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engine.R
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#' Engines of other languages
#'
#' This object controls how to execute the code from languages other than R
#' (when the chunk option \code{engine} is not \code{'R'}). Each component in
#' this object is a function that takes a list of current chunk options
#' (including the source code) and returns a character string to be written into
#' the output.
#'
#' The engine function has one argument \code{options}: the source code of the
#' current chunk is in \code{options$code}. Usually we can call external
#' programs to run the code via \code{\link{system2}}. Other chunk options are
#' also contained in this argument, e.g. \code{options$echo} and
#' \code{options$eval}, etc.
#'
#' In most cases, \code{options$engine} can be directly used in command line to
#' execute the code, e.g. \code{python} or \code{ruby}, but sometimes we may
#' want to specify the path of the engine program, in which case we can pass it
#' through the \code{engine.path} option. For example, \code{engine='ruby',
#' engine.path='/usr/bin/ruby1.9.1'}. Additional command line arguments can be
#' passed through \code{options$engine.opts}, e.g. \code{engine='ruby',
#' engine.opts='-v'}.
#'
#' See \code{str(knitr::knit_engines$get())} for a list of built-in language
#' engines.
#' @export
#' @note The Leiningen engine \code{lein} requires lein-exec plugin; see
#' \url{https://github.com/yihui/knitr/issues/1176} for details.
#' @references Usage: \url{https://yihui.org/knitr/objects/}; examples:
#' \url{https://yihui.org/knitr/demo/engines/}
#' @examples knit_engines$get('python'); knit_engines$get('awk')
#' names(knit_engines$get())
knit_engines = new_defaults()
#' Cache engines of other languages
#'
#' This object controls how to load cached environments from languages other
#' than R (when the chunk option \code{engine} is not \code{'R'}). Each
#' component in this object is a function that takes the current path to the
#' chunk cache and loads it into the language environment.
#'
#' The cache engine function has one argument \code{options}, a list containing
#' all chunk options. Note that \code{options$hash} is the path to the current
#' chunk cache with the chunk's hash, but without any file extension, and the
#' language engine may write a cache database to this path (with an extension).
#'
#' The cache engine function should load the cache environment and should know
#' the extension appropriate for the language.
#' @references See \url{https://github.com/rstudio/reticulate/pull/167} for an
#' implementation of a cache engine for Python.
#' @export
cache_engines = new_defaults()
#' An output wrapper for language engine output
#'
#' If you have designed a language engine, you may call this function in the end
#' to format and return the text output from your engine.
#'
#' For expert users, an advanced usage of this function is
#' \code{engine_output(options, out = LIST)} where \code{LIST} is a list that
#' has the same structure as the output of \code{evaluate::evaluate()}. In this
#' case, the arguments \code{code} and \code{extra} are ignored, and the list is
#' passed to \code{knitr::sew()} to return a character vector of final output.
#' @param options A list of chunk options. Usually this is just the object
#' \code{options} passed to the engine function; see
#' \code{\link{knit_engines}}.
#' @param code Source code of the chunk, to which the output hook \code{source}
#' is applied, unless the chunk option \code{echo} is \code{FALSE}.
#' @param out Text output from the engine, to which the hook \code{output} is
#' applied, unless the chunk option \code{results} is \code{'hide'}
#' @param extra Any additional text output that you want to include.
#' @return A character string generated from the source code and output using
#' the appropriate output hooks.
#' @export
#' @examples library(knitr)
#' engine_output(opts_chunk$merge(list(engine = 'Rscript')), code = '1 + 1', out = '[1] 2')
#' engine_output(opts_chunk$merge(list(echo = FALSE, engine = 'Rscript')), code = '1 + 1', out = '[1] 2')
#'
#' # expert use only
#' engine_output(opts_chunk$merge(list(engine = 'python')), out = list(structure(list(src = '1 + 1'), class = 'source'), '2'))
engine_output = function(options, code, out, extra = NULL) {
if (missing(code) && is.list(out)) return(unlist(sew(out, options)))
if (!is.logical(options$echo)) code = code[options$echo]
if (length(code) != 1L) code = one_string(code)
if (options$engine == 'sas' && length(out) > 1L && !grepl('[[:alnum:]]', out[2]))
out = tail(out, -3L)
if (length(out) != 1L) out = one_string(out)
out = sub('([^\n]+)$', '\\1\n', out)
if (options$engine == 'stata') {
out = gsub('\n+running.*profile\\.do', '', out)
out = sub('\\.\\.\\.\n+', '', out)
out = sub('\n\\. \nend of do-file\n', '', out)
}
one_string(c(
if (length(options$echo) > 1L || options$echo) knit_hooks$get('source')(code, options),
if (options$results != 'hide' && !is_blank(out)) {
if (options$engine == 'highlight') out else sew.character(out, options)
},
extra
))
}
## command-line tools
eng_interpreted = function(options) {
engine = options$engine
code = if (engine %in% c('highlight', 'Rscript', 'sas', 'haskell', 'stata')) {
f = wd_tempfile(engine, switch(engine, sas = '.sas', Rscript = '.R', stata = '.do', '.txt'))
write_utf8(c(switch(
engine,
sas = "OPTIONS NONUMBER NODATE PAGESIZE = MAX FORMCHAR = '|----|+|---+=|-/<>*' FORMDLIM=' ';title;",
NULL
), options$code), f)
on.exit(unlink(f), add = TRUE)
switch(
engine,
haskell = paste('-e', shQuote(paste(':script', f))),
sas = {
logf = sub('[.]sas$', '.lst', f)
on.exit(unlink(c(logf, sub('[.]sas$', '.log', f))), add = TRUE)
f
},
stata = {
logf = sub('[.]do$', '.log', f)
on.exit(unlink(c(logf)), add = TRUE)
sprintf(switch(
Sys.info()[['sysname']],
Windows = '/q /e do %s',
Darwin = paste('-q < %s >', shQuote(xfun::normalize_path(logf))),
Linux = '-q -e do %s',
'-q -b do %s'
), shQuote(normalizePath(f)))
},
f
)
} else paste(switch(
engine, bash = '-c', coffee = '-e', groovy = '-e', lein = 'exec -ep',
mysql = '-e', node = '-e', octave = '--eval', perl = '-E', php = '-r',
psql = '-c', python = '-c', ruby = '-e', scala = '-e', sh = '-c', zsh = '-c',
NULL
), shQuote(one_string(options$code)))
opts = get_engine_opts(options$engine.opts, engine)
# FIXME: for these engines, the correct order is options + code + file
code = if (engine %in% c('awk', 'gawk', 'sed', 'sas', 'psql', 'mysql'))
paste(code, opts) else paste(opts, code)
cmd = get_engine_path(options$engine.path, engine)
out = if (options$eval) {
if (options$message) message('running: ', cmd, ' ', code)
tryCatch(
system2(cmd, code, stdout = TRUE, stderr = TRUE, env = options$engine.env),
error = function(e) {
if (!options$error) stop(e)
paste('Error in running command', cmd)
}
)
} else ''
# chunk option error=FALSE means we need to signal the error
if (!options$error && !is.null(attr(out, 'status'))) stop(one_string(out))
if (options$eval && engine %in% c('sas', 'stata') && file.exists(logf))
out = c(read_utf8(logf), out)
engine_output(options, options$code, out)
}
# options$engine.path can be list(name1 = path1, name2 = path2, ...); similarly,
# options$engine.opts can be list(name1 = opts1, ...)
get_engine_opts = function(opts, engine, fallback = '') {
if (is.list(opts)) opts = opts[[engine]]
opts %n% fallback
}
get_engine_path = function(path, engine, fallback = engine) {
get_engine_opts(path, engine, fallback)
}
# execute an arbitrary command (optionally with arguments)
# engine.opts = list(command, input, ext, clean, args, args1, args2)
eng_exec = function(options) {
opts = options$engine.opts
if (!is.character(cmd <- opts$command %n% options$command)) stop(
"The command of the 'exec' engine must be a character string."
)
cmd = get_engine_path(options$engine.path, options$engine, cmd)
input = function(code, file) {
write_utf8(code, file)
file
}
if (is.character(i0 <- opts$input))
opts$input = function(code, file) input(code, i0)
# turn all chunk options into function except 'command'
opts = list_fun(opts, setdiff(names(opts), 'command'))
# default options
opts2 = list(
ext = identity, input = input, args = function(code, file) {
file
}, clean = function(file) {
unlink(file)
}, args1 = function() NULL, args2 = function() NULL,
output = function(options, code, output, file) {
engine_output(options, code, output)
}
)
opts = merge_list(opts2, opts)
cmd2 = basename(cmd) # in case command is a full path
ext = opts$ext(cmd2) # file extension
f = wd_tempfile(cmd2, paste0('.', ext))
if (is.function(opts$clean)) on.exit(opts$clean(f), add = TRUE)
f = opts$input(options$code, f)
a = c(opts$args1(), opts$args(options$code, f), opts$args2())
out = if (options$eval) {
if (options$message) message('running: ', paste(c(cmd, a), collapse = ' '))
f2 = wd_tempfile(cmd2) # capture stderr
on.exit(unlink(f2), add = TRUE)
tryCatch({
res = (if (options$error) suppressWarnings else identity)(
system2(cmd, shQuote(a), stdout = TRUE, stderr = f2, env = options$engine.env)
)
# check error in the content run
if (!is.null(attr(res, 'status')) && file.exists(f2) && file.size(f2) > 0) {
e = readLines(f2) # f2 may not be UTF-8
if (!options$error) stop(one_string(e)) else e
} else {
res
}
}, error = function(e) {
# error in the command run
if (!options$error) stop(e)
paste('Error in running command', cmd)
}
)
} else ''
# chunk option error=FALSE means we need to signal the error
if (!options$error && !is.null(attr(out, 'status'))) stop(one_string(out))
options = set_lang(options, eng2lang(xfun::sans_ext(cmd2)))
opts$output(options, options$code, out, f)
}
# turn elements of a list into functions: if an element is not a function, make
# it a function that returns the non-function value
list_fun = function(x, which = names(x)) {
for (i in which) {
if (!is.function(v <- x[[i]])) x[[i]] = local({
# a trick to avoid R's lazy evaluation (make a copy of v)
v2 = v; function(...) v2
})
}
x
}
## C, C++, and Fortran (via R CMD SHLIB)
eng_shlib = function(options) {
n = switch(options$engine, c = 'c', cc = 'cc', fortran = 'f', fortran95 = 'f95')
f = wd_tempfile(n, paste0('.', n))
write_utf8(options$code, f)
on.exit(unlink(c(f, with_ext(f, c('o', 'so', 'dll')))), add = TRUE)
if (options$eval) {
out = system(paste('R CMD SHLIB', f), intern = TRUE)
dyn.load(sub(sprintf('[.]%s$', n), .Platform$dynlib.ext, f))
} else out = ''
engine_output(options, options$code, out)
}
## Python
eng_python = function(options) {
if (isFALSE(options$python.reticulate)) {
eng_interpreted(options)
} else {
if (!loadable('reticulate')) warning2(
"The 'python' engine in knitr requires the reticulate package. ",
"If you do not want to use the reticulate package, set the chunk option ",
"python.reticulate = FALSE."
)
reticulate::eng_python(options)
}
}
cache_eng_python = function(options) {
if (isFALSE(options$python.reticulate)) return()
# TODO: change this hack to reticulate::cache_eng_python(options) after
# https://github.com/rstudio/reticulate/pull/167 is merged and released
if (!'cache_eng_python' %in% ls(asNamespace('reticulate'))) return()
fun = getFromNamespace('cache_eng_python', 'reticulate')
fun(options)
}
## Java
# e.g. see http://cran.rstudio.com/package=jvmr
## Rcpp
eng_Rcpp = function(options) {
sourceCpp = getFromNamespace('sourceCpp', 'Rcpp')
code = one_string(options$code)
# engine.opts is a list of arguments to be passed to Rcpp function, e.g.
# engine.opts=list(plugin='RcppArmadillo')
opts = options$engine.opts
# use custom cacheDir for sourceCpp if it's supported
cache = options$cache && ('cacheDir' %in% names(formals(sourceCpp)))
if (cache) {
opts$cacheDir = paste(valid_path(options$cache.path, options$label), 'sourceCpp', sep = '_')
opts$cleanupCacheDir = TRUE
}
if (!is.environment(opts$env)) opts$env = knit_global() # default env is knit_global()
if (options$eval) {
message('Building shared library for Rcpp code chunk...')
do.call(sourceCpp, c(list(code = code), opts))
}
engine_output(options, code, '')
}
## Julia
eng_julia = function(options) {
JuliaCall::eng_juliacall(options)
}
## Stan
## Compiles Stan model in the code chunk, creates a stanmodel object,
## and assigns it to a variable with the name given in engine.opts$x.
eng_stan = function(options) {
code = one_string(options$code)
opts = options$engine.opts
## name of the modelfit object returned by stan_model
if (is.null(x <- options$output.var)) {
warning("the option engine.opts$x is deprecated; use the chunk option output.var instead")
x = opts$x
}
if (!is.character(x) || length(x) != 1L) stop(
"the chunk option output.var must be a character string ",
"providing a name for the returned `stanmodel` object."
)
opts$x = NULL
if (options$eval) {
message("Creating a 'stanmodel' object ", x)
assign(
x,
do.call(getFromNamespace('stan_model', 'rstan'), c(list(model_code = code), opts)),
envir = knit_global()
)
}
engine_output(options, code, '')
}
## convert tikz string to PDF
eng_tikz = function(options) {
if (!options$eval) return(engine_output(options, options$code, ''))
lines = read_utf8(
options$engine.opts$template %n% system.file('misc', 'tikz2pdf.tex', package = 'knitr')
)
# add class options to template
lines = insert_template(
lines, '%% TIKZ_CLASSOPTION %%', options$engine.opts$classoption %n% 'tikz', TRUE
)
# insert code into preamble
lines = insert_template(
lines, '%% EXTRA_TIKZ_PREAMBLE_CODE %%', options$engine.opts$extra.preamble, TRUE
)
# insert tikz code into the tex template
s = insert_template(lines, '%% TIKZ_CODE %%', options$code)
write_utf8(s, texf <- wd_tempfile('tikz', '.tex'))
on.exit(unlink(texf), add = TRUE)
ext = dev2ext(options)
to_svg = ext == 'svg'
outf = if (to_svg) tinytex::latexmk(texf, 'latex') else tinytex::latexmk(texf)
fig = fig_path(if (to_svg) '.dvi' else '.pdf', options)
dir.create(dirname(fig), recursive = TRUE, showWarnings = FALSE)
file.rename(outf, fig)
fig2 = with_ext(fig, ext)
if (to_svg) {
# dvisvgm needs to be on the path
# dvisvgm for windows needs ghostscript bin dir on the path also
if (Sys.which('dvisvgm') == '') tinytex::tlmgr_install('dvisvgm')
if (system2('dvisvgm', c(
options$engine.opts$dvisvgm.opts, '-o', shQuote(fig2), fig
)) != 0) stop('Failed to compile ', fig, ' to ', fig2)
} else {
# convert to the desired output-format using magick
if (ext != 'pdf') magick::image_write(do.call(magick::image_convert, c(
list(magick::image_read_pdf(fig), ext), options$engine.opts$convert.opts
)), fig2)
}
fig = fig2
options$fig.num = 1L; options$fig.cur = 1L
extra = run_hook_plot(fig, options)
engine_output(options, options$code, '', extra)
}
## Commands that generate plots, e.g., GraphViz (dot), Asymptote, and Ditaa
eng_plot = function(options) {
options$command = cmd = options$engine
options$fig.ext = ext = dev2ext(options)
opts = list(
output = function(options, code, output, file) {
extra = if (options$eval) {
# move the generated plot (with a temp filename) to fig.path
f1 = with_ext(file, ext)
f2 = paste(fig_path(), ext, sep = '.')
xfun::dir_create(dirname(f2))
unlink(f2)
file.rename(f1, f2)
options$fig.num = 1L; options$fig.cur = 1L
run_hook_plot(f2, options)
}
engine_output(options, code, '', extra)
},
# better default for ditaa: https://github.com/yihui/knitr/pull/2092
args1 = if (cmd == 'ditta') c('-s', 2, '-T', '-S', '-E'),
args = function(code, file) {
f2 = with_ext(file, ext)
if (cmd == 'ditaa') return(c(file, f2))
if (cmd %in% c('dot', 'asy')) {
c(file, c(dot = '-T', asy = '-f')[cmd], ext, '-o', f2)
}
})
options$engine.opts = merge_list(opts, options$engine.opts)
eng_exec(options)
}
## Andre Simon's highlight
eng_highlight = function(options) {
# e.g. engine.opts can be '-S matlab -O latex'
if (is.null(options$engine.opts)) options$engine.opts = '-S text'
options$engine.opts[1L] = paste('-f', options$engine.opts[1L])
options$echo = FALSE; options$results = 'asis' # do not echo source code
res = eng_interpreted(options)
if (out_format('latex')) {
highlight_header()
sub('(.*)\\\\\\\\(.*)', '\\1\\2', res)
} else res
}
## save the code
eng_cat = function(options) {
cat2 = function(..., file = '', sep = '\n', lang = NULL) {
# do not write to stdout like the default behavior of cat()
if (!identical(file, '')) cat(..., file = file, sep = sep)
}
if (options$eval)
do.call(cat2, c(list(options$code), options$engine.opts))
options = set_lang(options, options$class.source)
if (is.null(options$lang)) return('')
engine_output(options, options$code, NULL)
}
## output the code without processing it
eng_asis = function(options) {
if (options$echo) one_string(options$code)
}
# write a block environment according to the output format
eng_block = function(options) {
if (isFALSE(options$echo)) return()
code = one_string(options$code)
to = pandoc_to()
is_pandoc = !is.null(to)
if (!is_pandoc) {
# not in R Markdown v2
to = out_format()
if (!(to %in% c('latex', 'html', 'markdown'))) to = NULL
}
if (is.null(to)) return(code)
if (to == 'beamer') to = 'latex'
if (is_html_output(to)) to = 'html'
type = options$type
if (is.null(type)) return(code)
# convert the chunk content to HTML or LaTeX (ideally I only need to specify
# the markdown extension, but it is not implemented yet for LaTeX:
# https://github.com/jgm/pandoc/issues/2453)
if (is_pandoc) code = pandoc_fragment(code, if (to == 'html') 'html4' else to)
l1 = options$latex.options
if (is.null(l1)) l1 = ''
h2 = options$html.tag %n% 'div'
h3 = options$html.before %n% ''
h4 = options$html.after %n% ''
# e.g. type = c(latex = 'marginfigure', html = 'marginnote')
if (to %in% names(type)) type = type[to]
# block level tags? this is an incomplete list, but should work for most cases
if (to == 'html') if (h2 %in% c('div', 'p', 'blockquote')) {
code = paste0('\n', code, '\n')
} else {
code = gsub('<p>', '<span style="display: block;">', code)
code = gsub('</p>', '</span>', code)
}
switch(
to,
latex = sprintf('\\begin{%s}%s\n%s\n\\end{%s}', type, l1, code, type),
html = sprintf('%s<%s class="%s">%s</%s>%s', h3, h2, type, code, h2, h4),
code
)
}
eng_block2 = function(options) {
if (isFALSE(options$echo)) return()
code = one_string(options$code); type = options$type
if (is.null(type)) return(code)
if (is.null(pandoc_to())) stop('The engine "block2" is for R Markdown only')
l1 = options$latex.options
if (is.null(l1)) l1 = ''
# protect environment options because Pandoc may escape the characters like
# {}; when encoded in integers, they won't be escaped, but will need to
# restore them later; see bookdown:::restore_block2
if (l1 != '') l1 = paste(
c('\\iffalse{', utf8ToInt(enc2utf8(l1)), '}\\fi{}'), collapse = '-'
)
h2 = options$html.tag %n% 'div'
h3 = options$html.before %n% ''
h4 = options$html.after %n% ''
h5 = options$html.before2 %n% ''
h6 = options$html.after2 %n% ''
if (is_latex_output()) {
h7 = h8 = '\n'
} else {
h7 = sprintf('<%s class="%s">', h2, type)
h8 = sprintf('</%s>', h2)
}
sprintf(
'\\BeginKnitrBlock{%s}%s%s%s%s%s%s%s%s\\EndKnitrBlock{%s}',
type, l1, h3, h7, h5, code, h6, h8, h4, type
)
}
# helper to create engines the wrap embedded html assets (e.g. css,js)
eng_html_asset = function(prefix, postfix) {
function(options) {
out = if (options$eval && is_html_output()) {
one_string(c(prefix, options$code, postfix))
}
options$results = 'asis'
engine_output(options, options$code, out)
}
}
# include js in a script tag (ignore if not html output)
eng_js = eng_html_asset('<script>', '</script>')
# include css in a style tag (ignore if not html output)
eng_css = eng_html_asset('<style type="text/css">', '</style>')
# perform basic sql parsing to determine if a sql query is an update query
is_sql_update_query = function(query) {
query = one_string(query)
# remove line comments
query = gsub('^\\s*--.*\n', '', query)
# remove multi-line comments
if (grepl('^\\s*\\/\\*.*', query)) query = gsub('.*\\*\\/', '', query)
grepl('^\\s*(INSERT|UPDATE|DELETE|CREATE|DROP|ALTER).*', query, ignore.case = TRUE)
}
# sql engine
eng_sql = function(options) {
# return chunk before interpolation eagerly to avoid connection option check
if (isFALSE(options$eval) && !isTRUE(options$sql.show_interpolated)) {
return(engine_output(options, options$code, ''))
}
# Return char vector of sql interpolation param names
varnames_from_sql = function(conn, sql) {
varPos = DBI::sqlParseVariables(conn, sql)
if (length(varPos$start) > 0) {
varNames = substring(sql, varPos$start, varPos$end)
sub('^\\?', '', varNames)
}
}
# Vectorized version of exists
mexists = function(x, env = knit_global(), inherits = TRUE) {
vapply(x, exists, logical(1), where = env, inherits = inherits)
}
# Interpolate a sql query based on the variables in an environment
interpolate_from_env = function(conn, sql, env = knit_global(), inherits = TRUE) {
names = unique(varnames_from_sql(conn, sql))
names_missing = names[!mexists(names, env, inherits)]
if (length(names_missing) > 0) {
stop("Object(s) not found: ", paste('"', names_missing, '"', collapse = ", "))
}
args = if (length(names) > 0) setNames(
mget(names, envir = env, inherits = inherits), names
)
do.call(DBI::sqlInterpolate, c(list(conn, sql), args))
}
# extract options
conn = options$connection
if (is.character(conn)) conn = get(conn, envir = knit_global())
if (is.null(conn)) stop2(
"The 'connection' option (DBI connection) is required for sql chunks."
)
varname = options$output.var
max.print = options$max.print %n% (opts_knit$get('sql.max.print') %n% 10)
if (is.na(max.print) || is.null(max.print))
max.print = -1
sql = one_string(options$code)
params = options$params
query = interpolate_from_env(conn, sql)
if (isFALSE(options$eval)) return(engine_output(options, query, ''))
data = tryCatch({
if (is_sql_update_query(query)) {
DBI::dbExecute(conn, query)
NULL
} else if (is.null(varname) && max.print > 0) {
# execute query -- when we are printing with an enforced max.print we
# use dbFetch so as to only pull down the required number of records
res = DBI::dbSendQuery(conn, query)
data = DBI::dbFetch(res, n = max.print)
DBI::dbClearResult(res)
data
} else {
if (length(params) == 0) {
DBI::dbGetQuery(conn, query)
} else {
# If params option is provided, parameters are not interplolated
DBI::dbGetQuery(conn, sql, params = params)
}
}
}, error = function(e) {
if (!options$error) stop(e)
e
})
if (inherits(data, "error"))
return(engine_output(options, query, one_string(data)))
# create output if needed (we have data and we aren't assigning it to a variable)
output = if (length(dim(data)) == 2 && ncol(data) > 0 && is.null(varname)) capture.output({
# apply max.print to data
display_data = if (max.print == -1) data else head(data, n = max.print)
# get custom sql print function
sql.print = opts_knit$get('sql.print')
# use kable for markdown
if (!is.null(sql.print)) {
options$results = 'asis'
cat(sql.print(data))
} else if (out_format('markdown')) {
# we are going to output raw markdown so set results = 'asis'
options$results = 'asis'
# force left alignment if the first column is an incremental id column
is_id = function(x) {
is.numeric(x) && length(x) > 1 && !anyNA(x) && all(diff(x) == 1)
}
if (is_id(display_data[[1]])) display_data[[1]] = as.character(display_data[[1]])
# wrap html output in a div so special styling can be applied
add_div = is_html_output() && getOption('knitr.sql.html_div', TRUE)
if (add_div) cat('<div class="knitsql-table">\n')
# determine records caption
caption = options$tab.cap
if (is.null(caption)) {
rows = nrow(data)
rows_formatted = formatC(rows, format = "d", big.mark = ',')
caption = if (max.print == -1 || rows < max.print) {
paste(rows_formatted, "records")
} else {
paste("Displaying records 1 -", rows_formatted)
}
}
# disable caption
if (identical(caption, NA)) caption = NULL
# print using kable
print(kable(display_data, caption = caption))
# terminate div
if (add_div) cat("\n</div>\n")
# otherwise use tibble if it's available
} else if (loadable('tibble')) {
print(tibble::as_tibble(display_data), n = max.print)
} else print(display_data) # fallback to standard print
})
if (options$results == 'hide') output = NULL
# assign varname if requested
if (!is.null(varname)) assign(varname, data, envir = knit_global())
# reset query to pre-interpolated if not expanding
if (!isTRUE(options$sql.show_interpolated)) query <- options$code
# return output
engine_output(options, query, output)
}
# go engine, added by @hodgesds https://github.com/yihui/knitr/pull/1330
eng_go = function(options) {
f = wd_tempfile('code', '.go')
write_utf8(code <- options$code, f)
on.exit(unlink(f), add = TRUE)
cmd = get_engine_path(options$engine.path, options$engine)
fmt_args = sprintf('fmt %s', f)
tryCatch(
system2(cmd, fmt_args, stdout = TRUE, stderr = TRUE, env = options$engine.env),
error = function(e) {
if (!options$error) stop(e)
}
)
run_args = sprintf(" run %s", f)
extra = if (options$eval) {
message('running: ', cmd, run_args)
tryCatch(
system2(cmd, run_args, stdout = TRUE, stderr = TRUE, env = options$engine.env),
error = function(e) {
if (!options$error) stop(e)
'Error in executing go code'
}
)
}
if (options$results == 'hide') extra = NULL
engine_output(options, code, extra)
}
# SASS / SCSS engine (contributed via https://github.com/yihui/knitr/pull/1666)
#
# Converts SASS / SCSS -> CSS (with same treatments as CSS engine) using either:
# LibSass sass R package (https://github.com/rstudio/sass) when
# + the package is installed
# + engine.opts does not set package = FALSE (e.g. engine.opts = list(package = FALSE))
# + an explicit path to the executable is not provided through engine.path, or
# dart-sass standalone executable (https://sass-lang.com/install) otherwise
#
# CSS output is compressed by default but formatting can be set through style in engine.opts
# For the sass R package, valid styles are "compressed","expanded", "nested", and "compact"
# For the executable, valid styles are "compressed" and "expanded"
# Please refer to respective package / executable documentation for more details
eng_sxss = function(options) {
# early exit if evaluated output not requested
options$results = 'asis'
if (!options$eval) return(engine_output(options, options$code, ''))
# create temporary file with input code
f = wd_tempfile('code', paste0('.', options$engine))
xfun::write_utf8(options$code , f)
on.exit(unlink(f), add = TRUE)
# process provided engine options
package = options$engine.opts$package %n% TRUE
style = options$engine.opts$style %n% "compressed"
cmd = get_engine_path(options$engine.path, "sass")
use_package = loadable("sass") && package && cmd == "sass"
style = match.arg(style, c("compressed", "expanded", if (use_package) c("compact", "nested")))
# convert sass/sxss -> css
if (use_package) {
message("Converting with the R package sass")
sass_fun = options$engine.opts$sass_fun %n% sass::sass
out = tryCatch(
sass_fun(sass::sass_file(f), options = sass::sass_options(output_style = style)),
error = function(e) {
if (!options$error) stop(e)
warning2(paste('Error in converting to CSS using sass R package:', e, sep = "\n"))
NULL
}
)
# remove final newline chars from output
if (!is.null(out)) out = sub("\\n$", "", out)
} else {
message("Converting sass with ", cmd)
style = paste0("--style=", style)
# attempt execution of sass
out = tryCatch(
system2(cmd, args = c(f, style), stdout = TRUE, stderr = TRUE),
error = function(e) {
if (!options$error) stop2(e)
warning2(paste('Error in converting to CSS using executable:', e, sep = "\n"))
NULL
}
)
# handle execution errors (status codes)
if (!is.null(attr(out, 'status')) && !options$error) stop2(one_string(out))
}
# wrap final output for correct rendering
final_out = if (!is.null(out) && is_html_output(excludes = 'markdown')) {
one_string(c('<style type="text/css">', out, '</style>'))
}
engine_output(options, options$code, final_out)
}
eng_bslib = function(options) {
if (!loadable("bslib")) {
stop2("The 'bslib' package must be installed in order for the knitr engine 'bslib' to work.")
}
if (!is.null(options$engine.opts$sass_fun)) {
stop2("The 'bslib' knitr engine does not allow for customization of the Sass compilation function.")
}
func = sass::sass_partial
formals(func)$bundle = quote(bslib::bs_global_get())
options$engine.opts$sass_fun = func
eng_sxss(options)
}
# Target Markdown engine contributed by @wlandau
# Thread: https://github.com/ropensci/targets/issues/503
# Usage: https://books.ropensci.org/targets/markdown.html
# Docs: https://docs.ropensci.org/targets/reference/tar_engine_knitr.html
eng_targets = function(options) {
targets::tar_engine_knitr(options)
}
# an Eviews engine based on EviewsR
eng_eviews = function(options) {
# EviewsR can't be installed in lower versions of R, hence I can't declare
# Suggests dependency in DESCRIPTION
f = getFromNamespace('eng_eviews', 'EviewsR')
f(options)
}
# a comment engine to return nothing
eng_comment = function(options) {}
# a verbatim engine that returns its chunk content verbatim
eng_verbatim = function(options) {
# change default for the cat engine
options$eval = FALSE
options = set_lang(options)
eng_cat(options)
}
set_lang = function(options, default = 'default') {
# specify the lang name in engine.opts = list(lang = ), or lang/language,
# or class.source; if all are empty, use 'default'
if (is.null(options$lang)) options$lang = options$engine.opts$lang %n% default
options
}
# embed a file verbatim
eng_embed = function(options) {
# if `file` is empty, use `code` as the list of files
if (is.null(f <- options$file)) {
f = gsub('^["\']|["\']$', '', options$code) # in case paths are quoted
if (length(f) == 0) return()
options$code = xfun::read_all(f)
}
# use the filename extension as the default language name
if (nchar(lang <- file_ext(f[1])) > 1) {
lang = sub('^R', '', lang) # Rmd -> md, Rhtml -> html, etc.
if (lang == 'nw') lang = 'tex'
}
options = set_lang(options, tolower(lang))
eng_verbatim(options)
}
# set engines for interpreted languages
local({
for (i in c(
'awk', 'bash', 'coffee', 'gawk', 'groovy', 'haskell', 'lein', 'mysql',
'node', 'octave', 'perl', 'php', 'psql', 'Rscript', 'ruby', 'sas',
'scala', 'sed', 'sh', 'stata', 'zsh'
)) knit_engines$set(setNames(list(eng_interpreted), i))
})
# additional engines
knit_engines$set(
asis = eng_asis,
asy = eng_plot,
block = eng_block,
block2 = eng_block2,
bslib = eng_bslib,
c = eng_shlib,
cat = eng_cat,
cc = eng_shlib,
comment = eng_comment,
css = eng_css,
ditaa = eng_plot,
dot = eng_plot,
embed = eng_embed,
eviews = eng_eviews,
exec = eng_exec,
fortran = eng_shlib,
fortran95 = eng_shlib,
go = eng_go,
highlight = eng_highlight,
js = eng_js,
julia = eng_julia,
python = eng_python,
R = eng_r,
Rcpp = eng_Rcpp,
sass = eng_sxss,
scss = eng_sxss,
sql = eng_sql,
stan = eng_stan,
targets = eng_targets,
tikz = eng_tikz,
verbatim = eng_verbatim
)
cache_engines$set(python = cache_eng_python)
get_engine = function(name) {
fun = knit_engines$get(name)
if (is.function(fun)) return(fun)
warning(
"Unknown language engine '", name,
"' (must be registered via knit_engines$set())."
)
function(options) {
engine_output(options, options$code, '')
}
}
cache_engine = function(options) {
cache_fun = cache_engines$get(options$engine)
if (!is.function(cache_fun)) return()
cache_fun(options)
}
# possible values for engines (for auto-completion in RStudio)
opts_chunk_attr$engine = as.list(sort(c('R', names(knit_engines$get()))))
opts_chunk_attr[c('engine.path', 'engine.opts')] = list('character', 'character')