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Package development

Source: vignettes/pkg_devel.Rmd
pkg_devel.Rmd

Introduction

This vignette contains code and annotations to develop a package, to prepare for package release, and to set up for a new version. It assumes the package has been set up as described in the vignette Package setup: vignette("pkg_setup", package = "develcoder").

Adding functions

Set up 

usethis::use_r("<func>")
devtools::document() # also runs devtools::load_all()
?<func>() # view help-page of the function

Do:

  • Manually update the NEWS file:
    ### Added functions - `<func>()` to ...
  • If the added function relies on other packages, you have to update the dependencies given in the DESCRIPTION file: see section Update dependencies.
  • When adding new function arguments to an existing function, it is best practice to place the new argument after existing arguments and use a default value that matches the old behaviour: then code written for the old version will work the same as before the change, even if it relies on positional matching, such that it is a non-breaking change.
  • When renaming functions, remember to also change their names in the _pkgdown.yml file if that file is used to create a custom index for the website (pkgdown::build_reference() warns about it if you forget).

Documentation 

#' Title
#'
#' Description
#'
#' @param x Vector of names to test.
#' @param allow_NA `TRUE` or `FALSE`: allow [NA]s of the correct type in `x`?
#' @param x,y Separate arguments by a comma without a space to create a single
#' description for multiple arguments.
#'
#' @details
#'
#' @returns
#' `TRUE` or `FALSE`, returned [invisibly][invisible].
#'
#' @section Side effects:
#' The directory indicated by the returned path is
#' [created][progutils::create_dir()] if it does not yet exist.
#'
#' @section Notes:
#' Some notes.
#'
#' @section Programming notes:
#' Some programming notes. Create a GitHub issue instead of To do / Wishlist
#' sections.
#'
#' @seealso
#' Section `Details` of [make.names()] and the [\R FAQ about valid names](
#' https://CRAN.R-project.org/doc/manuals/R-FAQ.html#What-are-valid-names_003f)
#' on the syntactical validity of names.
#'
#' @family collections of checks on type and length
#'
#' @examples
#' all_names(x = c("a", "b2a")) # TRUE
#'
#' @export
func_name <- function(x, allow_NA = TRUE) {
  stopifnot(checkinput::is_logical(allow_NA))
  <...>
}

Inherit documentation

It is possible to inherit sections of the documentation from other functions. Inherited sections are silently ignored if that section is also defined in the file itself.

#' @inherit is_number return
#' @inherit is_number details
#' @inheritSection is_logical Programming notes
#' @inheritSection is_logical @note

Inherit parameters

It is possible to inherit the description of parameters from other functions. Since roxygen2 8.0.0, it is possible to specify which arguments to inherit.

# inherit from a function in the current package
#' @inheritParams is_logical allow_NA

# inherit from a function in another package
#' @inheritParams utils::installed.packages fields

Add examples

Examples that create output files should write them to a temporary directory that is cleaned up afterwards. See the section Usage in practice in help("create_tempdir", package = "progutils") and section Add tests below.

Although examples rendered on a website created with pkgdown will display the output underneath the code, help-files accessed through help(<func>) will not, such that it might be useful to include a short comment regarding what feature of the output is notable.

To run all examples in a package:

devtools::run_examples()

To not run or not display code in examples, you can use the dontrun and dontshow tags, see the section Examples from the Writing R Extensions manual and the section about Examples in the book R packages.

Styling

Newlines can be forced using \cr.

For an overview of mathematical notation see https://rpruim.github.io/s341/S19/from-class/MathinRmd.html

Add tests

Background

For background on testing:

To attach a package during testing, use devtools::load_all(<pkg>). Alternatively, use attach(loadNamespace("<pkg>"), name = "<some_name>") which can be undone by detach("<some_name>").

Cleaning up

Tests that create output files should write them to a temporary directory that is cleaned up afterwards. See the section Usage in practice in help("create_tempdir", package = "progutils") and the vignette test fixtures from package testthat for more details. In addition, changed options and graphical parameters should be restored to their original state to prevent influencing subsequent code (see the entry in the CRAN cookbook for details). The following pattern shows how to do so for a single option or parameter:

orig_opt <- options(<option> = <value>)
orig_par <- par(<parameter> = <value>)
<do stuff>
par(orig_par)
options(<option> = orig_opt)

To reset all parameters at once, use orig_par <- par(no.readonly = TRUE). To restore options that are changed inside a function, add on.exit(par(orig_par)) immediately after changing the option.

Note that expect_silent(...) tests that no errors or warnings are emitted, not that no messages are emitted.

tinytest::expect_silent(expect_true(func_name(x = x, arg = arg)))
tinytest::expect_warning(
  expect_equal(func_name(x = "a", arg = arg), 3),
  pattern = "...", strict = TRUE, fixed = TRUE)
tinytest::expect_error(func_name(x = "a", arg = arg),
             pattern = "is_number(x) is not TRUE", fixed = TRUE)

The code below shows how to run tests.

# Run all tests of a package. Use 'devtools::test()' instead of
# 'tinytest::test_all()' if you used package 'testthat' to create tests.
tinytest::test_all()

# Run a specific test file, selecting the file by name
tinytest::run_test_file(fs::path(getwd(), "inst", "tinytest", "test_funcname.R"))
# Run specific test files, selecting the files by order
tinytest::run_test_file(
  list.files(fs::path(getwd(), "inst", "tinytest"), full.names = TRUE)[1:3])

Testing file paths

Testing file paths requires some thought because the file separator depends on the operating system (see .Platform$file.sep) and the backward slash is used as escape character in R such that it needs to be escaped itself by doubling them. Thus, a check on the presence of two successive slashes or backslashes in string string would use grepl(pattern = "//", x = string, fixed = TRUE) and grepl(pattern = "\\\\", x = string, fixed = TRUE), respectively. The message to point out their presence would be written as message("Successive '/' or '\\'") which would be printed as Successive '/' or '\'.

To circumvent the hassle of getting the correct type and number of slashes to compare with the path recorded in a message, check only for fixed parts of the message (e.g., "Repeated"), possibly followed by a check like tinytest::expect_true(fs::dir_exists(string)).

Update dependencies

First, you should consider if you really need a new dependency. Some additional effort in choosing dependencies or in coding can allow to depend on dependencies that themselves have not too many dependencies, which makes a project more stable over time. See the various contributions to the tinyverse.

Importing packages or functions

The standard way to use functions from other packages is to import the package (i.e., put it in the Imports: field of the DESCRIPTION file; this is done by
usethis::use_package("<pkg>", type = "Imports", min_version = "<version>")) and in code use the package name followed by two colons and the function name, e.g., utils::osVersion().

Using two colons to specify the package is not possible if the function is an operator: then it is necessary to also list the function in the NAMESPACE file, e.g., to add the line
#' @importFrom utils osVersion to the file R/<pkg>-package.R that was created by usethis::use_package_doc(). This is done by usethis::use_import_from(package = "utils", fun = "osVersion").

usethis::use_import_from(package = "utils", fun = "osVersion")
usethis::use_package("utils", type = "Suggests", min_version = "4.1.0")

Specifying minimum versions

Specifying a minimum package version when importing packages ensures that used features are actually present. Setting min_version = TRUE in usethis::use_package() uses the currently installed package version but that might be too strict as features are likely also present in older versions.

To check in which version used features were introduced, you can search the NEWS file of the relevant package for the function name to find the news item announcing its introduction. If that does not work, you can search for the function R file on the GitHub-page of the package and look in its history to see when it was created (or use the Blame feature to get a fine-grained overview of when code in that file was changed to see when a feature was introduced). Finally, you can also specify different minimum package versions in checks through GitHub actions and iteratively change them to find the minimum version that passes the check. Then specify that version as minimum version in your DESCRIPTION file.

Since R 4.6.0, read.dcf() recognises lines starting with # as comment lines, making it possible to use comments in the DESCRIPTION file to indicate why a particular package version is needed.

# Declare a minimum version for R itself
usethis::use_package("R", type = "Depends", min_version = "4.1.0")

# Declare a dependency on a package: 'use_package()' to declare a minimum
# version and 'use_dev_package()' to specify the remote repository to download
# the package from.
utils::packageVersion("checkinput")
usethis::use_package(package = "checkinput", type = "Imports", min_version = TRUE)
usethis::use_dev_package(package = "checkinput", type = "Imports",
                         remote = "github::JesseAlderliesten/checkinput")
utils::packageVersion("progutils")
usethis::use_package(package = "progutils", type = "Imports", min_version = TRUE)
usethis::use_dev_package(package = "progutils", type = "Imports",
                         remote = "github::JesseAlderliesten/progutils")
devtools::document()

Do:

  • Add the minimum declared R version to workflows for GitHub Actions, see the section Use GitHub Actions.

Adding vignettes

Set up 

usethis::use_vignette("my_vignette", title = "Some title")
# Add suggested dependencies on 'knitr' and 'rmarkdown'
usethis::use_package(package = "knitr", type = "Suggests")
usethis::use_package(package = "rmarkdown", type = "Suggests")
devtools::document()
pkgdown::build_article()
browseVignettes(package = basename(getwd()))

If no vignettes are visible after running browseVignettes(package = basename(getwd())), devtools::install() was probably run with the default argument build_vignettes = FALSE, use build_vignettes = TRUE instead: devtools::install(quick = FALSE, upgrade = FALSE, build_vignettes = TRUE). Run tools::pkgVignettes(package = "<pkg>") for information about the vignettes that R finds.

Use utils::vignette("<vignette_title>") (e.g., utils::vignette("pkg_devel")) to render a vignette in the help pane of RStudio. To do so with an Rd file, use tools::Rd2txt("path/to/file.Rd").

Styling

See the vignette RMarkdown and knitr: vignette("rmarkdown_knitr", package = "develcoder")) on using RMarkdown to style vignettes.

Put the next lines in the header of vignettes to get a table of contents:

output:
  rmarkdown::html_vignette:
  toc: true
toc_depth: 3

Linking

  • Link to another section in the same document:
    [<link text>][<Section title>] or [<Section title>].
  • Link to a help page of a package:
    help("<func>", package = "<pkg>") (unfortunately, help("<pkg>::<func>") does not work).
  • Link from a help-page to a vignette:
    The vignette *<vignette title>*: `vignette("<vignette>", package = "<pkg>")`
  • Link to another vignette in the same package:
    [<link text>](<vignette_filename>.html)

There is no official way to link from vignettes to help-pages or vice versa. pkgdown recognises calls like `<func>()` and `<pkg>::<func>()`, such that relevant links for such calls will be created on a package website (see the documentation for details).

Adding miscellaneous files

Non-standard files or folders should be added in the inst directory to pass R CMD checks. Those files and folders will be in the top directory in the installed package.

Preparing for updates

Check tests

Check if there are functions for which no test file was written and run all test files. Use devtools::test() instead of tinytest::test_all() if you used package testthat to create tests.

devtools::document()
tinytest::test_all() # or devtools::test() if testthat was used to create tests
develcoder::check_tests() # character(0) if all is fine

Automated checks

tools::CRAN_check_results(), tools::CRAN_check_details() and tools::CRAN_check_issues() give information about the current check status of CRAN packages. cransays (source code here) provides information about the status of packages during package submission to CRAN.

The next sections provide code to run checks from various packages.

devtools (local)

The default devtools::check() from devtools should be run often. devtools::check() uses the preferred approach of first building the package before checking it, whereas rcmdcheck::rcmdcheck() does not but is able to compare output from different checks.

See the CRAN cookbook and the appendix R-CMD-check from the book ‘R packages’ on how to proceed if checks fail.

The call to devtools::check() used below is more strict than the default, following suggestions from the Writing R extensions manual and from R packages (see the manual for details about the environment variables):

  • Using manual = TRUE to build and check the manual.

  • Using remote = TRUE (and thus incoming = TRUE) to run additional checks that are used by CRAN for new package submissions.

    These checks flag dependencies that are on GitHub, leading to NOTEs like
    Strong dependencies not in the CRAN or BioC software repositories: <pkg>,
    Suggests or Enhances not in mainstream repositories: <pkg>, and
    Unknown, possibly misspelled, fields in DESCRIPTION: 'Remotes'.
    If you do not intend to submit to CRAN, you can ignore these NOTEs.

    These checks also identify problems with linked URLs (i.e., not with URLs in comments). URLs:

    • should be accessible (e.g., point to public GitHub repositories, not to private repositories)
    • should be direct links, not redirects
    • should use the protocol https:// instead of http://
    • should use the canonical forms expected by CRAN, not the ‘simple’ forms displayed in the webbrowser:
      • https://CRAN.R-project.org/package=<pkg> for packages
      • https://CRAN.R-project.org/manuals.html to refer to manuals in general and URLs of the form https://CRAN.R-project.org/doc/manuals/r-release/R-exts.html to refer to a specific manual
      • https://CRAN.R-project.org/web/packages/policies.html to refer to the CRAN policies.

  • Using TRUE for environment variable _R_CHECK_DEPENDS_ONLY_ to run code while only using dependencies listed in the Depends and Imports fields of the DESCRIPTION file. This catches cases where a package that is listed in the Suggests field of the DESCRIPTION file is used in a vignette without being run conditionally through if(requireNamespace(<pkg>)) {<code>}.

  • Using TRUE for environment variable _R_CHECK_SUGGESTS_ONLY_ to run code while only using dependencies listed in the Depends, Imports and Suggests fields of the DESCRIPTION file.

devtools::document()
devtools::check(manual = TRUE, remote = TRUE)
devtools::check(manual = TRUE, remote = TRUE,
                env_vars = c("_R_CHECK_DEPENDS_ONLY_" = TRUE,
                             "_R_CHECK_SUGGESTS_ONLY_" = TRUE))
devtools::release_checks()
if(utils::packageVersion("devtools") >= "2.5.0") {
  # check for missing `\value` and `\examples` fields in `Rd` files
  devtools::check_doc_fields()
}

devtools (remote)

The following checks might be used to check the package on Windows or MacOS, respectively. devtools::check_win_release() emails a link to a webpage with the check results if the check is done. devtools::check_mac_release() links to a webpage where the results are shown if the check is done (the webpage might display ‘504 Gateway Time-out’ if it has not finished yet).

These checks might malfunction if your package has dependencies that are not on CRAN or BioConductor. Such dependencies should have been flagged above by devtools::check(manual = TRUE, remote = TRUE) as not in the CRAN or BioC software repositories or as not in mainstream repositories.

devtools::check_win_release()
devtools::check_mac_release()

codetools

Check R code for possible problems.

devtools::load_all()
# Return is invisible and silent if all is well
codetools::checkUsagePackage(pack = basename(getwd()),
                             all = TRUE, suppressParamAssigns = TRUE)

utils

Spell checking. This requires system libraries like Aspell.

checktor

Checktor provides various checks supplementing R CMD check.

checktor::checktor()

goodpractice

Runs checks of its own and checks from various other packages.

I do not use pkgcheck::pkgcheck() because their ‘own’ checks are largely covered by the checks from devtools used above, their checks from goodpractice are already covered here (see also this post on the relation between goodpractice and pkgcheck), and the checks from pkgstats are not very useful and require system libraries ctags-universal and GNU global. However, the pkgcheck GitHub action (see also here) might be useful.

# Select checks
# Show groups of checks: goodpractice::all_check_groups()
# Show all checks in some groups: goodpractice::checks_by_group(c("cyclocomp", "lintr"))
# Run all check from some groups:
# goodpractice::goodpractice(checks = goodpractice::checks_by_group(c("cyclocomp", "lintr")))
goodpractice_all_checks <- goodpractice::all_checks()
my_checks_goodpractice <- progutils::not_in(
  goodpractice_all_checks,
  c("covr", # time-consuming and wants 100% coverage
    "complexity_function_length", "cyclocomp", # I write complex functions
    # The lintr issue `Use == instead of %in% for scalar comparison` should be
    # ignored for 'x %in% y' if 'x' or 'y' might contain 'NA' that should be
    # removed: 'x %in% NA' and 'NA %in% y' return 'FALSE', whereas 'x == NA' and
    # 'NA == y' return 'NA'.
    "lintr_scalar_in_linter",
    "lintr_line_length_linter",
    "lintr_outer_negation_linter", # changes handling of NAs
    # flags data.frame() even if 'strings_as_factors' is not explicitly set
    "lintr_strings_as_factors_linter",
    "tidyverse_brace_linter",
    "tidyverse_function_left_parentheses_linter",
    "tidyverse_indentation_linter",
    "tidyverse_line_length_linter",
    "tidyverse_object_name_linter",
    "tidyverse_spaces_left_parentheses_linter",
    # does not find test-files in inst/tinytest, use check_test_files() instead.
    "tidyverse_test_file_names",
    "tidyverse_whitespace_linter",
    # Checks similar to those from 'rcmdcheck' and 'urlchecker' are also used by
    # devtools::check() that already has been run above
    goodpractice_all_checks[
      grepl(pattern = "^rcmdcheck_|^urlchecker_", x = goodpractice_all_checks)]
  )
)

res_goodpractice <- goodpractice::goodpractice(
  path = ".", checks = my_checks_goodpractice)
res_goodpractice_failed <- goodpractice::failed_checks(res_goodpractice)
res_goodpractice_failed

# Can also show output of selected checks through
# res_goodpractice$checks$<check_name>
res_goodpractice

Update package-wide documentation

DESCRIPTION

Run desc::desc_normalize() to normalize the DESCRIPTION file:

To show the DESCRIPTION file, use desc::desc() or utils::packageDescription(pkg = basename(getwd())). To only show the dependencies, use desc::desc_get_deps() or utils::packageDescription(pkg = basename(getwd()), fields = c("Depends", "Imports", "Suggests", "Enhances")).

Manually increment the package version in the DESCRIPTION file, or run R as administrator and then use usethis::use_version(). In the latter case, do not automatically commit the change, but do so manually to adjust the commit message to Bump to version x.y.z. Indicating the version number in the commit title makes it easier to find changes back later on (the pull request can have a description of the changes, i.e., the updated section of the NEWS file). See package lifecycle on how to add badges to packages and functions to indicate their lifecycle and its vignette Lifecycle stages, chapter Lifecycle, and the Semantic Versioning Specification on versioning.

CITATION

Update the CITATION.cff file to reflect the new package version (this code updates the citation file if it exists and otherwise uses the DESCRIPTION file to create a citation file):

cffr::cff_write(dependencies = FALSE) # Create or update a citation file

README

Install the development version of the package by running devtools::install() to ensure the updated version number without Git-commit ID will be included in the citation format in the README:

devtools::install(quick = FALSE, upgrade = FALSE, build_vignettes = TRUE)

Then Knit the README.Rmd to produce a README.md file. The citation in the README should then display the updated version number. The version badge at the top will still display the old version number, but that will change to the updated number when pushed to GitHub.

If the requirement that README.Rmd and README.md are staged at the same time was accidentally introduced, delete the the (hidden) file .git/hooks/pre-commit from the R-project folder (see the Description section in help("use_readme_rmd", package = "usethis") to remove that requirement.

NEWS

Restyle and publish the NEWS file.

Check reverse dependencies

Acknowledgement

This section reproduces a contribution by Ivan Krylov to the R-pkg-devel mailing list of 26 May 2026.

To check if packages that use your package still pass their checks if you made breaking changes, install the new version of your package, run tools::package_dependencies(reverse = TRUE, which = "most", recursive = "strong") to get the list of reverse dependencies, then use utils::download.packages(...) to obtain their latest tarballs and finally run tools::check_packages_in_dir() to check them.

tools::package_dependencies() and the related tools::dependsOnPkgs() only take packages from CRAN into account. devtools::revdep(pkg = <your pkg>, bioconductor = TRUE) also takes packages from BioConductor into account. To take other non-CRAN packages into account, use revdepcheck::revdep_check() or xfun::rev_check() (which has a GitHub Action: crandalf). If you find reverse dependencies that broke because of your changes, you can identify their maintainers using devtools::revdep_maintainers(pkg = <your pkg>) to notify them.

Locally test update 

devtools::document()
.libPaths() # Check if output of .libPaths() is correct.
# If the next line leads to the error 'lazy-load database
# '.../R/win-library/<X.Y>/<pkg>/R/<pkg>.rdb' is corrupt', you should restart R
# and again run the next line.
devtools::install(quick = FALSE, upgrade = FALSE, build_vignettes = TRUE)

# Load the package and view the help files as usual outside devtools:
library(basename(getwd()), character.only = TRUE)
browseVignettes(package = basename(getwd()))
?progutils::reorder_levels

Updating

Use GitHub Actions

To manually trigger GitHub Actions (GHA) set up workflow_dispatch (see section Automate checks in the vignette Package setup: vignette("pkg_setup", package = "develcoder")).

To check if a reverse dependency (i.e., a package that depends on a package you changed) that you created is still working fine: go to the Actions tab of the reverse dependency, select the action you want to trigger (e.g., check-standard.yaml), and use the Run workflow button shown at the top of the overview with workflow runs to run the GHA. You can select which branch it should run on but need to trigger it once manually on the main branch to be able to trigger it manually on other branches.

Scheduled jobs that failed can be rerun through the button Re-run jobs > Re-run failed jobs > Re-run jobs. If the GitHub actions page (e.g., https://github.com/JesseAlderliesten/develcoder/actions) indicates the package passes the R CMD checks whereas the badge on the README indicates it fails, make sure the R CMD check considers the main branch (i.e., if the devel branch passes but the main branch fails, the badge will have failing): use the Run workflow button to run the GHA on the main branch (see the previous paragraph).

If the package declares a dependency on a minimum R version, it is useful to specify the minimum declared R version to run in addition to the ones that are by default used in the template: for example, add - {os: ubuntu-latest, r: '4.1.0'} to section matrix: config: to also run the workflow with R 4.1.0 if your package declares R 4.1.0 as minimum version.

GHA: documentation and help

For more background on GitHub Actions, including an explanation of the syntax used in .yaml files, see the section about GitHub Actions in the book R packages, the GitHub reference and HowTo, and the section Use GitHub Actions in the vignette Package development: vignette("pkg_devel", package = "develcoder").

For help debugging build failures, see the Appendix R-CMD-check in the book R packages and the section Where to find help in the documentation of the actions package.

pkgdown website

See the documentation about package pkgdown and the chapter from the R packages book for further details.

# To manually update the website
pkgdown::build_site()

Open docs/index.html in a web browser to preview the website, or look at the files that constitute your package’s website are in the local docs directory.

Instead of manually updating the pkgdown website, one can use a GitHub Action workflow (e.g., pkgdown.yaml) that updates the website after a pull request or push. To set this up, run usethis::use_pkgdown_github_pages().

Styling

To create a thematic index instead of the default alphabetically ordered one, see the documentation and the example.

To customise the order in which Articles are listed, specify their order in the _pkgdown.yml file (run tools::pkgVignettes(package = "<pkg>")$names to get their names; see the documentation and for example the _pkgdown.yml file and non-alphabetical order of the articles in the checkrpkgs package.

To create a custom function index, include a section reference: in the _pkgdown.yml file with the desired headings and topics, see the documentation, an official example, and my own example. Then build the reference with pkgdown::build_reference() and view it locally by opening the file "<pkg>\docs\index.html" and browse to Reference to see the package index.

Merge devel-branch with main

To merge the devel branch with main (i.e., to incorporate the changes you made to the devel branch in the main branch), go the the devel branch on GitHub. Then use <Contribute> > Open Pull Request. Copy the updated NEWS in the description field and use the button Create pull request.

If the message No conflicts with base branch: Merging can be performed automatically, is displayed, you can use the green Merge pull request button, or change to Squash and merge.

Otherwise, the message This branch has conflicts that must be resolved will be displayed: follow the instructions to resolve the conflicts. Then push the button Commit merge. Then you should see No conflicts with base branch and you can proceed as described in the previous paragraph.

After a successful merge, you will see a message that you can delete the devel-branch, which you can do. To do so later, go to Pull requests, select the Closed tab, and scroll down to the button Delete branch.

Overwrite devel-branch after merge

In RStudio, open the relevant project to check there are no commits left. Then you can move to the main branch and Pull to get all updates you just committed to the main branch. Then click the New branch button in RStudio (besides the Switch branch icon indicating which branch (e.g., main or devel) you are using), use devel as branch name and click Create. You will be notified that devel already exists and asked if you want to overwrite it. If you have just merged devel into main, you can choose to overwrite it to have a new devel branch.

Set up a new branch

Instead of overwriting the devel-branch after merging into main, you can also create a completely new branch:

  • At the GitHub page of the package: Branch icon > green New branch button > specify a name for the branch > green Create new branch button.
  • Go back to the GitHub page of the package, and at the green Code button > copy URL to clipboard.
  • In RStudio: File > New project > Version control > Git and paste the copied URL in the Repository URL > Create Project.
  • Then (still in RStudio) in the Git menu change from main to the just-created branch.

Installing the updated package

Then you can delete the old package version from your PC (find.package("<pkg>") gives its location) and install the updated version following your own instructions on the GitHub pages of the relevant packages.

See also

Searching for packages

Troubleshooting

  • If running checks lead to the warning Warning in get_engine(options$engine): Unknown language engine '<name>' (must be registered via knit_engines$set()), you probably forgot to indicate the knit-engine when naming a code chunk:

    ```{use-sum}
1 + 1
```

    erroneously tries to use the engine use-sum, whereas the probably intended {r use-sum} correctly indicates that the r engine should be used and the code chunk should be named use-sum:

    ```{r use-sum}
1 + 1
```

    See sort(names(knitr::knit_engines$get())) for the available knit-engines.

  • If running checks lead to the error Failed with error: 'there is no package called '<pkg>'' Quitting from <filename>.Rmd:<line numbers> [<chunk name>], you probably forgot to use library(<pkg>) in a code chunck, used a package that is not declared as dependency in the DESCRIPTION file, or used a package that is declared as suggested dependency (i.e., is in the Suggests field of the DESCRIPTION file) without running that code conditionally on the presence of <pkg> through if(requireNamespace(<pkg>)) {<code>}. The latter is catched by using argument env_vars = c("_R_CHECK_DEPENDS_ONLY_" = TRUE) when running devtools::check().

  • If checks fail because of LaTeX errors when building the manual, you can use manual = FALSE.

  • If running devtools::document() leads to the error @section Could not resolve link to topic ":blank:" in the dependencies or base packages, regex-classes in example code are being interpreted as links. To prevent this, use backticks (`) to format a line as code, or wrap consecutive lines in \code{...}`.

  • Errors can arise if package development is not done from a clean R session. Use loadedNamespaces() to check which packages are loaded.

  • See also section Troubleshooting in the vignette about R packages in package checkrpkgs: Troubleshooting

Documentation and help

Guidelines on package development

Other useful resources