R CMD check

Mini-Lecture 16

Ben Baumer

Smith College

2024-10-29

Slack review

Dependencies

I’m still a bit unsure about dependencies. When and where do we have to import functions and when can we call libraries in the script?

• Use library() in scripts:
  • in data-raw/
• Use :: or @importFrom in package code:
  • in R/
  • add these packages to Imports

Dependencies (cont’d)

I’m still a bit unsure about dependencies. When and where do we have to import functions and when can we call libraries in the script?

• Use requireNamespace() in documentation code:
  • in vignettes/
  • in @examples
  • in tests/
  • add these packages to Suggests
• Don’t confuse Imports section of DESCRIPTION with import() directive in NAMESPACE

.Rbuildignore

I got lost on explaining .Rbuildignore.

• “Each line gives a Perl-compatible regular expression”

^.*\.Rproj$         # Automatically added by RStudio,
^\.Rproj\.user$     # used for temporary files. 
^README\.Rmd$       # An Rmarkdown file used to generate README.md
^cran-comments\.md$ # Comments for CRAN submission
^NEWS\.md$          # A news file written in Markdown

R CMD check

What is R CMD check?

• Runs over 50 automated checks

• Three types of problems:
  • Errors: must fix
  • Warnings: should really fix
  • Notes: should probably fix
• READ the error messages
  • Look them up in the book
  • Most won’t mean much until it happens to you
• Reach out with #questions

Errors you are likely to see

• Checking installed package size…
  • CRAN packages limited to 5 MB
• Checking package dependencies…
• Checking dependencies in R code…
  • Anything you use must appear in DESCRIPTION somewhere
  • Depends: probably do not use
  • Imports: dependencies in package
  • Suggests: packages used only in examples or vignettes

Errors you are likely to see

• Checking examples…
  • examples code has to run
  • can’t take too long
• Checking tests…
  • have to pass all tests
• Checking Rd sections…
  • have to document all exported functions
  • have to document all arguments
  • use @rdname to document multiple functions together

Example: macleish package

• Let’s take a quick tour!

Now

Homework

• Work on pull request