Nothing
R/render.R
In rmarkdown: Dynamic Documents for R
Defines functions
file_scope_split
resolve_df_print
id_prefix_from_args
merge_render_context
new_render_context
clear_render_context
init_render_context
render_context
knit_meta_reset
render_supporting_files
render
Documented in
render
render_supporting_files
#' R Markdown Metadata
#'
#' Rmd files include a metadata section (typically located at the top of the
#' file) that can specify (among other things) the title, author, and date of
#' the document. Metadata adheres to the \href{https://yaml.org}{YAML} format
#' and is delimited by lines containing three dashes (\code{---}). Here is an
#' example metadata section:
#' \preformatted{---
#' title: "Crop Analysis Q3 2013"
#' author: Martha Smith
#' date: October 23rd, 2013
#' ---
#' }
#' Note that the \code{title} field is quoted. This is because titles often
#' contained embedded colons (\code{:}) and colons followed by a space need to
#' be quoted in YAML.
#' @details When title, author, and date metadata is provided it's used to
#' automatically create a title section within output documents. If you don't
#' want this section included in your document then you should remove the
#' corresponding metadata fields.
#'
#' When generating PDF and Beamer output there are also a number of other
#' metadata fields that can be included to customize the appearance and theme
#' of PDF output. For more details see the documentation for
#' \code{\link{pdf_document}} and \code{\link{beamer_presentation}}.
#' @name rmd_metadata
NULL
#' The YAML metadata of the current R Markdown document
#'
#' The object \code{metadata} stores the YAML metadata of the current R Markdown
#' document as a list, which you may use in the R code chunks, e.g.
#' \code{rmarkdown::metadata$title} (the title of the document),
#' \code{rmarkdown::metadata$author}, and \code{rmarkdown::metadata$foo} (if you
#' have a YAML field named \code{foo}), etc.
#' @usage NULL
#' @examples rmarkdown::metadata
#' @export
metadata <- list()
#' Compiling R scripts to a notebook
#'
#' R Markdown can also compile R scripts to a notebook which includes
#' commentary, source code, and script output. Notebooks can be compiled to any
#' output format including HTML, PDF, and MS Word.
#'
#' @section Overview:
#' To compile a notebook from an R script you simply pass the script to
#' \code{\link{render}}. For example:
#' \preformatted{
#' rmarkdown::render("analysis.R")
#' rmarkdown::render("analysis.R", "pdf_document")
#' }
#' The first call to \code{\link{render}} creates an HTML document, whereas
#' the second creates a PDF document.
#'
#' By default the name of the script, username, and current date and time are
#' included in the header of the generated notebook. You can override this
#' default behavior by including explicit metadata in a specially formatted R
#' comment:
#' \preformatted{
#' #' ---
#' #' title: "Crop Analysis Q3 2013"
#' #' author: "John Smith"
#' #' date: "May 3rd, 2014"
#' #' ---
#' }
#' @section Including Markdown:
#' Note that the R comment used above to add a title, author, and date
#' includes a single-quote as a special prefix character. This is a
#' \pkg{roxygen2} style comment, and it's actually possible to include many
#' such comments in an R script, all of which will be converted to markdown
#' content within the generated notebook. For example:
#' \preformatted{#' A script comment that includes **markdown** formatting.}
#' Rather than displaying as an R comment in the compiled notebook any
#' \pkg{roxygen2} style comment will be treated as markdown and rendered
#' accordingly.
#' @section knitr Spin:
#' Including markdown within R comments is possible because \code{\link{render}}
#' calls the \code{\link[knitr:spin]{knitr spin}} function to convert the R
#' script to an Rmd file. The \code{spin} function also enables you to add
#' knitr
#' chunk options with another special comment prefix (\code{#+}).
#'
#' Here's an example of a script that uses the various features of \code{spin}:
#'
#' \url{https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R}
#'
#' For more details on \code{knitr::spin} see the following documentation:
#'
#' \url{https://yihui.org/knitr/demo/stitch/}
#' @name compile_notebook
NULL
#' Render R Markdown
#'
#' Render the input file to the specified output format using pandoc. If the
#' input requires knitting then \code{\link[knitr:knit]{knit}} is called prior
#' to pandoc.
#'
#' Note that the \pkg{knitr} \code{error} option is set to \code{FALSE} during
#' rendering (which is different from the \pkg{knitr} default value of
#' \code{TRUE}).
#'
#' For additional details on rendering R scripts see
#' \link[=compile_notebook]{Compiling R scripts to a notebook}.
#'
#' If no \code{output_format} parameter is specified then the output format is
#' read from the YAML front-matter of the input file. For example, the
#' following YAML would yield a PDF document:
#'
#' \preformatted{
#' output: pdf_document
#' }
#'
#' Additional format options can also be specified in metadata. For example:
#'
#' \preformatted{
#' output:
#' pdf_document:
#' toc: true
#' highlight: zenburn
#' }
#'
#' Multiple formats can be specified in metadata. If no \code{output_format}
#' is passed to \code{render} then the first one defined will be used:
#'
#' \preformatted{
#' output:
#' pdf_document:
#' toc: true
#' highlight: zenburn
#' html_document:
#' toc: true
#' theme: united
#' }
#'
#' Formats specified in metadata can be any one of the built in formats (e.g.
#' \code{\link{html_document}}, \code{\link{pdf_document}}) or a format defined
#' in another package (e.g. \code{pkg::custom_format}).
#'
#' If there is no format defined in the YAML then
#' \code{\link{html_document}} will be used.
#' @section R Markdown:
#' R Markdown supports all of the base pandoc markdown features as well as some
#' optional features for compatibility with GitHub Flavored Markdown (which
#' previous versions of R Markdown were based on). See
#' \code{\link{rmarkdown_format}} for details.
#' @seealso
#' \link[knitr:knit]{knit}, \link{output_format},
#' \url{https://pandoc.org}
#' @inheritParams default_output_format
#' @param input The input file to be rendered. This can be an R script (.R),
#' an R Markdown document (.Rmd), or a plain markdown document.
#' @param output_format The R Markdown output format to convert to. The option
#' \code{"all"} will render all formats defined within the file. The option can
#' be the name of a format (e.g. \code{"html_document"}) and that will render
#' the document to that single format. One can also use a vector of format
#' names to render to multiple formats. Alternatively, you can pass an output
#' format object (e.g. \code{html_document()}). If using \code{NULL} then the
#' output format is the first one defined in the YAML frontmatter in the input
#' file (this defaults to HTML if no format is specified there).
#' If you pass an output format object to \code{output_format}, the options
#' specified in the YAML header or \code{_output.yml} will be ignored and you
#' must explicitly set all the options you want when you construct the object.
#' If you pass a string, the output format will use the output parameters in
#' the YAML header or \code{_output.yml}.
#' @param output_file The name of the output file. If using \code{NULL} then the
#' output filename will be based on filename for the input file. If a filename
#' is provided, a path to the output file can also be provided. Note that the
#' \code{output_dir} option allows for specifying the output file path as well,
#' however, if also specifying the path, the directory must exist. If
#' \code{output_file} is specified but does not have a file extension, an
#' extension will be automatically added according to the output format. To
#' avoid the automatic file extension, put the \code{output_file} value in
#' \code{\link{I}()}, e.g., \code{I('my-output')}.
#' @param output_dir The output directory for the rendered \code{output_file}.
#' This allows for a choice of an alternate directory to which the output file
#' should be written (the default output directory of that of the input file).
#' If a path is provided with a filename in \code{output_file} the directory
#' specified here will take precedence. Please note that any directory path
#' provided will create any necessary directories if they do not exist.
#' @param output_options List of output options that can override the options
#' specified in metadata (e.g. could be used to force \code{self_contained} or
#' \code{mathjax = "local"}). Note that this is only valid when the output
#' format is read from metadata (i.e. not a custom format object passed to
#' \code{output_format}).
#' @param intermediates_dir Intermediate files directory. If a path is specified
#' then intermediate files will be written to that path. If \code{NULL},
#' intermediate files are written to the same directory as the input file.
#' @param knit_root_dir The working directory in which to knit the document;
#' uses knitr's \code{root.dir} knit option. If \code{NULL} then the behavior
#' will follow the knitr default, which is to use the parent directory of the
#' document.
#' @param runtime The runtime target for rendering. The \code{static} option
#' produces output intended for static files; \code{shiny} produces output
#' suitable for use in a Shiny document (see \code{\link{run}}). The default,
#' \code{auto}, allows the \code{runtime} target specified in the YAML metadata
#' to take precedence, and renders for a \code{static} runtime target otherwise.
#' @param clean Using \code{TRUE} will clean intermediate files that are created
#' during rendering.
#' @param params A list of named parameters that override custom params
#' specified within the YAML front-matter (e.g. specifying a dataset to read or
#' a date range to confine output to). Pass \code{"ask"} to start an
#' application that helps guide parameter configuration.
#' @param knit_meta (This option is reserved for expert use.) Metadata
#' generated by \pkg{knitr}.
#' @param envir The environment in which the code chunks are to be evaluated
#' during knitting (can use \code{\link{new.env}()} to guarantee an empty new
#' environment).
#' @param run_pandoc An option for whether to run pandoc to convert Markdown
#' output.
#' @param quiet An option to suppress printing during rendering from knitr,
#' pandoc command line and others. To only suppress printing of the last
#' "Output created: " message, you can set \code{rmarkdown.render.message} to
#' \code{FALSE}
#' @param encoding Ignored. The encoding is always assumed to be UTF-8.
#' @return
#' When \code{run_pandoc = TRUE}, the compiled document is written into
#' the output file, and the path of the output file is returned. When
#' \code{run_pandoc = FALSE}, the path of the Markdown output file, with
#' attributes \code{knit_meta} (the \pkg{knitr} meta data collected from code
#' chunks) and \code{intermediates} (the intermediate files/directories
#' generated by \code{render()}).
#' @examples
#' \dontrun{
#' library(rmarkdown)
#'
#' # Render the default (first) format defined in the file
#' render("input.Rmd")
#'
#' # Render all formats defined in the file
#' render("input.Rmd", "all")
#'
#' # Render a single format, using parameters for \code{html_document} from
#' # the YAML header parameters.
#' render("input.Rmd", "html_document")
#'
#' # Render a single format, ignoring parameters for \code{html_document} in
#' # the YAML header. Any parameters not passed as arguments to
#' # \code{html_document()} will be assigned to their default values, regardless
#' # of anything in the YAML header
#' render("input.Rmd", html_document(toc = TRUE, toc_depth = 2))
#'
#' # Render multiple formats
#' render("input.Rmd", c("html_document", "pdf_document"))
#' }
#' @export
render <- function(input,
output_format = NULL,
output_file = NULL,
output_dir = NULL,
output_options = NULL,
output_yaml = NULL,
intermediates_dir = NULL,
knit_root_dir = NULL,
runtime = c("auto", "static", "shiny", "shinyrmd", "shiny_prerendered"),
clean = TRUE,
params = NULL,
knit_meta = NULL,
envir = parent.frame(),
run_pandoc = TRUE,
quiet = FALSE,
encoding = "UTF-8") {
perf_timer_start("render")
init_render_context()
on.exit(clear_render_context(), add = TRUE)
# render() may call itself, e.g., in discover_rmd_resources(); in this case,
# we should not clean up temp files in the nested render() call, but wait
# until the top-level render() exits to clean up temp files
.globals$level <- .globals$level + 1L # increment level in a nested render()
on.exit({
.globals$level <- .globals$level - 1L
if (.globals$level == 0) clean_tmpfiles()
}, add = TRUE)
# check for "all" output formats
if (identical(output_format, "all")) {
output_format <- enumerate_output_formats(input)
if (is.null(output_format))
output_format <- "html_document"
}
# check for a list of output formats -- if there is more than one
# then recursively call this function with each format by name
if (is.character(output_format) && length(output_format) > 1) {
outputs <- character()
if (length(output_file) == 1) output_file <- rep(output_file, length(output_format))
for (i in seq_along(output_format)) {
# the output_file argument is intentionally ignored (we can't give
# the same name to each rendered output); copy the rest by name
output <- render(input = input,
output_format = output_format[i],
output_file = output_file[i],
output_dir = output_dir,
output_options = output_options,
intermediates_dir = intermediates_dir,
knit_root_dir = knit_root_dir,
runtime = runtime,
clean = clean,
params = params,
knit_meta = knit_meta,
envir = envir,
run_pandoc = run_pandoc,
quiet = quiet)
outputs <- c(outputs, output)
}
return(invisible(outputs))
}
# check for required version of pandoc if we are running pandoc
if (run_pandoc) {
required_pandoc <- "1.12.3"
pandoc_available(required_pandoc, error = TRUE)
}
# setup a cleanup function for intermediate files
intermediates <- c()
on.exit(if (clean) unlink(intermediates, recursive = TRUE), add = TRUE)
# ensure we have a directory to store intermediates
if (!is.null(intermediates_dir)) {
if (!dir_exists(intermediates_dir))
dir.create(intermediates_dir, recursive = TRUE)
intermediates_dir <- normalize_path(intermediates_dir)
}
intermediates_loc <- function(file) {
if (is.null(intermediates_dir))
file
else
file.path(intermediates_dir, file)
}
# resolve output directory before we change the working directory in
# preparation for rendering the document
if (!is.null(output_dir)) {
if (!dir_exists(output_dir))
dir.create(output_dir, recursive = TRUE)
output_dir <- normalize_path(output_dir)
}
# check whether this document requires a knit
requires_knit <- tolower(xfun::file_ext(input)) %in% c("r", "rmd", "rmarkdown", "qmd")
# remember the name of the original input document (we overwrite 'input' once
# we've knitted)
original_input <- normalize_path(input)
# if the input file has shell characters in its name then make a copy that
# doesn't have shell characters
if (grepl(.shell_chars_regex, basename(input))) {
# form the name of the file w/o shell characters
input_no_shell_chars <- intermediates_loc(
file_name_without_shell_chars(basename(input)))
if (file.exists(input_no_shell_chars)) {
stop2("The name of the input file cannot contain the special shell ",
"characters: ", .shell_chars_regex, " (attempted to copy to a ",
"version without those characters '", input_no_shell_chars, "' ",
"however that file already exists)")
}
file.copy(input, input_no_shell_chars, overwrite = TRUE)
intermediates <- c(intermediates, input_no_shell_chars)
input <- input_no_shell_chars
# if an intermediates directory wasn't explicit before, make it explicit now
if (is.null(intermediates_dir)) {
intermediates_dir <-
dirname(normalize_path(input_no_shell_chars))
}
}
# never use the original input directory as the intermediate directory,
# otherwise external resources discovered will be deleted as intermediate
# files later (because they are copied to the "intermediate" dir)
if (!is.null(intermediates_dir) &&
same_path(intermediates_dir, dirname(original_input)))
intermediates_dir <- NULL
# force evaluation of knitr root dir before we change directory context
force(knit_root_dir)
# execute within the input file's directory
oldwd <- setwd(dirname(abs_path(input)))
on.exit(setwd(oldwd), add = TRUE)
# reset the name of the input file to be relative and generate the name of
# the intermediate knitted file. The extension can be set as an option mainly for blogdown
# as `.md~` will be ignored.
input <- basename(input)
knit_input <- input
knit_output <- intermediates_loc(
file_with_meta_ext(input, "knit", getOption("rmarkdown.knit.ext", "md"))
)
intermediates <- c(intermediates, knit_output)
# track whether this was straight markdown input (to prevent keep_md later)
md_input <- identical(tolower(xfun::file_ext(input)), "md")
# if this is an R script then spin it first
if (identical(tolower(xfun::file_ext(input)), "r")) {
# make a copy of the file to spin
spin_input <- intermediates_loc(file_with_meta_ext(input, "spin", "R"))
file.copy(input, spin_input, overwrite = TRUE)
intermediates <- c(intermediates, spin_input)
# spin it
spin_rmd <- knitr::spin(spin_input,
knit = FALSE,
envir = envir,
format = "Rmd")
intermediates <- c(intermediates, spin_rmd)
knit_input <- spin_rmd
# append default metadata unless the field exists in YAML
meta1 <- yaml_front_matter(knit_input)
meta2 <- list(
title = input, author = Sys.info()[["user"]],
date = as.character(Sys.Date())
)
for (i in names(meta2)) if (!is.null(meta1[[i]])) meta2[[i]] <- NULL
if (length(meta2)) {
input_lines <- read_utf8(knit_input)
write_utf8(c(input_lines, '\n\n---', yaml::as.yaml(meta2), '---'), knit_input)
}
}
# read the input file
input_lines <- read_utf8(knit_input)
# read the yaml front matter
front_matter <- parse_yaml_front_matter(input_lines)
# metadata to be attached to the returned value of render() as an attribute
old_output_metadata <- output_metadata$get()
on.exit(output_metadata$restore(old_output_metadata), add = TRUE)
output_metadata$restore(as.list(front_matter[['rmd_output_metadata']]))
# if this is shiny_prerendered then modify the output format to
# be single-page and to output dependencies to the shiny.dep file
shiny_prerendered_dependencies <- list()
if (requires_knit && is_shiny_prerendered(front_matter$runtime,
front_matter$server)) {
# require shiny for the knit
if (requireNamespace("shiny")) {
if (!"package:shiny" %in% search())
attachNamespace("shiny")
}
else
stop("The shiny package is required for shiny documents")
# source global.R if it exists
global_r <- file.path.ci(".", "global.R")
if (file.exists(global_r)) {
source(global_r, local = envir)
}
# force various output options
output_options$self_contained <- FALSE
output_options$dependency_resolver <- function(deps) {
shiny_prerendered_dependencies <<- list(
deps = deps,
packages = get_loaded_packages()
)
list()
}
}
# if we haven't been passed a fully formed output format then
# resolve it by looking at the yaml
if (!is_output_format(output_format)) {
output_format <- output_format_from_yaml_front_matter(input_lines,
output_options,
output_format,
output_yaml,
output_file)
output_format <- create_output_format(output_format$name,
output_format$options)
}
pandoc_to <- output_format$pandoc$to
# generate outpout file based on input filename
output_auto <- pandoc_output_file(input, output_format$pandoc)
if (is.null(output_file) || is.na(output_file)) output_file <- output_auto else {
if (!inherits(output_file, "AsIs") && xfun::file_ext(output_file) == "")
output_file <- paste(output_file, xfun::file_ext(output_auto), sep = ".")
}
# if an output_dir was specified then concatenate it with the output file
if (!is.null(output_dir)) {
output_file <- file.path(output_dir, basename(output_file))
}
output_dir <- dirname(output_file)
# Stop the render process early if the output directory does not exist
if (!dir_exists(output_dir)) {
stop2("The directory '", output_dir, "' does not exist.")
}
# use output filename based files dir
files_dir_slash <- file.path(output_dir, knitr_files_dir(basename(output_file)))
files_dir <- pandoc_path_arg(files_dir_slash)
# default to no cache_dir (may be generated by the knit)
cache_dir <- NULL
# call any intermediate files generator, if we have an intermediates directory
# (do this before knitting in case the knit requires intermediates)
if (!is.null(intermediates_dir) &&
!is.null(output_format$intermediates_generator)) {
intermediates <- c(intermediates,
output_format$intermediates_generator(original_input,
intermediates_dir))
}
# reset knit_meta (and ensure it's always reset before exiting render)
old_knit_meta <- knit_meta_reset()
on.exit({
knit_meta_reset()
if (length(old_knit_meta)) {
knitr::knit_meta_add(old_knit_meta, attr(old_knit_meta, 'knit_meta_id'))
}
}, add = TRUE)
# presume that we're rendering as a static document unless specified
# otherwise in the parameters
runtime <- match.arg(runtime)
if (identical(runtime, "auto")) {
if (is_shiny_prerendered(front_matter$runtime, front_matter$server)) {
runtime <- "shiny_prerendered"
} else {
runtime <- front_matter$runtime %||% "static"
}
}
# set df_print
context <- render_context()
context$df_print <- resolve_df_print(output_format$df_print)
# make the front_matter available as 'metadata' within the knit environment
# (unless it is already defined there, in which case we emit a warning)
env <- environment(render)
metadata_this <- env$metadata
do.call("unlockBinding", list("metadata", env))
on.exit({
if (bindingIsLocked("metadata", env)) {
do.call("unlockBinding", list("metadata", env))
}
env$metadata <- metadata_this
lockBinding("metadata", env)
}, add = TRUE)
env$metadata <- front_matter
# call any pre_knit handler
if (!is.null(output_format$pre_knit)) {
if ('...' %in% names(formals(output_format$pre_knit))) {
output_format$pre_knit(input = original_input, metadata = front_matter)
} else {
warning("The 'pre_knit' function of the output format should have a '...' argument.")
output_format$pre_knit(input = original_input)
}
}
# function used to call post_knit handler
call_post_knit_handler <- function() {
if (!is.null(output_format$post_knit)) {
post_knit_extra_args <- output_format$post_knit(front_matter,
knit_input,
runtime,
encoding = 'UTF-8')
} else {
post_knit_extra_args <- NULL
}
c(output_format$pandoc$args, post_knit_extra_args)
}
# determine our id-prefix (add one if necessary for runtime: shiny)
id_prefix <- id_prefix_from_args(output_format$pandoc$args)
if (!nzchar(id_prefix) && is_shiny(runtime, front_matter[["server"]])) {
id_prefix <- "section-"
output_format$pandoc$args <- c(output_format$pandoc$args, rbind("--id-prefix", id_prefix))
}
# knit if necessary
if (requires_knit) {
# restore options and hooks after knit
optk <- knitr::opts_knit$get()
on.exit(knitr::opts_knit$restore(optk), add = TRUE)
optc <- knitr::opts_chunk$get()
on.exit(knitr::opts_chunk$restore(optc), add = TRUE)
hooks <- knitr::knit_hooks$get()
on.exit(knitr::knit_hooks$restore(hooks), add = TRUE)
ohooks <- knitr::opts_hooks$get()
on.exit(knitr::opts_hooks$restore(ohooks), add = TRUE)
templates <- knitr::opts_template$get()
on.exit(knitr::opts_template$restore(templates), add = TRUE)
# specify that htmltools::htmlPreserve() should use the Pandoc raw attribute
# by default (e.g. ```{=html}) rather than preservation tokens when pandoc
# >= v2.0.
if (pandoc2.0() && is.null(prev <- getOption("htmltools.preserve.raw"))) {
options(htmltools.preserve.raw = TRUE)
on.exit(options(htmltools.preserve.raw = prev), add = TRUE)
}
# run render on_exit (run after the knit hooks are saved so that
# any hook restoration can take precedence)
if (is.function(output_format$on_exit))
on.exit(output_format$on_exit(), add = TRUE)
# default rendering and chunk options
knitr::render_markdown()
knitr::opts_chunk$set(tidy = FALSE, error = FALSE)
# the retina option does not make sense to non-HTML output formats
if (!grepl('[.]html$', output_file)) knitr::opts_chunk$set(fig.retina = NULL)
# store info about the final output format in opts_knit
knitr::opts_knit$set(
rmarkdown.pandoc.from = output_format$pandoc$from,
rmarkdown.pandoc.to = pandoc_to,
rmarkdown.pandoc.args = output_format$pandoc$args,
rmarkdown.pandoc.id_prefix = id_prefix,
rmarkdown.keep_md = output_format$keep_md,
rmarkdown.df_print = output_format$df_print,
rmarkdown.version = 2,
rmarkdown.runtime = runtime
)
# read root directory from argument (has precedence) or front matter
root_dir <- knit_root_dir
if (is.null(root_dir))
root_dir <- front_matter$knit_root_dir
if (!is.null(root_dir))
knitr::opts_knit$set(root.dir = root_dir)
# use filename based figure and cache directories
base_pandoc_to <- gsub('[-+].*', '', pandoc_to)
if (base_pandoc_to == 'html4') base_pandoc_to <- 'html'
knitr::opts_chunk$set(fig.path = paste0(
pandoc_path_arg(files_dir_slash, backslash = FALSE),
"/figure-", base_pandoc_to, "/"
))
cache_dir <- knitr_cache_dir(input, base_pandoc_to)
knitr::opts_chunk$set(cache.path = cache_dir)
# strip the trailing slash from cache_dir so that file.exists() and unlink()
# check on it later works on windows
cache_dir <- gsub("/$", "", cache_dir)
# merge user options and hooks
if (!is.null(output_format$knitr)) {
knitr::opts_knit$set(as.list(output_format$knitr$opts_knit))
knitr::opts_chunk$set(adjust_dev(as.list(output_format$knitr$opts_chunk)))
knitr::opts_template$set(as.list(output_format$knitr$opts_template))
knitr::knit_hooks$set(as.list(output_format$knitr$knit_hooks))
knitr::opts_hooks$set(as.list(output_format$knitr$opts_hooks))
}
# setting the runtime (static/shiny) type
knitr::opts_knit$set(rmarkdown.runtime = runtime)
# install evaluate hook for shiny_prerendred
if (is_shiny_prerendered(runtime)) {
# remove uncached .RData (will be recreated from context="data" chunks)
shiny_prerendered_remove_uncached_data(original_input)
# set the cache option hook and evaluate hook
knitr::opts_hooks$set(label = shiny_prerendered_option_hook(original_input))
knitr::knit_hooks$set(evaluate = shiny_prerendered_evaluate_hook(original_input))
}
# install global chunk handling for runtime: shiny (evaluate the 'global'
# chunk only once, and in the global environment)
if (is_shiny_classic(runtime) && !is.null(shiny::getDefaultReactiveDomain())) {
# install evaluate hook to ensure that the 'global' chunk for this source
# file is evaluated only once and is run outside of a user reactive domain
knitr::knit_hooks$set(evaluate = function(code, envir, ...) {
# check for 'global' chunk label
if (identical(knitr::opts_current$get("label"), "global")) {
# check list of previously evaluated global chunks
code_string <- one_string(code)
if (!code_string %in% .globals$evaluated_global_chunks) {
# save it in our list of evaluated global chunks
.globals$evaluated_global_chunks <-
c(.globals$evaluated_global_chunks, code_string)
# evaluate with no reactive domain to prevent any shiny code (e.g.
# a reactive timer) from attaching to the current user session
# (resulting in it's destruction when that session ends)
shiny::withReactiveDomain(NULL, {
evaluate::evaluate(code, envir = globalenv(), ...)
})
} else {
list()
}
# delegate to standard evaluate for everything else
} else {
evaluate::evaluate(code, envir, ...)
}
})
}
# make the params available within the knit environment
# (only do this if there are parameters in the front matter
# so we don't require recent knitr for all users)
if (!is.null(front_matter$params)) {
params <- knit_params_get(input_lines, params)
# bail if an object called 'params' exists in this environment,
# and it seems to be an unrelated user-created object. store
# references so we can restore them post-render
hasParams <- exists("params", envir = envir, inherits = FALSE)
envirParams <- NULL
if (hasParams) {
envirParams <- get("params", envir = envir, inherits = FALSE)
isKnownParamsObject <-
inherits(envirParams, "knit_param_list") ||
inherits(envirParams, "knit_param")
if (!isKnownParamsObject) {
stop2("params object already exists in knit environment ",
"so can't be overwritten by render params")
}
}
# make the params available in the knit environment
assign("params", params, envir = envir)
lockBinding("params", envir)
on.exit({
if (exists("params", envir = envir, inherits = FALSE)) {
do.call("unlockBinding", list("params", envir))
if (hasParams)
assign("params", envirParams, envir = envir)
else
remove("params", envir = envir)
}
}, add = TRUE)
}
# call onKnit hooks (normalize to list)
sapply(as.list(getHook("rmarkdown.onKnit")), function(hook) {
tryCatch(hook(input = original_input), error = function(e) NULL)
})
on.exit({
sapply(as.list(getHook("rmarkdown.onKnitCompleted")), function(hook) {
tryCatch(hook(input = original_input), error = function(e) NULL)
})
}, add = TRUE)
perf_timer_start("knitr")
# perform the knit
input <- knitr::knit(knit_input,
knit_output,
envir = envir,
quiet = quiet)
perf_timer_stop("knitr")
front_matter <- yaml_front_matter(input)
# call post_knit handler
output_format$pandoc$args <- call_post_knit_handler()
# pull any R Markdown warnings from knit_meta and emit
rmd_warnings <- knit_meta_reset(class = "rmd_warning")
for (rmd_warning in rmd_warnings) {
message("Warning: ", rmd_warning)
}
# pull out shiny_prerendered_contexts and append them as script tags
shiny_prerendered_append_contexts(runtime, input)
# collect remaining knit_meta
knit_meta <- knit_meta_reset()
} else {
output_format$pandoc$args <- call_post_knit_handler()
}
# if this isn't html and there are html dependencies then flag an error
if (!(is_pandoc_to_html(output_format$pandoc) ||
identical(tolower(xfun::file_ext(output_file)), "html"))) {
if (has_html_dependencies(knit_meta)) {
if (!isTRUE(front_matter$always_allow_html)) {
stop2("Functions that produce HTML output found in document targeting ",
pandoc_to, " output.\nPlease change the output type ",
"of this document to HTML.\n",
"If your aiming to have some HTML widgets shown in non-HTML format as a screenshot,\n",
"please install webshot or webshot2 R package for knitr to do the screenshot.\n",
"Alternatively, you can allow HTML output in non-HTML formats\n",
"by adding this option to the YAML front-matter of\nyour rmarkdown file:\n\n",
" always_allow_html: true\n\n",
"Note however that the HTML output will not be visible in non-HTML formats.\n\n"
)
}
}
if (!identical(runtime, "static")) {
stop2("Runtime '", runtime, "' is not supported for ",
pandoc_to, " output.\nPlease change the output type ",
"of this document to HTML.")
}
}
# clean the files_dir if we've either been asking to clean supporting files or
# the knitr cache is active; clean the figure-* dir instead of the whole
# files_dir if other subdirs are generated by another format and still needed:
# https://github.com/rstudio/rmarkdown/issues/1472 and also #1503
intermediates_fig <- if (output_format$clean_supporting && !dir_exists(cache_dir)) {
# unlink does not support / at the end of file path
fig_path <- gsub("/$", "", knitr::opts_chunk$get('fig.path'))
# existing figure folder(s), can be character(0)
# if no figure is generated, clean the whole files_dir (#1664)
files_dir_fig <- list.files(files_dir, '^figure-.+')
if (length(files_dir_fig) < 1 || identical(files_dir_fig, basename(fig_path))) {
files_dir
} else {
fig_path
}
}
intermediates <- c(intermediates, intermediates_fig)
if (run_pandoc) {
# set env vars required during Pandoc processing
lua_env_vars <- xfun::set_envvar(c(RMARKDOWN_LUA_SHARED = pkg_file_lua("shared.lua")))
on.exit(xfun::set_envvar(lua_env_vars), add = TRUE)
perf_timer_start("pre-processor")
if (has_dependencies(knit_meta, "output_format_dependency")) {
output_format <- merge_output_format_dependencies(output_format, knit_meta)
}
# call any pre_processor
if (!is.null(output_format$pre_processor)) {
extra_args <- output_format$pre_processor(front_matter,
input,
runtime,
knit_meta,
files_dir,
output_dir)
output_format$pandoc$args <- c(output_format$pandoc$args, extra_args)
}
# write shiny_prerendered_dependencies if we have them
if (is_shiny_prerendered(runtime)) {
shiny_prerendered_append_dependencies(input,
shiny_prerendered_dependencies,
files_dir,
output_dir)
# Include special comment in header for correc insertion of HTML dependencies
# during shiny_prerendered process (See `shiny_prerendered_html()`).
# This should be the last header-includes to be set.
# Context in https://github.com/rstudio/rmarkdown/pull/2249
output_format$pandoc$args <- c(output_format$pandoc$args,
pandoc_include_args(in_header = pkg_file("rmd/h/shiny-header.html")))
}
perf_timer_stop("pre-processor")
need_bibtex <- grepl('[.](pdf|tex)$', output_file) &&
any(c('--natbib', '--biblatex') %in% output_format$pandoc$args)
perf_timer_start("pandoc")
convert <- function(output, citeproc = FALSE) {
# temporarily move figures and bib files to the intermediate dir if
# specified: https://github.com/rstudio/rmarkdown/issues/500
if (!is.null(intermediates_dir)) {
figures_dir <- gsub('/$', '', knitr::opts_chunk$get("fig.path"))
files <- list.files(figures_dir, full.names = TRUE, recursive = TRUE)
# https://github.com/rstudio/rmarkdown/issues/1358
if (citeproc) files <- c(files, front_matter[['bibliography']])
for (f in files) {
intermediates <<- c(intermediates, copy_file_with_dir(f, intermediates_dir))
}
}
# ensure we expand paths (for Windows where leading `~/` does
# not get expanded by pandoc)
input <- path.expand(input)
output <- path.expand(output)
pandoc_args <- output_format$pandoc$args
# if Lua filters are provided, add the command line switch
if (!is.null(lua_filters <- output_format$pandoc$lua_filters)) {
lua_filters <- pandoc_lua_filter_args(lua_filters)
}
pandoc_args <- c(lua_filters, pandoc_args)
# in case the output format turns on the --file-scope flag, run its
# file_scope function to split the input into multiple files
input_files <- input
if (is.function(output_format$file_scope)) {
input_files <- file_scope_split(input, output_format$file_scope)
# ignore if input_files has not really been splitted
if (length(input_files) > 1) {
# add the --file-scope option
pandoc_args <- c(pandoc_args, "--file-scope")
# cleanup the split files after render
on.exit(unlink(input_files), add = TRUE)
}
}
# use the convert function from the output format if provided
if (!is.function(convert_fun <- output_format$pandoc$convert_fun))
convert_fun <- pandoc_convert
convert_it <- function(output) convert_fun(
output = output, input_files, pandoc_to, output_format$pandoc$from,
citeproc, pandoc_args, !quiet
)
# if we don't detect any invalid shell characters in the
# target path, then just call pandoc directly
if (!grepl(.shell_chars_regex, output) && !grepl(.shell_chars_regex, input)) {
return(convert_it(output))
}
# render to temporary file (preserve extension)
# this also ensures we don't pass a file path with invalid
# characters to our pandoc invocation
ext <- xfun::file_ext(output)
if (ext != '') ext <- paste0('.', ext)
# render to a path in the current working directory
# (avoid passing invalid characters to shell)
pandoc_output_tmp <- basename(tempfile("pandoc", getwd(), ext))
# clean up temporary file on exit
on.exit(unlink(pandoc_output_tmp), add = TRUE)
# call pandoc to render file
status <- convert_it(pandoc_output_tmp)
# construct output path (when passed only a file name to '--output',
# pandoc seems to render in the same directory as the input file)
pandoc_output_tmp_path <- file.path(dirname(input), pandoc_output_tmp)
# rename output file to desired location
renamed <- suppressWarnings(file.rename(pandoc_output_tmp_path, output))
# rename can fail if the temporary directory and output path
# lie on different volumes; in such a case attempt a file copy
# see: https://github.com/rstudio/rmarkdown/issues/705
if (!renamed) {
copied <- file.copy(pandoc_output_tmp_path, output, overwrite = TRUE)
if (!copied) {
stop("failed to copy rendered pandoc artefact to '", output, "'")
}
}
# return status
status
}
texfile <- file_with_ext(output_file, "tex")
# determine whether we need to run citeproc (based on whether we have
# references in the input)
run_citeproc <- citeproc_required(front_matter, input_lines)
# if the output format is LaTeX, first convert .md to .tex, and then convert
# .tex to .pdf via latexmk() if PDF output is requested (in rmarkdown <=
# v1.8, we used to call Pandoc to convert .md to .tex and .pdf separately)
if (output_format$pandoc$keep_tex || knitr::is_latex_output()) {
# do not use pandoc-citeproc if needs to build bibliography
convert(texfile, run_citeproc && !need_bibtex)
# patch the .tex output generated from the default Pandoc LaTeX template
if (!("--template" %in% output_format$pandoc$args)) patch_tex_output(texfile)
fix_horiz_rule(texfile)
# unless the output file has the extension .tex, we assume it is PDF
if (!grepl('[.]tex$', output_file)) {
latexmk(texfile, output_format$pandoc$latex_engine, '--biblatex' %in% output_format$pandoc$args)
file.rename(file_with_ext(texfile, "pdf"), output_file)
# clean up the tex file if necessary
if (!output_format$pandoc$keep_tex) {
texfile <- normalize_path(texfile)
on.exit(unlink(texfile), add = TRUE)
}
}
} else {
convert(output_file, run_citeproc)
}
# pandoc writes the output alongside the input, so if we rendered from an
# intermediate directory, move the output file
if (!is.null(intermediates_dir)) {
intermediate_output <- file.path(intermediates_dir, basename(output_file))
if (file.exists(intermediate_output)) {
move_dir(intermediate_output, output_file)
}
}
perf_timer_stop("pandoc")
perf_timer_start("post-processor")
# if there is a post-processor then call it
if (!is.null(output_format$post_processor))
output_file <- output_format$post_processor(front_matter,
input,
output_file,
clean,
!quiet)
if (!quiet && getOption('rmarkdown.render.message', TRUE)) {
message("\nOutput created: ", relative_to(oldwd, output_file))
}
perf_timer_stop("post-processor")
}
perf_timer_stop("render")
# write markdown output if requested
if (output_format$keep_md && !md_input) {
file.copy(input, file_with_ext(output_file, "md"), overwrite = TRUE)
}
if (run_pandoc) {
# return the full path to the output file
output_file <- abs_path(output_file)
# attach the metadata specified as rmd_output_metadata in YAML
if (length(output_meta <- output_metadata$get()))
attr(output_file, 'rmd_output_metadata') <- output_meta
invisible(output_file)
} else {
# make sure the markdown output and fig dir are not cleaned up
intermediates <- setdiff(intermediates, c(input, intermediates_fig))
# did not run pandoc; returns the markdown output with attributes of the
# knitr meta data and intermediate files
invisible(structure(input,
knit_meta = knit_meta,
files_dir = files_dir,
intermediates_dir = intermediates_fig,
intermediates = intermediates))
}
}
#' Render supporting files for an input document
#'
#' Render (copy) required supporting files for an input document to the
#' \code{_files} directory that is associated with the document.
#'
#' @param from The directory from which the files should be copied.
#' @param files_dir The directory that will receive the copied files.
#' @param rename_to An option to rename the source directory after the copy
#' operation is complete.
#' @return The relative path to the supporting files. This path is suitable
#' for inclusion in HTML\code{href} and \code{src} attributes.
#' @export
render_supporting_files <- function(from, files_dir, rename_to = NULL) {
# auto-create directory for supporting files
if (!dir_exists(files_dir))
dir.create(files_dir)
# target directory is based on the dirname of the path or the rename_to
# value if it was provided
target_stage_dir <- file.path(files_dir, basename(from))
target_dir <- file.path(files_dir, ifelse(is.null(rename_to),
basename(from),
rename_to))
# copy the directory if it hasn't already been copied
if (!dir_exists(target_dir) && !dir_exists(target_stage_dir)) {
file.copy(from = from,
to = files_dir,
recursive = TRUE,
copy.mode = FALSE)
if (!is.null(rename_to)) {
file.rename(from = target_stage_dir,
to = target_dir)
}
}
# return the target dir (used to form links in the HTML)
target_dir
}
# reset knitr meta output (returns any meta output generated since the last
# call to knit_meta_reset), optionally scoped to a specific output class
knit_meta_reset <- function(class = NULL) {
knitr::knit_meta(class, clean = TRUE)
}
# render context (render-related state can be stuffed here)
.render_context <- NULL # initialized in .onLoad
render_context <- function() {
.render_context$peek()
}
init_render_context <- function() {
.render_context$push(new_render_context())
}
clear_render_context <- function() {
.render_context$pop()
}
new_render_context <- function() {
env <- new.env(parent = emptyenv())
env$chunk.index <- 1
env
}
merge_render_context <- function(context) {
elements <- ls(envir = render_context(), all.names = TRUE)
for (el in elements)
context[[el]] <- get(el, envir = render_context())
context
}
id_prefix_from_args <- function(args) {
# scan for id-prefix argument
for (i in 1:length(args)) {
arg <- args[[i]]
if (identical(arg, "--id-prefix") && (i < length(args)))
return(args[[i + 1]])
}
# default to empty string
""
}
resolve_df_print <- function(df_print) {
# available methods
valid_methods <- c("default", "kable", "tibble", "paged")
# if we are passed NULL then select the first method
if (is.null(df_print))
df_print <- valid_methods[[1]]
# if we are passed all of valid_methods then select the first one
if (identical(valid_methods, df_print))
df_print <- valid_methods[[1]]
if (!is.function(df_print)) {
if (df_print == "kable")
df_print <- knitr::kable
else if (df_print == "tibble") {
if (!requireNamespace("tibble", quietly = TRUE))
stop("Printing 'tibble' without 'tibble' package available")
df_print <- function(x) print(tibble::as_tibble(x))
}
else if (df_print == "paged")
df_print <- function(x) {
if (!identical(knitr::opts_current$get("paged.print"), FALSE)) {
knitr::asis_output(paged_table_html(x))
}
else {
print(x)
}
}
else if (df_print == "default")
df_print <- print
else
stop2('Invalid value for df_print (valid values are ',
paste(valid_methods, collapse = ", "))
}
df_print
}
# package level globals
.globals <- new.env(parent = emptyenv())
.globals$evaluated_global_chunks <- character()
.globals$level <- 0L
#' The output metadata object
#'
#' This object provides a mechanism for users to attach metadata as an attribute
#' (named \code{rmd_output_metadata}) of the returned value of
#' \code{\link{render}()}. The initial value of the metadata comes from in the
#' \code{rmd_output_metadata} field of the YAML frontmatter of an R Markdown
#' document. The metadata can be queried via the
#' \code{output_metadata$get()} method, and modified via the
#' \code{output_metadata$set()} method.
#' @format NULL
#' @usage NULL
#' @keywords NULL
#' @export
output_metadata = knitr:::new_defaults()
file_scope_split <- function(input, fun) {
inputs <- if (length(formals(fun)) == 1L) {
fun(input) # for the backward compatibility
} else {
fun(input, NULL) # the second argument implies current file scope
}
# file_scope_fun should split the input file in several
# do nothing if not and return input file unsplited
if (length(inputs) <= 1) return(input)
# write the split content into *.split.md files
input_files <- lapply(inputs, function(f) {
file <- file_with_meta_ext(f$name, "split", "md")
file <- file.path(dirname(input), file)
write_utf8(f$content, file)
file
})
unlist(input_files)
}
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Defines functions file_scope_split resolve_df_print id_prefix_from_args merge_render_context new_render_context clear_render_context init_render_context render_context knit_meta_reset render_supporting_files render
Documented in render render_supporting_files
#' R Markdown Metadata
#'
#' Rmd files include a metadata section (typically located at the top of the
#' file) that can specify (among other things) the title, author, and date of
#' the document. Metadata adheres to the \href{https://yaml.org}{YAML} format
#' and is delimited by lines containing three dashes (\code{---}). Here is an
#' example metadata section:
#' \preformatted{---
#' title: "Crop Analysis Q3 2013"
#' author: Martha Smith
#' date: October 23rd, 2013
#' ---
#' }
#' Note that the \code{title} field is quoted. This is because titles often
#' contained embedded colons (\code{:}) and colons followed by a space need to
#' be quoted in YAML.
#' @details When title, author, and date metadata is provided it's used to
#' automatically create a title section within output documents. If you don't
#' want this section included in your document then you should remove the
#' corresponding metadata fields.
#'
#' When generating PDF and Beamer output there are also a number of other
#' metadata fields that can be included to customize the appearance and theme
#' of PDF output. For more details see the documentation for
#' \code{\link{pdf_document}} and \code{\link{beamer_presentation}}.
#' @name rmd_metadata
NULL
#' The YAML metadata of the current R Markdown document
#'
#' The object \code{metadata} stores the YAML metadata of the current R Markdown
#' document as a list, which you may use in the R code chunks, e.g.
#' \code{rmarkdown::metadata$title} (the title of the document),
#' \code{rmarkdown::metadata$author}, and \code{rmarkdown::metadata$foo} (if you
#' have a YAML field named \code{foo}), etc.
#' @usage NULL
#' @examples rmarkdown::metadata
#' @export
metadata <- list()
#' Compiling R scripts to a notebook
#'
#' R Markdown can also compile R scripts to a notebook which includes
#' commentary, source code, and script output. Notebooks can be compiled to any
#' output format including HTML, PDF, and MS Word.
#'
#' @section Overview:
#' To compile a notebook from an R script you simply pass the script to
#' \code{\link{render}}. For example:
#' \preformatted{
#' rmarkdown::render("analysis.R")
#' rmarkdown::render("analysis.R", "pdf_document")
#' }
#' The first call to \code{\link{render}} creates an HTML document, whereas
#' the second creates a PDF document.
#'
#' By default the name of the script, username, and current date and time are
#' included in the header of the generated notebook. You can override this
#' default behavior by including explicit metadata in a specially formatted R
#' comment:
#' \preformatted{
#' #' ---
#' #' title: "Crop Analysis Q3 2013"
#' #' author: "John Smith"
#' #' date: "May 3rd, 2014"
#' #' ---
#' }
#' @section Including Markdown:
#' Note that the R comment used above to add a title, author, and date
#' includes a single-quote as a special prefix character. This is a
#' \pkg{roxygen2} style comment, and it's actually possible to include many
#' such comments in an R script, all of which will be converted to markdown
#' content within the generated notebook. For example:
#' \preformatted{#' A script comment that includes **markdown** formatting.}
#' Rather than displaying as an R comment in the compiled notebook any
#' \pkg{roxygen2} style comment will be treated as markdown and rendered
#' accordingly.
#' @section knitr Spin:
#' Including markdown within R comments is possible because \code{\link{render}}
#' calls the \code{\link[knitr:spin]{knitr spin}} function to convert the R
#' script to an Rmd file. The \code{spin} function also enables you to add
#' knitr
#' chunk options with another special comment prefix (\code{#+}).
#'
#' Here's an example of a script that uses the various features of \code{spin}:
#'
#' \url{https://github.com/yihui/knitr/blob/master/inst/examples/knitr-spin.R}
#'
#' For more details on \code{knitr::spin} see the following documentation:
#'
#' \url{https://yihui.org/knitr/demo/stitch/}
#' @name compile_notebook
NULL
#' Render R Markdown
#'
#' Render the input file to the specified output format using pandoc. If the
#' input requires knitting then \code{\link[knitr:knit]{knit}} is called prior
#' to pandoc.
#'
#' Note that the \pkg{knitr} \code{error} option is set to \code{FALSE} during
#' rendering (which is different from the \pkg{knitr} default value of
#' \code{TRUE}).
#'
#' For additional details on rendering R scripts see
#' \link[=compile_notebook]{Compiling R scripts to a notebook}.
#'
#' If no \code{output_format} parameter is specified then the output format is
#' read from the YAML front-matter of the input file. For example, the
#' following YAML would yield a PDF document:
#'
#' \preformatted{
#' output: pdf_document
#' }
#'
#' Additional format options can also be specified in metadata. For example:
#'
#' \preformatted{
#' output:
#' pdf_document:
#' toc: true
#' highlight: zenburn
#' }
#'
#' Multiple formats can be specified in metadata. If no \code{output_format}
#' is passed to \code{render} then the first one defined will be used:
#'
#' \preformatted{
#' output:
#' pdf_document:
#' toc: true
#' highlight: zenburn
#' html_document:
#' toc: true
#' theme: united
#' }
#'
#' Formats specified in metadata can be any one of the built in formats (e.g.
#' \code{\link{html_document}}, \code{\link{pdf_document}}) or a format defined
#' in another package (e.g. \code{pkg::custom_format}).
#'
#' If there is no format defined in the YAML then
#' \code{\link{html_document}} will be used.
#' @section R Markdown:
#' R Markdown supports all of the base pandoc markdown features as well as some
#' optional features for compatibility with GitHub Flavored Markdown (which
#' previous versions of R Markdown were based on). See
#' \code{\link{rmarkdown_format}} for details.
#' @seealso
#' \link[knitr:knit]{knit}, \link{output_format},
#' \url{https://pandoc.org}
#' @inheritParams default_output_format
#' @param input The input file to be rendered. This can be an R script (.R),
#' an R Markdown document (.Rmd), or a plain markdown document.
#' @param output_format The R Markdown output format to convert to. The option
#' \code{"all"} will render all formats defined within the file. The option can
#' be the name of a format (e.g. \code{"html_document"}) and that will render
#' the document to that single format. One can also use a vector of format
#' names to render to multiple formats. Alternatively, you can pass an output
#' format object (e.g. \code{html_document()}). If using \code{NULL} then the
#' output format is the first one defined in the YAML frontmatter in the input
#' file (this defaults to HTML if no format is specified there).
#' If you pass an output format object to \code{output_format}, the options
#' specified in the YAML header or \code{_output.yml} will be ignored and you
#' must explicitly set all the options you want when you construct the object.
#' If you pass a string, the output format will use the output parameters in
#' the YAML header or \code{_output.yml}.
#' @param output_file The name of the output file. If using \code{NULL} then the
#' output filename will be based on filename for the input file. If a filename
#' is provided, a path to the output file can also be provided. Note that the
#' \code{output_dir} option allows for specifying the output file path as well,
#' however, if also specifying the path, the directory must exist. If
#' \code{output_file} is specified but does not have a file extension, an
#' extension will be automatically added according to the output format. To
#' avoid the automatic file extension, put the \code{output_file} value in
#' \code{\link{I}()}, e.g., \code{I('my-output')}.
#' @param output_dir The output directory for the rendered \code{output_file}.
#' This allows for a choice of an alternate directory to which the output file
#' should be written (the default output directory of that of the input file).
#' If a path is provided with a filename in \code{output_file} the directory
#' specified here will take precedence. Please note that any directory path
#' provided will create any necessary directories if they do not exist.
#' @param output_options List of output options that can override the options
#' specified in metadata (e.g. could be used to force \code{self_contained} or
#' \code{mathjax = "local"}). Note that this is only valid when the output
#' format is read from metadata (i.e. not a custom format object passed to
#' \code{output_format}).
#' @param intermediates_dir Intermediate files directory. If a path is specified
#' then intermediate files will be written to that path. If \code{NULL},
#' intermediate files are written to the same directory as the input file.
#' @param knit_root_dir The working directory in which to knit the document;
#' uses knitr's \code{root.dir} knit option. If \code{NULL} then the behavior
#' will follow the knitr default, which is to use the parent directory of the
#' document.
#' @param runtime The runtime target for rendering. The \code{static} option
#' produces output intended for static files; \code{shiny} produces output
#' suitable for use in a Shiny document (see \code{\link{run}}). The default,
#' \code{auto}, allows the \code{runtime} target specified in the YAML metadata
#' to take precedence, and renders for a \code{static} runtime target otherwise.
#' @param clean Using \code{TRUE} will clean intermediate files that are created
#' during rendering.
#' @param params A list of named parameters that override custom params
#' specified within the YAML front-matter (e.g. specifying a dataset to read or
#' a date range to confine output to). Pass \code{"ask"} to start an
#' application that helps guide parameter configuration.
#' @param knit_meta (This option is reserved for expert use.) Metadata
#' generated by \pkg{knitr}.
#' @param envir The environment in which the code chunks are to be evaluated
#' during knitting (can use \code{\link{new.env}()} to guarantee an empty new
#' environment).
#' @param run_pandoc An option for whether to run pandoc to convert Markdown
#' output.
#' @param quiet An option to suppress printing during rendering from knitr,
#' pandoc command line and others. To only suppress printing of the last
#' "Output created: " message, you can set \code{rmarkdown.render.message} to
#' \code{FALSE}
#' @param encoding Ignored. The encoding is always assumed to be UTF-8.
#' @return
#' When \code{run_pandoc = TRUE}, the compiled document is written into
#' the output file, and the path of the output file is returned. When
#' \code{run_pandoc = FALSE}, the path of the Markdown output file, with
#' attributes \code{knit_meta} (the \pkg{knitr} meta data collected from code
#' chunks) and \code{intermediates} (the intermediate files/directories
#' generated by \code{render()}).
#' @examples
#' \dontrun{
#' library(rmarkdown)
#'
#' # Render the default (first) format defined in the file
#' render("input.Rmd")
#'
#' # Render all formats defined in the file
#' render("input.Rmd", "all")
#'
#' # Render a single format, using parameters for \code{html_document} from
#' # the YAML header parameters.
#' render("input.Rmd", "html_document")
#'
#' # Render a single format, ignoring parameters for \code{html_document} in
#' # the YAML header. Any parameters not passed as arguments to
#' # \code{html_document()} will be assigned to their default values, regardless
#' # of anything in the YAML header
#' render("input.Rmd", html_document(toc = TRUE, toc_depth = 2))
#'
#' # Render multiple formats
#' render("input.Rmd", c("html_document", "pdf_document"))
#' }
#' @export
render <- function(input,
output_format = NULL,
output_file = NULL,
output_dir = NULL,
output_options = NULL,
output_yaml = NULL,
intermediates_dir = NULL,
knit_root_dir = NULL,
runtime = c("auto", "static", "shiny", "shinyrmd", "shiny_prerendered"),
clean = TRUE,
params = NULL,
knit_meta = NULL,
envir = parent.frame(),
run_pandoc = TRUE,
quiet = FALSE,
encoding = "UTF-8") {
perf_timer_start("render")
init_render_context()
on.exit(clear_render_context(), add = TRUE)
# render() may call itself, e.g., in discover_rmd_resources(); in this case,
# we should not clean up temp files in the nested render() call, but wait
# until the top-level render() exits to clean up temp files
.globals$level <- .globals$level + 1L # increment level in a nested render()
on.exit({
.globals$level <- .globals$level - 1L
if (.globals$level == 0) clean_tmpfiles()
}, add = TRUE)
# check for "all" output formats
if (identical(output_format, "all")) {
output_format <- enumerate_output_formats(input)
if (is.null(output_format))
output_format <- "html_document"
}
# check for a list of output formats -- if there is more than one
# then recursively call this function with each format by name
if (is.character(output_format) && length(output_format) > 1) {
outputs <- character()
if (length(output_file) == 1) output_file <- rep(output_file, length(output_format))
for (i in seq_along(output_format)) {
# the output_file argument is intentionally ignored (we can't give
# the same name to each rendered output); copy the rest by name
output <- render(input = input,
output_format = output_format[i],
output_file = output_file[i],
output_dir = output_dir,
output_options = output_options,
intermediates_dir = intermediates_dir,
knit_root_dir = knit_root_dir,
runtime = runtime,
clean = clean,
params = params,
knit_meta = knit_meta,
envir = envir,
run_pandoc = run_pandoc,
quiet = quiet)
outputs <- c(outputs, output)
}
return(invisible(outputs))
}
# check for required version of pandoc if we are running pandoc
if (run_pandoc) {
required_pandoc <- "1.12.3"
pandoc_available(required_pandoc, error = TRUE)
}
# setup a cleanup function for intermediate files
intermediates <- c()
on.exit(if (clean) unlink(intermediates, recursive = TRUE), add = TRUE)
# ensure we have a directory to store intermediates
if (!is.null(intermediates_dir)) {
if (!dir_exists(intermediates_dir))
dir.create(intermediates_dir, recursive = TRUE)
intermediates_dir <- normalize_path(intermediates_dir)
}
intermediates_loc <- function(file) {
if (is.null(intermediates_dir))
file
else
file.path(intermediates_dir, file)
}
# resolve output directory before we change the working directory in
# preparation for rendering the document
if (!is.null(output_dir)) {
if (!dir_exists(output_dir))
dir.create(output_dir, recursive = TRUE)
output_dir <- normalize_path(output_dir)
}
# check whether this document requires a knit
requires_knit <- tolower(xfun::file_ext(input)) %in% c("r", "rmd", "rmarkdown", "qmd")
# remember the name of the original input document (we overwrite 'input' once
# we've knitted)
original_input <- normalize_path(input)
# if the input file has shell characters in its name then make a copy that
# doesn't have shell characters
if (grepl(.shell_chars_regex, basename(input))) {
# form the name of the file w/o shell characters
input_no_shell_chars <- intermediates_loc(
file_name_without_shell_chars(basename(input)))
if (file.exists(input_no_shell_chars)) {
stop2("The name of the input file cannot contain the special shell ",
"characters: ", .shell_chars_regex, " (attempted to copy to a ",
"version without those characters '", input_no_shell_chars, "' ",
"however that file already exists)")
}
file.copy(input, input_no_shell_chars, overwrite = TRUE)
intermediates <- c(intermediates, input_no_shell_chars)
input <- input_no_shell_chars
# if an intermediates directory wasn't explicit before, make it explicit now
if (is.null(intermediates_dir)) {
intermediates_dir <-
dirname(normalize_path(input_no_shell_chars))
}
}
# never use the original input directory as the intermediate directory,
# otherwise external resources discovered will be deleted as intermediate
# files later (because they are copied to the "intermediate" dir)
if (!is.null(intermediates_dir) &&
same_path(intermediates_dir, dirname(original_input)))
intermediates_dir <- NULL
# force evaluation of knitr root dir before we change directory context
force(knit_root_dir)
# execute within the input file's directory
oldwd <- setwd(dirname(abs_path(input)))
on.exit(setwd(oldwd), add = TRUE)
# reset the name of the input file to be relative and generate the name of
# the intermediate knitted file. The extension can be set as an option mainly for blogdown
# as `.md~` will be ignored.
input <- basename(input)
knit_input <- input
knit_output <- intermediates_loc(
file_with_meta_ext(input, "knit", getOption("rmarkdown.knit.ext", "md"))
)
intermediates <- c(intermediates, knit_output)
# track whether this was straight markdown input (to prevent keep_md later)
md_input <- identical(tolower(xfun::file_ext(input)), "md")
# if this is an R script then spin it first
if (identical(tolower(xfun::file_ext(input)), "r")) {
# make a copy of the file to spin
spin_input <- intermediates_loc(file_with_meta_ext(input, "spin", "R"))
file.copy(input, spin_input, overwrite = TRUE)
intermediates <- c(intermediates, spin_input)
# spin it
spin_rmd <- knitr::spin(spin_input,
knit = FALSE,
envir = envir,
format = "Rmd")
intermediates <- c(intermediates, spin_rmd)
knit_input <- spin_rmd
# append default metadata unless the field exists in YAML
meta1 <- yaml_front_matter(knit_input)
meta2 <- list(
title = input, author = Sys.info()[["user"]],
date = as.character(Sys.Date())
)
for (i in names(meta2)) if (!is.null(meta1[[i]])) meta2[[i]] <- NULL
if (length(meta2)) {
input_lines <- read_utf8(knit_input)
write_utf8(c(input_lines, '\n\n---', yaml::as.yaml(meta2), '---'), knit_input)
}
}
# read the input file
input_lines <- read_utf8(knit_input)
# read the yaml front matter
front_matter <- parse_yaml_front_matter(input_lines)
# metadata to be attached to the returned value of render() as an attribute
old_output_metadata <- output_metadata$get()
on.exit(output_metadata$restore(old_output_metadata), add = TRUE)
output_metadata$restore(as.list(front_matter[['rmd_output_metadata']]))
# if this is shiny_prerendered then modify the output format to
# be single-page and to output dependencies to the shiny.dep file
shiny_prerendered_dependencies <- list()
if (requires_knit && is_shiny_prerendered(front_matter$runtime,
front_matter$server)) {
# require shiny for the knit
if (requireNamespace("shiny")) {
if (!"package:shiny" %in% search())
attachNamespace("shiny")
}
else
stop("The shiny package is required for shiny documents")
# source global.R if it exists
global_r <- file.path.ci(".", "global.R")
if (file.exists(global_r)) {
source(global_r, local = envir)
}
# force various output options
output_options$self_contained <- FALSE
output_options$dependency_resolver <- function(deps) {
shiny_prerendered_dependencies <<- list(
deps = deps,
packages = get_loaded_packages()
)
list()
}
}
# if we haven't been passed a fully formed output format then
# resolve it by looking at the yaml
if (!is_output_format(output_format)) {
output_format <- output_format_from_yaml_front_matter(input_lines,
output_options,
output_format,
output_yaml,
output_file)
output_format <- create_output_format(output_format$name,
output_format$options)
}
pandoc_to <- output_format$pandoc$to
# generate outpout file based on input filename
output_auto <- pandoc_output_file(input, output_format$pandoc)
if (is.null(output_file) || is.na(output_file)) output_file <- output_auto else {
if (!inherits(output_file, "AsIs") && xfun::file_ext(output_file) == "")
output_file <- paste(output_file, xfun::file_ext(output_auto), sep = ".")
}
# if an output_dir was specified then concatenate it with the output file
if (!is.null(output_dir)) {
output_file <- file.path(output_dir, basename(output_file))
}
output_dir <- dirname(output_file)
# Stop the render process early if the output directory does not exist
if (!dir_exists(output_dir)) {
stop2("The directory '", output_dir, "' does not exist.")
}
# use output filename based files dir
files_dir_slash <- file.path(output_dir, knitr_files_dir(basename(output_file)))
files_dir <- pandoc_path_arg(files_dir_slash)
# default to no cache_dir (may be generated by the knit)
cache_dir <- NULL
# call any intermediate files generator, if we have an intermediates directory
# (do this before knitting in case the knit requires intermediates)
if (!is.null(intermediates_dir) &&
!is.null(output_format$intermediates_generator)) {
intermediates <- c(intermediates,
output_format$intermediates_generator(original_input,
intermediates_dir))
}
# reset knit_meta (and ensure it's always reset before exiting render)
old_knit_meta <- knit_meta_reset()
on.exit({
knit_meta_reset()
if (length(old_knit_meta)) {
knitr::knit_meta_add(old_knit_meta, attr(old_knit_meta, 'knit_meta_id'))
}
}, add = TRUE)
# presume that we're rendering as a static document unless specified
# otherwise in the parameters
runtime <- match.arg(runtime)
if (identical(runtime, "auto")) {
if (is_shiny_prerendered(front_matter$runtime, front_matter$server)) {
runtime <- "shiny_prerendered"
} else {
runtime <- front_matter$runtime %||% "static"
}
}
# set df_print
context <- render_context()
context$df_print <- resolve_df_print(output_format$df_print)
# make the front_matter available as 'metadata' within the knit environment
# (unless it is already defined there, in which case we emit a warning)
env <- environment(render)
metadata_this <- env$metadata
do.call("unlockBinding", list("metadata", env))
on.exit({
if (bindingIsLocked("metadata", env)) {
do.call("unlockBinding", list("metadata", env))
}
env$metadata <- metadata_this
lockBinding("metadata", env)
}, add = TRUE)
env$metadata <- front_matter
# call any pre_knit handler
if (!is.null(output_format$pre_knit)) {
if ('...' %in% names(formals(output_format$pre_knit))) {
output_format$pre_knit(input = original_input, metadata = front_matter)
} else {
warning("The 'pre_knit' function of the output format should have a '...' argument.")
output_format$pre_knit(input = original_input)
}
}
# function used to call post_knit handler
call_post_knit_handler <- function() {
if (!is.null(output_format$post_knit)) {
post_knit_extra_args <- output_format$post_knit(front_matter,
knit_input,
runtime,
encoding = 'UTF-8')
} else {
post_knit_extra_args <- NULL
}
c(output_format$pandoc$args, post_knit_extra_args)
}
# determine our id-prefix (add one if necessary for runtime: shiny)
id_prefix <- id_prefix_from_args(output_format$pandoc$args)
if (!nzchar(id_prefix) && is_shiny(runtime, front_matter[["server"]])) {
id_prefix <- "section-"
output_format$pandoc$args <- c(output_format$pandoc$args, rbind("--id-prefix", id_prefix))
}
# knit if necessary
if (requires_knit) {
# restore options and hooks after knit
optk <- knitr::opts_knit$get()
on.exit(knitr::opts_knit$restore(optk), add = TRUE)
optc <- knitr::opts_chunk$get()
on.exit(knitr::opts_chunk$restore(optc), add = TRUE)
hooks <- knitr::knit_hooks$get()
on.exit(knitr::knit_hooks$restore(hooks), add = TRUE)
ohooks <- knitr::opts_hooks$get()
on.exit(knitr::opts_hooks$restore(ohooks), add = TRUE)
templates <- knitr::opts_template$get()
on.exit(knitr::opts_template$restore(templates), add = TRUE)
# specify that htmltools::htmlPreserve() should use the Pandoc raw attribute
# by default (e.g. ```{=html}) rather than preservation tokens when pandoc
# >= v2.0.
if (pandoc2.0() && is.null(prev <- getOption("htmltools.preserve.raw"))) {
options(htmltools.preserve.raw = TRUE)
on.exit(options(htmltools.preserve.raw = prev), add = TRUE)
}
# run render on_exit (run after the knit hooks are saved so that
# any hook restoration can take precedence)
if (is.function(output_format$on_exit))
on.exit(output_format$on_exit(), add = TRUE)
# default rendering and chunk options
knitr::render_markdown()
knitr::opts_chunk$set(tidy = FALSE, error = FALSE)
# the retina option does not make sense to non-HTML output formats
if (!grepl('[.]html$', output_file)) knitr::opts_chunk$set(fig.retina = NULL)
# store info about the final output format in opts_knit
knitr::opts_knit$set(
rmarkdown.pandoc.from = output_format$pandoc$from,
rmarkdown.pandoc.to = pandoc_to,
rmarkdown.pandoc.args = output_format$pandoc$args,
rmarkdown.pandoc.id_prefix = id_prefix,
rmarkdown.keep_md = output_format$keep_md,
rmarkdown.df_print = output_format$df_print,
rmarkdown.version = 2,
rmarkdown.runtime = runtime
)
# read root directory from argument (has precedence) or front matter
root_dir <- knit_root_dir
if (is.null(root_dir))
root_dir <- front_matter$knit_root_dir
if (!is.null(root_dir))
knitr::opts_knit$set(root.dir = root_dir)
# use filename based figure and cache directories
base_pandoc_to <- gsub('[-+].*', '', pandoc_to)
if (base_pandoc_to == 'html4') base_pandoc_to <- 'html'
knitr::opts_chunk$set(fig.path = paste0(
pandoc_path_arg(files_dir_slash, backslash = FALSE),
"/figure-", base_pandoc_to, "/"
))
cache_dir <- knitr_cache_dir(input, base_pandoc_to)
knitr::opts_chunk$set(cache.path = cache_dir)
# strip the trailing slash from cache_dir so that file.exists() and unlink()
# check on it later works on windows
cache_dir <- gsub("/$", "", cache_dir)
# merge user options and hooks
if (!is.null(output_format$knitr)) {
knitr::opts_knit$set(as.list(output_format$knitr$opts_knit))
knitr::opts_chunk$set(adjust_dev(as.list(output_format$knitr$opts_chunk)))
knitr::opts_template$set(as.list(output_format$knitr$opts_template))
knitr::knit_hooks$set(as.list(output_format$knitr$knit_hooks))
knitr::opts_hooks$set(as.list(output_format$knitr$opts_hooks))
}
# setting the runtime (static/shiny) type
knitr::opts_knit$set(rmarkdown.runtime = runtime)
# install evaluate hook for shiny_prerendred
if (is_shiny_prerendered(runtime)) {
# remove uncached .RData (will be recreated from context="data" chunks)
shiny_prerendered_remove_uncached_data(original_input)
# set the cache option hook and evaluate hook
knitr::opts_hooks$set(label = shiny_prerendered_option_hook(original_input))
knitr::knit_hooks$set(evaluate = shiny_prerendered_evaluate_hook(original_input))
}
# install global chunk handling for runtime: shiny (evaluate the 'global'
# chunk only once, and in the global environment)
if (is_shiny_classic(runtime) && !is.null(shiny::getDefaultReactiveDomain())) {
# install evaluate hook to ensure that the 'global' chunk for this source
# file is evaluated only once and is run outside of a user reactive domain
knitr::knit_hooks$set(evaluate = function(code, envir, ...) {
# check for 'global' chunk label
if (identical(knitr::opts_current$get("label"), "global")) {
# check list of previously evaluated global chunks
code_string <- one_string(code)
if (!code_string %in% .globals$evaluated_global_chunks) {
# save it in our list of evaluated global chunks
.globals$evaluated_global_chunks <-
c(.globals$evaluated_global_chunks, code_string)
# evaluate with no reactive domain to prevent any shiny code (e.g.
# a reactive timer) from attaching to the current user session
# (resulting in it's destruction when that session ends)
shiny::withReactiveDomain(NULL, {
evaluate::evaluate(code, envir = globalenv(), ...)
})
} else {
list()
}
# delegate to standard evaluate for everything else
} else {
evaluate::evaluate(code, envir, ...)
}
})
}
# make the params available within the knit environment
# (only do this if there are parameters in the front matter
# so we don't require recent knitr for all users)
if (!is.null(front_matter$params)) {
params <- knit_params_get(input_lines, params)
# bail if an object called 'params' exists in this environment,
# and it seems to be an unrelated user-created object. store
# references so we can restore them post-render
hasParams <- exists("params", envir = envir, inherits = FALSE)
envirParams <- NULL
if (hasParams) {
envirParams <- get("params", envir = envir, inherits = FALSE)
isKnownParamsObject <-
inherits(envirParams, "knit_param_list") ||
inherits(envirParams, "knit_param")
if (!isKnownParamsObject) {
stop2("params object already exists in knit environment ",
"so can't be overwritten by render params")
}
}
# make the params available in the knit environment
assign("params", params, envir = envir)
lockBinding("params", envir)
on.exit({
if (exists("params", envir = envir, inherits = FALSE)) {
do.call("unlockBinding", list("params", envir))
if (hasParams)
assign("params", envirParams, envir = envir)
else
remove("params", envir = envir)
}
}, add = TRUE)
}
# call onKnit hooks (normalize to list)
sapply(as.list(getHook("rmarkdown.onKnit")), function(hook) {
tryCatch(hook(input = original_input), error = function(e) NULL)
})
on.exit({
sapply(as.list(getHook("rmarkdown.onKnitCompleted")), function(hook) {
tryCatch(hook(input = original_input), error = function(e) NULL)
})
}, add = TRUE)
perf_timer_start("knitr")
# perform the knit
input <- knitr::knit(knit_input,
knit_output,
envir = envir,
quiet = quiet)
perf_timer_stop("knitr")
front_matter <- yaml_front_matter(input)
# call post_knit handler
output_format$pandoc$args <- call_post_knit_handler()
# pull any R Markdown warnings from knit_meta and emit
rmd_warnings <- knit_meta_reset(class = "rmd_warning")
for (rmd_warning in rmd_warnings) {
message("Warning: ", rmd_warning)
}
# pull out shiny_prerendered_contexts and append them as script tags
shiny_prerendered_append_contexts(runtime, input)
# collect remaining knit_meta
knit_meta <- knit_meta_reset()
} else {
output_format$pandoc$args <- call_post_knit_handler()
}
# if this isn't html and there are html dependencies then flag an error
if (!(is_pandoc_to_html(output_format$pandoc) ||
identical(tolower(xfun::file_ext(output_file)), "html"))) {
if (has_html_dependencies(knit_meta)) {
if (!isTRUE(front_matter$always_allow_html)) {
stop2("Functions that produce HTML output found in document targeting ",
pandoc_to, " output.\nPlease change the output type ",
"of this document to HTML.\n",
"If your aiming to have some HTML widgets shown in non-HTML format as a screenshot,\n",
"please install webshot or webshot2 R package for knitr to do the screenshot.\n",
"Alternatively, you can allow HTML output in non-HTML formats\n",
"by adding this option to the YAML front-matter of\nyour rmarkdown file:\n\n",
" always_allow_html: true\n\n",
"Note however that the HTML output will not be visible in non-HTML formats.\n\n"
)
}
}
if (!identical(runtime, "static")) {
stop2("Runtime '", runtime, "' is not supported for ",
pandoc_to, " output.\nPlease change the output type ",
"of this document to HTML.")
}
}
# clean the files_dir if we've either been asking to clean supporting files or
# the knitr cache is active; clean the figure-* dir instead of the whole
# files_dir if other subdirs are generated by another format and still needed:
# https://github.com/rstudio/rmarkdown/issues/1472 and also #1503
intermediates_fig <- if (output_format$clean_supporting && !dir_exists(cache_dir)) {
# unlink does not support / at the end of file path
fig_path <- gsub("/$", "", knitr::opts_chunk$get('fig.path'))
# existing figure folder(s), can be character(0)
# if no figure is generated, clean the whole files_dir (#1664)
files_dir_fig <- list.files(files_dir, '^figure-.+')
if (length(files_dir_fig) < 1 || identical(files_dir_fig, basename(fig_path))) {
files_dir
} else {
fig_path
}
}
intermediates <- c(intermediates, intermediates_fig)
if (run_pandoc) {
# set env vars required during Pandoc processing
lua_env_vars <- xfun::set_envvar(c(RMARKDOWN_LUA_SHARED = pkg_file_lua("shared.lua")))
on.exit(xfun::set_envvar(lua_env_vars), add = TRUE)
perf_timer_start("pre-processor")
if (has_dependencies(knit_meta, "output_format_dependency")) {
output_format <- merge_output_format_dependencies(output_format, knit_meta)
}
# call any pre_processor
if (!is.null(output_format$pre_processor)) {
extra_args <- output_format$pre_processor(front_matter,
input,
runtime,
knit_meta,
files_dir,
output_dir)
output_format$pandoc$args <- c(output_format$pandoc$args, extra_args)
}
# write shiny_prerendered_dependencies if we have them
if (is_shiny_prerendered(runtime)) {
shiny_prerendered_append_dependencies(input,
shiny_prerendered_dependencies,
files_dir,
output_dir)
# Include special comment in header for correc insertion of HTML dependencies
# during shiny_prerendered process (See `shiny_prerendered_html()`).
# This should be the last header-includes to be set.
# Context in https://github.com/rstudio/rmarkdown/pull/2249
output_format$pandoc$args <- c(output_format$pandoc$args,
pandoc_include_args(in_header = pkg_file("rmd/h/shiny-header.html")))
}
perf_timer_stop("pre-processor")
need_bibtex <- grepl('[.](pdf|tex)$', output_file) &&
any(c('--natbib', '--biblatex') %in% output_format$pandoc$args)
perf_timer_start("pandoc")
convert <- function(output, citeproc = FALSE) {
# temporarily move figures and bib files to the intermediate dir if
# specified: https://github.com/rstudio/rmarkdown/issues/500
if (!is.null(intermediates_dir)) {
figures_dir <- gsub('/$', '', knitr::opts_chunk$get("fig.path"))
files <- list.files(figures_dir, full.names = TRUE, recursive = TRUE)
# https://github.com/rstudio/rmarkdown/issues/1358
if (citeproc) files <- c(files, front_matter[['bibliography']])
for (f in files) {
intermediates <<- c(intermediates, copy_file_with_dir(f, intermediates_dir))
}
}
# ensure we expand paths (for Windows where leading `~/` does
# not get expanded by pandoc)
input <- path.expand(input)
output <- path.expand(output)
pandoc_args <- output_format$pandoc$args
# if Lua filters are provided, add the command line switch
if (!is.null(lua_filters <- output_format$pandoc$lua_filters)) {
lua_filters <- pandoc_lua_filter_args(lua_filters)
}
pandoc_args <- c(lua_filters, pandoc_args)
# in case the output format turns on the --file-scope flag, run its
# file_scope function to split the input into multiple files
input_files <- input
if (is.function(output_format$file_scope)) {
input_files <- file_scope_split(input, output_format$file_scope)
# ignore if input_files has not really been splitted
if (length(input_files) > 1) {
# add the --file-scope option
pandoc_args <- c(pandoc_args, "--file-scope")
# cleanup the split files after render
on.exit(unlink(input_files), add = TRUE)
}
}
# use the convert function from the output format if provided
if (!is.function(convert_fun <- output_format$pandoc$convert_fun))
convert_fun <- pandoc_convert
convert_it <- function(output) convert_fun(
output = output, input_files, pandoc_to, output_format$pandoc$from,
citeproc, pandoc_args, !quiet
)
# if we don't detect any invalid shell characters in the
# target path, then just call pandoc directly
if (!grepl(.shell_chars_regex, output) && !grepl(.shell_chars_regex, input)) {
return(convert_it(output))
}
# render to temporary file (preserve extension)
# this also ensures we don't pass a file path with invalid
# characters to our pandoc invocation
ext <- xfun::file_ext(output)
if (ext != '') ext <- paste0('.', ext)
# render to a path in the current working directory
# (avoid passing invalid characters to shell)
pandoc_output_tmp <- basename(tempfile("pandoc", getwd(), ext))
# clean up temporary file on exit
on.exit(unlink(pandoc_output_tmp), add = TRUE)
# call pandoc to render file
status <- convert_it(pandoc_output_tmp)
# construct output path (when passed only a file name to '--output',
# pandoc seems to render in the same directory as the input file)
pandoc_output_tmp_path <- file.path(dirname(input), pandoc_output_tmp)
# rename output file to desired location
renamed <- suppressWarnings(file.rename(pandoc_output_tmp_path, output))
# rename can fail if the temporary directory and output path
# lie on different volumes; in such a case attempt a file copy
# see: https://github.com/rstudio/rmarkdown/issues/705
if (!renamed) {
copied <- file.copy(pandoc_output_tmp_path, output, overwrite = TRUE)
if (!copied) {
stop("failed to copy rendered pandoc artefact to '", output, "'")
}
}
# return status
status
}
texfile <- file_with_ext(output_file, "tex")
# determine whether we need to run citeproc (based on whether we have
# references in the input)
run_citeproc <- citeproc_required(front_matter, input_lines)
# if the output format is LaTeX, first convert .md to .tex, and then convert
# .tex to .pdf via latexmk() if PDF output is requested (in rmarkdown <=
# v1.8, we used to call Pandoc to convert .md to .tex and .pdf separately)
if (output_format$pandoc$keep_tex || knitr::is_latex_output()) {
# do not use pandoc-citeproc if needs to build bibliography
convert(texfile, run_citeproc && !need_bibtex)
# patch the .tex output generated from the default Pandoc LaTeX template
if (!("--template" %in% output_format$pandoc$args)) patch_tex_output(texfile)
fix_horiz_rule(texfile)
# unless the output file has the extension .tex, we assume it is PDF
if (!grepl('[.]tex$', output_file)) {
latexmk(texfile, output_format$pandoc$latex_engine, '--biblatex' %in% output_format$pandoc$args)
file.rename(file_with_ext(texfile, "pdf"), output_file)
# clean up the tex file if necessary
if (!output_format$pandoc$keep_tex) {
texfile <- normalize_path(texfile)
on.exit(unlink(texfile), add = TRUE)
}
}
} else {
convert(output_file, run_citeproc)
}
# pandoc writes the output alongside the input, so if we rendered from an
# intermediate directory, move the output file
if (!is.null(intermediates_dir)) {
intermediate_output <- file.path(intermediates_dir, basename(output_file))
if (file.exists(intermediate_output)) {
move_dir(intermediate_output, output_file)
}
}
perf_timer_stop("pandoc")
perf_timer_start("post-processor")
# if there is a post-processor then call it
if (!is.null(output_format$post_processor))
output_file <- output_format$post_processor(front_matter,
input,
output_file,
clean,
!quiet)
if (!quiet && getOption('rmarkdown.render.message', TRUE)) {
message("\nOutput created: ", relative_to(oldwd, output_file))
}
perf_timer_stop("post-processor")
}
perf_timer_stop("render")
# write markdown output if requested
if (output_format$keep_md && !md_input) {
file.copy(input, file_with_ext(output_file, "md"), overwrite = TRUE)
}
if (run_pandoc) {
# return the full path to the output file
output_file <- abs_path(output_file)
# attach the metadata specified as rmd_output_metadata in YAML
if (length(output_meta <- output_metadata$get()))
attr(output_file, 'rmd_output_metadata') <- output_meta
invisible(output_file)
} else {
# make sure the markdown output and fig dir are not cleaned up
intermediates <- setdiff(intermediates, c(input, intermediates_fig))
# did not run pandoc; returns the markdown output with attributes of the
# knitr meta data and intermediate files
invisible(structure(input,
knit_meta = knit_meta,
files_dir = files_dir,
intermediates_dir = intermediates_fig,
intermediates = intermediates))
}
}
#' Render supporting files for an input document
#'
#' Render (copy) required supporting files for an input document to the
#' \code{_files} directory that is associated with the document.
#'
#' @param from The directory from which the files should be copied.
#' @param files_dir The directory that will receive the copied files.
#' @param rename_to An option to rename the source directory after the copy
#' operation is complete.
#' @return The relative path to the supporting files. This path is suitable
#' for inclusion in HTML\code{href} and \code{src} attributes.
#' @export
render_supporting_files <- function(from, files_dir, rename_to = NULL) {
# auto-create directory for supporting files
if (!dir_exists(files_dir))
dir.create(files_dir)
# target directory is based on the dirname of the path or the rename_to
# value if it was provided
target_stage_dir <- file.path(files_dir, basename(from))
target_dir <- file.path(files_dir, ifelse(is.null(rename_to),
basename(from),
rename_to))
# copy the directory if it hasn't already been copied
if (!dir_exists(target_dir) && !dir_exists(target_stage_dir)) {
file.copy(from = from,
to = files_dir,
recursive = TRUE,
copy.mode = FALSE)
if (!is.null(rename_to)) {
file.rename(from = target_stage_dir,
to = target_dir)
}
}
# return the target dir (used to form links in the HTML)
target_dir
}
# reset knitr meta output (returns any meta output generated since the last
# call to knit_meta_reset), optionally scoped to a specific output class
knit_meta_reset <- function(class = NULL) {
knitr::knit_meta(class, clean = TRUE)
}
# render context (render-related state can be stuffed here)
.render_context <- NULL # initialized in .onLoad
render_context <- function() {
.render_context$peek()
}
init_render_context <- function() {
.render_context$push(new_render_context())
}
clear_render_context <- function() {
.render_context$pop()
}
new_render_context <- function() {
env <- new.env(parent = emptyenv())
env$chunk.index <- 1
env
}
merge_render_context <- function(context) {
elements <- ls(envir = render_context(), all.names = TRUE)
for (el in elements)
context[[el]] <- get(el, envir = render_context())
context
}
id_prefix_from_args <- function(args) {
# scan for id-prefix argument
for (i in 1:length(args)) {
arg <- args[[i]]
if (identical(arg, "--id-prefix") && (i < length(args)))
return(args[[i + 1]])
}
# default to empty string
""
}
resolve_df_print <- function(df_print) {
# available methods
valid_methods <- c("default", "kable", "tibble", "paged")
# if we are passed NULL then select the first method
if (is.null(df_print))
df_print <- valid_methods[[1]]
# if we are passed all of valid_methods then select the first one
if (identical(valid_methods, df_print))
df_print <- valid_methods[[1]]
if (!is.function(df_print)) {
if (df_print == "kable")
df_print <- knitr::kable
else if (df_print == "tibble") {
if (!requireNamespace("tibble", quietly = TRUE))
stop("Printing 'tibble' without 'tibble' package available")
df_print <- function(x) print(tibble::as_tibble(x))
}
else if (df_print == "paged")
df_print <- function(x) {
if (!identical(knitr::opts_current$get("paged.print"), FALSE)) {
knitr::asis_output(paged_table_html(x))
}
else {
print(x)
}
}
else if (df_print == "default")
df_print <- print
else
stop2('Invalid value for df_print (valid values are ',
paste(valid_methods, collapse = ", "))
}
df_print
}
# package level globals
.globals <- new.env(parent = emptyenv())
.globals$evaluated_global_chunks <- character()
.globals$level <- 0L
#' The output metadata object
#'
#' This object provides a mechanism for users to attach metadata as an attribute
#' (named \code{rmd_output_metadata}) of the returned value of
#' \code{\link{render}()}. The initial value of the metadata comes from in the
#' \code{rmd_output_metadata} field of the YAML frontmatter of an R Markdown
#' document. The metadata can be queried via the
#' \code{output_metadata$get()} method, and modified via the
#' \code{output_metadata$set()} method.
#' @format NULL
#' @usage NULL
#' @keywords NULL
#' @export
output_metadata = knitr:::new_defaults()
file_scope_split <- function(input, fun) {
inputs <- if (length(formals(fun)) == 1L) {
fun(input) # for the backward compatibility
} else {
fun(input, NULL) # the second argument implies current file scope
}
# file_scope_fun should split the input file in several
# do nothing if not and return input file unsplited
if (length(inputs) <= 1) return(input)
# write the split content into *.split.md files
input_files <- lapply(inputs, function(f) {
file <- file_with_meta_ext(f$name, "split", "md")
file <- file.path(dirname(input), file)
write_utf8(f$content, file)
file
})
unlist(input_files)
}
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