Update Everything
This lesson is called Update Everything, part of the R in 3 Months (Spring 2026) course. This lesson is called Update Everything, part of the R in 3 Months (Spring 2026) course.
Transcript
Click on the transcript to go to that point in the video. Please note that transcripts are auto generated and may contain minor inaccuracies.
Loading transcript...
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.
Have any questions? Put them below and we will help you out!
Course Content
148 Lessons
1
Welcome to Fundamentals of R
01:20
2
Update Everything
02:26
3
Start a New Project
02:38
4
The Tidyverse
03:24
5
Pipes
03:52
6
select()
04:43
7
mutate()
03:22
8
filter()
10:18
9
Quiz
10
summarize()
05:38
11
Grouped Summaries
04:24
12
arrange()
02:50
13
Create a New Data Frame
03:30
14
Quiz
15
Bring it All Together (Data Wrangling)
07:09
16
Week 2 Project Assignment
13:10
17
Week 2 Coworking Session (Spring 2026)
18
Week 2 Live Session (Spring 2026)
59:16
1
The Grammar of Graphics
04:36
2
Scatterplots
03:40
3
Histograms
04:51
4
Bar Charts
04:53
5
Quiz
6
Setting color and fill Aesthetic Properties
02:43
7
Setting color and fill Scales
05:12
8
Quiz
9
Setting x and y Scales
02:58
10
Adding Text to Plots
05:50
11
Plot Labels
02:59
12
Themes
02:10
13
Facets
02:56
14
Save Plots
02:49
15
Bring it All Together (Data Visualization)
06:14
16
Week 3 Project Assignment
06:02
17
Week 3 Coworking Session (Spring 2026)
18
Week 3 Live Session (Spring 2026)
1:00:46
1
Downloading and Importing Data
08:13
2
Overview of Tidy Data
05:03
3
Tidy Data Rule #1: Every Column is a Variable
06:26
4
Tidy Data Rule #3: Every Cell is a Single Value
09:27
5
Tidy Data Rule #2: Every Row is an Observation
04:05
6
Quiz
7
Week 6 Coworking Session (Spring 2026)
8
Week 6 Live Session (Spring 2026)
59:31
1
Best Practices in Data Visualization
03:38
2
Tidy Data
02:25
3
Pipe Data in ggplot
08:18
4
Reorder Plots to Highlight Findings
03:50
5
Line Charts
04:13
6
Use Color to Highlight Findings
08:23
7
Declutter
07:53
8
Add Descriptive Labels to Your Plots
09:18
9
Use Titles to Highlight Findings
08:30
10
Use Annotations to Explain
06:35
11
Quiz
12
Week 9 Coworking Session (Spring 2026)
13
Week 9 Live Session (Spring 2026)
59:10
1
Advanced Markdown
07:10
2
Tables
15:48
3
Advanced YAML and Code Chunk Options
05:42
4
Inline R Code
03:42
5
Making Your Reports Shine: Word Edition
05:08
6
Making Your Reports Shine: PDF Edition
07:37
7
Making Your Reports Shine: HTML Edition
06:08
8
Presentations
11:12
9
Dashboards
06:20
10
Websites
08:11
11
Publishing Your Work
02:37
12
Quarto Extensions
06:38
13
Parameterized Reporting, Part 1
07:02
14
Parameterized Reporting, Part 2
04:03
15
Parameterized Reporting, Part 3
06:22
16
Quiz
17
Week 12 Coworking Session (Spring 2026)
18
Week 12 Live Session (Spring 2026)
57:26
1
Working with labelled data
05:35
2
Understanding Documentation Pages
05:20
3
Factors in R
11:18
4
Add citations to Quarto documents
10:42
5
Change titles of facet plots
08:16
6
Population pyramid plot
04:24
7
Why use Git - example case
06:13
8
How to access data not on GitHub
13:46
9
Dealing with merge conflicts in GitHub Desktop
03:22
10
Crosstabs
06:58
11
Difference between == and %in%
03:17
12
Quarto - rendering and working directories
13:05
13
Using Function Arguments
13:06
You need to be signed-in to comment on this post. Login.
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
classpackage 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:
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
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?
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.