Merged origin/master into abhsarma-master

.Rbuildignore

@@ -23,4 +23,3 @@ Makefile
 ^codecov\.yml$
 ^NEWS\.md$
 ^cran-comments\.md$
-vignettes/knitr-refcard.lyx

.Rinstignore

@@ -1,2 +1 @@
 knitr-intro.lyx
-knitr-refcard.lyx

.github/workflows/R-CMD-check.yaml

@@ -56,8 +56,6 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-tinytex@v2-branch
         env:
           # install full prebuilt version

.github/workflows/knitr-examples.yaml

@@ -91,7 +91,7 @@ jobs:
           make integration
         shell: bash
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: knitr-examples

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: knitr
 Type: Package
 Title: A General-Purpose Package for Dynamic Report Generation in R
-Version: 1.48.1
+Version: 1.48.7
 Authors@R: c(
     person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
     person("Abhraneel", "Sarma", role = "ctb"),
@@ -120,7 +120,7 @@ Imports:
     highr (>= 0.11),
     methods,
     tools,
-    xfun (>= 0.44),
+    xfun (>= 0.48),
     yaml (>= 2.1.19)
 Suggests:
     bslib,
@@ -134,6 +134,7 @@ Suggests:
     jpeg,
     JuliaCall (>= 0.11.1),
     magick,
+    litedown,
     markdown (>= 1.3),
     png,
     ragg,
@@ -156,7 +157,7 @@ License: GPL
 URL: https://yihui.org/knitr/
 BugReports: https://github.com/yihui/knitr/issues
 Encoding: UTF-8
-VignetteBuilder: knitr
+VignetteBuilder: litedown, knitr
 SystemRequirements: Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org).
     The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).
 Collate:

Makefile

@@ -44,12 +44,6 @@ examples:
 	cd inst/examples;\
 	Rscript knit-all.R
 
-vignettes:
-	cd vignettes;\
-	lyx -e knitr knitr-refcard.lyx;\
-	sed -i '/\\usepackage{breakurl}/ d' knitr-refcard.Rnw;\
-	mv knitr-refcard.Rnw assets/template-refcard.tex
-
 clean:
 	cd ..;\
 	$(RM) -r $(PKGNAME).Rcheck/

NAMESPACE

@@ -156,6 +156,7 @@ import(utils)
 importFrom(xfun,attr)
 importFrom(xfun,file_ext)
 importFrom(xfun,file_string)
+importFrom(xfun,html_escape)
 importFrom(xfun,is_R_CMD_check)
 importFrom(xfun,is_abs_path)
 importFrom(xfun,is_windows)

NEWS.md

@@ -1,5 +1,30 @@
 # CHANGES IN knitr VERSION 1.49
 
+## NEW FEATURES
+
+- In-chunk references of the form `<<label>>` can be disabled via the chunk option `ref.chunk = FALSE` now (thanks, @jennybc @gadenbuie, #2360).
+
+- Added support for `fig.alt` for LaTeX output, i.e., using `\includegraphics[alt={alt text}]` (thanks, @capnrefsmmat, #2378).
+
+## BUG FIXES
+
+- In-chunk references of the form `<<label>>` should not be resolved if `label` is not found in the document (thanks, @jennybc @gadenbuie, #2360).
+
+- `asis_output()` was not passed to the `output` hook (thanks, @cderv, #2332).
+
+- Avoid partial matching of the `Date/Publication` field when generating `citation('knitr')`, otherwise R will emit a warning when `options(warnPartialMatchDollar = TRUE)` (thanks, @fkohrt, #2361).
+
+## MAJOR CHANGES
+
+- Unbalanced chunk delimiters (fences) in R Markdown documents are strictly prohibited now.
+
+- For code chunks with `error = TRUE`, `purl()` and `hook_purl()` will wrap the code in `try({...})` (thanks, @bastistician #2338, @jeroen #2368).
+
+## MINOR CHANGES
+
+- Changed the format of the reference card from PDF to HTML so building this package will not require LaTeX. See `vignette('knitr-refcard', package = 'knitr')`.
+
+- Switched the vignette engine from **knitr** to `litedown::vignette` for some package vignettes.
 
 # CHANGES IN knitr VERSION 1.48
 
@@ -2165,7 +2190,7 @@
 
 ## DOCUMENTATION
 
-- added a simple reference card: http://cran.rstudio.com/web/packages/knitr/vignettes/knitr-refcard.pdf
+- added a simple reference card: `vignette('knitr-refcard', package = 'knitr')`
 
 # CHANGES IN knitr VERSION 0.7
 

R/block.R

@@ -52,7 +52,8 @@ call_block = function(block) {
 
   if (opts_knit$get('progress')) print_block(block)
 
-  params[['code']] = parse_chunk(params[['code']]) # parse sub-chunk references
+  if (!isFALSE(params$ref.chunk))
+    params[['code']] = parse_chunk(params[['code']]) # parse sub-chunk references
 
   ohooks = opts_hooks$get()
   for (opt in names(ohooks)) {
@@ -255,7 +256,7 @@ eng_r = function(options) {
   res = if (is_blank(code)) list() else if (isFALSE(ev)) {
     as.source(code)
   } else if (cache.exists && isFALSE(options$cache.rebuild)) {
-    fix_evaluate(cache$output(options$hash, 'list'), options$cache == 1)
+    cache$output(options$hash, 'list')
   } else in_input_dir(
     evaluate(
       code, envir = env, new_device = FALSE,
@@ -603,12 +604,18 @@ tangle_block = function(x) {
     eval(parse_only(unlist(str_extract(code, 'read_chunk\\(([^)]+)\\)'))))
   }
   code = parse_chunk(code)
-  if (isFALSE(ev)) code = comment_out(code, params$comment, newline = FALSE)
+  code = tangle_mask(code, ev, x$params$error)
   if (opts_knit$get('documentation') == 0L) return(one_string(code))
   # e.g. when documentation 1 or 2 with purl()
   label_code(code, x)
 }
 
+tangle_mask = function(code, eval, error) {
+  if (isFALSE(eval)) code = comment_out(code, '#', newline = FALSE)
+  if (isTRUE(error)) code = c('try({', code, '})')
+  code
+}
+
 tangle_inline = function(x) {
   output = if (opts_knit$get('documentation') == 2L) {
     output = paste("#'", gsub('\n', "\n#' ", x$input, fixed = TRUE))

R/highlight.R

@@ -6,7 +6,7 @@ hilight_source = function(x, format, options) {
     } else {
       res = try(highr::hi_andre(x, options$engine, format))
       if (inherits(res, 'try-error')) {
-        if (format == 'html') highr:::escape_html(x) else highr:::escape_latex(x)
+        if (format == 'html') html_escape(x) else highr:::escape_latex(x)
       } else {
         highlight_header()
         n = length(res)

R/hooks-asciidoc.R

@@ -36,7 +36,9 @@ hooks_asciidoc = function() {
   hook.error = function(x, options) {
     sprintf('\n[CAUTION]\n====\n.Error\n%s\n====\n', gsub('^.*Error: ', '', x))
   }
-  hook.output = function(x, options) sprintf('\n----\n%s----\n', x)
+  hook.output = function(x, options) {
+    if (output_asis(x, options)) x else sprintf('\n----\n%s----\n', x)
+  }
   list(
     source = hook.source, output = hook.output, message = hook.message,
     warning = hook.warning, error = hook.error, plot = hook_plot_asciidoc

R/hooks-extra.R

@@ -146,8 +146,10 @@ hook_purl = function(before, options, ...) {
     .knitEnv$tangle.params = NULL
   }
 
-  code = options$code
-  if (isFALSE(options$eval)) code = comment_out(code, '# ', newline = FALSE)
+  # `options` contains merged chunk options, but we need to check if
+  # `error=TRUE` in local chunk options, so retrieve options from knit_code
+  error = attr(knit_code$get(options$label), 'chunk_opts')[['error']]
+  code = tangle_mask(options$code, options$eval, error)
   if (is.character(output)) {
     code = c(
       if (file.exists(output)) read_utf8(output),

R/hooks-html.R

@@ -62,7 +62,7 @@ hook_animation = function(options) {
   if (length(cap) == 0) cap = ''
   if (alt) {
     alt = options$fig.alt %n% cap
-    return(if (escape) escape_html(alt) else alt)
+    return(if (escape) html_escape(alt) else alt)
   }
   if (is_blank(cap)) return(cap)
   paste0(create_label(
@@ -252,9 +252,10 @@ hooks_html = function() {
   hook = function(name) {
     force(name)
     function(x, options) {
+      if (name == 'output' && output_asis(x, options)) return(x)
       x = if (name == 'source') {
         c(hilight_source(x, 'html', options), '')
-      } else escape_html(x)
+      } else html_escape(x)
       x = one_string(x)
       sprintf('<div class="%s"><pre class="knitr %s">%s</pre></div>\n', name, tolower(options$engine), x)
     }

R/hooks-latex.R

@@ -162,9 +162,10 @@ hook_plot_tex = function(x, options) {
   # maxwidth does not work with animations
   if (animate && identical(ow, '\\maxwidth')) ow = NULL
   if (is.numeric(ow)) ow = paste0(ow, 'px')
-  size = paste(c(sprintf('width=%s', ow),
-                 sprintf('height=%s', options$out.height),
-                 options$out.extra), collapse = ',')
+  size = paste(c(
+    sprintf('width=%s', ow), sprintf('height=%s', options$out.height),
+    sprintf('alt={%s}', escape_percent(options$fig.alt)), options$out.extra
+  ), collapse = ',')
 
   paste0(
     fig1, align1, sub1, resize1,

R/hooks-md.R

@@ -175,6 +175,7 @@ hooks_markdown = function(strict = FALSE, fence_char = '`') {
   hook.o = function(class) {
     force(class)
     function(x, options) {
+      if (class == 'output' && output_asis(x, options)) return(x)
       hook.t(x, options[[paste0('attr.', class)]], options[[paste0('class.', class)]])
     }
   }
@@ -277,19 +278,22 @@ hooks_jekyll = function(highlight = c('pygments', 'prettify', 'none'), extra = '
   }, prettify = {
     hook.r = function(x, options) {
       paste0(
-        '\n\n<pre><code class="prettyprint ', extra, '">', escape_html(x),
+        '\n\n<pre><code class="prettyprint ', extra, '">', html_escape(x),
         '</code></pre>\n\n'
       )
     }
     hook.t = function(x, options) paste0(
-      '\n\n<pre><code>', escape_html(x), '</code></pre>\n\n'
+      '\n\n<pre><code>', html_escape(x), '</code></pre>\n\n'
     )
   })
   source = function(x, options) {
     x = one_string(hilight_source(x, 'markdown', options))
     hook.r(x, options)
   }
   merge_list(hook.m, list(
-    source = source, output = hook.t, warning = hook.t, message = hook.t, error = hook.t
+    source = source, warning = hook.t, message = hook.t, error = hook.t,
+    output = function(x, options) {
+      if (output_asis(x, options)) x else hook.t(x, options)
+    }
   ))
 }

R/hooks-rst.R

@@ -42,7 +42,9 @@ hooks_rst = function(strict = FALSE) {
       (if (strict) hook.s else hook.t)(x, options)
     },
     warning = hook.s, error = hook.s, message = hook.s,
-    output = hook.s, inline = hook.i, plot = hook_plot_rst
+    inline = hook.i, plot = hook_plot_rst, output = function(x, options) {
+      if (output_asis(x, options)) x else hook.s(x, options)
+    }
   )
 }
 

R/hooks-textile.R

@@ -33,6 +33,7 @@ hooks_textile = function() {
     function(x, options) {
       if (name == 'source') x = c(hilight_source(x, 'textile', options), '')
       x = one_string(x)
+      if (name == 'output' && output_asis(x, options)) return(x)
       sprintf('bc(knitr %s %s#%s).. %s\np(knitr_end). \n\n',
               tolower(options$engine), name, options$label, x)
     }

R/output.R

@@ -132,7 +132,7 @@ knit = function(
   oconc = knit_concord$get(); on.exit(knit_concord$set(oconc), add = TRUE)
 
   if (child_mode()) {
-    setwd(opts_knit$get('output.dir')) # always restore original working dir
+    setwd(opts_knit$get('output.dir') %n% '.') # always restore original working dir
     # in child mode, input path needs to be adjusted
     if (in.file && !is_abs_path(input)) {
       input = paste0(opts_knit$get('child.path'), input)
@@ -512,8 +512,7 @@ sew.knit_asis = function(x, options, inline = FALSE, ...) {
     }
   }
   x = wrap_asis(x, options)
-  if (!out_format('latex') || inline) return(x)
-  # latex output need the \end{kframe} trick
+  if (inline) return(x)
   options$results = 'asis'
   knit_hooks$get('output')(x, options)
 }
@@ -646,7 +645,7 @@ sew.knit_embed_url = function(x, options = opts_chunk$get(), inline = FALSE, ...
   if (length(extra <- options$out.extra)) extra = paste('', extra, collapse = '')
   add_html_caption(options, sprintf(
     '<iframe src="%s" width="%s" height="%s" data-external="1"%s></iframe>',
-    escape_html(x$url), options$out.width %n% '100%', x$height %n% '400px',
+    html_escape(x$url), options$out.width %n% '100%', x$height %n% '400px',
     extra %n% ''
   ))
 }

R/package.R

@@ -24,7 +24,7 @@
 #'   \code{knit} + \code{R} (while \code{Sweave} = \code{S} + \code{weave}).
 #' @references Full documentation and demos: \url{https://yihui.org/knitr/};
 #'   FAQ's: \url{https://yihui.org/knitr/faq/}
-#' @importFrom xfun attr file_ext is_windows loadable parse_only
+#' @importFrom xfun attr file_ext html_escape is_windows loadable parse_only
 #'   sans_ext try_silent with_ext read_utf8 write_utf8 file_string
 #'   is_R_CMD_check is_abs_path
 '_PACKAGE'

R/parser.R

@@ -399,12 +399,13 @@ strip_white = function(x, test_strip = is_blank) {
 parse_chunk = function(x, rc = knit_patterns$get('ref.chunk')) {
   if (length(x) == 0L) return(x)
   x = c(x)  # drop attributes of code (e.g. chunk_opts)
-  if (!group_pattern(rc) || !any(idx <- grepl(rc, x))) return(x)
+  if (!group_pattern(rc) || length(idx <- grep(rc, x)) == 0) return(x)
 
   labels = sub(rc, '\\1', x[idx])
-  code = knit_code$get(labels)
+  code = knit_code$get()
+  i = labels %in% names(code)
+  idx = idx[i]; code = code[labels[i]]
   indent = gsub('^(\\s*).*', '\\1', x[idx])
-  if (length(labels) <= 1L) code = list(code)
   code = mapply(indent_block, code, indent, SIMPLIFY = FALSE, USE.NAMES = FALSE)
 
   x = as.list(x)
@@ -469,17 +470,14 @@ match_chunk_end = function(pattern, line, i, b, lines) {
     if (!any(match_chunk_begin(pattern, lines[i + 1:(k - 1)], '^\\1`*\\\\{')))
       return(FALSE)
   }
-  # TODO: clean up the exceptions here (although perhaps some may never update again)
-  signal = if (getOption('knitr.unbalanced.chunk', FALSE)) warning2 else stop2
-  signal(
+  stop2(
     'The closing fence on line ', i, ' ("', line, '") in ', current_input(),
     ' does not match the opening fence "',
     gsub('\\^(\\s*`+).*', '\\1', pattern), '" on line ', b, '. You are recommended to ',
     'fix either the opening or closing fence of the code chunk to use exactly ',
     'the same numbers of backticks and same level of indentation (or blockquote). ',
     'See https://yihui.org/en/2021/10/unbalanced-delimiters/ for more info.'
   )
-  TRUE
 }
 
 #' Get all chunk labels in a document

R/plot.R

@@ -281,38 +281,6 @@ reduce_plot_opts = function(options) {
   options
 }
 
-# the memory address of a NativeSymbolInfo object will be lost if it is saved to
-# disk; see http://markmail.org/message/zat2r2pfsvhrsfqz for the full
-# discussion; the hack below was stolen (with permission) from RStudio:
-# https://github.com/rstudio/rstudio/blob/master/src/cpp/r/R/Tools.R
-fix_recordedPlot = function(plot) {
-  # restore native symbols for R >= 3.0
-  for (i in seq_along(plot[[1]])) {
-    # get the symbol then test if it's a native symbol
-    symbol = plot[[1]][[i]][[2]][[1]]
-    if (inherits(symbol, 'NativeSymbolInfo')) {
-      # determine the dll that the symbol lives in
-      name = symbol[[if (is.null(symbol$package)) 'dll' else 'package']][['name']]
-      pkgDLL = getLoadedDLLs()[[name]]
-      # reconstruct the native symbol and assign it into the plot
-      nativeSymbol = getNativeSymbolInfo(
-        name = symbol$name, PACKAGE = pkgDLL, withRegistrationInfo = TRUE
-      )
-      plot[[1]][[i]][[2]][[1]] <- nativeSymbol
-    }
-  }
-  attr(plot, 'pid') = Sys.getpid()
-  plot
-}
-
-# fix plots in evaluate() results
-fix_evaluate = function(list, fix = TRUE) {
-  if (!fix) return(list)
-  lapply(list, function(x) {
-    if (evaluate::is.recordedplot(x)) fix_recordedPlot(x) else x
-  })
-}
-
 # remove the plots from the evaluate results for the case of cache=2; if we only
 # want to keep high-level plots, we need MD5 digests of the plot components so
 # that we will be able to filter out low-level changes later