From 1d1719d4d0f4edfebb7d591583f7e65dc900990a Mon Sep 17 00:00:00 2001 From: wlandau-lilly Date: Tue, 17 Oct 2023 09:59:22 -0400 Subject: [PATCH] Remove links --- R/build_times.R | 2 +- R/cache.R | 4 ++-- R/deprecated.R | 24 ++++++++++++------------ R/drake_build.R | 2 +- R/drake_config.R | 15 +++++++-------- R/drake_example.R | 10 +++++----- R/drake_plan.R | 18 +++++++++--------- R/drake_plan_helpers.R | 12 ++++++------ R/make.R | 8 ++++---- R/package.R | 4 ++-- R/transform_plan.R | 6 +++--- R/use_drake.R | 8 ++++---- man/build_drake_graph.Rd | 2 +- man/build_times.Rd | 2 +- man/drake-package.Rd | 4 ++-- man/drake_cache.Rd | 2 +- man/drake_config.Rd | 15 +++++++-------- man/drake_debug.Rd | 2 +- man/drake_envir.Rd | 4 ++-- man/drake_example.Rd | 6 +++--- man/drake_examples.Rd | 4 ++-- man/drake_history.Rd | 2 +- man/drake_plan.Rd | 20 ++++++++++---------- man/drake_plan_source.Rd | 2 +- man/drake_triggers.Rd | 2 +- man/evaluate_plan.Rd | 2 +- man/expand_plan.Rd | 2 +- man/expose_imports.Rd | 4 ++-- man/file_in.Rd | 4 ++-- man/file_out.Rd | 4 ++-- man/gather_by.Rd | 2 +- man/gather_plan.Rd | 2 +- man/id_chr.Rd | 4 ++-- man/ignore.Rd | 4 ++-- man/knitr_in.Rd | 4 ++-- man/load_main_example.Rd | 2 +- man/make.Rd | 23 +++++++++++------------ man/map_plan.Rd | 2 +- man/new_drake_settings.Rd | 11 +++++------ man/no_deps.Rd | 4 ++-- man/plan_analyses.Rd | 2 +- man/plan_summaries.Rd | 2 +- man/readd.Rd | 2 +- man/reduce_by.Rd | 2 +- man/reduce_plan.Rd | 2 +- man/target.Rd | 20 ++++++++++---------- man/transform_plan.Rd | 2 +- man/transformations.Rd | 4 ++-- man/trigger.Rd | 4 ++-- man/use_drake.Rd | 8 ++++---- 50 files changed, 149 insertions(+), 153 deletions(-) diff --git a/R/build_times.R b/R/build_times.R index afa94aa3e..135f37b89 100644 --- a/R/build_times.R +++ b/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`) #' 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. diff --git a/R/cache.R b/R/cache.R index faa076171..e8cbec3ee 100644 --- a/R/cache.R +++ b/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` diff --git a/R/deprecated.R b/R/deprecated.R index b07e92fad..ca202490a 100644 --- a/R/deprecated.R +++ b/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`. #' 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 +#' 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` #' 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` #' 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` #' 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` #' 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` #' 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` #' 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` #' 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` #' 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 , -#' especially , # 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. diff --git a/R/drake_build.R b/R/drake_build.R index e2ebb9ff2..4be1f37d7 100644 --- a/R/drake_build.R +++ b/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 ). +#' (see `https://github.com/ropensci/drake/issues/587`). #' @export #' @seealso [drake_build()] #' @return The value of the target right after it is built. diff --git a/R/drake_config.R b/R/drake_config.R index 23f6967eb..444846c26 100644 --- a/R/drake_config.R +++ b/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`. #' #' @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`. #' 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`. #' 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: -#' # 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. diff --git a/R/drake_example.R b/R/drake_example.R index d3a0e67bd..38d2bee0e 100644 --- a/R/drake_example.R +++ b/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 . +#' 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`. #' @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`. #' @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`. #' The `drake_examples()` function downloads the list of examples -#' from , +#' from `https://wlandau.github.io/drake-examples/examples.md`, #' so you need an internet connection. #' @export #' @seealso [drake_example()], [make()] diff --git a/R/drake_plan.R b/R/drake_plan.R index f142ea262..c35cae0d0 100644 --- a/R/drake_plan.R +++ b/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 -#' # 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: (). # 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: . +#' Details: `https://books.ropensci.org/drake/triggers.html`. #' - `hpc`: logical values (`TRUE`/`FALSE`/`NA`) whether to send each target #' to parallel workers. -#' Visit +#' 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` #' 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 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: ), # nolint -#' supply a trigger (), # 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 -#' # . # nolint +#' # `https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way`. # nolint #' drake_plan( #' data = target( #' simulate(nrows), diff --git a/R/drake_plan_helpers.R b/R/drake_plan_helpers.R index 92e77e7d8..2c23698c0 100644 --- a/R/drake_plan_helpers.R +++ b/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`. #' 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` #' @param dynamic A call to [map()], [cross()], or [group()] #' to apply a *dynamic* transformation. Details: -#' +#' `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` #' @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 -#' # 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 diff --git a/R/make.R b/R/make.R index 35f5e0ce8..bb906ff1e 100644 --- a/R/make.R +++ b/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`. #' 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`) #' you can safely run the command in its own special `callr::r()` process. -#' Example: . # 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: ) # 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: diff --git a/R/package.R b/R/package.R index 9bfaeafee..373afbca1 100644 --- a/R/package.R +++ b/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`) #' 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 +#' @references `https://github.com/ropensci/drake` #' @useDynLib drake, .registration = TRUE #' @importFrom base64url base32_decode base32_encode #' @importFrom digest getVDigest diff --git a/R/transform_plan.R b/R/transform_plan.R index f869d82fc..737667f61 100644 --- a/R/transform_plan.R +++ b/R/transform_plan.R @@ -5,13 +5,13 @@ #' of targets with transformations such as #' `map()`, `split()`, `cross()`, and `combine()`. #' @details For details, see -#' . +#' `https://books.ropensci.org/drake/plans.html#large-plans`. #' @section Transformations: #' `drake` has special syntax for generating large plans. #' Your code will look something like #' `drake_plan(y = target(f(x), transform = map(x = c(1, 2, 3)))` #' You can read about this interface at -#' . # nolint +#' `https://books.ropensci.org/drake/plans.html#large-plans`. # nolint #' @section Static branching: #' In static branching, you define batches of targets #' based on information you know in advance. @@ -153,7 +153,7 @@ NULL #' @description Evaluate the `map()`, `cross()`, `split()` and #' `combine()` operations in the `transform` column of a #' `drake` plan. -#' @details # nolint +#' @details `https://books.ropensci.org/drake/plans.html#large-plans` # nolint #' @export #' @seealso drake_plan, map, split, cross, combine #' @param plan A `drake` plan with a `transform` column diff --git a/R/use_drake.R b/R/use_drake.R index 3e95185c6..23ce1a304 100644 --- a/R/use_drake.R +++ b/R/use_drake.R @@ -2,19 +2,19 @@ #' `r lifecycle::badge("questioning")` #' @description Add top-level R script files to use `drake` #' in your data analysis project. For details, read -#' +#' `https://books.ropensci.org/drake/projects.html` #' @details Files written: #' 1. `make.R`: a suggested main R script for batch mode. #' 2. `_drake.R`: a configuration R script for -#' the [`r_*()`](https://docs.ropensci.org/drake/reference/r_make.html) functions documented at # nolint -#' . # nolint +#' the `r_*()` functions documented at # nolint +#' `https://books.ropensci.org/drake/projects.html#safer-interactivity`. # nolint #' Remarks: #' - There is nothing magical about the name, `make.R`. #' You can call it whatever you want. #' - Other supporting scripts, such as `R/packages.R`, #' `R/functions.R`, and `R/plan.R`, are not included. #' - You can find examples at -#' +#' `https://github.com/wlandau/drake-examples` #' and download examples with [`drake_example()`] #' (e.g. `drake_example("main")`). #' @export diff --git a/man/build_drake_graph.Rd b/man/build_drake_graph.Rd index d934ac41e..c6dd00b3f 100644 --- a/man/build_drake_graph.Rd +++ b/man/build_drake_graph.Rd @@ -54,7 +54,7 @@ done so far. You can experiment with \code{\link[=predict_runtime]{predict_runtime()}} to help decide on an appropriate number of jobs. For details, visit -\url{https://books.ropensci.org/drake/time.html}.} +\verb{https://books.ropensci.org/drake/time.html}.} \item{console_log_file}{Deprecated in favor of \code{log_make}.} diff --git a/man/build_times.Rd b/man/build_times.Rd index a883203ff..7996e449e 100644 --- a/man/build_times.Rd +++ b/man/build_times.Rd @@ -55,7 +55,7 @@ Applies to targets in your plan, not imports or files. } \details{ Times for dynamic targets -(\url{https://books.ropensci.org/drake/dynamic.html}) +(\verb{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. diff --git a/man/drake-package.Rd b/man/drake-package.Rd index be40a6c48..9684e3388 100644 --- a/man/drake-package.Rd +++ b/man/drake-package.Rd @@ -7,7 +7,7 @@ \title{drake: A pipeline toolkit for reproducible computation at scale.} \description{ drake is a pipeline toolkit -(\url{https://github.com/pditommaso/awesome-pipeline}) +(\verb{https://github.com/pditommaso/awesome-pipeline}) and a scalable, R-focused solution for reproducibility and high-performance computing. } @@ -49,7 +49,7 @@ readd(mean_mpg_by_cyl) } } \references{ -\url{https://github.com/ropensci/drake} +\verb{https://github.com/ropensci/drake} } \author{ William Michael Landau \email{will.landau@gmail.com} diff --git a/man/drake_cache.Rd b/man/drake_cache.Rd index 3f453944e..50aeaae15 100644 --- a/man/drake_cache.Rd +++ b/man/drake_cache.Rd @@ -40,7 +40,7 @@ Some methods and objects are new or overwritten. Here are the ones relevant to users. \itemize{ \item \code{history}: \code{drake}'s history (which powers \code{\link[=drake_history]{drake_history()}}) -is a \href{https://github.com/wlandau/txtq}{\code{txtq}}. Access it +is a \code{txtq}. Access it with \code{drake_cache()$history}. \item \code{import()}: The \code{import()} method is a function that can import targets, function dependencies, etc. from one decorated \code{storr} diff --git a/man/drake_config.Rd b/man/drake_config.Rd index 3d682dcf2..10f4a1799 100644 --- a/man/drake_config.Rd +++ b/man/drake_config.Rd @@ -107,9 +107,8 @@ See also \code{\link[=drake_cache]{drake_cache()}}.} \item{fetch_cache}{Deprecated.} \item{parallelism}{Character scalar, type of parallelism to use. -For detailed explanations, see the -\href{https://books.ropensci.org/drake/hpc.html}{high-performance computing chapter} # nolint -of the user manual. +For detailed explanations, see +\verb{https://books.ropensci.org/drake/hpc.html}. You could also supply your own scheduler function if you want to experiment or aggressively optimize. @@ -130,7 +129,7 @@ whenever \code{drake}'s unexported core functions are updated. You can experiment with \code{\link[=predict_runtime]{predict_runtime()}} to help decide on an appropriate number of jobs. For details, visit -\url{https://books.ropensci.org/drake/time.html}.} +\verb{https://books.ropensci.org/drake/time.html}.} \item{jobs_preprocess}{Number of parallel jobs for processing the imports and doing other preprocessing tasks.} @@ -217,7 +216,7 @@ on your workflow. Use at your own peril.} \item{lazy_load}{An old feature, currently being questioned. For the current recommendations on memory management, see -\url{https://books.ropensci.org/drake/memory.html#memory-strategies}. +\verb{https://books.ropensci.org/drake/memory.html#memory-strategies}. The \code{lazy_load} argument is either a character vector or a logical. For dynamic targets, the behavior is always \code{"eager"} (see below). So the \code{lazy_load} argument is for static targets only. @@ -327,7 +326,7 @@ Same as the \code{template} argument of \code{clustermq::Q()} and Enabled for \code{clustermq} only (\code{make(parallelism = "clustermq")}), not \code{future} or \code{batchtools} so far. For more information, see the \code{clustermq} package: -\url{https://github.com/mschubert/clustermq}. +\verb{https://github.com/mschubert/clustermq}. Some template placeholders such as \code{{{ job_name }}} and \code{{{ n_jobs }}} cannot be set this way.} @@ -431,7 +430,7 @@ if \code{envir} is \code{getNamespace("packagename")}.} \item{history}{Logical, whether to record the build history of your targets. You can also supply a -\href{https://github.com/wlandau/txtq}{\code{txtq}}, which is +\code{txtq}, which is how \code{drake} records history. Must be \code{TRUE} for \code{\link[=drake_history]{drake_history()}} to work later.} @@ -520,7 +519,7 @@ with \code{build_times = FALSE}.} \item{format}{Character, an optional custom storage format for targets without an explicit \code{target(format = ...)} in the plan. Details about formats: -\url{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint} +\verb{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint} \item{lock_cache}{Logical, whether to lock the cache before running \code{make()} etc. It is usually recommended to keep cache locking on. diff --git a/man/drake_debug.Rd b/man/drake_debug.Rd index f7bc36f18..739fb3c3b 100644 --- a/man/drake_debug.Rd +++ b/man/drake_debug.Rd @@ -41,7 +41,7 @@ Not valid for dynamic branching. and then runs its command in debug mode (see \code{browser()}, \code{debug()}, and \code{debugonce()}). This function does not store the target's value in the cache -(see \url{https://github.com/ropensci/drake/issues/587}). +(see \verb{https://github.com/ropensci/drake/issues/587}). } \examples{ \dontrun{ diff --git a/man/drake_envir.Rd b/man/drake_envir.Rd index c3a23d620..068bc565b 100644 --- a/man/drake_envir.Rd +++ b/man/drake_envir.Rd @@ -37,8 +37,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/drake_example.Rd b/man/drake_example.Rd index f8be0aded..44d25744c 100644 --- a/man/drake_example.Rd +++ b/man/drake_example.Rd @@ -16,7 +16,7 @@ drake_example( \arguments{ \item{example}{Name of the example. The possible values are the names of the folders at -\url{https://github.com/wlandau/drake-examples}.} +\verb{https://github.com/wlandau/drake-examples}.} \item{to}{Character scalar, the folder containing the code files for the example. @@ -36,12 +36,12 @@ to download quietly or print progress.} } \description{ The \code{drake_example()} function downloads a -folder from \url{https://github.com/wlandau/drake-examples}. +folder from \verb{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 \code{README} file. Other instructions are available in the files at -\url{https://github.com/wlandau/drake-examples}. +\verb{https://github.com/wlandau/drake-examples}. } \examples{ \dontrun{ diff --git a/man/drake_examples.Rd b/man/drake_examples.Rd index 77d64f3aa..1ff26aa89 100644 --- a/man/drake_examples.Rd +++ b/man/drake_examples.Rd @@ -17,9 +17,9 @@ Names of all the drake examples. } \description{ You can find the code files of the examples at -\url{https://github.com/wlandau/drake-examples}. +\verb{https://github.com/wlandau/drake-examples}. The \code{drake_examples()} function downloads the list of examples -from \url{https://wlandau.github.io/drake-examples/examples.md}, +from \verb{https://wlandau.github.io/drake-examples/examples.md}, so you need an internet connection. } \examples{ diff --git a/man/drake_history.Rd b/man/drake_history.Rd index 607b40ef5..502ce1011 100644 --- a/man/drake_history.Rd +++ b/man/drake_history.Rd @@ -13,7 +13,7 @@ See also \code{\link[=drake_cache]{drake_cache()}}.} \item{history}{Logical, whether to record the build history of your targets. You can also supply a -\href{https://github.com/wlandau/txtq}{\code{txtq}}, which is +\code{txtq}, which is how \code{drake} records history. Must be \code{TRUE} for \code{\link[=drake_history]{drake_history()}} to work later.} diff --git a/man/drake_plan.Rd b/man/drake_plan.Rd index 14580b21a..d3982ba04 100644 --- a/man/drake_plan.Rd +++ b/man/drake_plan.Rd @@ -70,7 +70,7 @@ R code to produce it. \details{ Besides \code{"target"} and \code{"command"}, \code{\link[=drake_plan]{drake_plan()}} understands a special set of optional columns. For details, visit -\url{https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan} # nolint +\verb{https://books.ropensci.org/drake/plans.html#special-custom-columns-in-your-plan} # nolint } \section{Columns}{ @@ -87,19 +87,19 @@ but \code{drake} looks for them at various points in the workflow. \itemize{ \item \code{transform}: a call to \code{\link[=map]{map()}}, \code{\link[=split]{split()}}, \code{\link[=cross]{cross()}}, or \code{\link[=combine]{combine()}} to create and manipulate large collections of targets. -Details: (\url{https://books.ropensci.org/drake/plans.html#large-plans}). # nolint +Details: (\verb{https://books.ropensci.org/drake/plans.html#large-plans}). # nolint \item \code{format}: set a storage format to save big targets more efficiently. See the "Formats" section of this help file for more details. \item \code{trigger}: rule to decide whether a target needs to run. It is recommended that you define this one with \code{target()}. -Details: \url{https://books.ropensci.org/drake/triggers.html}. +Details: \verb{https://books.ropensci.org/drake/triggers.html}. \item \code{hpc}: logical values (\code{TRUE}/\code{FALSE}/\code{NA}) whether to send each target to parallel workers. -Visit \url{https://books.ropensci.org/drake/hpc.html#selectivity} +Visit \verb{https://books.ropensci.org/drake/hpc.html#selectivity} to learn more. \item \code{resources}: target-specific lists of resources for a computing cluster. See -\url{https://books.ropensci.org/drake/hpc.html#advanced-options} +\verb{https://books.ropensci.org/drake/hpc.html#advanced-options} for details. \item \code{caching}: overrides the \code{caching} argument of \code{\link[=make]{make()}} for each target individually. Possible values: @@ -144,7 +144,7 @@ Then, \code{drake} will watch for changes to those files in subsequent calls to \code{make()}. This is a more flexible alternative to \code{file_in()} and \code{file_out()}, and it is compatible with dynamic branching. -See \url{https://github.com/ropensci/drake/pull/1178} for an example. +See \verb{https://github.com/ropensci/drake/pull/1178} for an example. \item \code{"fst"}: save big data frames fast. Requires the \code{fst} package. Note: this format strips non-data-frame attributes such as the \item \code{"fst_tbl"}: Like \code{"fst"}, but for \code{tibble} objects. @@ -184,8 +184,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced @@ -208,7 +208,7 @@ Intended for advanced custom memory management. Your code will look something like \verb{drake_plan(y = target(f(x), transform = map(x = c(1, 2, 3)))} You can read about this interface at -\url{https://books.ropensci.org/drake/plans.html#large-plans}. # nolint +\verb{https://books.ropensci.org/drake/plans.html#large-plans}. # nolint } \section{Static branching}{ @@ -302,7 +302,7 @@ plan <- drake_plan( # Use transformations to generate large plans. # Read more at -# . # nolint +# `https://books.ropensci.org/drake/plans.html#create-large-plans-the-easy-way`. # nolint drake_plan( data = target( simulate(nrows), diff --git a/man/drake_plan_source.Rd b/man/drake_plan_source.Rd index 3eed9a79c..e583dfdd2 100644 --- a/man/drake_plan_source.Rd +++ b/man/drake_plan_source.Rd @@ -17,7 +17,7 @@ is a call to \code{\link[=drake_plan]{drake_plan()}} that produces the plan you \description{ You supply a plan, and \code{\link[=drake_plan_source]{drake_plan_source()}} supplies code to generate that plan. If you have the -\href{https://github.com/r-lib/prettycode}{\code{prettycode} package}, +\code{prettycode} package, installed, you also get nice syntax highlighting in the console when you print it. } diff --git a/man/drake_triggers.Rd b/man/drake_triggers.Rd index 3f433fdb5..9d29f754b 100644 --- a/man/drake_triggers.Rd +++ b/man/drake_triggers.Rd @@ -36,7 +36,7 @@ in your workflow.} choice of specialized data format changes: for example, if you use \code{target(format = "qs")} one instance and \code{target(format = "fst")} the next. See -\url{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint +\verb{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint for details on formats.} \item{condition}{R code (expression or language object) diff --git a/man/evaluate_plan.Rd b/man/evaluate_plan.Rd index ada205f00..00696a322 100644 --- a/man/evaluate_plan.Rd +++ b/man/evaluate_plan.Rd @@ -66,7 +66,7 @@ A workflow plan data frame with the wildcards evaluated. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/expand_plan.Rd b/man/expand_plan.Rd index acf9f07f8..26eb4073b 100644 --- a/man/expand_plan.Rd +++ b/man/expand_plan.Rd @@ -28,7 +28,7 @@ An expanded workflow plan data frame (with replicated targets). \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/expose_imports.Rd b/man/expose_imports.Rd index 6b52a99c1..c55e36dda 100644 --- a/man/expose_imports.Rd +++ b/man/expose_imports.Rd @@ -40,8 +40,8 @@ so \code{drake} can watch them for changes. This used to be the standard way to make \code{drake} compatible with workflows implemented as custom analysis packages. Now, the recommendation is to supply \code{getNamespace("yourPackage")} to the \code{envir} argument of \code{\link[=make]{make()}} -and friends. Read \url{https://github.com/ropensci/drake/issues/1286}, -especially \url{https://github.com/ropensci/drake/issues/1286#issuecomment-649088321}, # nolint +and friends. Read \verb{https://github.com/ropensci/drake/issues/1286}, +especially \verb{https://github.com/ropensci/drake/issues/1286#issuecomment-649088321}, # nolint for details. } \examples{ diff --git a/man/file_in.Rd b/man/file_in.Rd index c4003b752..3145e4721 100644 --- a/man/file_in.Rd +++ b/man/file_in.Rd @@ -41,8 +41,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/file_out.Rd b/man/file_out.Rd index 310a0020b..fdb904cfe 100644 --- a/man/file_out.Rd +++ b/man/file_out.Rd @@ -27,8 +27,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/gather_by.Rd b/man/gather_by.Rd index 52d377493..21eab1302 100644 --- a/man/gather_by.Rd +++ b/man/gather_by.Rd @@ -51,7 +51,7 @@ A workflow plan data frame. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/gather_plan.Rd b/man/gather_plan.Rd index 267ec6c11..8ac398181 100644 --- a/man/gather_plan.Rd +++ b/man/gather_plan.Rd @@ -27,7 +27,7 @@ prespecified targets into one additional target downstream. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/id_chr.Rd b/man/id_chr.Rd index 57e384553..41fa390bb 100644 --- a/man/id_chr.Rd +++ b/man/id_chr.Rd @@ -22,8 +22,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/ignore.Rd b/man/ignore.Rd index 09c023567..9b0aca580 100644 --- a/man/ignore.Rd +++ b/man/ignore.Rd @@ -34,8 +34,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/knitr_in.Rd b/man/knitr_in.Rd index 9a284231f..12b6904b8 100644 --- a/man/knitr_in.Rd +++ b/man/knitr_in.Rd @@ -35,8 +35,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/load_main_example.Rd b/man/load_main_example.Rd index e39f99e89..444d619fe 100644 --- a/man/load_main_example.Rd +++ b/man/load_main_example.Rd @@ -30,7 +30,7 @@ A \code{\link[=drake_config]{drake_config()}} configuration list. } \description{ The main example lives at -\url{https://github.com/wlandau/drake-examples/tree/main/main}. +\verb{https://github.com/wlandau/drake-examples/tree/main/main}. Use \code{drake_example("main")} to download its code. This function also writes/overwrites the files \code{report.Rmd} and \code{raw_data.xlsx}. diff --git a/man/make.Rd b/man/make.Rd index d466053bf..96fe82d65 100644 --- a/man/make.Rd +++ b/man/make.Rd @@ -108,9 +108,8 @@ See also \code{\link[=drake_cache]{drake_cache()}}.} \item{fetch_cache}{Deprecated.} \item{parallelism}{Character scalar, type of parallelism to use. -For detailed explanations, see the -\href{https://books.ropensci.org/drake/hpc.html}{high-performance computing chapter} # nolint -of the user manual. +For detailed explanations, see +\verb{https://books.ropensci.org/drake/hpc.html}. You could also supply your own scheduler function if you want to experiment or aggressively optimize. @@ -131,7 +130,7 @@ whenever \code{drake}'s unexported core functions are updated. You can experiment with \code{\link[=predict_runtime]{predict_runtime()}} to help decide on an appropriate number of jobs. For details, visit -\url{https://books.ropensci.org/drake/time.html}.} +\verb{https://books.ropensci.org/drake/time.html}.} \item{jobs_preprocess}{Number of parallel jobs for processing the imports and doing other preprocessing tasks.} @@ -220,7 +219,7 @@ on your workflow. Use at your own peril.} \item{lazy_load}{An old feature, currently being questioned. For the current recommendations on memory management, see -\url{https://books.ropensci.org/drake/memory.html#memory-strategies}. +\verb{https://books.ropensci.org/drake/memory.html#memory-strategies}. The \code{lazy_load} argument is either a character vector or a logical. For dynamic targets, the behavior is always \code{"eager"} (see below). So the \code{lazy_load} argument is for static targets only. @@ -330,7 +329,7 @@ Same as the \code{template} argument of \code{clustermq::Q()} and Enabled for \code{clustermq} only (\code{make(parallelism = "clustermq")}), not \code{future} or \code{batchtools} so far. For more information, see the \code{clustermq} package: -\url{https://github.com/mschubert/clustermq}. +\verb{https://github.com/mschubert/clustermq}. Some template placeholders such as \code{{{ job_name }}} and \code{{{ n_jobs }}} cannot be set this way.} @@ -434,7 +433,7 @@ if \code{envir} is \code{getNamespace("packagename")}.} \item{history}{Logical, whether to record the build history of your targets. You can also supply a -\href{https://github.com/wlandau/txtq}{\code{txtq}}, which is +\code{txtq}, which is how \code{drake} records history. Must be \code{TRUE} for \code{\link[=drake_history]{drake_history()}} to work later.} @@ -523,7 +522,7 @@ with \code{build_times = FALSE}.} \item{format}{Character, an optional custom storage format for targets without an explicit \code{target(format = ...)} in the plan. Details about formats: -\url{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint} +\verb{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint} \item{lock_cache}{Logical, whether to lock the cache before running \code{make()} etc. It is usually recommended to keep cache locking on. @@ -579,7 +578,7 @@ ideally with the help of a main R script. This script should begin in a fresh R session, load your packages and functions in a dependable manner, and then run \code{make()}. Example: -\url{https://github.com/wlandau/drake-examples/tree/main/gsp}. +\verb{https://github.com/wlandau/drake-examples/tree/main/gsp}. Batch mode, especially within a container, is particularly helpful. Interactive R sessions are still useful, @@ -612,15 +611,15 @@ prior to \code{make()}, not in any functions or commands that get called during \code{make()} itself. For each target that is still problematic (e.g. -\url{https://github.com/rstudio/gt/issues/297}) +\verb{https://github.com/rstudio/gt/issues/297}) you can safely run the command in its own special \code{callr::r()} process. -Example: \url{https://github.com/rstudio/gt/issues/297#issuecomment-497778735}. # nolint +Example: \verb{https://github.com/rstudio/gt/issues/297#issuecomment-497778735}. # nolint If that fails, you can run \code{make(plan, lock_envir = FALSE)} to suppress environment-locking for all targets. However, this is not usually recommended. There are legitimate use cases for \code{lock_envir = FALSE} -(example: \url{https://books.ropensci.org/drake/hpc.html#parallel-computing-within-targets}) # nolint +(example: \verb{https://books.ropensci.org/drake/hpc.html#parallel-computing-within-targets}) # nolint but most workflows should stick with the default \code{lock_envir = TRUE}. } diff --git a/man/map_plan.Rd b/man/map_plan.Rd index 2d78f867d..972643a2e 100644 --- a/man/map_plan.Rd +++ b/man/map_plan.Rd @@ -38,7 +38,7 @@ A workflow plan data frame. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/new_drake_settings.Rd b/man/new_drake_settings.Rd index 10cda3fbc..04e80f2d6 100644 --- a/man/new_drake_settings.Rd +++ b/man/new_drake_settings.Rd @@ -71,7 +71,7 @@ a target is built during \code{\link[=make]{make()}}.} You can experiment with \code{\link[=predict_runtime]{predict_runtime()}} to help decide on an appropriate number of jobs. For details, visit -\url{https://books.ropensci.org/drake/time.html}.} +\verb{https://books.ropensci.org/drake/time.html}.} \item{jobs_preprocess}{Number of parallel jobs for processing the imports and doing other preprocessing tasks.} @@ -81,7 +81,7 @@ if targets fail.} \item{lazy_load}{An old feature, currently being questioned. For the current recommendations on memory management, see -\url{https://books.ropensci.org/drake/memory.html#memory-strategies}. +\verb{https://books.ropensci.org/drake/memory.html#memory-strategies}. The \code{lazy_load} argument is either a character vector or a logical. For dynamic targets, the behavior is always \code{"eager"} (see below). So the \code{lazy_load} argument is for static targets only. @@ -194,9 +194,8 @@ Also see the \code{garbage_collection} argument of \code{make()} and \code{drake_config()}.} \item{parallelism}{Character scalar, type of parallelism to use. -For detailed explanations, see the -\href{https://books.ropensci.org/drake/hpc.html}{high-performance computing chapter} # nolint -of the user manual. +For detailed explanations, see +\verb{https://books.ropensci.org/drake/hpc.html}. You could also supply your own scheduler function if you want to experiment or aggressively optimize. @@ -344,7 +343,7 @@ Same as the \code{template} argument of \code{clustermq::Q()} and Enabled for \code{clustermq} only (\code{make(parallelism = "clustermq")}), not \code{future} or \code{batchtools} so far. For more information, see the \code{clustermq} package: -\url{https://github.com/mschubert/clustermq}. +\verb{https://github.com/mschubert/clustermq}. Some template placeholders such as \code{{{ job_name }}} and \code{{{ n_jobs }}} cannot be set this way.} diff --git a/man/no_deps.Rd b/man/no_deps.Rd index 8cc06428a..d598c8764 100644 --- a/man/no_deps.Rd +++ b/man/no_deps.Rd @@ -28,8 +28,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced diff --git a/man/plan_analyses.Rd b/man/plan_analyses.Rd index f1751d1d0..a9a3133b1 100644 --- a/man/plan_analyses.Rd +++ b/man/plan_analyses.Rd @@ -26,7 +26,7 @@ An evaluated workflow plan data frame of analysis targets. } \description{ Use \code{\link[=drake_plan]{drake_plan()}} instead. -See \url{https://books.ropensci.org/drake/plans.html#large-plans} +See \verb{https://books.ropensci.org/drake/plans.html#large-plans} for details. } \details{ diff --git a/man/plan_summaries.Rd b/man/plan_summaries.Rd index 586ebdb3b..953515406 100644 --- a/man/plan_summaries.Rd +++ b/man/plan_summaries.Rd @@ -38,7 +38,7 @@ analyses of multiple datasets in multiple ways. } \description{ Use \code{\link[=drake_plan]{drake_plan()}} with transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for details. } \details{ diff --git a/man/readd.Rd b/man/readd.Rd index 545efc01b..2f23b1ab1 100644 --- a/man/readd.Rd +++ b/man/readd.Rd @@ -160,7 +160,7 @@ When you call \code{\link[=make]{make()}} to run your project, You may want to inspect the targets afterwards, possibly in an interactive R session. However, the files in the \code{.drake} folder are organized in a special format created by the -\href{https://github.com/richfitz/storr}{\code{storr}} package, +\code{storr} package, which is not exactly human-readable. To retrieve a target for manual viewing, use \code{\link[=readd]{readd()}}. To load one or more targets into your session, use \code{\link[=loadd]{loadd()}}. diff --git a/man/reduce_by.Rd b/man/reduce_by.Rd index 8794e3c74..c1f68b86f 100644 --- a/man/reduce_by.Rd +++ b/man/reduce_by.Rd @@ -63,7 +63,7 @@ A workflow plan data frame. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/reduce_plan.Rd b/man/reduce_plan.Rd index 8a271ec68..5d974d76d 100644 --- a/man/reduce_plan.Rd +++ b/man/reduce_plan.Rd @@ -47,7 +47,7 @@ prespecified targets into one additional target downstream. \description{ Deprecated on 2019-05-16. Use \code{\link[=drake_plan]{drake_plan()}} transformations instead. See -\url{https://books.ropensci.org/drake/plans.html#large-plans} +\verb{https://books.ropensci.org/drake/plans.html#large-plans} for the details. } \details{ diff --git a/man/target.Rd b/man/target.Rd index d957b4e55..ec0ad7411 100644 --- a/man/target.Rd +++ b/man/target.Rd @@ -12,11 +12,11 @@ target(command = NULL, transform = NULL, dynamic = NULL, ...) \item{transform}{A call to \code{\link[=map]{map()}}, \code{\link[=split]{split()}}, \code{\link[=cross]{cross()}}, or \code{\link[=combine]{combine()}} to apply a \emph{static} transformation. Details: -\url{https://books.ropensci.org/drake/static.html}} +\verb{https://books.ropensci.org/drake/static.html}} \item{dynamic}{A call to \code{\link[=map]{map()}}, \code{\link[=cross]{cross()}}, or \code{\link[=group]{group()}} to apply a \emph{dynamic} transformation. Details: -\url{https://books.ropensci.org/drake/dynamic.html}} +\verb{https://books.ropensci.org/drake/dynamic.html}} \item{...}{Optional columns of the plan for a given target. See the Columns section of this help file for a selection @@ -33,7 +33,7 @@ Its most common use is to invoke static branching and dynamic branching, and it can also set the values of custom columns such as \code{format}, \code{elapsed}, \code{retries}, and \code{max_expand}. Details are at -\url{https://books.ropensci.org/drake/plans.html#special-columns}. +\verb{https://books.ropensci.org/drake/plans.html#special-columns}. Note: \code{drake_plan(my_target = my_command())} is equivalent to \verb{drake_plan(my_target = target(my_command())}. @@ -57,19 +57,19 @@ but \code{drake} looks for them at various points in the workflow. \itemize{ \item \code{transform}: a call to \code{\link[=map]{map()}}, \code{\link[=split]{split()}}, \code{\link[=cross]{cross()}}, or \code{\link[=combine]{combine()}} to create and manipulate large collections of targets. -Details: (\url{https://books.ropensci.org/drake/plans.html#large-plans}). # nolint +Details: (\verb{https://books.ropensci.org/drake/plans.html#large-plans}). # nolint \item \code{format}: set a storage format to save big targets more efficiently. See the "Formats" section of this help file for more details. \item \code{trigger}: rule to decide whether a target needs to run. It is recommended that you define this one with \code{target()}. -Details: \url{https://books.ropensci.org/drake/triggers.html}. +Details: \verb{https://books.ropensci.org/drake/triggers.html}. \item \code{hpc}: logical values (\code{TRUE}/\code{FALSE}/\code{NA}) whether to send each target to parallel workers. -Visit \url{https://books.ropensci.org/drake/hpc.html#selectivity} +Visit \verb{https://books.ropensci.org/drake/hpc.html#selectivity} to learn more. \item \code{resources}: target-specific lists of resources for a computing cluster. See -\url{https://books.ropensci.org/drake/hpc.html#advanced-options} +\verb{https://books.ropensci.org/drake/hpc.html#advanced-options} for details. \item \code{caching}: overrides the \code{caching} argument of \code{\link[=make]{make()}} for each target individually. Possible values: @@ -102,8 +102,8 @@ with its own help file. \itemize{ \item \code{\link[=target]{target()}}: give the target more than just a command. Using \code{\link[=target]{target()}}, you can apply a transformation -(examples: \url{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint -supply a trigger (\url{https://books.ropensci.org/drake/triggers.html}), # nolint +(examples: \verb{https://books.ropensci.org/drake/plans.html#large-plans}), # nolint +supply a trigger (\verb{https://books.ropensci.org/drake/triggers.html}), # nolint or set any number of custom columns. \item \code{\link[=file_in]{file_in()}}: declare an input file dependency. \item \code{\link[=file_out]{file_out()}}: declare an output file to be produced @@ -140,7 +140,7 @@ Then, \code{drake} will watch for changes to those files in subsequent calls to \code{make()}. This is a more flexible alternative to \code{file_in()} and \code{file_out()}, and it is compatible with dynamic branching. -See \url{https://github.com/ropensci/drake/pull/1178} for an example. +See \verb{https://github.com/ropensci/drake/pull/1178} for an example. \item \code{"fst"}: save big data frames fast. Requires the \code{fst} package. Note: this format strips non-data-frame attributes such as the \item \code{"fst_tbl"}: Like \code{"fst"}, but for \code{tibble} objects. diff --git a/man/transform_plan.Rd b/man/transform_plan.Rd index cdcef85f8..92dbfc76e 100644 --- a/man/transform_plan.Rd +++ b/man/transform_plan.Rd @@ -43,7 +43,7 @@ Evaluate the \code{map()}, \code{cross()}, \code{split()} and \code{drake} plan. } \details{ -\url{https://books.ropensci.org/drake/plans.html#large-plans} # nolint +\verb{https://books.ropensci.org/drake/plans.html#large-plans} # nolint } \examples{ plan1 <- drake_plan( diff --git a/man/transformations.Rd b/man/transformations.Rd index a3b2f670d..bbb999ca1 100644 --- a/man/transformations.Rd +++ b/man/transformations.Rd @@ -61,7 +61,7 @@ of targets with transformations such as } \details{ For details, see -\url{https://books.ropensci.org/drake/plans.html#large-plans}. +\verb{https://books.ropensci.org/drake/plans.html#large-plans}. } \section{Transformations}{ @@ -69,7 +69,7 @@ For details, see Your code will look something like \verb{drake_plan(y = target(f(x), transform = map(x = c(1, 2, 3)))} You can read about this interface at -\url{https://books.ropensci.org/drake/plans.html#large-plans}. # nolint +\verb{https://books.ropensci.org/drake/plans.html#large-plans}. # nolint } \section{Static branching}{ diff --git a/man/trigger.Rd b/man/trigger.Rd index 20bb64e7a..a3a74df93 100644 --- a/man/trigger.Rd +++ b/man/trigger.Rd @@ -37,7 +37,7 @@ in your workflow.} choice of specialized data format changes: for example, if you use \code{target(format = "qs")} one instance and \code{target(format = "fst")} the next. See -\url{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint +\verb{https://books.ropensci.org/drake/plans.html#special-data-formats-for-targets} # nolint for details on formats.} \item{condition}{R code (expression or language object) @@ -77,7 +77,7 @@ in your \code{\link[=drake_plan]{drake_plan()}} or the \code{trigger} argument t \code{\link[=make]{make()}} or \code{\link[=drake_config]{drake_config()}}. For details, see the chapter on triggers in the user manual: -\url{https://books.ropensci.org/drake/triggers.html} +\verb{https://books.ropensci.org/drake/triggers.html} } \details{ A target always builds if it has not been built before. diff --git a/man/use_drake.Rd b/man/use_drake.Rd index 1397262ba..58efd94f2 100644 --- a/man/use_drake.Rd +++ b/man/use_drake.Rd @@ -13,15 +13,15 @@ use_drake(open = interactive()) \description{ Add top-level R script files to use \code{drake} in your data analysis project. For details, read -\url{https://books.ropensci.org/drake/projects.html} +\verb{https://books.ropensci.org/drake/projects.html} } \details{ Files written: \enumerate{ \item \code{make.R}: a suggested main R script for batch mode. \item \verb{_drake.R}: a configuration R script for -the \href{https://docs.ropensci.org/drake/reference/r_make.html}{\verb{r_*()}} functions documented at # nolint -\url{https://books.ropensci.org/drake/projects.html#safer-interactivity}. # nolint +the \verb{r_*()} functions documented at # nolint +\verb{https://books.ropensci.org/drake/projects.html#safer-interactivity}. # nolint Remarks: } \itemize{ @@ -30,7 +30,7 @@ You can call it whatever you want. \item Other supporting scripts, such as \code{R/packages.R}, \code{R/functions.R}, and \code{R/plan.R}, are not included. \item You can find examples at -\url{https://github.com/wlandau/drake-examples} +\verb{https://github.com/wlandau/drake-examples} and download examples with \code{\link[=drake_example]{drake_example()}} (e.g. \code{drake_example("main")}). }