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wlandau-lilly committed Oct 17, 2023
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2 changes: 1 addition & 1 deletion R/build_times.R
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Expand Up @@ -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.
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4 changes: 2 additions & 2 deletions R/cache.R
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Expand Up @@ -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()].
Expand Down Expand Up @@ -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`
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24 changes: 12 additions & 12 deletions R/deprecated.R
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Expand Up @@ -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`.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion R/drake_build.R
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Expand Up @@ -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.
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15 changes: 7 additions & 8 deletions R/drake_config.R
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Expand Up @@ -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.
Expand All @@ -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.
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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.
#'
Expand Down Expand Up @@ -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.
#'
Expand Down Expand Up @@ -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.
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10 changes: 5 additions & 5 deletions R/drake_example.R
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@@ -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()`.
Expand Down Expand Up @@ -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()]
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18 changes: 9 additions & 9 deletions R/drake_plan.R
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Expand Up @@ -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
#'
Expand All @@ -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:
Expand Down Expand Up @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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),
Expand Down
12 changes: 6 additions & 6 deletions R/drake_plan_helpers.R
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Expand Up @@ -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())`.
Expand All @@ -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.
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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8 changes: 4 additions & 4 deletions R/make.R
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Expand Up @@ -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,
Expand Down Expand Up @@ -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:
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4 changes: 2 additions & 2 deletions R/package.R
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@@ -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
Expand Down Expand Up @@ -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
Expand Down
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