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updating the R habitat


Habitat by Patrice Ouellet is licensed under CC BY-NC-ND 2.0

contents

prerequisites
stay current
update R
update RStudio
update R packages
conclusion
references

prerequisites

Start every work session by launching portfolio.Rproj

You have set up a package library independent of the R installation, for example, at C:/R/library, as instructed here.

Packages

install.packages("installr")
install.packages("devtools")

stay current

Running old software can be considerably harder than running new software.

R updates about twice a year.

Get current at the start of a new project, but avoid updating if you are approaching a project deadline.

Read more about it at Maintaining R, a chapter in (Bryan and Hester, 2019).

update R

On a Windows machine, we update R using the R GUI running as an administrator.

  • Navigate to your most recent Rgui.exe file located in your Programs directory, e.g., C:\Program Files\R\R-3.5.3\bin\x64\Rgui.exe
  • Right-click on Rgui.exe and run as administrator

In the R GUI window that appears, run the commands

.libPaths("C:/R/library")
library("installr")
updateR()

OK all defaults except the libraries questions. We are using the C:/R/libr ary directory for packages—independent of the R installation. So we can answer “no” to the library questions in the R update.

update RStudio

Check for updates from the menu Help > Check for Updates.

If Check for Updates does not appear in the menu,

  • Find the current version of RStudio from the menu Help > About RStudio
  • Navigate to the RStudio website, find out what the current version is.

If you decide to update RStudio, close RStudio on your machine, download the new version, and run the RStudio-n.n.n.exe as an administrator (n.n.n is the current version number).

update R packages

When updating packages, if a window pops up asking about compilation,

  • NO saves time
  • YES gets you the latest version but can be time-consuming. Don’t say yes if you are in a hurry to get some work done.

From within RStudio

  • From the RStudio pane, Select Packages > Update
  • OR, from the menu, Tools > Check for Package updates …

CRAN packages only

  • Copy and paste these lines in the Console
  • Follow the instructions that appear to select the packages to update
update.packages(lib.loc = "C:/R/library", 
    ask = FALSE, 
    checkBuilt = TRUE)

GitHub packages (and CRAN packages)

  • Copy and paste these lines in the Console
  • Follow the instructions that appear to select the packages to update
devtools::update_packages(packages = TRUE, 
    lib.loc = "C:/R/library",
    ask = FALSE)

conclusion

To conclude the course, I offer two additional short pages of final thoughts

references

Bryan J and Hester J (2019) What They Forgot to Teach You About R. https://whattheyforgot.org/

Wickham H and Grolemund G (2017) R for Data Science. O’Reilly Media, Inc., Sebastopol, CA https://r4ds.had.co.nz/

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