wflow_build: Build the site

In workflowr: A Framework for Reproducible and Collaborative Data Science

Build the site

Description

wflow_build builds the website from the files in the analysis directory. This is intended to be used when developing your code to preview the changes. When you are ready to commit the files, use wflow_publish.

Usage

wflow_build(
  files = NULL,
  make = is.null(files),
  update = FALSE,
  republish = FALSE,
  combine = "or",
  view = getOption("workflowr.view"),
  clean_fig_files = FALSE,
  delete_cache = FALSE,
  seed = 12345,
  log_dir = NULL,
  verbose = FALSE,
  local = FALSE,
  dry_run = FALSE,
  project = "."
)

Arguments

files	character (default: NULL). Files to build. Only allows files in the analysis directory with the extension Rmd or rmd. If files is NULL, the default behavior is to build all outdated files (see argument make below). Supports file globbing. The files are always built in the order they are listed.
make	logical (default: is.null(files)). When make = TRUE, build any files that have been modified more recently than their corresponding HTML files (inspired by Make). This is the default action if no files are specified.
update	logical (default: FALSE). Build any files that have been committed more recently than their corresponding HTML files (and do not have any unstaged or staged changes). This ensures that the commit version ID inserted into the HTML corresponds to the exact version of the source file that was used to produce it.
republish	logical (default: FALSE). Build all published R Markdown files (that do not have any unstaged or staged changes). Useful for site-wide changes like updating the theme, navigation bar, or any other setting in _site.yml.
combine	character (default: "or"). Determine how to combine the files from the arguments files, make (wflow_build() only), update, and republish. When combine is "or", any file specified by at least one of these arguments will be built. When combine is "and", only files specified by all of these arguments will be built.
view	logical (default: getOption("workflowr.view")). View the website with wflow_view after building files. If only one file is built, it is opened. If more than one file is built, the main index page is opened. Not applicable if no files are built or if dry_run = TRUE.
clean_fig_files	logical (default: FALSE). Delete existing figure files for each R Markdown file prior to building it. This ensures that only relevant figure files are saved. As you develop an analysis, it is easy to generate lots of unused plots due to changes in the number of code chunks and their names. However, if you are caching chunks during code development, this could cause figures to disappear. Note that wflow_publish uses clean_fig_files = TRUE to ensure the results can be reproduced.
delete_cache	logical (default: FALSE). Delete the cache directory (if it exists) for each R Markdown file prior to building it.
seed	numeric (default: 12345). The seed to set before building each file. Passed to set.seed. DEPRECATED: The seed set here has no effect if you are using wflow_html as the output format defined in _site.yml. This argument is for backwards compatibility with previous versions of workflowr.
log_dir	character (default: NULL). The directory to save log files from building files. It will be created if necessary and ignored if local = TRUE. The default is to use a directory named workflowr in tempdir.
verbose	logical (default: FALSE). Display the build log directly in the R console as each file is built. This is useful for monitoring long-running code chunks.
local	logical (default: FALSE). Build files locally in the R console. This should only be used for debugging purposes. The default is to build each file in its own separate fresh R process to ensure each file is reproducible in isolation. This is done using callr::r_safe.
dry_run	logical (default: FALSE). List the files to be built, without building them.
project	character (default: ".") By default the function assumes the current working directory is within the project. If this is not true, you'll need to provide the path to the project directory.

Details

wflow_build has multiple, non-mutually exclusive options for deciding which files to build. If multiple options are used, then the argument combine determines which files will be built. If combine == "or" (the default), then any file specified by at least one of the arguments will be built. In contrast, if combine == "and", then only files specified by all of the arguments will be built. The argument make is the most useful for interactively performing your analysis. The other options are more useful when you are ready to publish specific files with wflow_publish (which passes these arguments to wflow_build). Here are the options for specifying files to be built:

• Files specified via the argument files

• make = TRUE - Files which have been modified more recently than their corresponding HTML files

• update = TRUE - Previously published files which have been committed more recently than their corresponding HTML files. However, files which currently have staged or unstaged changes are not included.

• republish = TRUE - All published files. However, files which currently have staged or unstaged changes are not included.

Under the hood, wflow_build is a wrapper for render_site from the package rmarkdown. By default (local = FALSE), the code is executed in an isolated R session. This is done using callr::r_safe.

Value

An object of class wflow_build, which is a list with the following elements:

• files: The input argument files

• make: The input argument make

• update: The input argument update

• republish: The input argument republish

• view: The input argument view

• clean_fig_files: The input argument clean_fig_files

• delete_cache: The input argument delete_cache

• seed: The input argument seed

• log_dir: The directory where the log files were saved

• verbose: The input argument verbose

• local: The input argument local

• dry_run: The input argument dry_run

• built: The relative paths to the built R Markdown files

• html: The relative paths to the corresponding HTML files

Comparison to RStudio Knit button

wflow_build is intentionally designed to be similar to clicking on the Knit button in RStudio. Both isolate the code execution in a separate R process, thus ensuring the results are not dependent on the state of the current R session. However, they do differ in a few ways:

Number of files

The RStudio Knit button only builds the current Rmd file open in the editor. In contrast, wflow_build can build any number of Rmd files (each in their own separate R process) with a single invocation, including accepting file globs.

System and user profiles

The two methods diverge the most in their use of .Rprofile files. wflow_build ignores any system or user profiles (i.e. ~/.Rprofile on Linux/macOS or ~/Documents/.Rprofile on Windows). This is the default behavior of callr::r_safe, which it calls to run the separate R process. This is ideal for reproducibility. Otherwise the results could be affected by custom settings made only on the user's machine. In contrast, the RStudio Knit button loads any system or user level profiles, consistent with its role as a development tool.

Project-specific profiles

A project-specific .Rprofile is treated differently than system or user profiles. wflow_build only loads a project-specific .Rprofile if it is located in the current working directory in which wflow_build is invoked. This may be confusing if this differs from the directory in which the code in the Rmd is actually executed (the option knit_root_dir defined in _workflowr.yml). The RStudio Knit button only loads a project-specific .Rprofile if it is located in the same directory as its setting "Knit Directory" is configured. For example, if "Knit Directory" is set to "Document Directory", it will ignore any .Rprofile in the root of the project. But it would load the .Rprofile if "Knit Directory" was changed to "Project Directory".

The main takeaway from the above is that you should try to limit settings and options defined in .Rprofile to affect the interactive R experience and superficial behavior, e.g. the option max.print to limit the number of lines that can be printed to the console. Any critical settings that affect the results of the analysis should be explicitly set in the Rmd file.

See Also

wflow_publish

Examples

## Not run: 

# Build any files which have been modified
wflow_build() # equivalent to wflow_build(make = TRUE)
# Build a single file
wflow_build("file.Rmd")
# Build multiple files
wflow_build(c("file1.Rmd", "file2.Rmd"))
# Build multiple files using a file glob
wflow_build("file*.Rmd")
# Build every published file
wflow_build(republish = TRUE)
# Build file.Rmd and any files which have been modified
wflow_build("file.Rmd", make = TRUE)

## End(Not run)

workflowr documentation built on Aug. 23, 2023, 1:09 a.m.