diff --git a/DESCRIPTION b/DESCRIPTION index c744db6f1..051974065 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -66,3 +66,4 @@ Remotes: r-lib/covr, r-lib/rcmdcheck RoxygenNote: 6.1.0 +Roxygen: list(markdown = TRUE) diff --git a/R/R.r b/R/R.r index 99e7cb723..ee32e0359 100644 --- a/R/R.r +++ b/R/R.r @@ -3,8 +3,8 @@ #' Devtools sets a number of environmental variables to ensure consistent #' between the current R session and the new session, and to ensure that #' everything behaves the same across systems. It also suppresses a common -#' warning on windows, and sets \code{NOT_CRAN} so you can tell that your -#' code is not running on CRAN. If \code{NOT_CRAN} has been set externally, it +#' warning on windows, and sets `NOT_CRAN` so you can tell that your +#' code is not running on CRAN. If `NOT_CRAN` has been set externally, it #' is not overwritten. #' #' @keywords internal diff --git a/R/bash.r b/R/bash.r index 5e769e4d1..7f20ec01e 100644 --- a/R/bash.r +++ b/R/bash.r @@ -1,7 +1,7 @@ #' Open bash shell in package directory. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @export bash <- function(pkg = ".") { pkg <- as.package(pkg) diff --git a/R/build-manual.R b/R/build-manual.R index 56ab13739..e5380f496 100644 --- a/R/build-manual.R +++ b/R/build-manual.R @@ -1,11 +1,11 @@ #' Create package pdf manual #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information. +#' [as.package()] for more information. #' @param path path in which to produce package manual. -#' If \code{NULL}, defaults to the parent directory of the package. +#' If `NULL`, defaults to the parent directory of the package. #' -#' @seealso \code{\link{Rd2pdf}} +#' @seealso [Rd2pdf()] #' @export build_manual <- function(pkg = ".", path = NULL) { pkg <- as.package(pkg) diff --git a/R/check-devtools.r b/R/check-devtools.r index b4ed3f452..4ea6bf059 100644 --- a/R/check-devtools.r +++ b/R/check-devtools.r @@ -1,10 +1,10 @@ #' Custom devtools release checks. #' #' This function performs additional checks prior to release. It is called -#' automatically by \code{\link{release}()}. +#' automatically by [release()]. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information. +#' [as.package()] for more information. #' @keywords internal #' @export release_checks <- function(pkg = ".", built_path = NULL) { diff --git a/R/check-doc.r b/R/check-doc.r index 679a58223..8147af0f6 100644 --- a/R/check-doc.r +++ b/R/check-doc.r @@ -1,12 +1,12 @@ -#' Check documentation, as \code{R CMD check} does. +#' Check documentation, as `R CMD check` does. #' #' This function attempts to run the documentation related checks in the -#' same way that \code{R CMD check} does. Unfortunately it can't run them +#' same way that `R CMD check` does. Unfortunately it can't run them #' all because some tests require the package to be loaded, and the way #' they attempt to load the code conflicts with how devtools does it. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @return Nothing. This function is called purely for it's side effects: if # no errors there will be no output. #' @export diff --git a/R/check-git.r b/R/check-git.r index 8e21f00c0..05452299d 100644 --- a/R/check-git.r +++ b/R/check-git.r @@ -1,10 +1,10 @@ #' Git checks. #' #' This function performs Git checks checks prior to release. It is called -#' automatically by \code{\link{release}()}. +#' automatically by [release()]. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information. +#' [as.package()] for more information. #' @keywords internal git_checks <- function(pkg = ".") { pkg <- as.package(pkg) diff --git a/R/check-results.R b/R/check-results.R index 032a27b51..ac1f67b36 100644 --- a/R/check-results.R +++ b/R/check-results.R @@ -106,17 +106,17 @@ trunc_middle <- function(x, n_max = 25, n_top = 10, n_bottom = 10) { #' Parses R CMD check log file for ERRORs, WARNINGs and NOTEs #' -#' Extracts check messages from the \code{00check.log} file generated by -#' \code{R CMD check}. +#' Extracts check messages from the `00check.log` file generated by +#' `R CMD check`. #' -#' @param path check path, e.g., value of the \code{check_dir} argument in a -#' call to \code{\link{check}} +#' @param path check path, e.g., value of the `check_dir` argument in a +#' call to [check()] #' @param error,warning,note logical, indicates if errors, warnings and/or #' notes should be returned #' @return a character vector with the relevant messages, can have length zero #' if no messages are found #' -#' @seealso \code{\link{check}}, \code{\link{revdep_check}} +#' @seealso [check()], [revdep_check()] #' @export check_failures <- function(path, error = TRUE, warning = TRUE, note = TRUE) { check_dir <- file.path(path, "00check.log") diff --git a/R/check-win.r b/R/check-win.r index bcea75a72..a0316c7d1 100644 --- a/R/check-win.r +++ b/R/check-win.r @@ -1,17 +1,17 @@ #' Build windows binary package. #' #' This function works by bundling source package, and then uploading to -#' \url{http://win-builder.r-project.org/}. Once building is complete you'll +#' . Once building is complete you'll #' receive a link to the built package in the email address listed in the #' maintainer field. It usually takes around 30 minutes. As a side effect, -#' win-build also runs \code{R CMD check} on the package, so \code{build_win} +#' win-build also runs `R CMD check` on the package, so `build_win` #' is also useful to check that your package is ok on windows. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @inheritParams pkgbuild::build -#' @param quiet If \code{TRUE}, suppresses output. -#' @param ... Additional arguments passed to \code{\link[pkgbuild]{build}}. +#' @param quiet If `TRUE`, suppresses output. +#' @param ... Additional arguments passed to [pkgbuild::build()]. #' @family build functions #' @name check_win NULL diff --git a/R/check.r b/R/check.r index 73ccfc6cd..c3b245b5b 100644 --- a/R/check.r +++ b/R/check.r @@ -1,15 +1,15 @@ #' Build and check a package, cleaning up automatically on success. #' -#' \code{check} automatically builds and checks a source package, using all -#' known best practices. \code{check_built} checks an already built package. +#' `check` automatically builds and checks a source package, using all +#' known best practices. `check_built` checks an already built package. #' -#' Passing \code{R CMD check} is essential if you want to submit your package +#' Passing `R CMD check` is essential if you want to submit your package #' to CRAN: you must not have any ERRORs or WARNINGs, and you want to ensure #' that there are as few NOTEs as possible. If you are not submitting to CRAN, #' at least ensure that there are no ERRORs or WARNINGs: these typically #' represent serious problems. #' -#' \code{check} automatically builds a package before calling \code{check_built} +#' `check` automatically builds a package before calling `check_built` #' as this is the recommended way to check packages. Note that this process #' runs in an independent realisation of R, so nothing in your current #' workspace will affect the process. @@ -22,34 +22,34 @@ #' \itemize{ #' #' \item The standard environment variables set by devtools: -#' \code{\link{r_env_vars}}. Of particular note for package tests is the -#' \code{NOT_CRAN} env var which lets you know that your tests are not +#' [r_env_vars()]. Of particular note for package tests is the +#' `NOT_CRAN` env var which lets you know that your tests are not #' running on cran, and hence can take a reasonable amount of time. #' #' \item Debugging flags for the compiler, set by #' \code{\link{compiler_flags}(FALSE)}. #' -#' \item If \code{aspell} is found \code{_R_CHECK_CRAN_INCOMING_USE_ASPELL_} -#' is set to \code{TRUE}. If no spell checker is installed, a warning is +#' \item If `aspell` is found `_R_CHECK_CRAN_INCOMING_USE_ASPELL_` +#' is set to `TRUE`. If no spell checker is installed, a warning is #' issued.) #' -#' \item env vars set by arguments \code{incoming}, \code{remote} and -#' \code{force_suggests} +#' \item env vars set by arguments `incoming`, `remote` and +#' `force_suggests` #' } #' #' @return An object containing errors, warnings, and notes. #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param document If \code{NA} and the package uses roxygen2, will -#' rerun \code{\link{document}} prior to checking. Use \code{TRUE} -#' and \code{FALSE} to override this default. -#' @param build_args Additional arguments passed to \code{R CMD build} +#' [as.package()] for more information +#' @param document If `NA` and the package uses roxygen2, will +#' rerun [document()] prior to checking. Use `TRUE` +#' and `FALSE` to override this default. +#' @param build_args Additional arguments passed to `R CMD build` #' @param check_dir the directory in which the package is checked -#' compatibility. \code{args = "--output=/foo/bar"} can be used to change the +#' compatibility. `args = "--output=/foo/bar"` can be used to change the #' check directory. -#' @param ... Additional arguments passed on to \code{\link[pkgbuild]{build}()}. +#' @param ... Additional arguments passed on to [pkgbuild::build()]. #' @param cleanup Deprecated. -#' @seealso \code{\link{release}} if you want to send the checked package to +#' @seealso [release()] if you want to send the checked package to #' CRAN. #' @export check <- function(pkg = ".", @@ -131,24 +131,24 @@ check <- function(pkg = ".", #' @export #' @rdname check #' @param path Path to built package. -#' @param cran if \code{TRUE} (the default), check using the same settings as +#' @param cran if `TRUE` (the default), check using the same settings as #' CRAN uses. -#' @param remote Sets \code{_R_CHECK_CRAN_INCOMING_REMOTE_} env var. -#' If \code{TRUE}, performs a number of CRAN incoming checks that require +#' @param remote Sets `_R_CHECK_CRAN_INCOMING_REMOTE_` env var. +#' If `TRUE`, performs a number of CRAN incoming checks that require #' remote access. -#' @param incoming Sets \code{_R_CHECK_CRAN_INCOMING_} env var. -#' If \code{TRUE}, performs a number of CRAN incoming checks. -#' @param force_suggests Sets \code{_R_CHECK_FORCE_SUGGESTS_}. If -#' \code{FALSE} (the default), check will proceed even if all suggested +#' @param incoming Sets `_R_CHECK_CRAN_INCOMING_` env var. +#' If `TRUE`, performs a number of CRAN incoming checks. +#' @param force_suggests Sets `_R_CHECK_FORCE_SUGGESTS_`. If +#' `FALSE` (the default), check will proceed even if all suggested #' packages aren't found. -#' @param run_dont_test Sets \code{--run-donttest} so that tests surrounded in +#' @param run_dont_test Sets `--run-donttest` so that tests surrounded in #' \code{\\dontest\{\}} are also tested. This is important for CRAN #' submission. -#' @param manual If \code{FALSE}, don't build and check manual -#' (\code{--no-manual}). -#' @param args Additional arguments passed to \code{R CMD check} -#' @param env_vars Environment variables set during \code{R CMD check} -#' @param quiet if \code{TRUE} suppresses output from this function. +#' @param manual If `FALSE`, don't build and check manual +#' (`--no-manual`). +#' @param args Additional arguments passed to `R CMD check` +#' @param env_vars Environment variables set during `R CMD check` +#' @param quiet if `TRUE` suppresses output from this function. #' @inheritParams rcmdcheck::rcmdcheck check_built <- function(path = NULL, cran = TRUE, remote = FALSE, incoming = remote, force_suggests = FALSE, diff --git a/R/dev-mode.r b/R/dev-mode.r index 14328427a..d5f7f1f56 100644 --- a/R/dev-mode.r +++ b/R/dev-mode.r @@ -1,14 +1,14 @@ #' Activate and deactivate development mode. #' -#' When activated, \code{dev_mode} creates a new library for storing installed -#' packages. This new library is automatically created when \code{dev_mode} is +#' When activated, `dev_mode` creates a new library for storing installed +#' packages. This new library is automatically created when `dev_mode` is #' activated if it does not already exist. #' This allows you to test development packages in a sandbox, without #' interfering with the other packages you have installed. #' -#' @param on turn dev mode on (\code{TRUE}) or off (\code{FALSE}). If omitted -#' will guess based on whether or not \code{path} is in -#' \code{\link{.libPaths}} +#' @param on turn dev mode on (`TRUE`) or off (`FALSE`). If omitted +#' will guess based on whether or not `path` is in +#' [.libPaths()] #' @param path directory to library. #' @export #' @examples diff --git a/R/document.r b/R/document.r index f77e6c410..d3982f632 100644 --- a/R/document.r +++ b/R/document.r @@ -1,14 +1,14 @@ #' Use roxygen to document a package. #' -#' This function is a wrapper for the \code{\link[roxygen2]{roxygenize}()} +#' This function is a wrapper for the [roxygen2::roxygenize()] #' function from the roxygen2 package. See the documentation and vignettes of #' that package to learn how to use roxygen. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @inheritParams roxygen2::roxygenise -#' @seealso \code{\link[roxygen2]{roxygenize}}, -#' \code{browseVignettes("roxygen2")} +#' @seealso [roxygen2::roxygenize()], +#' `browseVignettes("roxygen2")` #' @export document <- function(pkg = ".", roclets = NULL) { check_suggested("roxygen2") diff --git a/R/github.R b/R/github.R index c2348f4d5..23b655358 100644 --- a/R/github.R +++ b/R/github.R @@ -84,7 +84,7 @@ github_tag <- function(username, repo, ref = "master") { #' Retrieve Github personal access token. #' #' A github personal access token -#' Looks in env var \code{GITHUB_PAT} +#' Looks in env var `GITHUB_PAT` #' #' @keywords internal #' @export diff --git a/R/install.r b/R/install.r index e06cdf81a..75032e789 100644 --- a/R/install.r +++ b/R/install.r @@ -1,58 +1,58 @@ #' Install a local development package. #' -#' Uses \code{R CMD INSTALL} to install the package. Will also try to install +#' Uses `R CMD INSTALL` to install the package. Will also try to install #' dependencies of the package from CRAN, if they're not already installed. #' #' By default, installation takes place using the current package directory. #' If you have compiled code, this means that artefacts of compilation will be -#' created in the \code{src/} directory. If you want to avoid this, you can -#' use \code{build = TRUE} to first build a package bundle and then install +#' created in the `src/` directory. If you want to avoid this, you can +#' use `build = TRUE` to first build a package bundle and then install #' it from a temporary directory. This is slower, but keeps the source #' directory pristine. #' #' If the package is loaded, it will be reloaded after installation. This is -#' not always completely possible, see \code{\link{reload}} for caveats. +#' not always completely possible, see [reload()] for caveats. #' -#' To install a package in a non-default library, use \code{\link[withr]{with_libpaths}}. +#' To install a package in a non-default library, use [withr::with_libpaths()]. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param reload if \code{TRUE} (the default), will automatically reload the +#' [as.package()] for more information +#' @param reload if `TRUE` (the default), will automatically reload the #' package after installing. -#' @param quick if \code{TRUE} skips docs, multiple-architectures, +#' @param quick if `TRUE` skips docs, multiple-architectures, #' demos, and vignettes, to make installation as fast as possible. -#' @param build if \code{TRUE} \code{\link[pkgbuild]{build}}s the package first: +#' @param build if `TRUE` [pkgbuild::build()]s the package first: #' this ensures that the installation is completely clean, and prevents any -#' binary artefacts (like \file{.o}, \code{.so}) from appearing in your local +#' binary artefacts (like \file{.o}, `.so`) from appearing in your local #' package directory, but is considerably slower, because every compile has #' to start from scratch. #' @param args An optional character vector of additional command line -#' arguments to be passed to \code{R CMD INSTALL}. This defaults to the -#' value of the option \code{"devtools.install.args"}. -#' @param quiet if \code{TRUE} suppresses output from this function. -#' @param dependencies \code{logical} indicating to also install uninstalled -#' packages which this \code{pkg} depends on/links to/suggests. See -#' argument \code{dependencies} of \code{\link{install.packages}}. -#' @param upgrade If \code{TRUE}, the default, will also update +#' arguments to be passed to `R CMD INSTALL`. This defaults to the +#' value of the option `"devtools.install.args"`. +#' @param quiet if `TRUE` suppresses output from this function. +#' @param dependencies `logical` indicating to also install uninstalled +#' packages which this `pkg` depends on/links to/suggests. See +#' argument `dependencies` of [install.packages()]. +#' @param upgrade If `TRUE`, the default, will also update #' any out of date dependencies. -#' @param build_vignettes if \code{TRUE}, will build vignettes. Normally it is -#' \code{build} that's responsible for creating vignettes; this argument makes +#' @param build_vignettes if `TRUE`, will build vignettes. Normally it is +#' `build` that's responsible for creating vignettes; this argument makes #' sure vignettes are built even if a build never happens (i.e. because -#' \code{local = TRUE}). -#' @param keep_source If \code{TRUE} will keep the srcrefs from an installed +#' `local = TRUE`). +#' @param keep_source If `TRUE` will keep the srcrefs from an installed #' package. This is useful for debugging (especially inside of RStudio). -#' It defaults to the option \code{"keep.source.pkgs"}. +#' It defaults to the option `"keep.source.pkgs"`. #' @param threads number of concurrent threads to use for installing #' dependencies. -#' It defaults to the option \code{"Ncpus"} or \code{1} if unset. +#' It defaults to the option `"Ncpus"` or `1` if unset. #' @param force whether to force installation of dependencies even if they #' have not been updated from the previously installed version. -#' @param ... additional arguments passed to \code{\link{install.packages}} -#' when installing dependencies. \code{pkg} is installed with -#' \code{R CMD INSTALL}. +#' @param ... additional arguments passed to [install.packages()] +#' when installing dependencies. `pkg` is installed with +#' `R CMD INSTALL`. #' @family package installation -#' @seealso \code{\link{update_packages}} to update installed packages from the -#' source location and \code{\link{with_debug}} to install packages with +#' @seealso [update_packages()] to update installed packages from the +#' source location and [with_debug()] to install packages with #' debugging flags set. #' @export install <- diff --git a/R/lint.r b/R/lint.r index d3ed3a6cf..37429d3fe 100644 --- a/R/lint.r +++ b/R/lint.r @@ -1,18 +1,18 @@ #' Lint all source files in a package. #' #' The default lintings correspond to the style guide at -#' \url{http://r-pkgs.had.co.nz/r.html#style}, however it is possible to -#' override any or all of them using the \code{linters} parameter. +#' , however it is possible to +#' override any or all of them using the `linters` parameter. #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @param cache store the lint results so repeated lints of the same content #' use the previous results. -#' @param ... additional arguments passed to \code{\link[lintr]{lint_package}} -#' @seealso \code{\link[lintr]{lint_package}}, \code{\link[lintr]{lint}} +#' @param ... additional arguments passed to [lintr::lint_package()] +#' @seealso [lintr::lint_package()], [lintr::lint()] #' @details -#' The lintr cache is by default stored in \code{~/.R/lintr_cache/} (this can -#' be configured by setting \code{options(lintr.cache_directory)}). It can be -#' cleared by calling \code{\link[lintr]{clear_cache}}. +#' The lintr cache is by default stored in `~/.R/lintr_cache/` (this can +#' be configured by setting `options(lintr.cache_directory)`). It can be +#' cleared by calling [lintr::clear_cache()]. #' @export lint <- function(pkg = ".", cache = TRUE, ...) { check_suggested("lintr") diff --git a/R/missing-s3.r b/R/missing-s3.r index d62b4e389..3aac532ff 100644 --- a/R/missing-s3.r +++ b/R/missing-s3.r @@ -3,7 +3,7 @@ #' The method is heuristic - looking for objs with a period in their name. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @export missing_s3 <- function(pkg = ".") { pkg <- as.package(pkg) diff --git a/R/package.r b/R/package.r index 9ad35999a..3de88ba2d 100644 --- a/R/package.r +++ b/R/package.r @@ -7,7 +7,7 @@ #' } #' @param x object to coerce to a package #' @param create only relevant if a package structure does not exist yet: if -#' \code{TRUE}, create a package structure; if \code{NA}, ask the user +#' `TRUE`, create a package structure; if `NA`, ask the user #' (in interactive mode only) #' @export #' @keywords internal @@ -21,7 +21,7 @@ as.package <- function(x = NULL, create = NA) { #' Find file in a package. #' #' It always starts by walking up the path until it finds the root directory, -#' i.e. a directory containing \code{DESCRIPTION}. If it cannot find the root +#' i.e. a directory containing `DESCRIPTION`. If it cannot find the root #' directory, or it can't find the specified path, it will throw an error. #' #' @param ... Components of the path. diff --git a/R/pkgload.R b/R/pkgload.R index 55d3274d4..cadc2d382 100644 --- a/R/pkgload.R +++ b/R/pkgload.R @@ -1,5 +1,5 @@ #' @inherit pkgload::load_all -#' @param ... Additional arguments passed to [pkgload::load]. +#' @param ... Additional arguments passed to [pkgload::load_all()]. #' @export load_all <- function(path = ".", reset = TRUE, recompile = FALSE, export_all = TRUE, helpers = TRUE, quiet = FALSE, ...) { diff --git a/R/r-hub.R b/R/r-hub.R index 9a20829d2..03ffbf3b4 100644 --- a/R/r-hub.R +++ b/R/r-hub.R @@ -1,9 +1,9 @@ #' Run CRAN checks for package on r-hub #' -#' It runs \code{\link{build}} on the package, with the arguments specified -#' in \code{args}, and then submits it to the r-hub builder at -#' \url{https://builder.r-hub.io}. The \code{interactive} option controls +#' It runs [build()] on the package, with the arguments specified +#' in `args`, and then submits it to the r-hub builder at +#' . The `interactive` option controls #' whether the function waits for the check output. Regardless, after the #' check is complete, r-hub sends an email with the results to the package #' maintainer. @@ -11,21 +11,21 @@ #' @section About email validation on r-hub: #' To build and check R packages on r-hub, you need to validate your #' email address. This is because r-hub sends out emails about build -#' results. See more at \code{\link[rhub]{validate_email}}. +#' results. See more at [rhub::validate_email()]. #' -#' @param platforms R-hub platforms to run the check on. If \code{NULL} +#' @param platforms R-hub platforms to run the check on. If `NULL` #' uses default list of CRAN checkers (one for each major platform, and #' one with extra checks if you have compiled code). You can also specify -#' your own, see \code{\link[rhub]{platforms}} for a complete list. +#' your own, see [rhub::platforms()] for a complete list. #' @param email email address to notify, defaults to the maintainer #' address in the package. #' @param interactive whether to show the status of the build #' interactively. R-hub will send an email to the package maintainer's #' email address, regardless of whether the check is interactive or not. -#' @param ... extra arguments, passed to \code{\link[pkgbuild]{build}}. +#' @param ... extra arguments, passed to [pkgbuild::build()]. #' @inheritParams check #' @family build functions, rhub functions -#' @return a \code{rhub_check} object. +#' @return a `rhub_check` object. #' #' @export diff --git a/R/release.r b/R/release.r index ad728e0d2..f813cb94c 100644 --- a/R/release.r +++ b/R/release.r @@ -5,19 +5,19 @@ #' The package release process will: #' #' \itemize{ -#' \item Confirm that the package passes \code{R CMD check} on relevant platoforms +#' \item Confirm that the package passes `R CMD check` on relevant platoforms #' \item Confirm that important files are up-to-date #' \item Build the package #' \item Submit the package to CRAN, using comments in "cran-comments.md" #' } #' #' You can add arbitrary extra questions by defining an (un-exported) function -#' called \code{release_questions()} that returns a character vector +#' called `release_questions()` that returns a character vector #' of additional questions to ask. #' #' You also need to read the CRAN repository policy at -#' \url{https://cran.r-project.org/web/packages/policies.html} and make -#' sure you're in line with the policies. \code{release} tries to automate as +#' and make +#' sure you're in line with the policies. `release` tries to automate as #' many of polices as possible, but it's impossible to be completely #' comprehensive, and they do change in between releases of devtools. #' @@ -29,12 +29,12 @@ #' the mail. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param check if \code{TRUE}, run checking, otherwise omit it. This +#' [as.package()] for more information +#' @param check if `TRUE`, run checking, otherwise omit it. This #' is useful if you've just checked your package and you're ready to #' release it. #' @param args An optional character vector of additional command -#' line arguments to be passed to \code{R CMD build}. +#' line arguments to be passed to `R CMD build`. #' @export release <- function(pkg = ".", check = FALSE, args = NULL) { pkg <- as.package(pkg) @@ -287,11 +287,11 @@ cran_submission_url <- "http://xmpalantir.wu.ac.at/cransubmit/index2.php" #' will receive an email asking you to confirm submission - this is used #' to check that the package is submitted by the maintainer. #' -#' It's recommended that you use \code{\link{release}()} rather than this +#' It's recommended that you use [release()] rather than this #' function as it performs more checks prior to submission. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @inheritParams release #' @export #' @keywords internal diff --git a/R/reload.r b/R/reload.r index d1ba504d1..2357fad47 100644 --- a/R/reload.r +++ b/R/reload.r @@ -2,13 +2,13 @@ #' #' This attempts to unload and reload a package. If the package is not loaded #' already, it does nothing. It's not always possible to cleanly unload a -#' package: see the caveats in \code{\link{unload}} for some of the +#' package: see the caveats in [unload()] for some of the #' potential failure points. If in doubt, restart R and reload the package -#' with \code{\link{library}}. +#' with [library()]. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param quiet if \code{TRUE} suppresses output from this function. +#' [as.package()] for more information +#' @param quiet if `TRUE` suppresses output from this function. #' @examples #' \dontrun{ #' # Reload package that is in current directory diff --git a/R/revdep.R b/R/revdep.R index 68b7af5ff..99578be4c 100755 --- a/R/revdep.R +++ b/R/revdep.R @@ -13,15 +13,15 @@ #' current package. #' @param ignore A character vector of package names to ignore. These packages #' will not appear in returned vector. This is used in -#' \code{\link{revdep_check}} to avoid packages with installation problems +#' [revdep_check()] to avoid packages with installation problems #' or extremely long check times. #' @param dependencies A character vector listing the types of dependencies #' to follow. -#' @param bioconductor If \code{TRUE} also look for dependencies amongst +#' @param bioconductor If `TRUE` also look for dependencies amongst #' bioconductor packages. -#' @param recursive If \code{TRUE} look for full set of recursive dependencies. +#' @param recursive If `TRUE` look for full set of recursive dependencies. #' @inheritParams tools::dependsOnPkgs -#' @seealso \code{\link{revdep_check}()} to run R CMD check on all reverse +#' @seealso [revdep_check()] to run R CMD check on all reverse #' dependencies. #' @export #' @examples diff --git a/R/run-examples.r b/R/run-examples.r index b72d9ea76..5406d1a12 100644 --- a/R/run-examples.r +++ b/R/run-examples.r @@ -6,23 +6,23 @@ #' making it possible to run all examples from an R function. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @param start Where to start running the examples: this can either be the -#' name of \code{Rd} file to start with (with or without extensions), or +#' name of `Rd` file to start with (with or without extensions), or #' a topic name. If omitted, will start with the (lexicographically) first #' file. This is useful if you have a lot of examples and don't want to #' rerun them every time you fix a problem. #' @family example functions #' @param show DEPRECATED. -#' @param test if \code{TRUE}, code in \code{\\donttest{}} will be commented -#' out. If \code{FALSE}, code in \code{\\testonly{}} will be commented out. -#' @param run if \code{TRUE}, code in \code{\\dontrun{}} will be commented +#' @param test if `TRUE`, code in \code{\\donttest{}} will be commented +#' out. If `FALSE`, code in \code{\\testonly{}} will be commented out. +#' @param run if `TRUE`, code in \code{\\dontrun{}} will be commented #' out. -#' @param fresh if \code{TRUE}, will be run in a fresh R session. This has +#' @param fresh if `TRUE`, will be run in a fresh R session. This has #' the advantage that there's no way the examples can depend on anything in -#' the current session, but interactive code (like \code{\link{browser}}) +#' the current session, but interactive code (like [browser()]) #' won't work. -#' @param document if \code{TRUE}, \code{\link{document}} will be run to ensure +#' @param document if `TRUE`, [document()] will be run to ensure #' examples are updated before running them. #' @keywords programming #' @export diff --git a/R/run-source.r b/R/run-source.r index 78c077f47..8ec16531c 100644 --- a/R/run-source.r +++ b/R/run-source.r @@ -1,6 +1,6 @@ #' Run a script through some protocols such as http, https, ftp, etc. #' -#' If a SHA-1 hash is specified with the \code{sha1} argument, then this +#' If a SHA-1 hash is specified with the `sha1` argument, then this #' function will check the SHA-1 hash of the downloaded file to make sure it #' matches the expected value, and throw an error if it does not match. If the #' SHA-1 hash is not specified, it will print a message displaying the hash of @@ -11,10 +11,10 @@ #' as secure as the full hash. #' #' @param url url -#' @param ... other options passed to \code{\link{source}} +#' @param ... other options passed to [source()] #' @param sha1 The (prefix of the) SHA-1 hash of the file at the remote URL. #' @export -#' @seealso \code{\link{source_gist}} +#' @seealso [source_gist()] #' @examples #' \dontrun{ #' @@ -66,21 +66,21 @@ source_url <- function(url, ..., sha1 = NULL) { #' \dQuote{Gist is a simple way to share snippets and pastes with others. #' All gists are git repositories, so they are automatically versioned, #' forkable and usable as a git repository.} -#' \url{https://gist.github.com/} +#' #' #' @param id either full url (character), gist ID (numeric or character of #' numeric). -#' @param ... other options passed to \code{\link{source}} +#' @param ... other options passed to [source()] #' @param filename if there is more than one R file in the gist, which one to -#' source (filename ending in '.R')? Default \code{NULL} will source the +#' source (filename ending in '.R')? Default `NULL` will source the #' first file. #' @param sha1 The SHA-1 hash of the file at the remote URL. This is highly #' recommend as it prevents you from accidentally running code that's not -#' what you expect. See \code{\link{source_url}} for more information on +#' what you expect. See [source_url()] for more information on #' using a SHA-1 hash. -#' @param quiet if \code{FALSE}, the default, prints informative messages. +#' @param quiet if `FALSE`, the default, prints informative messages. #' @export -#' @seealso \code{\link{source_url}} +#' @seealso [source_url()] #' @examples #' \dontrun{ #' # You can run gists given their id diff --git a/R/save-all.R b/R/save-all.R index a41445304..dd3cc9b75 100644 --- a/R/save-all.R +++ b/R/save-all.R @@ -1,10 +1,10 @@ #' Save all documents in an active IDE session. #' #' Helper function wrapping IDE-specific calls to save all documents in the -#' active session. In this form, callers of \code{save_all()} don't need to +#' active session. In this form, callers of `save_all()` don't need to #' execute any IDE-specific code. This function can be extened to include #' other IDE implementations of their equivalent -#' \code{rstudioapi::documentSaveAll()} methods. +#' `rstudioapi::documentSaveAll()` methods. #' @return NULL save_all <- function() { if (rstudioapi::hasFun("documentSaveAll")) { diff --git a/R/session-info.r b/R/session-info.r index 2af8e35bf..a97733c32 100644 --- a/R/session-info.r +++ b/R/session-info.r @@ -30,12 +30,12 @@ dev_packages <- function() { #' Print session information #' -#' This is \code{\link{sessionInfo}()} re-written from scratch to both exclude +#' This is [sessionInfo()] re-written from scratch to both exclude #' data that's rarely useful (e.g., the full collate string or base packages #' loaded) and include stuff you'd like to know (e.g., where a package was #' installed from). #' -#' @param pkgs Either a vector of package names or NULL. If \code{NULL}, +#' @param pkgs Either a vector of package names or NULL. If `NULL`, #' displays all loaded packages. If a character vector, also, includes #' all dependencies of the package. #' @param include_base Include base packages in summary? By default this is diff --git a/R/show-news.r b/R/show-news.r index a176307e7..10831bef2 100644 --- a/R/show-news.r +++ b/R/show-news.r @@ -1,10 +1,10 @@ #' Show package news #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param latest if \code{TRUE}, only show the news for the most recent +#' [as.package()] for more information +#' @param latest if `TRUE`, only show the news for the most recent #' version. -#' @param ... other arguments passed on to \code{news} +#' @param ... other arguments passed on to `news` #' @export show_news <- function(pkg = ".", latest = TRUE, ...) { pkg <- as.package(pkg) diff --git a/R/spell-check.R b/R/spell-check.R index ab6d7f39b..4db3ef5c6 100644 --- a/R/spell-check.R +++ b/R/spell-check.R @@ -3,7 +3,7 @@ #' Runs a spell check on text fields in the package description file, manual #' pages, and optionally vignettes. Wraps the \link[spelling:spell_check_package]{spelling} #' package. -#' manual pages. Hunspell includes dictionaries for \code{en_US} and \code{en_GB} +#' manual pages. Hunspell includes dictionaries for `en_US` and `en_GB` #' by default. Other languages require installation of a custom dictionary, see #' the \href{https://cran.r-project.org/package=hunspell/vignettes/intro.html#system_dictionaries}{hunspell vignette} #' for details. @@ -11,7 +11,7 @@ #' @export #' @rdname spell_check #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @param vignettes include vignettes in the spell check; passed to #' \link[spelling:spell_check_package]{spelling::spell_check_package} spell_check <- function(pkg = ".", vignettes = TRUE) { diff --git a/R/system.r b/R/system.r index 189424903..09a2214a1 100644 --- a/R/system.r +++ b/R/system.r @@ -1,13 +1,13 @@ #' Run a system command and check if it succeeds. #' -#' @param cmd Command to run. Will be quoted by \code{\link{shQuote}()}. +#' @param cmd Command to run. Will be quoted by [shQuote()]. #' @param args A character vector of arguments. #' @param env_vars A named character vector of environment variables. #' @param path Path in which to execute the command -#' @param quiet If \code{FALSE}, the command to be run will be echoed. -#' @param throw If \code{TRUE}, will throw an error if the command fails +#' @param quiet If `FALSE`, the command to be run will be echoed. +#' @param throw If `TRUE`, will throw an error if the command fails #' (i.e. the return value is not 0). -#' @param ... additional arguments passed to \code{\link[base]{system}} +#' @param ... additional arguments passed to [base::system()] #' @keywords internal #' @export #' @return The exit status of the command, invisibly. @@ -41,8 +41,8 @@ system_check <- function(cmd, args = character(), env_vars = character(), } #' @noRd -#' @param out_file Path of file to which output is written if \code{quiet} is -#' \code{TRUE} +#' @param out_file Path of file to which output is written if `quiet` is +#' `TRUE` system2_check <- function(cmd, args = character(), env_vars = character(), path = ".", quiet = FALSE, throw = TRUE, out_file = NULL, ...) { @@ -85,7 +85,7 @@ system2_check <- function(cmd, args = character(), env_vars = character(), #' Run a system command and capture the output. #' #' @inheritParams system_check -#' @param ... additional arguments passed to \code{\link[base]{system}} +#' @param ... additional arguments passed to [base::system()] #' @return command output if the command succeeds, an error will be thrown if #' the command fails. #' @keywords internal diff --git a/R/uninstall.r b/R/uninstall.r index 85485355c..2eb8307b4 100644 --- a/R/uninstall.r +++ b/R/uninstall.r @@ -1,16 +1,16 @@ #' Uninstall a local development package. #' -#' Uses \code{remove.package} to uninstall the package. +#' Uses `remove.package` to uninstall the package. #' To uninstall a package from a non-default library, -#' use \code{\link[withr]{with_libpaths}}. +#' use [withr::with_libpaths()]. #' #' @inheritParams install -#' @param unload if \code{TRUE} (the default), will automatically unload the +#' @param unload if `TRUE` (the default), will automatically unload the #' package prior to uninstalling. -#' @param ... additional arguments passed to \code{\link{remove.packages}}. +#' @param ... additional arguments passed to [remove.packages()]. #' @export #' @family package installation -#' @seealso \code{\link{with_debug}} to install packages with debugging flags +#' @seealso [with_debug()] to install packages with debugging flags #' set. uninstall <- function(pkg = ".", unload = TRUE, quiet = FALSE, ...) { pkg <- as.package(pkg) diff --git a/R/vignettes.r b/R/vignettes.r index a61922b07..b32de1617 100644 --- a/R/vignettes.r +++ b/R/vignettes.r @@ -1,32 +1,32 @@ #' Build package vignettes. #' -#' Builds package vignettes using the same algorithm that \code{R CMD build} +#' Builds package vignettes using the same algorithm that `R CMD build` #' does. This means including non-Sweave vignettes, using makefiles (if #' present), and copying over extra files. The files are copied in the 'doc' #' directory and an vignette index is created in 'Meta/vignette.rds', as they #' would be in a built package. 'doc' and 'Meta' are added to -#' \code{.Rbuildignore}, so will not be included in the built package. These +#' `.Rbuildignore`, so will not be included in the built package. These #' files can be checked into version control, so they can be viewed with -#' \code{browseVignettes()} and \code{vignette()} if the package has been -#' loaded with \code{load_all()} without needing to re-build them locally. +#' `browseVignettes()` and `vignette()` if the package has been +#' loaded with `load_all()` without needing to re-build them locally. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information -#' @param quiet If \code{TRUE}, suppresses most output. Set to \code{FALSE} +#' [as.package()] for more information +#' @param quiet If `TRUE`, suppresses most output. Set to `FALSE` #' if you need to debug. -#' @param install If \code{TRUE}, install the package before building +#' @param install If `TRUE`, install the package before building #' vignettes. -#' @param keep_md If \code{TRUE}, move md intermediates as well as rendered +#' @param keep_md If `TRUE`, move md intermediates as well as rendered #' outputs. Most useful when using the `keep_md` YAML option for Rmarkdown #' outputs. See -#' \url{https://bookdown.org/yihui/rmarkdown/html-document.html#keeping-markdown}. +#' . #' @inheritParams tools::buildVignettes #' @inheritParams remotes::install_deps #' @keywords programming -#' @seealso \code{\link{clean_vignettes}} to remove the pdfs in +#' @seealso [clean_vignettes()] to remove the pdfs in #' \file{doc} created from vignettes #' @export -#' @seealso \code{\link{clean_vignettes}} to remove build tex/pdf files. +#' @seealso [clean_vignettes()] to remove build tex/pdf files. build_vignettes <- function(pkg = ".", dependencies = "VignetteBuilder", clean = TRUE, @@ -92,7 +92,7 @@ create_vignette_index <- function(pkg, vigns) { #' with a name that exists in \file{vignettes} are removed. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @export clean_vignettes <- function(pkg = ".") { pkg <- as.package(pkg) diff --git a/R/wd.r b/R/wd.r index eae45303e..45882bb22 100644 --- a/R/wd.r +++ b/R/wd.r @@ -1,7 +1,7 @@ #' Set working directory. #' #' @param pkg package description, can be path or package name. See -#' \code{\link{as.package}} for more information +#' [as.package()] for more information #' @param path path within package. Leave empty to change working directory #' to package directory. #' @export diff --git a/R/zzz.r b/R/zzz.r index adc8e72e8..aa4c6cb50 100644 --- a/R/zzz.r +++ b/R/zzz.r @@ -8,29 +8,29 @@ NULL #' #' @section Package options: #' -#' Devtools uses the following \code{\link{options}} to configure behaviour: +#' Devtools uses the following [options()] to configure behaviour: #' #' \itemize{ -#' \item \code{devtools.path}: path to use for \code{\link{dev_mode}} +#' \item `devtools.path`: path to use for [dev_mode()] #' -#' \item \code{devtools.name}: your name, used when signing draft +#' \item `devtools.name`: your name, used when signing draft #' emails. #' -#' \item \code{devtools.install.args}: a string giving extra arguments passed -#' to \code{R CMD install} by \code{\link{install}}. +#' \item `devtools.install.args`: a string giving extra arguments passed +#' to `R CMD install` by [install()]. #' -#' \item \code{devtools.desc.author}: a string providing a default Authors@@R +#' \item `devtools.desc.author`: a string providing a default Authors@@R #' string to be used in new \file{DESCRIPTION}s. Should be a R code, and -#' look like \code{"Hadley Wickham [aut, cre]"}. See -#' \code{\link[utils]{as.person}} for more details. +#' look like `"Hadley Wickham [aut, cre]"`. See +#' [utils::as.person()] for more details. #' -#' \item \code{devtools.desc.license}: a default license string to use for +#' \item `devtools.desc.license`: a default license string to use for #' new packages. #' -#' \item \code{devtools.desc.suggests}: a character vector listing packages to +#' \item `devtools.desc.suggests`: a character vector listing packages to #' to add to suggests by defaults for new packages. # -#' \item \code{devtools.desc}: a named list listing any other +#' \item `devtools.desc`: a named list listing any other #' extra options to add to \file{DESCRIPTION} #' #' } diff --git a/man/as.package.Rd b/man/as.package.Rd index 49df7f6e0..1fec39ea2 100644 --- a/man/as.package.Rd +++ b/man/as.package.Rd @@ -16,8 +16,8 @@ as.package(x = NULL, create = NA) \description{ Possible specifications of package: \itemize{ - \item path - \item package object +\item path +\item package object } } \keyword{internal} diff --git a/man/bash.Rd b/man/bash.Rd index f7882325a..f28c618a3 100644 --- a/man/bash.Rd +++ b/man/bash.Rd @@ -8,7 +8,7 @@ bash(pkg = ".") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} } \description{ Open bash shell in package directory. diff --git a/man/build.Rd b/man/build.Rd index c0e92cc05..439c41806 100644 --- a/man/build.Rd +++ b/man/build.Rd @@ -29,7 +29,7 @@ or \code{R CMD install} if \code{binary = TRUE}.} \item{quiet}{if \code{TRUE} suppresses output from this function.} -\item{...}{Additional arguments passed to [pkgbuild::build].} +\item{...}{Additional arguments passed to \link[pkgbuild:build]{pkgbuild::build}.} } \value{ a string giving the location (including file name) of the built diff --git a/man/build_manual.Rd b/man/build_manual.Rd index fd61fc397..20c5dbeba 100644 --- a/man/build_manual.Rd +++ b/man/build_manual.Rd @@ -8,7 +8,7 @@ build_manual(pkg = ".", path = NULL) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information.} +\code{\link[=as.package]{as.package()}} for more information.} \item{path}{path in which to produce package manual. If \code{NULL}, defaults to the parent directory of the package.} @@ -17,5 +17,5 @@ If \code{NULL}, defaults to the parent directory of the package.} Create package pdf manual } \seealso{ -\code{\link{Rd2pdf}} +\code{\link[=Rd2pdf]{Rd2pdf()}} } diff --git a/man/build_readme.Rd b/man/build_readme.Rd index f3671963e..bbae75bf5 100644 --- a/man/build_readme.Rd +++ b/man/build_readme.Rd @@ -11,9 +11,9 @@ build_readme(path = ".", quiet = TRUE, ...) \item{quiet}{if \code{TRUE} suppresses output from this function.} -\item{...}{additional arguments passed to [rmarkdown::render()]} +\item{...}{additional arguments passed to \code{\link[rmarkdown:render]{rmarkdown::render()}}} } \description{ -`build_readme()` is a wrapper around [rmarkdown::render()], it generates the +\code{build_readme()} is a wrapper around \code{\link[rmarkdown:render]{rmarkdown::render()}}, it generates the README.md from a README.Rmd file. } diff --git a/man/build_site.Rd b/man/build_site.Rd index ac2be6c58..711861eff 100644 --- a/man/build_site.Rd +++ b/man/build_site.Rd @@ -11,9 +11,9 @@ build_site(path = ".", quiet = TRUE, ...) \item{quiet}{if \code{TRUE} suppresses output from this function.} -\item{...}{additional arguments passed to [pkgdown::build_site()]} +\item{...}{additional arguments passed to \code{\link[pkgdown:build_site]{pkgdown::build_site()}}} } \description{ -`build_site()` is a shortcut for [pkgdown::build_site()], it generates the - static HTML documentation. +\code{build_site()} is a shortcut for \code{\link[pkgdown:build_site]{pkgdown::build_site()}}, it generates the +static HTML documentation. } diff --git a/man/build_vignettes.Rd b/man/build_vignettes.Rd index 1e558cd99..5906dec85 100644 --- a/man/build_vignettes.Rd +++ b/man/build_vignettes.Rd @@ -10,7 +10,7 @@ build_vignettes(pkg = ".", dependencies = "VignetteBuilder", } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{dependencies}{Which dependencies do you want to check? Can be a character vector (selecting from "Depends", "Imports", @@ -33,7 +33,7 @@ if you need to debug.} vignettes.} \item{keep_md}{If \code{TRUE}, move md intermediates as well as rendered -outputs. Most useful when using the `keep_md` YAML option for Rmarkdown +outputs. Most useful when using the \code{keep_md} YAML option for Rmarkdown outputs. See \url{https://bookdown.org/yihui/rmarkdown/html-document.html#keeping-markdown}.} } @@ -49,9 +49,9 @@ files can be checked into version control, so they can be viewed with loaded with \code{load_all()} without needing to re-build them locally. } \seealso{ -\code{\link{clean_vignettes}} to remove the pdfs in - \file{doc} created from vignettes +\code{\link[=clean_vignettes]{clean_vignettes()}} to remove the pdfs in +\file{doc} created from vignettes -\code{\link{clean_vignettes}} to remove build tex/pdf files. +\code{\link[=clean_vignettes]{clean_vignettes()}} to remove build tex/pdf files. } \keyword{programming} diff --git a/man/check.Rd b/man/check.Rd index fc65d9c5c..cc9b6c82f 100644 --- a/man/check.Rd +++ b/man/check.Rd @@ -19,15 +19,15 @@ check_built(path = NULL, cran = TRUE, remote = FALSE, } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{document}{If \code{NA} and the package uses roxygen2, will -rerun \code{\link{document}} prior to checking. Use \code{TRUE} +rerun \code{\link[=document]{document()}} prior to checking. Use \code{TRUE} and \code{FALSE} to override this default.} \item{build_args}{Additional arguments passed to \code{R CMD build}} -\item{...}{Additional arguments passed on to \code{\link[pkgbuild]{build}()}.} +\item{...}{Additional arguments passed on to \code{\link[pkgbuild:build]{pkgbuild::build()}}.} \item{manual}{If \code{FALSE}, don't build and check manual (\code{--no-manual}).} @@ -99,24 +99,24 @@ with how check works on CRAN. This includes: \itemize{ - \item The standard environment variables set by devtools: - \code{\link{r_env_vars}}. Of particular note for package tests is the - \code{NOT_CRAN} env var which lets you know that your tests are not - running on cran, and hence can take a reasonable amount of time. +\item The standard environment variables set by devtools: +\code{\link[=r_env_vars]{r_env_vars()}}. Of particular note for package tests is the +\code{NOT_CRAN} env var which lets you know that your tests are not +running on cran, and hence can take a reasonable amount of time. - \item Debugging flags for the compiler, set by - \code{\link{compiler_flags}(FALSE)}. +\item Debugging flags for the compiler, set by +\code{\link{compiler_flags}(FALSE)}. - \item If \code{aspell} is found \code{_R_CHECK_CRAN_INCOMING_USE_ASPELL_} - is set to \code{TRUE}. If no spell checker is installed, a warning is - issued.) +\item If \code{aspell} is found \code{_R_CHECK_CRAN_INCOMING_USE_ASPELL_} +is set to \code{TRUE}. If no spell checker is installed, a warning is +issued.) - \item env vars set by arguments \code{incoming}, \code{remote} and - \code{force_suggests} +\item env vars set by arguments \code{incoming}, \code{remote} and +\code{force_suggests} } } \seealso{ -\code{\link{release}} if you want to send the checked package to - CRAN. +\code{\link[=release]{release()}} if you want to send the checked package to +CRAN. } diff --git a/man/check_failures.Rd b/man/check_failures.Rd index 79471c7cc..9e312e313 100644 --- a/man/check_failures.Rd +++ b/man/check_failures.Rd @@ -8,19 +8,19 @@ check_failures(path, error = TRUE, warning = TRUE, note = TRUE) } \arguments{ \item{path}{check path, e.g., value of the \code{check_dir} argument in a -call to \code{\link{check}}} +call to \code{\link[=check]{check()}}} \item{error, warning, note}{logical, indicates if errors, warnings and/or notes should be returned} } \value{ a character vector with the relevant messages, can have length zero - if no messages are found +if no messages are found } \description{ Extracts check messages from the \code{00check.log} file generated by \code{R CMD check}. } \seealso{ -\code{\link{check}}, \code{\link{revdep_check}} +\code{\link[=check]{check()}}, \code{\link[=revdep_check]{revdep_check()}} } diff --git a/man/check_man.Rd b/man/check_man.Rd index 4c4e0b166..60e981dd8 100644 --- a/man/check_man.Rd +++ b/man/check_man.Rd @@ -8,7 +8,7 @@ check_man(pkg = ".") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} } \value{ Nothing. This function is called purely for it's side effects: if diff --git a/man/check_rhub.Rd b/man/check_rhub.Rd index 27c2d4eb8..0ba255251 100644 --- a/man/check_rhub.Rd +++ b/man/check_rhub.Rd @@ -9,12 +9,12 @@ check_rhub(pkg = ".", platforms = NULL, email = NULL, } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{platforms}{R-hub platforms to run the check on. If \code{NULL} uses default list of CRAN checkers (one for each major platform, and one with extra checks if you have compiled code). You can also specify -your own, see \code{\link[rhub]{platforms}} for a complete list.} +your own, see \code{\link[rhub:platforms]{rhub::platforms()}} for a complete list.} \item{email}{email address to notify, defaults to the maintainer address in the package.} @@ -23,13 +23,13 @@ address in the package.} interactively. R-hub will send an email to the package maintainer's email address, regardless of whether the check is interactive or not.} -\item{...}{extra arguments, passed to \code{\link[pkgbuild]{build}}.} +\item{...}{extra arguments, passed to \code{\link[pkgbuild:build]{pkgbuild::build()}}.} } \value{ a \code{rhub_check} object. } \description{ -It runs \code{\link{build}} on the package, with the arguments specified +It runs \code{\link[=build]{build()}} on the package, with the arguments specified in \code{args}, and then submits it to the r-hub builder at \url{https://builder.r-hub.io}. The \code{interactive} option controls whether the function waits for the check output. Regardless, after the @@ -40,7 +40,7 @@ maintainer. To build and check R packages on r-hub, you need to validate your email address. This is because r-hub sends out emails about build -results. See more at \code{\link[rhub]{validate_email}}. +results. See more at \code{\link[rhub:validate_email]{rhub::validate_email()}}. } \concept{build functions, rhub functions} diff --git a/man/check_win.Rd b/man/check_win.Rd index 7a18c5496..133fd0457 100644 --- a/man/check_win.Rd +++ b/man/check_win.Rd @@ -15,7 +15,7 @@ check_win_oldrelease(pkg = ".", args = NULL, quiet = FALSE, ...) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{args}{An optional character vector of additional command line arguments to be passed to \code{R CMD build} if \code{binary = FALSE}, @@ -23,7 +23,7 @@ or \code{R CMD install} if \code{binary = TRUE}.} \item{quiet}{If \code{TRUE}, suppresses output.} -\item{...}{Additional arguments passed to \code{\link[pkgbuild]{build}}.} +\item{...}{Additional arguments passed to \code{\link[pkgbuild:build]{pkgbuild::build()}}.} } \description{ This function works by bundling source package, and then uploading to diff --git a/man/clean_vignettes.Rd b/man/clean_vignettes.Rd index d78429db5..418482813 100644 --- a/man/clean_vignettes.Rd +++ b/man/clean_vignettes.Rd @@ -8,7 +8,7 @@ clean_vignettes(pkg = ".") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} } \description{ This uses a fairly rudimentary algorithm where any files in \file{doc} diff --git a/man/dev_mode.Rd b/man/dev_mode.Rd index 83fc9a7b7..5f31e6ff9 100644 --- a/man/dev_mode.Rd +++ b/man/dev_mode.Rd @@ -9,7 +9,7 @@ dev_mode(on = NULL, path = getOption("devtools.path")) \arguments{ \item{on}{turn dev mode on (\code{TRUE}) or off (\code{FALSE}). If omitted will guess based on whether or not \code{path} is in -\code{\link{.libPaths}}} +\code{\link[=.libPaths]{.libPaths()}}} \item{path}{directory to library.} } diff --git a/man/devtools.Rd b/man/devtools.Rd index 040463915..581fe0a63 100644 --- a/man/devtools.Rd +++ b/man/devtools.Rd @@ -11,29 +11,29 @@ Collection of package development tools. \section{Package options}{ -Devtools uses the following \code{\link{options}} to configure behaviour: +Devtools uses the following \code{\link[=options]{options()}} to configure behaviour: \itemize{ - \item \code{devtools.path}: path to use for \code{\link{dev_mode}} +\item \code{devtools.path}: path to use for \code{\link[=dev_mode]{dev_mode()}} - \item \code{devtools.name}: your name, used when signing draft - emails. +\item \code{devtools.name}: your name, used when signing draft +emails. - \item \code{devtools.install.args}: a string giving extra arguments passed - to \code{R CMD install} by \code{\link{install}}. +\item \code{devtools.install.args}: a string giving extra arguments passed +to \code{R CMD install} by \code{\link[=install]{install()}}. - \item \code{devtools.desc.author}: a string providing a default Authors@R - string to be used in new \file{DESCRIPTION}s. Should be a R code, and - look like \code{"Hadley Wickham [aut, cre]"}. See - \code{\link[utils]{as.person}} for more details. +\item \code{devtools.desc.author}: a string providing a default Authors@R +string to be used in new \file{DESCRIPTION}s. Should be a R code, and +look like \code{"Hadley Wickham [aut, cre]"}. See +\code{\link[utils:as.person]{utils::as.person()}} for more details. - \item \code{devtools.desc.license}: a default license string to use for - new packages. +\item \code{devtools.desc.license}: a default license string to use for +new packages. - \item \code{devtools.desc.suggests}: a character vector listing packages to - to add to suggests by defaults for new packages. - \item \code{devtools.desc}: a named list listing any other - extra options to add to \file{DESCRIPTION} +\item \code{devtools.desc.suggests}: a character vector listing packages to +to add to suggests by defaults for new packages. +\item \code{devtools.desc}: a named list listing any other +extra options to add to \file{DESCRIPTION} } } diff --git a/man/document.Rd b/man/document.Rd index 3ac28571c..609bc01c9 100644 --- a/man/document.Rd +++ b/man/document.Rd @@ -8,7 +8,7 @@ document(pkg = ".", roclets = NULL) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{roclets}{Character vector of roclet names to use with package. This defaults to \code{NULL}, which will use the \code{roclets} fields in @@ -16,11 +16,11 @@ the list provided in the \code{Roxygen} DESCRIPTION field. If none are specified, defaults to \code{c("collate", "namespace", "rd")}.} } \description{ -This function is a wrapper for the \code{\link[roxygen2]{roxygenize}()} +This function is a wrapper for the \code{\link[roxygen2:roxygenize]{roxygen2::roxygenize()}} function from the roxygen2 package. See the documentation and vignettes of that package to learn how to use roxygen. } \seealso{ -\code{\link[roxygen2]{roxygenize}}, - \code{browseVignettes("roxygen2")} +\code{\link[roxygen2:roxygenize]{roxygen2::roxygenize()}}, +\code{browseVignettes("roxygen2")} } diff --git a/man/git_checks.Rd b/man/git_checks.Rd index 2cd7e8fd8..2ceddf5cb 100644 --- a/man/git_checks.Rd +++ b/man/git_checks.Rd @@ -8,10 +8,10 @@ git_checks(pkg = ".") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information.} +\code{\link[=as.package]{as.package()}} for more information.} } \description{ This function performs Git checks checks prior to release. It is called -automatically by \code{\link{release}()}. +automatically by \code{\link[=release]{release()}}. } \keyword{internal} diff --git a/man/install.Rd b/man/install.Rd index fda3f57d0..aa2d4e5b8 100644 --- a/man/install.Rd +++ b/man/install.Rd @@ -12,7 +12,7 @@ install(pkg = ".", reload = TRUE, quick = FALSE, build = TRUE, } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{reload}{if \code{TRUE} (the default), will automatically reload the package after installing.} @@ -20,7 +20,7 @@ package after installing.} \item{quick}{if \code{TRUE} skips docs, multiple-architectures, demos, and vignettes, to make installation as fast as possible.} -\item{build}{if \code{TRUE} \code{\link[pkgbuild]{build}}s the package first: +\item{build}{if \code{TRUE} \code{\link[pkgbuild:build]{pkgbuild::build()}}s the package first: this ensures that the installation is completely clean, and prevents any binary artefacts (like \file{.o}, \code{.so}) from appearing in your local package directory, but is considerably slower, because every compile has @@ -34,7 +34,7 @@ value of the option \code{"devtools.install.args"}.} \item{dependencies}{\code{logical} indicating to also install uninstalled packages which this \code{pkg} depends on/links to/suggests. See -argument \code{dependencies} of \code{\link{install.packages}}.} +argument \code{dependencies} of \code{\link[=install.packages]{install.packages()}}.} \item{upgrade}{If \code{TRUE}, the default, will also update any out of date dependencies.} @@ -55,7 +55,7 @@ It defaults to the option \code{"Ncpus"} or \code{1} if unset.} \item{force}{whether to force installation of dependencies even if they have not been updated from the previously installed version.} -\item{...}{additional arguments passed to \code{\link{install.packages}} +\item{...}{additional arguments passed to \code{\link[=install.packages]{install.packages()}} when installing dependencies. \code{pkg} is installed with \code{R CMD INSTALL}.} } @@ -72,13 +72,13 @@ it from a temporary directory. This is slower, but keeps the source directory pristine. If the package is loaded, it will be reloaded after installation. This is -not always completely possible, see \code{\link{reload}} for caveats. +not always completely possible, see \code{\link[=reload]{reload()}} for caveats. -To install a package in a non-default library, use \code{\link[withr]{with_libpaths}}. +To install a package in a non-default library, use \code{\link[withr:with_libpaths]{withr::with_libpaths()}}. } \seealso{ -\code{\link{update_packages}} to update installed packages from the -source location and \code{\link{with_debug}} to install packages with +\code{\link[=update_packages]{update_packages()}} to update installed packages from the +source location and \code{\link[=with_debug]{with_debug()}} to install packages with debugging flags set. Other package installation: \code{\link{uninstall}} diff --git a/man/install_dev_deps.Rd b/man/install_dev_deps.Rd index 3512ed506..e0a274f03 100644 --- a/man/install_dev_deps.Rd +++ b/man/install_dev_deps.Rd @@ -8,7 +8,7 @@ install_dev_deps(pkg = ".", ...) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{...}{additional arguments passed to \code{\link[utils:install.packages]{utils::install.packages()}}.} } diff --git a/man/lint.Rd b/man/lint.Rd index 75c462fff..e95450de6 100644 --- a/man/lint.Rd +++ b/man/lint.Rd @@ -8,12 +8,12 @@ lint(pkg = ".", cache = TRUE, ...) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{cache}{store the lint results so repeated lints of the same content use the previous results.} -\item{...}{additional arguments passed to \code{\link[lintr]{lint_package}}} +\item{...}{additional arguments passed to \code{\link[lintr:lint_package]{lintr::lint_package()}}} } \description{ The default lintings correspond to the style guide at @@ -23,8 +23,8 @@ override any or all of them using the \code{linters} parameter. \details{ The lintr cache is by default stored in \code{~/.R/lintr_cache/} (this can be configured by setting \code{options(lintr.cache_directory)}). It can be -cleared by calling \code{\link[lintr]{clear_cache}}. +cleared by calling \code{\link[lintr:clear_cache]{lintr::clear_cache()}}. } \seealso{ -\code{\link[lintr]{lint_package}}, \code{\link[lintr]{lint}} +\code{\link[lintr:lint_package]{lintr::lint_package()}}, \code{\link[lintr:lint]{lintr::lint()}} } diff --git a/man/load_all.Rd b/man/load_all.Rd index 090b90b1b..6a8d0a4a1 100644 --- a/man/load_all.Rd +++ b/man/load_all.Rd @@ -28,7 +28,7 @@ in the NAMESPACE file.} \item{quiet}{if \code{TRUE} suppresses output from this function.} -\item{...}{Additional arguments passed to [pkgload::load].} +\item{...}{Additional arguments passed to \code{\link[pkgload:load_all]{pkgload::load_all()}}.} } \description{ \code{load_all} loads a package. It roughly simulates what happens diff --git a/man/loaded_packages.Rd b/man/loaded_packages.Rd index 7793cc86e..fd48140b5 100644 --- a/man/loaded_packages.Rd +++ b/man/loaded_packages.Rd @@ -8,7 +8,7 @@ loaded_packages() } \value{ A data frame with columns package and path, giving the name of - each package and the path it was loaded from. +each package and the path it was loaded from. } \description{ Return a vector of names of attached packages diff --git a/man/missing_s3.Rd b/man/missing_s3.Rd index a17b906d3..e01a69879 100644 --- a/man/missing_s3.Rd +++ b/man/missing_s3.Rd @@ -8,7 +8,7 @@ missing_s3(pkg = ".") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} } \description{ The method is heuristic - looking for objs with a period in their name. diff --git a/man/release.Rd b/man/release.Rd index aef5f9dff..337bd2656 100644 --- a/man/release.Rd +++ b/man/release.Rd @@ -8,7 +8,7 @@ release(pkg = ".", check = FALSE, args = NULL) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{check}{if \code{TRUE}, run checking, otherwise omit it. This is useful if you've just checked your package and you're ready to @@ -24,10 +24,10 @@ Run automated and manual tests, then post package to CRAN. The package release process will: \itemize{ - \item Confirm that the package passes \code{R CMD check} on relevant platoforms - \item Confirm that important files are up-to-date - \item Build the package - \item Submit the package to CRAN, using comments in "cran-comments.md" +\item Confirm that the package passes \code{R CMD check} on relevant platoforms +\item Confirm that important files are up-to-date +\item Build the package +\item Submit the package to CRAN, using comments in "cran-comments.md" } You can add arbitrary extra questions by defining an (un-exported) function diff --git a/man/release_checks.Rd b/man/release_checks.Rd index d5bba8196..951031632 100644 --- a/man/release_checks.Rd +++ b/man/release_checks.Rd @@ -8,10 +8,10 @@ release_checks(pkg = ".", built_path = NULL) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information.} +\code{\link[=as.package]{as.package()}} for more information.} } \description{ This function performs additional checks prior to release. It is called -automatically by \code{\link{release}()}. +automatically by \code{\link[=release]{release()}}. } \keyword{internal} diff --git a/man/reload.Rd b/man/reload.Rd index 06ed99f6d..8e8e49785 100644 --- a/man/reload.Rd +++ b/man/reload.Rd @@ -8,16 +8,16 @@ reload(pkg = ".", quiet = FALSE) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{quiet}{if \code{TRUE} suppresses output from this function.} } \description{ This attempts to unload and reload a package. If the package is not loaded already, it does nothing. It's not always possible to cleanly unload a -package: see the caveats in \code{\link{unload}} for some of the +package: see the caveats in \code{\link[=unload]{unload()}} for some of the potential failure points. If in doubt, restart R and reload the package -with \code{\link{library}}. +with \code{\link[=library]{library()}}. } \examples{ \dontrun{ diff --git a/man/revdep.Rd b/man/revdep.Rd index 5c78a189f..c3f9c1c4a 100644 --- a/man/revdep.Rd +++ b/man/revdep.Rd @@ -24,7 +24,7 @@ to follow.} \item{ignore}{A character vector of package names to ignore. These packages will not appear in returned vector. This is used in -\code{\link{revdep_check}} to avoid packages with installation problems +\code{\link[=revdep_check]{revdep_check()}} to avoid packages with installation problems or extremely long check times.} \item{bioconductor}{If \code{TRUE} also look for dependencies amongst @@ -47,6 +47,6 @@ revdep("ggplot2", ignore = c("xkcd", "zoo")) } } \seealso{ -\code{\link{revdep_check}()} to run R CMD check on all reverse - dependencies. +\code{\link[=revdep_check]{revdep_check()}} to run R CMD check on all reverse +dependencies. } diff --git a/man/run_examples.Rd b/man/run_examples.Rd index df139ebfe..f62e2de29 100644 --- a/man/run_examples.Rd +++ b/man/run_examples.Rd @@ -9,7 +9,7 @@ run_examples(pkg = ".", start = NULL, show = TRUE, test = FALSE, } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{start}{Where to start running the examples: this can either be the name of \code{Rd} file to start with (with or without extensions), or @@ -27,14 +27,14 @@ out.} \item{fresh}{if \code{TRUE}, will be run in a fresh R session. This has the advantage that there's no way the examples can depend on anything in -the current session, but interactive code (like \code{\link{browser}}) +the current session, but interactive code (like \code{\link[=browser]{browser()}}) won't work.} -\item{document}{if \code{TRUE}, \code{\link{document}} will be run to ensure +\item{document}{if \code{TRUE}, \code{\link[=document]{document()}} will be run to ensure examples are updated before running them.} } \description{ -One of the most frustrating parts of `R CMD check` is getting all of your +One of the most frustrating parts of \code{R CMD check} is getting all of your examples to pass - whenever one fails you need to fix the problem and then restart the whole process. This function makes it a little easier by making it possible to run all examples from an R function. diff --git a/man/session_info.Rd b/man/session_info.Rd index ae765b409..d530a0a70 100644 --- a/man/session_info.Rd +++ b/man/session_info.Rd @@ -15,7 +15,7 @@ all dependencies of the package.} false since base packages should always match the R version.} } \description{ -This is \code{\link{sessionInfo}()} re-written from scratch to both exclude +This is \code{\link[=sessionInfo]{sessionInfo()}} re-written from scratch to both exclude data that's rarely useful (e.g., the full collate string or base packages loaded) and include stuff you'd like to know (e.g., where a package was installed from). diff --git a/man/show_news.Rd b/man/show_news.Rd index a936a8832..fef1064ea 100644 --- a/man/show_news.Rd +++ b/man/show_news.Rd @@ -8,7 +8,7 @@ show_news(pkg = ".", latest = TRUE, ...) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{latest}{if \code{TRUE}, only show the news for the most recent version.} diff --git a/man/source_gist.Rd b/man/source_gist.Rd index b580bcc14..1a2113273 100644 --- a/man/source_gist.Rd +++ b/man/source_gist.Rd @@ -10,7 +10,7 @@ source_gist(id, ..., filename = NULL, sha1 = NULL, quiet = FALSE) \item{id}{either full url (character), gist ID (numeric or character of numeric).} -\item{...}{other options passed to \code{\link{source}}} +\item{...}{other options passed to \code{\link[=source]{source()}}} \item{filename}{if there is more than one R file in the gist, which one to source (filename ending in '.R')? Default \code{NULL} will source the @@ -18,15 +18,15 @@ first file.} \item{sha1}{The SHA-1 hash of the file at the remote URL. This is highly recommend as it prevents you from accidentally running code that's not -what you expect. See \code{\link{source_url}} for more information on +what you expect. See \code{\link[=source_url]{source_url()}} for more information on using a SHA-1 hash.} \item{quiet}{if \code{FALSE}, the default, prints informative messages.} } \description{ \dQuote{Gist is a simple way to share snippets and pastes with others. - All gists are git repositories, so they are automatically versioned, - forkable and usable as a git repository.} +All gists are git repositories, so they are automatically versioned, +forkable and usable as a git repository.} \url{https://gist.github.com/} } \examples{ @@ -52,5 +52,5 @@ source_gist(6872663, filename = "hi.r", sha1 = "54f1db27e60") } } \seealso{ -\code{\link{source_url}} +\code{\link[=source_url]{source_url()}} } diff --git a/man/source_url.Rd b/man/source_url.Rd index 30e5b9417..630d53996 100644 --- a/man/source_url.Rd +++ b/man/source_url.Rd @@ -9,7 +9,7 @@ source_url(url, ..., sha1 = NULL) \arguments{ \item{url}{url} -\item{...}{other options passed to \code{\link{source}}} +\item{...}{other options passed to \code{\link[=source]{source()}}} \item{sha1}{The (prefix of the) SHA-1 hash of the file at the remote URL.} } @@ -39,5 +39,5 @@ source_url("https://gist.github.com/hadley/6872663/raw/hi.r", } } \seealso{ -\code{\link{source_gist}} +\code{\link[=source_gist]{source_gist()}} } diff --git a/man/spell_check.Rd b/man/spell_check.Rd index 5996f3e7d..57bb2c3f4 100644 --- a/man/spell_check.Rd +++ b/man/spell_check.Rd @@ -8,7 +8,7 @@ spell_check(pkg = ".", vignettes = TRUE) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{vignettes}{include vignettes in the spell check; passed to \link[spelling:spell_check_package]{spelling::spell_check_package}} diff --git a/man/submit_cran.Rd b/man/submit_cran.Rd index f66295ed5..2b0557413 100644 --- a/man/submit_cran.Rd +++ b/man/submit_cran.Rd @@ -8,7 +8,7 @@ submit_cran(pkg = ".", args = NULL) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{args}{An optional character vector of additional command line arguments to be passed to \code{R CMD build}.} @@ -19,7 +19,7 @@ will receive an email asking you to confirm submission - this is used to check that the package is submitted by the maintainer. } \details{ -It's recommended that you use \code{\link{release}()} rather than this +It's recommended that you use \code{\link[=release]{release()}} rather than this function as it performs more checks prior to submission. } \keyword{internal} diff --git a/man/system_check.Rd b/man/system_check.Rd index 95eda5d79..fa209496d 100644 --- a/man/system_check.Rd +++ b/man/system_check.Rd @@ -8,7 +8,7 @@ system_check(cmd, args = character(), env_vars = character(), path = ".", quiet = FALSE, throw = TRUE, ...) } \arguments{ -\item{cmd}{Command to run. Will be quoted by \code{\link{shQuote}()}.} +\item{cmd}{Command to run. Will be quoted by \code{\link[=shQuote]{shQuote()}}.} \item{args}{A character vector of arguments.} @@ -21,7 +21,7 @@ system_check(cmd, args = character(), env_vars = character(), \item{throw}{If \code{TRUE}, will throw an error if the command fails (i.e. the return value is not 0).} -\item{...}{additional arguments passed to \code{\link[base]{system}}} +\item{...}{additional arguments passed to \code{\link[base:system]{base::system()}}} } \value{ The exit status of the command, invisibly. diff --git a/man/system_output.Rd b/man/system_output.Rd index e62916c55..d57e21992 100644 --- a/man/system_output.Rd +++ b/man/system_output.Rd @@ -8,7 +8,7 @@ system_output(cmd, args = character(), env_vars = character(), path = ".", quiet = FALSE, ...) } \arguments{ -\item{cmd}{Command to run. Will be quoted by \code{\link{shQuote}()}.} +\item{cmd}{Command to run. Will be quoted by \code{\link[=shQuote]{shQuote()}}.} \item{args}{A character vector of arguments.} @@ -18,11 +18,11 @@ system_output(cmd, args = character(), env_vars = character(), \item{quiet}{If \code{FALSE}, the command to be run will be echoed.} -\item{...}{additional arguments passed to \code{\link[base]{system}}} +\item{...}{additional arguments passed to \code{\link[base:system]{base::system()}}} } \value{ command output if the command succeeds, an error will be thrown if - the command fails. +the command fails. } \description{ Run a system command and capture the output. diff --git a/man/uninstall.Rd b/man/uninstall.Rd index 681b81975..8ef365d46 100644 --- a/man/uninstall.Rd +++ b/man/uninstall.Rd @@ -8,23 +8,23 @@ uninstall(pkg = ".", unload = TRUE, quiet = FALSE, ...) } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{unload}{if \code{TRUE} (the default), will automatically unload the package prior to uninstalling.} \item{quiet}{if \code{TRUE} suppresses output from this function.} -\item{...}{additional arguments passed to \code{\link{remove.packages}}.} +\item{...}{additional arguments passed to \code{\link[=remove.packages]{remove.packages()}}.} } \description{ Uses \code{remove.package} to uninstall the package. To uninstall a package from a non-default library, -use \code{\link[withr]{with_libpaths}}. +use \code{\link[withr:with_libpaths]{withr::with_libpaths()}}. } \seealso{ -\code{\link{with_debug}} to install packages with debugging flags - set. +\code{\link[=with_debug]{with_debug()}} to install packages with debugging flags +set. Other package installation: \code{\link{install}} } diff --git a/man/wd.Rd b/man/wd.Rd index 962e66fe3..c866c0a69 100644 --- a/man/wd.Rd +++ b/man/wd.Rd @@ -8,7 +8,7 @@ wd(pkg = ".", path = "") } \arguments{ \item{pkg}{package description, can be path or package name. See -\code{\link{as.package}} for more information} +\code{\link[=as.package]{as.package()}} for more information} \item{path}{path within package. Leave empty to change working directory to package directory.}