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Introduction to Git and GitHub
- What is Git? What is GitHub?
- Why Should You Learn to Use Git and GitHub?
- Update Everything
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Git
- Install Git
- Configure Git
- Create a Local Git Repository
- Commits
- Commit History
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GitHub
- GitHub Repositories
- Connect RStudio and GitHub
- Push an RStudio Project to a GitHub Repository
- Pull a GitHub Repository to an RStudio Project
- Keep RStudio and GitHub in Sync
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Collaborating with Git and GitHub
- Why Use GitHub vs Dropbox, Google Drive, Box, etc?
- Dealing with Common Problems: Can't Pull Code from GitHub
- Dealing with Common Problems: Merge Conflicts
- Dealing with Common Problems: Can't Push Code to GitHub
- Let's Keep Bad Things from Happening in the First Place
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Branches
- What are Branches and Why Should We Use Them?
- Branch Names
- How to Create Branches
- Using Pull Requests to Merge a Branch Into Main
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Project Management with GitHub
- GitHub Issues
- How to Organize Issues
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Wrapping Up
- Other Cool Stuff You Can Do with GitHub
Using Git and GitHub with R
Update Everything
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This lesson is called Update Everything, part of the Using Git and GitHub with R course. This lesson is called Update Everything, part of the Using Git and GitHub with R course.
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Your Turn
Update/re-install all of your R packages
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Matt M
October 17, 2021
at 1:15 and 2:45, you mention "link below" for R and RStudio. I don't see link below (but obviously could still get there).
When updating packages, several keep showing up as having newer versions available. gtsummary, insight, prismatic, rvest, and usethis. I've hit Select All and Install Updates several times. But when I click on Update Packages again, the same 5 show up.
David Keyes
October 18, 2021
Thanks! I just updated the Your Turn instructions to include the links.
On the package updates, if you quit RStudio and open it back up, do you still see those packages as needing to be updated?
Matt M
October 19, 2021
Yes, I've restarted RStudio (and my computer) and still see them as needing to be updated.
David Keyes
October 19, 2021
Very strange! First of all, the most important thing is to have the gitcreds and usethis packages up to date. As long as you have the latest versions of those, you should be fine.
However, if we do want to figure out what's going on, let's do this: If you type
install.packages("PACKAGE NAME")
in the console, that should also update your package. Why don't you try that with one package and lee me know if it works?Ben Skutnik
October 6, 2022
Do those packages warn you about a non-zero exit status when you do try to update them?
David Keyes
October 6, 2022
They should warn you if they don't update correctly. Are you getting that message?
Matthew Reichardt
October 18, 2022
Often when I update packages, not everything updates, so if I click on update packages again, I still see some listed. Sometimes I can manually remove them and manually re-install them, but that doesn't always work. For example, after I updated R and RStudio, and then ran update packages, I am still seeing commonmark has an installed version of 1.8.0 and an available version of 1.8.1, but nothing I can seem to do updates to the newer version.
Charlie Hadley
October 19, 2022
Hi Matt,
Are you describing using the point and click interface for modifying packages in the "Packages" tab?
Thanks, Charlie
Matthew Reichardt
October 19, 2022
Hi Charlie, Yes, I think. When packages are not updated with the update button, I've had some luck manually removing the package, by clicking the "X" button in the packages tab and then running install.packages() for what I just removed. This, however, doesn't always work and is, obviously, cumbersome to do.
Charlie Hadley
October 20, 2022
Unfortunately, I think the Packages tab is just not fit for purpose. It cause me frustration when I experimented with it and now actively encourage others against using it.
Instead, we can use remove.packages("ggtext") in the console to remove a package and install.packages("ggtext") to both install and update a package. If there's a new version of a package when you run install.packages() it will get you the new version. I'd recommend restarting RStudio between removing and installing packages. This can be done by selecting Session in the menu bar and selecting "Restart R".
Cheers, Charlie
Matt Kropp
October 25, 2022
Can I just use the top menu and click help-> Check for Updates to update R Studio?
David Keyes
October 25, 2022
That works too!