Update Everything

This lesson is called Update Everything, part of the Fundamentals of R course. This lesson is called Update Everything, part of the Fundamentals of R course.

Transcript

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Your Turn

Update R
Update Positron
Update all packages using the Positron R Package Manager extension.

Learn More

If you want more guidance on downloading the newest version of R and Positron, check out Getting Started with R.

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Suzy Letourneau • September 28, 2026

I was able to update packages using the extension that David described in the video, and it said everything was up to date. But I also tried going through the little box icon in the sidebar for Packages, and choosing "Update all packages" and there is a list of about 10 packages that give a warning saying they will not be updated. These include: class, cluster, KernSmooth, lattice, MASS, matric, nlme, nnet, spatial, and survival. Is this because these packages are no longer supported or something like that? I'm also curious whether using the extension is better than the sidebar option in general.

Here is an example of one of the error messages: Warning: package 'class' in library '/Library/Frameworks/R.framework/Versions/4.6/Resources/library' will not be updated

Gracielle Higino Coach • September 30, 2026

Hi Suzy! That's a good question. This warning message is very cryptic, and it seems to be a thing with Windows users. It might be a matter of permissions, but it's odd that the Packages tool is not flagging these packages as old. Could you see which version the class package is showing, for example? You can check that in the extension or on the little box icon. If it's not 7.3-24, we should investigate further.

One thing you can try is running the following code and then check the package version again:

update.packages(oldPkgs = old.packages(), ask = FALSE)

In terms of if it's better to use the extension or the package icon window, it seems like the extension didn't have a new release since early this year, although there are clues that they are preparing a new release. This means that probably the integrated tool in Positron might be more up-to-date at this point. This lesson was recorded a year ago and the package window was not integrated into Positron just yet, so we needed an extension to check for packages updates in a more interactive way.

Mallik Janthak • October 3, 2026

Positron R package manager Identifier kv9898.positron-r-package-manager Version 0.2.6 has the following message, 'Maintenance notice: Recent versions of Positron include built-in package managers for R and Python. This project is no longer maintained. Version 0.2.6 is provided as a security update to address a dependency vulnerability.' What are the alternative ways of updating packages?

Mallik Janthak • October 3, 2026

Gracielle Higino Coach • October 5, 2026

Hi Mallik! Positron now has a built-in package manager that you can use to update packages. It's turned on by default and you can see a little box icon on the main pane. If you can't see it, check if you have this feature enabled here. More information about this can be found here on this page.