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Bookdown, quarto and other scripts dependencies

Sébastien Rochette

2024-07-02

Source: vignettes/b-bookdown-and-scripts.Rmd
b-bookdown-and-scripts.Rmd

Load package {attachment}

Use “dev/dev_history.R”

When building your package, create a file called “dev_history.R” in a “dev/” directory. You will store all “manual” calls to devtools::xxx and usethis::xxx in this script.
Its first line should be :

usethis::use_build_ignore("dev")

You can then call {attachment} in this file to help you build your description file.

Use {attachment} with {bookdown} / {pagedown} / {quarto} dependencies

Dependencies of your Bookdown can be automatically installed if you use a “DESCRIPTION” file.
Indeed, you can use this procedure to create the DESCRIPTION file for local installation or for Continuous Integration with GitLab Pages or GitHub Actions. See for instance, the GitLab CI workflows in {gitlabr}: https://github.com/ThinkR-open/gitlabr/tree/main/inst/gitlab-ci

  1. Create a “DESCRIPTION” file
usethis::use_description()
  1. Fill the “DESCRIPTION” file using attachment::att_to_desc_from_is(). Note that to include it directly in CI (as proposed in {gitlabr} templates), you may need to set att_to_desc_from_is(must.exist = FALSE).
    Note that att_from_rmds() also works for “.qmd” documents. You can use att_from_qmds() if you want, although for now there is no difference and it will also parse “.Rmd” documents. 
# bookdown Imports are in Rmds
imports <- c("bookdown", attachment::att_from_rmds("."))

attachment::att_to_desc_from_is(
  path.d = "DESCRIPTION",
  imports = imports, suggests = NULL, 
  must.exist = FALSE
)
  1. Install dependencies from the DESCRIPTION file
# install.packages("remotes")
remotes::install_deps()
  1. Build your {bookdown} / {pagedown} / {quarto}

Propose content for “Remotes” field

An interest of using DESCRIPTION to list your bookdown dependencies is to use packages from other sources than CRAN and list them in the ‘Remotes’ field.
Here comes set_remotes_to_desc(), which adds packages that were installed from other source than CRAN to Remotes: field in DESCRIPTION.

You can run it after att_to_desc_from_is().

attachment::att_to_desc_from_is(
  path.d = "DESCRIPTION",
  imports = imports, suggests = NULL, 
  must.exist = FALSE
) %>%
  set_remotes_to_desc()

Get all packages listed in “namespace”

You can get the list of packages in your package with att_from_namespace()

Get all packages added using pkg::function or library/require

This reads all files in directories of R scripts (default to R directory of a package)

Get all packages called in your Rmd

If you have vignette, you may want to list extra libraries, not listed in your “Depends” list. This function applies to any Rmd file, of course.

Get all packages called in your Rmd and show them in this same Rmd

Of course, you can also use {attachment} out of a package to list all package dependencies of R scripts using att_from_rscripts() or Rmd files using att_from_rmds().
If you want to run att_from_rmds() inside a Rmd as for this vignette, you will need to set att_from_rmds(inside_rmd = TRUE)

dummypackage <- system.file("dummypackage", package = "attachment")

att_from_rmds(path = file.path(dummypackage, "vignettes"), inside_rmd = TRUE)
#> [1] "knitr"     "rmarkdown" "glue"