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block.R
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block.R
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# process chunks and inline text
process_group = function(x) {
if (inherits(x, 'block')) call_block(x) else {
x = call_inline(x)
knit_hooks$get('text')(x)
}
}
call_block = function(block) {
# now try eval all options except those in eval.after and their aliases
af = opts_knit$get('eval.after'); al = opts_knit$get('aliases')
if (!is.null(al) && !is.null(af)) af = c(af, names(al[af %in% al]))
params = opts_chunk$merge(block$params)
params = dot_names(params)
for (o in setdiff(names(params), af)) {
params[o] = list(eval_lang(params[[o]]))
# also update original options before being merged with opts_chunk
if (o %in% names(block$params)) block$params[o] = params[o]
}
label = ref.label = params$label
if (!is.null(params$ref.label)) {
ref.label = sc_split(params$ref.label)
# ref.label = I() implies opts.label = ref.label
if (inherits(params$ref.label, 'AsIs') && is.null(params$opts.label))
params$opts.label = ref.label
}
params[['code']] = get_code(params, label, ref.label)
# opts.label = TRUE means inheriting chunk options from ref.label
if (isTRUE(params$opts.label)) params$opts.label = ref.label
# expand chunk options defined via opts_template and reference chunks
params2 = NULL
for (lab in params$opts.label) {
# referenced chunk options (if any) override template options
params3 = merge_list(opts_template$get(lab), attr(knit_code$get(lab), 'chunk_opts'))
params2 = merge_list(params2, params3)
}
if (length(params2)) {
# local options override referenced options
params2 = merge_list(params2, block$params)
# then override previously merged opts_chunk options
params = merge_list(params, params2)
# in case any options are not evaluated
for (o in setdiff(names(params), af)) params[o] = list(eval_lang(params[[o]]))
}
# save current chunk options in opts_current
optc = opts_current$get(); on.exit(opts_current$restore(optc), add = TRUE)
opts_current$restore(params)
if (opts_knit$get('progress')) print_block(block)
params[['code']] = parse_chunk(params[['code']]) # parse sub-chunk references
ohooks = opts_hooks$get()
for (opt in names(ohooks)) {
hook = ohooks[[opt]]
if (!is.function(hook)) {
warning("The option hook '", opt, "' should be a function")
next
}
if (!is.null(params[[opt]])) params = as.strict_list(hook(params))
if (!is.list(params))
stop("The option hook '", opt, "' should return a list of chunk options")
}
params = fix_options(params) # for compatibility
if (!is.null(params$child)) {
if (!is_blank(params[['code']]) && getOption('knitr.child.warning', TRUE)) warning(
"The chunk '", params$label, "' has the 'child' option, ",
"and this code chunk must be empty. Its code will be ignored."
)
if (!params$eval) return('')
cmds = lapply(sc_split(params$child), knit_child, options = block$params)
out = one_string(unlist(cmds))
return(out)
}
# Check cache
if (params$cache > 0) {
content = c(
params[if (params$cache < 3) cache1.opts else setdiff(names(params), cache0.opts)],
75L, if (params$cache == 2) params[cache2.opts]
)
if (params$engine == 'R' && isFALSE(params$cache.comments)) {
content[['code']] = parse_only(content[['code']])
}
hash = paste(valid_path(params$cache.path, label), digest(content), sep = '_')
params$hash = hash
if (cache$exists(hash, params$cache.lazy) &&
isFALSE(params$cache.rebuild) &&
params$engine != 'Rcpp') {
if (opts_knit$get('verbose')) message(' loading cache from ', hash)
cache$load(hash, lazy = params$cache.lazy)
cache_engine(params)
if (!params$include) return('')
if (params$cache == 3) return(cache$output(hash))
}
if (params$engine == 'R')
cache$library(params$cache.path, save = FALSE) # load packages
} else if (label %in% names(dep_list$get()) && !isFALSE(opts_knit$get('warn.uncached.dep')))
warning2('code chunks must not depend on the uncached chunk "', label, '"')
params$params.src = block$params.src
opts_current$restore(params) # save current options
# prevent users from modifying opts_current (#1798)
opts_current$lock(); on.exit(opts_current$lock(FALSE), add = TRUE)
# set local options() for the current R chunk
if (is.list(params$R.options)) {
op = options(params$R.options); on.exit(options(op), add = TRUE)
}
block_exec(params)
}
# if chunk option 'file' is provided, read the file(s) as the chunk body;
# otherwise if 'code' is provided, use it; if neither 'file' nor 'code' is
# provided, use the chunk body
get_code = function(params, label, ref.label) {
code = params[['code']]; file = params[['file']]
if (is.null(code) && is.null(file))
return(unlist(knit_code$get(ref.label), use.names = FALSE))
if (!is.null(file)) code = in_input_dir(xfun::read_all(file))
set_code(label, code)
code
}
# replace code in knit_code but preserve attributes
set_code = function(label, code) {
res = knit_code$get(label)
attributes(code) = attributes(res)
knit_code$set(setNames(list(code), label))
}
# options that should affect cache when cache level = 1,2
cache1.opts = c('code', 'eval', 'cache', 'cache.path', 'cache.globals', 'message', 'warning', 'error')
# more options affecting cache level 2
cache2.opts = c('fig.keep', 'fig.path', 'fig.ext', 'dev', 'dpi', 'dev.args', 'fig.width', 'fig.height')
# options that should not affect cache
cache0.opts = c('include', 'out.width.px', 'out.height.px', 'cache.rebuild')
block_exec = function(options) {
if (options$engine == 'R') return(eng_r(options))
# when code is not R language
res.before = run_hooks(before = TRUE, options)
engine = get_engine(options$engine)
# special case: quarto-dev/quarto-cli#5994
if (is_quarto() && options$engine %in% c('dot', 'mermaid', 'ojs')) {
options$code = c(options$yaml.code, options$code)
options$yaml.code = NULL
}
output = in_input_dir(engine(options))
if (is.list(output)) output = unlist(output)
res.after = run_hooks(before = FALSE, options)
output = paste(c(res.before, output, res.after), collapse = '')
output = knit_hooks$get('chunk')(output, options)
if (options$cache) {
cache.exists = cache$exists(options$hash, options$cache.lazy)
if (options$cache.rebuild || !cache.exists) block_cache(options, output, switch(
options$engine,
'stan' = options$output.var, 'sql' = options$output.var, character(0)
))
}
if (options$include) output else ''
}
#' Engine for R
#'
#' This function handles the execution of R code blocks (when the chunk option
#' \code{engine} is \code{'R'}) and generates the R output for each code block.
#'
#' This engine function has one argument \code{options}: the source code of the
#' current chunk is in \code{options$code}. It returns a processed output that
#' can consist of data frames (as tables), graphs, or character output. This
#' function is intended for advanced use to allow developers to extend R, and
#' customize the pipeline with which R code is executed and processed within
#' knitr.
#'
#' @param options A list of chunk options. Usually this is just the object
#' \code{options} associated with the current code chunk.
#' @noRd
eng_r = function(options) {
# eval chunks (in an empty envir if cache)
env = knit_global()
obj.before = ls(globalenv(), all.names = TRUE) # global objects before chunk
keep = options$fig.keep
keep.idx = NULL
if (is.logical(keep)) keep = which(keep)
if (is.numeric(keep)) {
keep.idx = keep
keep = "index"
}
if (keep.pars <- opts_knit$get('global.par')) on.exit({
opts_knit$set(global.pars = par(no.readonly = TRUE))
}, add = TRUE)
tmp.fig = tempfile(); on.exit(unlink(tmp.fig), add = TRUE)
# open a device to record plots if not using a global device or no device is
# open, and close this device if we don't want to use a global device
if (!opts_knit$get('global.device') || is.null(dev.list())) {
# reset current device if any is open (#2166)
if (!is.null(dev.list())) {
dv0 = dev.cur(); on.exit(dev.set(dv0), add = TRUE)
}
chunk_device(options, keep != 'none', tmp.fig)
dv = dev.cur()
if (!opts_knit$get('global.device')) on.exit(dev.off(dv), add = TRUE)
showtext(options) # showtext support
}
# preserve par() settings from the last code chunk
if (keep.pars) par2(opts_knit$get('global.pars'))
res.before = run_hooks(before = TRUE, options, env) # run 'before' hooks
code = options$code
echo = options$echo # tidy code if echo
if (!isFALSE(echo) && !isFALSE(options$tidy) && length(code)) {
tidy.method = if (isTRUE(options$tidy)) 'formatR' else options$tidy
if (is.character(tidy.method)) tidy.method = switch(
tidy.method,
formatR = function(code, ...) {
if (!loadable('formatR')) stop2(
'The formatR package is required by the chunk option tidy = TRUE but ',
'not installed; tidy = TRUE will be ignored.'
)
formatR::tidy_source(text = code, output = FALSE, ...)$text.tidy
},
styler = function(code, ...) unclass(styler::style_text(text = code, ...))
)
res = try_silent(do.call(tidy.method, c(list(code), options$tidy.opts)))
if (!inherits(res, 'try-error')) code = res else warning(
"Failed to tidy R code in chunk '", options$label, "'. Reason:\n", res
)
}
# only evaluate certain lines
if (is.numeric(ev <- options$eval)) {
# group source code into syntactically complete expressions
if (isFALSE(options$tidy)) code = sapply(xfun::split_source(code), one_string)
iss = seq_along(code)
code = comment_out(code, '##', setdiff(iss, iss[ev]), newline = FALSE)
}
# guess plot file type if it is NULL
if (keep != 'none') options$fig.ext = dev2ext(options)
cache.exists = cache$exists(options$hash, options$cache.lazy)
evaluate = knit_hooks$get('evaluate')
# return code with class 'source' if not eval chunks
res = if (is_blank(code)) list() else if (isFALSE(ev)) {
as.source(code)
} else if (cache.exists && isFALSE(options$cache.rebuild)) {
fix_evaluate(cache$output(options$hash, 'list'), options$cache == 1)
} else in_input_dir(
evaluate(
code, envir = env, new_device = FALSE,
keep_warning = if (is.numeric(options$warning)) TRUE else options$warning,
keep_message = if (is.numeric(options$message)) TRUE else options$message,
stop_on_error = if (is.numeric(options$error)) options$error else {
if (options$error && options$include) 0L else 2L
},
output_handler = knit_handlers(options$render, options)
)
)
if (options$cache %in% 1:2 && (!cache.exists || isTRUE(options$cache.rebuild))) {
# make a copy for cache=1,2; when cache=2, we do not really need plots
res.orig = if (options$cache == 2) remove_plot(res, keep == 'high') else res
}
# eval other options after the chunk
if (!isFALSE(ev))
for (o in opts_knit$get('eval.after'))
options[o] = list(eval_lang(options[[o]], env))
# remove some components according options
if (isFALSE(echo)) {
res = Filter(Negate(evaluate::is.source), res)
} else if (is.numeric(echo)) {
# choose expressions to echo using a numeric vector
res = if (isFALSE(ev)) {
as.source(code[echo])
} else {
filter_evaluate(res, echo, evaluate::is.source)
}
}
if (options$results == 'hide') res = Filter(Negate(is.character), res)
if (options$results == 'hold') {
i = vapply(res, is.character, logical(1))
if (any(i)) res = c(res[!i], merge_character(res[i]))
}
res = filter_evaluate(res, options$warning, evaluate::is.warning)
res = filter_evaluate(res, options$message, evaluate::is.message)
# rearrange locations of figures
res = rearrange_figs(res, keep, keep.idx, options$fig.show)
# number of plots in this chunk
if (is.null(options$fig.num))
options$fig.num = if (length(res)) sum(sapply(res, function(x) {
if (inherits(x, 'knit_image_paths')) return(length(x))
if (is_plot_output(x)) return(1)
0
})) else 0L
# merge neighbor elements of the same class into one element
for (cls in c('source', 'message', 'warning')) res = merge_class(res, cls)
if (isTRUE(options$fig.beforecode)) res = fig_before_code(res)
on.exit({
plot_counter(reset = TRUE)
shot_counter(reset = TRUE)
opts_knit$delete('plot_files')
}, add = TRUE) # restore plot number
output = unlist(sew(res, options)) # wrap all results together
res.after = run_hooks(before = FALSE, options, env) # run 'after' hooks
output = paste(c(res.before, output, res.after), collapse = '') # insert hook results
output = knit_hooks$get('chunk')(output, options)
if (options$cache > 0) {
# if cache.vars has been specifically provided, only cache these vars and no
# need to look for objects in globalenv()
obj.new = if (is.null(options$cache.vars)) setdiff(ls(globalenv(), all.names = TRUE), obj.before)
copy_env(globalenv(), env, obj.new)
objs = if (isFALSE(ev) || length(code) == 0) character(0) else
options$cache.vars %n% codetools::findLocalsList(parse_only(code))
# make sure all objects to be saved exist in env
objs = intersect(c(objs, obj.new), ls(env, all.names = TRUE))
if (options$autodep) {
# you shall manually specify global object names if find_symbols() is not reliable
cache$objects(
objs, cache_globals(options$cache.globals, code), options$label,
options$cache.path
)
dep_auto(labels = options$label)
}
if (options$cache < 3) {
if (options$cache.rebuild || !cache.exists) block_cache(options, res.orig, objs)
} else block_cache(options, output, objs)
}
if (options$include) output else if (is.null(s <- options$indent)) '' else s
}
block_cache = function(options, output, objects) {
hash = options$hash
outname = cache_output_name(hash)
assign(outname, output, envir = knit_global())
purge_cache(options)
cache$library(options$cache.path, save = TRUE)
cache$save(objects, outname, hash, lazy = options$cache.lazy)
}
purge_cache = function(options) {
# purge my old cache and cache of chunks dependent on me
cache$purge(paste0(valid_path(
options$cache.path, c(options$label, dep_list$get(options$label))
), '_????????????????????????????????'))
}
cache_globals = function(option, code) {
if (is.character(option)) option else {
(if (isFALSE(option)) find_symbols else find_globals)(code)
}
}
# open a graphical device for a chunk to record plots
chunk_device = function(options, record = TRUE, tmp = tempfile()) {
width = options$fig.width[1L]
height = options$fig.height[1L]
dev = fallback_dev(options$dev)
dev.args = options$dev.args
dpi = options$dpi
# actually I should adjust the recording device according to dev, but here I
# have only considered devices like png and tikz (because the measurement
# results can be very different especially with the latter, see #1066), the
# cairo_pdf device (#1235), and svg (#1705)
if (identical(dev, 'png')) {
do.call(grDevices::png, c(list(
filename = tmp, width = width, height = height, units = 'in', res = dpi
), get_dargs(dev.args, 'png')))
} else if (identical(dev, 'ragg_png')) {
do.call(ragg_png_dev, c(list(
filename = tmp, width = width, height = height, units = 'in', res = dpi
), get_dargs(dev.args, 'ragg_png')))
} else if (identical(dev, 'tikz')) {
dargs = c(list(
file = tmp, width = width, height = height
), get_dargs(dev.args, 'tikz'))
dargs$sanitize = options$sanitize; dargs$standAlone = options$external
if (is.null(dargs$verbose)) dargs$verbose = FALSE
do.call(tikz_dev, dargs)
} else if (identical(dev, 'cairo_pdf')) {
do.call(grDevices::cairo_pdf, c(list(
filename = tmp, width = width, height = height
), get_dargs(dev.args, 'cairo_pdf')))
} else if (identical(dev, 'svg')) {
do.call(grDevices::svg, c(list(
filename = tmp, width = width, height = height
), get_dargs(dev.args, 'svg')))
} else if (identical(dev, 'svglite')) {
do.call(svglite::svglite, c(list(
filename = tmp, width = width, height = height
), get_dargs(dev.args, 'svglite')))
} else if (identical(getOption('device'), pdf_null)) {
if (!is.null(dev.args)) {
dev.args = get_dargs(dev.args, 'pdf')
dev.args = dev.args[intersect(names(dev.args), names(formals(pdf)))]
}
do.call(pdf_null, c(list(width = width, height = height), dev.args))
} else dev.new(width = width, height = height)
dev.control(displaylist = if (record) 'enable' else 'inhibit')
}
# fall back to a usable device (e.g., during R CMD check)
fallback_dev = function(dev) {
if (length(dev) != 1 || !getOption('knitr.device.fallback', is_R_CMD_check()))
return(dev)
choices = list(
svg = c('png', 'jpeg', 'bmp'), cairo_pdf = c('pdf'), cairo_ps = c('postscript'),
png = c('jpeg', 'svg', 'bmp'), jpeg = c('png', 'svg', 'bmp')
)
# add choices provided by users
choices = merge_list(choices, getOption('knitr.device.choices'))
if (!dev %in% names(choices)) return(dev) # no fallback devices available
# first test if the specified device actually works
if (dev_available(dev)) return(dev)
for (d in choices[[dev]]) if (dev_available(d)) {
warning2("The device '", dev, "' is not operational; falling back to '", d, "'.")
return(d)
}
dev # no fallback device found; you'll to run into an error soon
}
# filter out some results based on the numeric chunk option as indices
filter_evaluate = function(res, opt, test) {
if (length(res) == 0 || !is.numeric(opt) || !any(idx <- sapply(res, test)))
return(res)
idx = which(idx)
idx = setdiff(idx, na.omit(idx[opt])) # indices of elements to remove
if (length(idx) == 0) res else res[-idx]
}
# find recorded plots in the output of evaluate()
find_recordedplot = function(x) {
vapply(x, is_plot_output, logical(1))
}
is_plot_output = function(x) {
evaluate::is.recordedplot(x) ||
inherits(x, c('knit_image_paths', 'html_screenshot', 'knit_other_plot'))
}
# move plots before source code
fig_before_code = function(x) {
s = vapply(x, evaluate::is.source, logical(1))
if (length(s) == 0 || !any(s)) return(x)
s = which(s)
f = which(find_recordedplot(x))
f = f[f >= min(s)] # only move those plots after the first code block
for (i in f) {
j = max(s[s < i])
tmp = x[i]; x[[i]] = NULL; x = append(x, tmp, j - 1)
s = which(vapply(x, evaluate::is.source, logical(1)))
}
x
}
rearrange_figs = function(res, keep, idx, show) {
figs = find_recordedplot(res)
if (!any(figs)) return(res) # no figures
if (keep == 'none') return(res[!figs]) # remove all
if (show == 'hold') {
res = c(res[!figs], res[figs]) # move to the end
figs = find_recordedplot(res)
}
if (sum(figs) <= 1) return(res) # return early if only 1 figure to keep
switch(
keep,
first = res[-tail(which(figs), -1L)],
last = res[-head(which(figs), -1L)],
high = merge_low_plot(res, figs), # merge low-level plotting changes
index = {
i = which(figs)[-idx]
if (length(i) > 0) res[-i] else res # keep only selected
},
res
)
}
# merge neighbor elements of the same class in a list returned by evaluate()
merge_class = function(res, class = c('source', 'message', 'warning')) {
class = match.arg(class)
idx = if (length(res)) which(sapply(res, inherits, what = class))
if ((n <- length(idx)) <= 1) return(res)
k1 = idx[1]; k2 = NULL; res1 = res[[k1]]
el = c(source = 'src', message = 'message', warning = 'message')[class]
for (i in 1:(n - 1)) {
idx2 = idx[i + 1]; idx1 = idx[i]
if (idx2 - idx1 == 1) {
res2 = res[[idx2]]
# merge warnings/messages only if next one is identical to previous one
if (class == 'source' || identical(res1, res2) ||
(class == 'message' && !grepl('\n$', tail(res1[[el]], 1)))) {
res[[k1]][[el]] = c(res[[k1]][[el]], res2[[el]])
k2 = c(k2, idx2)
} else {
k1 = idx2
res1 = res[[k1]]
}
} else k1 = idx2
}
if (length(k2)) res = res[-k2] # remove lines that have been merged back
res
}
# merge character output for output='hold', if the subsequent character is of
# the same class(es) as the previous one (e.g. should not merge normal
# characters with asis_output())
merge_character = function(res) {
if ((n <- length(res)) <= 1) return(res)
k = NULL
for (i in 1:(n - 1)) {
cls = class(res[[i]])
if (identical(cls, class(res[[i + 1]]))) {
res[[i + 1]] = paste0(res[[i]], res[[i + 1]])
class(res[[i + 1]]) = cls
k = c(k, i)
}
}
if (length(k)) res = res[-k]
res
}
call_inline = function(block) {
optc = opts_current$get(); on.exit(opts_current$restore(optc), add = TRUE)
params = opts_chunk$merge(list(label = unnamed_chunk()))
opts_current$restore(params)
if (opts_knit$get('progress')) print_inline(block)
in_input_dir(inline_exec(block))
}
inline_exec = function(
block, envir = knit_global(), hook = knit_hooks$get('inline'),
hook_eval = knit_hooks$get('evaluate.inline')
) {
# run inline code and substitute original texts
code = block$code; input = block$input
if ((n <- length(code)) == 0) return(input) # untouched if no code is found
code.src = block$code.src
ans = character(n)
for (i in 1:n) {
tryCatch(parse_only(code[i]), error = function(e) {
stop2('Failed to parse the inline R code: ', code.src[i], '\nReason: ', e$message)
})
res = hook_eval(code[i], envir)
if (inherits(res, c('knit_asis', 'knit_asis_url'))) res = sew(res, inline = TRUE)
tryCatch(as.character(res), error = function(e) {
stop2("The inline value cannot be coerced to character: ", code[i])
})
if (length(res)) ans[i] = paste(hook(res), collapse = '')
}
# replace with evaluated results
str_replace(input, block$location, ans)
}
process_tangle = function(x) {
if (inherits(x, 'block')) tangle_block(x) else tangle_inline(x)
}
tangle_block = function(x) {
params = opts_chunk$merge(x$params)
for (o in c('purl', 'eval', 'child')) {
if (inherits(try(params[o] <- list(eval_lang(params[[o]]))), 'try-error')) {
params[['purl']] = FALSE # if any of these options cannot be determined, don't purl
}
}
if (isFALSE(params$purl)) return('')
label = params$label; ev = params$eval
if (params$engine != 'R') return(
one_string(comment_out(knit_code$get(label), params$comment, newline = FALSE))
)
code = if (!isFALSE(ev) && !is.null(params$child)) {
cmds = lapply(sc_split(params$child), knit_child)
one_string(unlist(cmds))
} else knit_code$get(label)
# read external code if exists
if (!isFALSE(ev) && length(code) && any(grepl('read_chunk\\(.+\\)', code))) {
eval(parse_only(unlist(str_extract(code, 'read_chunk\\(([^)]+)\\)'))))
}
code = parse_chunk(code)
if (isFALSE(ev)) code = comment_out(code, params$comment, newline = FALSE)
if (opts_knit$get('documentation') == 0L) return(one_string(code))
# e.g. when documentation 1 or 2 with purl()
label_code(code, x)
}
tangle_inline = function(x) {
output = if (opts_knit$get('documentation') == 2L) {
output = paste("#'", gsub('\n', "\n#' ", x$input, fixed = TRUE))
} else ''
code = x$code
if (length(code) == 0L) return(output)
if (getOption('knitr.purl.inline', FALSE)) output = c(output, code)
idx = grepl('knit_child\\(.+\\)', code)
if (any(idx)) {
cout = sapply(code[idx], function(z) eval(parse_only(z)))
output = c(output, cout, '')
}
one_string(output)
}
# add a label [and extra chunk options] to a code chunk
label_code = function(code, options) {
comments = paste0(
'## ----', options$params.src,
strrep('-', max(getOption('width') - 11L - nchar(options$params.src), 0L)),
'----'
)
one_string(c(comments, options$params.chunk, code, ''))
}
as.source = function(code) {
list(structure(list(src = code), class = 'source'))
}