AI keeps suggesting it). When set up through usethis package, it is reasonably secure method. If both the "publish button" and the "use_github()" options above fail (despite restarting Positron) I would go ahead and attempt this route.

The storage in .renviron is the oldest of the approaches was used by one of the earliest R packages, which is why Gemini remembers it. Of the options, it is the least secure of the options (passwords in plain text in a hidden file with consistent naming). I would try troubleshooting the other routes multiple times before settling on this approach.

[okolupaev]

I run into the same personal access token error towards the end of the Git walkthrough (MacOS 15.6.1).

This is the instructions suggested by Claude that resolved the issue for me.

Put these lines lines of code together

[Oscar-Kai]

Dear David,

Yes i managed to log myself to Pistron it shows Oscar-Kai(GitHub)

Unfortunately i cannot paste the screen shot through snipping tools

[Oscar-Kai]

OOH untill you hit he reply button is whene the screen short is seen okey!

[Oscar-Kai]

Dear David,

I am still stuck here at the token.its giving me an error of bad credentials i have not moved an inch since last time

[Oscar-Kai]

Dear David,

I am afaraid i have not moved after the token issue.

I now experience a bad credential issue. Copied below is my screen shot. I need an urgent help now.

[DavidRach]

@Oscar-Kai, not quite sure what is going on, since not sure what version of a token route was taken.

One thing to try is the following:

Uninstall the following R packages in the console tab using

remove.packages("devtools")
remove.packages("remotes")
remove.packages("usethis")

Then close and reopen Positron. Proceed to reinstall all three of the above packages using

install.packages("devtools")

Replacing in remotes and usethis between the parenthesis respectively for their own lines. If anything wants to update, select update all. If any errors occur, screenshot and share them.

Once everything is reinstalled, make sure your Git user name and email were set correctly.

Finally, once this is done, run the following in the terminal tab

quarto check

And take a screenshot of all the outputs. Hopefully this will help identify some more info about what might be going on.

As mentioned in the last course email, I am swamped at work and middle of major paper revisions that are due. Answering questions and troubleshooting issues will consequently sporadic until this changes.

Best-
David