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‎R/build_times.R

+1-1
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@@ -2,7 +2,7 @@
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#' `r lifecycle::badge("stable")`
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#' @description Applies to targets in your plan, not imports or files.
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#' @details Times for dynamic targets
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#' (<https://books.ropensci.org/drake/dynamic.html>)
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#' (`https://books.ropensci.org/drake/dynamic.html`)
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#' only reflect the time it takes
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#' to post-process the sub-targets (typically very fast)
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#' and exclude the time it takes to build the sub-targets themselves.

‎R/cache.R

+2-2
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@@ -15,7 +15,7 @@
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#' You may want to inspect the targets afterwards, possibly in an
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#' interactive R session. However, the files in the `.drake` folder
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#' are organized in a special format created by the
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#' [`storr`](https://github.com/richfitz/storr) package,
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#' `storr` package,
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#' which is not exactly human-readable.
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#' To retrieve a target for manual viewing, use [readd()].
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#' To load one or more targets into your session, use [loadd()].
@@ -784,7 +784,7 @@ is_imported_cache <- Vectorize(function(target, cache) {
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#' Some methods and objects are new or overwritten. Here
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#' are the ones relevant to users.
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#' - `history`: `drake`'s history (which powers [drake_history()])
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#' is a [`txtq`](https://github.com/wlandau/txtq). Access it
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#' is a `txtq`. Access it
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#' with `drake_cache()$history`.
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#' - `import()`: The `import()` method is a function that can import
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#' targets, function dependencies, etc. from one decorated `storr`

‎R/deprecated.R

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@@ -526,7 +526,7 @@ deprecate_targets_only <- function(targets_only) {
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#' @title Load the main example.
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#' `r lifecycle::badge("deprecated")`
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#' @description The main example lives at
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#' <https://github.com/wlandau/drake-examples/tree/main/main>.
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#' `https://github.com/wlandau/drake-examples/tree/main/main`.
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#' Use `drake_example("main")` to download its code.
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#' This function also writes/overwrites
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#' the files `report.Rmd` and `raw_data.xlsx`.
@@ -1457,7 +1457,7 @@ target_namespaces <- function(
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#' @title Specialized wildcard for analyses
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#' `r lifecycle::badge("deprecated")`
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#' @description Use [drake_plan()] instead.
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#' See <https://books.ropensci.org/drake/plans.html#large-plans>
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#' See `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for details.
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#' @details 2019-01-13
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#' @export
@@ -1495,7 +1495,7 @@ plan_analyses <- function(plan, datasets, sep = "_") {
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#' @title Specialized wildcard for summaries
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#' `r lifecycle::badge("deprecated")`
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#' @description Use [drake_plan()] with transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for details.
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#' @details 2019-01-13
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#' @export
@@ -1787,7 +1787,7 @@ drake_cache_log_file <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#'
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#' @details The commands in workflow plan data frames can have
@@ -2010,7 +2010,7 @@ check_wildcard_rules <- function(rules) {
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#'
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#' @details Duplicates the rows of a workflow plan data frame.
@@ -2062,7 +2062,7 @@ expand_plan <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#' @details `map_plan()` is like `base::Map()`:
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#' it takes a function name and a grid of arguments, and
@@ -2139,7 +2139,7 @@ map_plan <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#' @details Creates a new workflow plan to aggregate
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#' existing targets in the supplied plan.
@@ -2186,7 +2186,7 @@ gather_plan <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#' @details Perform several calls to `gather_plan()`
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#' based on groupings from columns in the plan,
@@ -2262,7 +2262,7 @@ gather_by <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
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#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#' @details Creates a new workflow plan data frame with the
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#' commands to do a reduction (i.e. to repeatedly apply a binary
@@ -2336,7 +2336,7 @@ reduce_plan <- function(
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#' `r lifecycle::badge("deprecated")`
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#' @description Deprecated on 2019-05-16. Use [drake_plan()]
23382338
#' transformations instead. See
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#' <https://books.ropensci.org/drake/plans.html#large-plans>
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#' `https://books.ropensci.org/drake/plans.html#large-plans`
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#' for the details.
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#' @details Perform several calls to `reduce_plan()`
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#' based on groupings from columns in the plan,
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26972697
#' way to make `drake` compatible with workflows implemented as custom
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#' analysis packages. Now, the recommendation is to supply
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#' `getNamespace("yourPackage")` to the `envir` argument of [make()]
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#' and friends. Read <https://github.com/ropensci/drake/issues/1286>,
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#' especially <https://github.com/ropensci/drake/issues/1286#issuecomment-649088321>, # nolint
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#' and friends. Read `https://github.com/ropensci/drake/issues/1286`,
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#' especially `https://github.com/ropensci/drake/issues/1286#issuecomment-649088321`, # nolint
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#' for details.
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#' @export
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#' @return The environment that the exposed imports are loaded into.

‎R/drake_build.R

+1-1
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@@ -79,7 +79,7 @@ body(drake_build) <- config_util_body(drake_build_impl)
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#' and then runs its command in debug mode (see `browser()`,
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#' `debug()`, and `debugonce()`). This function does not
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#' store the target's value in the cache
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#' (see <https://github.com/ropensci/drake/issues/587>).
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#' (see `https://github.com/ropensci/drake/issues/587`).
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#' @export
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#' @seealso [drake_build()]
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#' @return The value of the target right after it is built.

‎R/drake_config.R

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@@ -54,9 +54,8 @@
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#' in `plan` and just import objects and files.
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#'
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#' @param parallelism Character scalar, type of parallelism to use.
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#' For detailed explanations, see the
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#' [high-performance computing chapter](https://books.ropensci.org/drake/hpc.html) # nolint
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#' of the user manual.
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#' For detailed explanations, see
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#' `https://books.ropensci.org/drake/hpc.html`.
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#'
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#' You could also supply your own scheduler function
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#' if you want to experiment or aggressively optimize.
@@ -75,7 +74,7 @@
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#' You can experiment with [predict_runtime()]
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#' to help decide on an appropriate number of jobs.
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#' For details, visit
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#' <https://books.ropensci.org/drake/time.html>.
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#' `https://books.ropensci.org/drake/time.html`.
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#'
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#' @param jobs_preprocess Number of parallel jobs for processing the imports
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#' and doing other preprocessing tasks.
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#'
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#' @param lazy_load An old feature, currently being questioned.
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#' For the current recommendations on memory management, see
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#' <https://books.ropensci.org/drake/memory.html#memory-strategies>.
163+
#' `https://books.ropensci.org/drake/memory.html#memory-strategies`.
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#' The `lazy_load` argument is either a character vector or a logical.
166165
#' For dynamic targets, the behavior is always `"eager"` (see below).
167166
#' So the `lazy_load` argument is for static targets only.
@@ -333,7 +332,7 @@
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#' Enabled for `clustermq` only (`make(parallelism = "clustermq")`),
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#' not `future` or `batchtools` so far.
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#' For more information, see the `clustermq` package:
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#' <https://github.com/mschubert/clustermq>.
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#' `https://github.com/mschubert/clustermq`.
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#' Some template placeholders such as `{{ job_name }}` and `{{ n_jobs }}`
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#' cannot be set this way.
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#'
@@ -385,7 +384,7 @@
385384
#'
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#' @param history Logical, whether to record the build history
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#' of your targets. You can also supply a
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#' [`txtq`](https://github.com/wlandau/txtq), which is
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#' `txtq`, which is
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#' how `drake` records history.
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#' Must be `TRUE` for [drake_history()] to work later.
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#'
@@ -471,7 +470,7 @@
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#' @param format Character, an optional custom storage format for targets
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#' without an explicit `target(format = ...)` in the plan. Details
473472
#' about formats:
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#' <https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets> # nolint
473+
#' `https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets` # nolint
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#'
476475
#' @param lock_cache Logical, whether to lock the cache before running `make()`
477476
#' etc. It is usually recommended to keep cache locking on.

‎R/drake_example.R

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#' @title Download the files of an example `drake` project.
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#' `r lifecycle::badge("stable")`
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#' @description The `drake_example()` function downloads a
4-
#' folder from <https://github.com/wlandau/drake-examples>.
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#' folder from `https://github.com/wlandau/drake-examples`.
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#' By default, it creates a new folder with the example name
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#' in your current working directory. After the files are written,
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#' have a look at the enclosed `README` file.
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#' Other instructions are available in the files at
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#' <https://github.com/wlandau/drake-examples>.
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#' `https://github.com/wlandau/drake-examples`.
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#' @seealso [drake_examples()], [make()]
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#' @export
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#' @return `NULL`
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#' @param example Name of the example.
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#' The possible values are the names of the folders at
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#' <https://github.com/wlandau/drake-examples>.
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#' `https://github.com/wlandau/drake-examples`.
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#' @param to Character scalar,
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#' the folder containing the code files for the example.
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#' passed to the `exdir` argument of `utils::unzip()`.
@@ -62,9 +62,9 @@ drake_example <- function(
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#' @title List the names of all the drake examples.
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#' `r lifecycle::badge("stable")`
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#' @description You can find the code files of the examples at
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#' <https://github.com/wlandau/drake-examples>.
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#' `https://github.com/wlandau/drake-examples`.
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#' The `drake_examples()` function downloads the list of examples
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#' from <https://wlandau.github.io/drake-examples/examples.md>,
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#' from `https://wlandau.github.io/drake-examples/examples.md`,
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#' so you need an internet connection.
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#' @export
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#' @seealso [drake_example()], [make()]

‎R/drake_plan.R

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#'
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#' @details Besides `"target"` and `"command"`, [drake_plan()]
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#' understands a special set of optional columns. For details, visit
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#' <https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan> # nolint
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#' `https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan` # nolint
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#'
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#' @seealso make, drake_config, transform_plan, map, split, cross, combine
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#'
@@ -26,19 +26,19 @@
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#' but `drake` looks for them at various points in the workflow.
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#' - `transform`: a call to [map()], [split()], [cross()], or
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#' [combine()] to create and manipulate large collections of targets.
29-
#' Details: (<https://books.ropensci.org/drake/plans.html#large-plans>). # nolint
29+
#' Details: (`https://books.ropensci.org/drake/plans.html#large-plans`). # nolint
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#' - `format`: set a storage format to save big targets more efficiently.
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#' See the "Formats" section of this help file for more details.
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#' - `trigger`: rule to decide whether a target needs to run.
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#' It is recommended that you define this one with `target()`.
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#' Details: <https://books.ropensci.org/drake/triggers.html>.
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#' Details: `https://books.ropensci.org/drake/triggers.html`.
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#' - `hpc`: logical values (`TRUE`/`FALSE`/`NA`) whether to send each target
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#' to parallel workers.
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#' Visit <https://books.ropensci.org/drake/hpc.html#selectivity>
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#' Visit `https://books.ropensci.org/drake/hpc.html#selectivity`
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#' to learn more.
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#' - `resources`: target-specific lists of resources for a computing cluster.
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#' See
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#' <https://books.ropensci.org/drake/hpc.html#advanced-options>
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#' `https://books.ropensci.org/drake/hpc.html#advanced-options`
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#' for details.
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#' - `caching`: overrides the `caching` argument of [make()] for each target
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#' individually. Possible values:
@@ -76,7 +76,7 @@
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#' subsequent calls to `make()`. This is a more flexible
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#' alternative to `file_in()` and `file_out()`, and it is
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#' compatible with dynamic branching.
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#' See <https://github.com/ropensci/drake/pull/1178> for an example.
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#' See `https://github.com/ropensci/drake/pull/1178` for an example.
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#' - `"fst"`: save big data frames fast. Requires the `fst` package.
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#' Note: this format strips non-data-frame attributes such as the
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#' - `"fst_tbl"`: Like `"fst"`, but for `tibble` objects.
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112112
#' with its own help file.
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#' - [target()]: give the target more than just a command.
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#' Using [target()], you can apply a transformation
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#' (examples: <https://books.ropensci.org/drake/plans.html#large-plans>), # nolint
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#' supply a trigger (<https://books.ropensci.org/drake/triggers.html>), # nolint
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#' (examples: `https://books.ropensci.org/drake/plans.html#large-plans`), # nolint
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#' supply a trigger (`https://books.ropensci.org/drake/triggers.html`), # nolint
117117
#' or set any number of custom columns.
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#' - [file_in()]: declare an input file dependency.
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#' - [file_out()]: declare an output file to be produced
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#'
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#' # Use transformations to generate large plans.
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#' # Read more at
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#' # <https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way>. # nolint
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#' # `https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way`. # nolint
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#' drake_plan(
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#' data = target(
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#' simulate(nrows),

‎R/drake_plan_helpers.R

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

‎R/make.R

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

‎R/package.R

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

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