Remove links

R/build_times.R

@@ -2,7 +2,7 @@
 #' `r lifecycle::badge("stable")`
 #' @description Applies to targets in your plan, not imports or files.
 #' @details Times for dynamic targets
-#'   (<https://books.ropensci.org/drake/dynamic.html>)
+#'   (`https://books.ropensci.org/drake/dynamic.html`)
 #'   only reflect the time it takes
 #'   to post-process the sub-targets (typically very fast)
 #'   and exclude the time it takes to build the sub-targets themselves.

R/cache.R

@@ -15,7 +15,7 @@
 #'   You may want to inspect the targets afterwards, possibly in an
 #'   interactive R session. However, the files in the `.drake` folder
 #'   are organized in a special format created by the
-#'   [`storr`](https://github.com/richfitz/storr) package,
+#'   `storr` package,
 #'   which is not exactly human-readable.
 #'   To retrieve a target for manual viewing, use [readd()].
 #'   To load one or more targets into your session, use [loadd()].
@@ -784,7 +784,7 @@ is_imported_cache <- Vectorize(function(target, cache) {
 #'   Some methods and objects are new or overwritten. Here
 #'   are the ones relevant to users.
 #'   - `history`: `drake`'s history (which powers [drake_history()])
-#'     is a [`txtq`](https://github.com/wlandau/txtq). Access it
+#'     is a `txtq`. Access it
 #'     with `drake_cache()$history`.
 #'   - `import()`: The `import()` method is a function that can import
 #'     targets, function dependencies, etc. from one decorated `storr`

R/deprecated.R

@@ -526,7 +526,7 @@ deprecate_targets_only <- function(targets_only) {
 #' @title Load the main example.
 #' `r lifecycle::badge("deprecated")`
 #' @description The main example lives at
-#' <https://github.com/wlandau/drake-examples/tree/main/main>.
+#' `https://github.com/wlandau/drake-examples/tree/main/main`.
 #' Use `drake_example("main")` to download its code.
 #' This function also writes/overwrites
 #' the files `report.Rmd` and `raw_data.xlsx`.
@@ -1457,7 +1457,7 @@ target_namespaces <- function(
 #' @title Specialized wildcard for analyses
 #' `r lifecycle::badge("deprecated")`
 #' @description Use [drake_plan()] instead.
-#'   See <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   See `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for details.
 #' @details 2019-01-13
 #' @export
@@ -1495,7 +1495,7 @@ plan_analyses <- function(plan, datasets, sep = "_") {
 #' @title Specialized wildcard for summaries
 #' `r lifecycle::badge("deprecated")`
 #' @description Use [drake_plan()] with transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for details.
 #' @details 2019-01-13
 #' @export
@@ -1787,7 +1787,7 @@ drake_cache_log_file <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #'
 #' @details The commands in workflow plan data frames can have
@@ -2010,7 +2010,7 @@ check_wildcard_rules <- function(rules) {
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #'
 #' @details Duplicates the rows of a workflow plan data frame.
@@ -2062,7 +2062,7 @@ expand_plan <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #' @details `map_plan()` is like `base::Map()`:
 #'   it takes a function name and a grid of arguments, and
@@ -2139,7 +2139,7 @@ map_plan <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #' @details Creates a new workflow plan to aggregate
 #'   existing targets in the supplied plan.
@@ -2186,7 +2186,7 @@ gather_plan <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #' @details Perform several calls to `gather_plan()`
 #'   based on groupings from columns in the plan,
@@ -2262,7 +2262,7 @@ gather_by <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #' @details Creates a new workflow plan data frame with the
 #'   commands to do a reduction (i.e. to repeatedly apply a binary
@@ -2336,7 +2336,7 @@ reduce_plan <- function(
 #' `r lifecycle::badge("deprecated")`
 #' @description Deprecated on 2019-05-16. Use [drake_plan()]
 #'   transformations instead. See
-#'   <https://books.ropensci.org/drake/plans.html#large-plans>
+#'   `https://books.ropensci.org/drake/plans.html#large-plans`
 #'   for the details.
 #' @details Perform several calls to `reduce_plan()`
 #'   based on groupings from columns in the plan,
@@ -2697,8 +2697,8 @@ progress <- function(
 #'   way to make `drake` compatible with workflows implemented as custom
 #'   analysis packages. Now, the recommendation is to supply
 #'   `getNamespace("yourPackage")` to the `envir` argument of [make()]
-#'   and friends. Read <https://github.com/ropensci/drake/issues/1286>,
-#'   especially <https://github.com/ropensci/drake/issues/1286#issuecomment-649088321>, # nolint
+#'   and friends. Read `https://github.com/ropensci/drake/issues/1286`,
+#'   especially `https://github.com/ropensci/drake/issues/1286#issuecomment-649088321`, # nolint
 #'   for details.
 #' @export
 #' @return The environment that the exposed imports are loaded into.

R/drake_build.R

@@ -79,7 +79,7 @@ body(drake_build) <- config_util_body(drake_build_impl)
 #'   and then runs its command in debug mode (see `browser()`,
 #'   `debug()`, and `debugonce()`). This function does not
 #'   store the target's value in the cache
-#'   (see <https://github.com/ropensci/drake/issues/587>).
+#'   (see `https://github.com/ropensci/drake/issues/587`).
 #' @export
 #' @seealso [drake_build()]
 #' @return The value of the target right after it is built.

R/drake_config.R

@@ -54,9 +54,8 @@
 #'   in `plan` and just import objects and files.
 #'
 #' @param parallelism Character scalar, type of parallelism to use.
-#'   For detailed explanations, see the
-#'   [high-performance computing chapter](https://books.ropensci.org/drake/hpc.html) # nolint
-#'   of the user manual.
+#'   For detailed explanations, see
+#'   `https://books.ropensci.org/drake/hpc.html`.
 #'
 #'   You could also supply your own scheduler function
 #'   if you want to experiment or aggressively optimize.
@@ -75,7 +74,7 @@
 #'   You can experiment with [predict_runtime()]
 #'   to help decide on an appropriate number of jobs.
 #'   For details, visit
-#'   <https://books.ropensci.org/drake/time.html>.
+#'   `https://books.ropensci.org/drake/time.html`.
 #'
 #' @param jobs_preprocess Number of parallel jobs for processing the imports
 #'   and doing other preprocessing tasks.
@@ -161,7 +160,7 @@
 #'
 #' @param lazy_load An old feature, currently being questioned.
 #'   For the current recommendations on memory management, see
-#'   <https://books.ropensci.org/drake/memory.html#memory-strategies>.
+#'   `https://books.ropensci.org/drake/memory.html#memory-strategies`.
 #'   The `lazy_load` argument is either a character vector or a logical.
 #'   For dynamic targets, the behavior is always `"eager"` (see below).
 #'   So the `lazy_load` argument is for static targets only.
@@ -333,7 +332,7 @@
 #'   Enabled for `clustermq` only (`make(parallelism = "clustermq")`),
 #'   not `future` or `batchtools` so far.
 #'   For more information, see the `clustermq` package:
-#'   <https://github.com/mschubert/clustermq>.
+#'   `https://github.com/mschubert/clustermq`.
 #'   Some template placeholders such as `{{ job_name }}` and `{{ n_jobs }}`
 #'   cannot be set this way.
 #'
@@ -385,7 +384,7 @@
 #'
 #' @param history Logical, whether to record the build history
 #'   of your targets. You can also supply a
-#'   [`txtq`](https://github.com/wlandau/txtq), which is
+#'   `txtq`, which is
 #'   how `drake` records history.
 #'   Must be `TRUE` for [drake_history()] to work later.
 #'
@@ -471,7 +470,7 @@
 #' @param format Character, an optional custom storage format for targets
 #'   without an explicit `target(format = ...)` in the plan. Details
 #'   about formats:
-#'   <https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets> # nolint
+#'   `https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets` # nolint
 #'
 #' @param lock_cache Logical, whether to lock the cache before running `make()`
 #'   etc. It is usually recommended to keep cache locking on.

R/drake_example.R

@@ -1,18 +1,18 @@
 #' @title Download the files of an example `drake` project.
 #' `r lifecycle::badge("stable")`
 #' @description The `drake_example()` function downloads a
-#'   folder from <https://github.com/wlandau/drake-examples>.
+#'   folder from `https://github.com/wlandau/drake-examples`.
 #'   By default, it creates a new folder with the example name
 #'   in your current working directory. After the files are written,
 #'   have a look at the enclosed `README` file.
 #'   Other instructions are available in the files at
-#'   <https://github.com/wlandau/drake-examples>.
+#'   `https://github.com/wlandau/drake-examples`.
 #' @seealso [drake_examples()], [make()]
 #' @export
 #' @return `NULL`
 #' @param example Name of the example.
 #'   The possible values are the names of the folders at
-#'   <https://github.com/wlandau/drake-examples>.
+#'   `https://github.com/wlandau/drake-examples`.
 #' @param to Character scalar,
 #'   the folder containing the code files for the example.
 #'   passed to the `exdir` argument of `utils::unzip()`.
@@ -62,9 +62,9 @@ drake_example <- function(
 #' @title List the names of all the drake examples.
 #' `r lifecycle::badge("stable")`
 #' @description You can find the code files of the examples at
-#'   <https://github.com/wlandau/drake-examples>.
+#'   `https://github.com/wlandau/drake-examples`.
 #'   The `drake_examples()` function downloads the list of examples
-#'   from <https://wlandau.github.io/drake-examples/examples.md>,
+#'   from `https://wlandau.github.io/drake-examples/examples.md`,
 #'   so you need an internet connection.
 #' @export
 #' @seealso [drake_example()], [make()]

R/drake_plan.R

@@ -9,7 +9,7 @@
 #'
 #' @details Besides `"target"` and `"command"`, [drake_plan()]
 #'   understands a special set of optional columns. For details, visit
-#'   <https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan> # nolint
+#'   `https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan` # nolint
 #'
 #' @seealso make, drake_config, transform_plan, map, split, cross, combine
 #'
@@ -26,19 +26,19 @@
 #' but `drake` looks for them at various points in the workflow.
 #' - `transform`: a call to [map()], [split()], [cross()], or
 #'   [combine()] to create and manipulate large collections of targets.
-#'   Details: (<https://books.ropensci.org/drake/plans.html#large-plans>). # nolint
+#'   Details: (`https://books.ropensci.org/drake/plans.html#large-plans`). # nolint
 #' - `format`: set a storage format to save big targets more efficiently.
 #'   See the "Formats" section of this help file for more details.
 #' - `trigger`: rule to decide whether a target needs to run.
 #'   It is recommended that you define this one with `target()`.
-#'   Details: <https://books.ropensci.org/drake/triggers.html>.
+#'   Details: `https://books.ropensci.org/drake/triggers.html`.
 #' - `hpc`: logical values (`TRUE`/`FALSE`/`NA`) whether to send each target
 #'   to parallel workers.
-#'   Visit <https://books.ropensci.org/drake/hpc.html#selectivity>
+#'   Visit `https://books.ropensci.org/drake/hpc.html#selectivity`
 #'   to learn more.
 #' - `resources`: target-specific lists of resources for a computing cluster.
 #'   See
-#'   <https://books.ropensci.org/drake/hpc.html#advanced-options>
+#'   `https://books.ropensci.org/drake/hpc.html#advanced-options`
 #'   for details.
 #' - `caching`: overrides the `caching` argument of [make()] for each target
 #'   individually. Possible values:
@@ -76,7 +76,7 @@
 #'     subsequent calls to `make()`. This is a more flexible
 #'     alternative to `file_in()` and `file_out()`, and it is
 #'     compatible with dynamic branching.
-#'     See <https://github.com/ropensci/drake/pull/1178> for an example.
+#'     See `https://github.com/ropensci/drake/pull/1178` for an example.
 #'   - `"fst"`: save big data frames fast. Requires the `fst` package.
 #'     Note: this format strips non-data-frame attributes such as the
 #'   - `"fst_tbl"`: Like `"fst"`, but for `tibble` objects.
@@ -112,8 +112,8 @@
 #' with its own help file.
 #' - [target()]: give the target more than just a command.
 #'   Using [target()], you can apply a transformation
-#'   (examples: <https://books.ropensci.org/drake/plans.html#large-plans>), # nolint
-#'   supply a trigger (<https://books.ropensci.org/drake/triggers.html>), # nolint
+#'   (examples: `https://books.ropensci.org/drake/plans.html#large-plans`), # nolint
+#'   supply a trigger (`https://books.ropensci.org/drake/triggers.html`), # nolint
 #'   or set any number of custom columns.
 #' - [file_in()]: declare an input file dependency.
 #' - [file_out()]: declare an output file to be produced
@@ -190,7 +190,7 @@
 #'
 #' # Use transformations to generate large plans.
 #' # Read more at
-#' # <https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way>. # nolint
+#' # `https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way`. # nolint
 #' drake_plan(
 #'   data = target(
 #'     simulate(nrows),

R/drake_plan_helpers.R

@@ -6,7 +6,7 @@
 #'   and dynamic branching, and it can also set the values
 #'   of custom columns such as `format`, `elapsed`, `retries`,
 #'   and `max_expand`. Details are at
-#'   <https://books.ropensci.org/drake/plans.html#special-columns>.
+#'   `https://books.ropensci.org/drake/plans.html#special-columns`.
 #'   Note: `drake_plan(my_target = my_command())`
 #'   is equivalent to
 #'   `drake_plan(my_target = target(my_command())`.
@@ -22,10 +22,10 @@
 #' @param command The command to build the target.
 #' @param transform A call to [map()], [split()], [cross()], or [combine()]
 #'   to apply a *static* transformation. Details:
-#'   <https://books.ropensci.org/drake/static.html>
+#'   `https://books.ropensci.org/drake/static.html`
 #' @param dynamic A call to [map()], [cross()], or [group()]
 #'   to apply a *dynamic* transformation. Details:
-#'   <https://books.ropensci.org/drake/dynamic.html>
+#'   `https://books.ropensci.org/drake/dynamic.html`
 #' @param ... Optional columns of the plan for a given target.
 #'   See the Columns section of this help file for a selection
 #'   of special columns that `drake` understands.
@@ -104,7 +104,7 @@ target <- function(
 #'   [make()] or [drake_config()].
 #'   For details, see the chapter on triggers
 #'   in the user manual:
-#'   <https://books.ropensci.org/drake/triggers.html>
+#'   `https://books.ropensci.org/drake/triggers.html`
 #' @details
 #'   A target always builds if it has not been built before.
 #'   Triggers allow you to customize the conditions
@@ -142,7 +142,7 @@ target <- function(
 #'   choice of specialized data format changes: for example,
 #'   if you use `target(format = "qs")` one instance and
 #'   `target(format = "fst")` the next. See
-#'   <https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets> # nolint
+#'   `https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets` # nolint
 #'   for details on formats.
 #' @param condition R code (expression or language object)
 #'   that returns a logical. The target will rebuild
@@ -894,7 +894,7 @@ plan_to_text <- function(plan) {
 #' `r lifecycle::badge("stable")`
 #' @description You supply a plan, and [drake_plan_source()]
 #'   supplies code to generate that plan. If you have the
-#'   [`prettycode` package](https://github.com/r-lib/prettycode),
+#'   `prettycode` package,
 #'   installed, you also get nice syntax highlighting in the console
 #'   when you print it.
 #' @export

R/make.R

@@ -21,7 +21,7 @@
 #' This script should begin in a fresh R session,
 #' load your packages and functions in a dependable manner,
 #' and then run `make()`. Example:
-#' <https://github.com/wlandau/drake-examples/tree/main/gsp>.
+#' `https://github.com/wlandau/drake-examples/tree/main/gsp`.
 #' Batch mode, especially within a container, is particularly helpful.
 #'
 #' Interactive R sessions are still useful,
@@ -51,15 +51,15 @@
 #' during `make()` itself.
 #'
 #' For each target that is still problematic  (e.g.
-#' <https://github.com/rstudio/gt/issues/297>)
+#' `https://github.com/rstudio/gt/issues/297`)
 #' you can safely run the command in its own special `callr::r()` process.
-#' Example: <https://github.com/rstudio/gt/issues/297#issuecomment-497778735>. # nolint
+#' Example: `https://github.com/rstudio/gt/issues/297#issuecomment-497778735`. # nolint
 #'
 #' If that fails, you can run `make(plan, lock_envir = FALSE)`
 #' to suppress environment-locking for all targets.
 #' However, this is not usually recommended.
 #' There are legitimate use cases for `lock_envir = FALSE`
-#' (example: <https://books.ropensci.org/drake/hpc.html#parallel-computing-within-targets>) # nolint
+#' (example: `https://books.ropensci.org/drake/hpc.html#parallel-computing-within-targets`) # nolint
 #' but most workflows should stick with the default `lock_envir = TRUE`.
 #'
 #' @section Cache locking:

R/package.R

@@ -1,7 +1,7 @@
 #' drake: A pipeline toolkit for reproducible computation at scale.
 #' @docType package
 #' @description drake is a pipeline toolkit
-#' (<https://github.com/pditommaso/awesome-pipeline>)
+#' (`https://github.com/pditommaso/awesome-pipeline`)
 #' and a scalable, R-focused solution for reproducibility
 #' and high-performance computing.
 #' @name drake-package
@@ -43,7 +43,7 @@
 #' readd(mean_mpg_by_cyl)
 #' })
 #' }
-#' @references <https://github.com/ropensci/drake>
+#' @references `https://github.com/ropensci/drake`
 #' @useDynLib drake, .registration = TRUE
 #' @importFrom base64url base32_decode base32_encode
 #' @importFrom digest getVDigest