Merge branch 'master' into error-formatting-enhance

* master:
  make negative times 0
  replace highr:::spaces() with strrep() in base R
  support chunk options message/warning = NA
  close #2204: drop the support for cairoDevice
  amend 1a0f2cc: make line_count() a few times faster
  Replace several stringr-based function calls with base equivalents (#2202, #1549)
  see if this fix the ruby gems issue https://github.com/yihui/knitr/actions/runs/3682745993/jobs/6230638404
  stop importing xfun::isFALSE() and define isFALSE() only for R < 3.5.0
  Add labels to the default progress bar and allow users to provide a custom progress bar (#2196)

.github/workflows/knitr-examples.yaml

@@ -61,9 +61,6 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get install -y libpoppler-cpp-dev graphviz asymptote highlight coffeescript scala optipng ghostscript
-          # downgrade ruby to remove deprecated
-          # https://github.com/rubygems/rubygems/issues/3068
-          sudo gem update --system 3.0.8
 
       - name: Install CTAN dependencies
         run: |

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: knitr
 Type: Package
 Title: A General-Purpose Package for Dynamic Report Generation in R
-Version: 1.41.1
+Version: 1.41.5
 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"),
@@ -196,4 +196,4 @@ Collate:
     'utils-upload.R'
     'utils-vignettes.R'
     'zzz.R'
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -159,7 +159,6 @@ import(utils)
 importFrom(xfun,attr)
 importFrom(xfun,file_ext)
 importFrom(xfun,file_string)
-importFrom(xfun,isFALSE)
 importFrom(xfun,is_R_CMD_check)
 importFrom(xfun,is_abs_path)
 importFrom(xfun,is_windows)

NEWS.md

@@ -1,13 +1,23 @@
 # CHANGES IN knitr VERSION 1.42
 
+## NEW FEATURES
+
+- Users can specify a custom progress bar for `knit()` now. The default is still a text progress bar created from `utils::txtProgressBar()`. To specify a custom progress bar, set `options(knitr.progress.fun = function(total, labels) {})`. This function should take arguments `total` (the total number of chunks) and `labels` (the vector of chunk labels), create a progress bar, and return a list of two methods: `list(update = function(i) {}, done = function() {})`. The `update()` method takes `i` (index of the current chunk) as the input and updates the progress bar. The `done()` method closes the progress bar. See https://yihui.org/knitr/options/#global-r-options for documentation and examples.
+
+- The default text progress bar is still written to `stdout()` by default, but can also be written to other connections or `stderr()` now. To do so, set `options(knitr.progress.output = )` to a connection or `stderr()`.
+
 ## MAJOR CHANGES
 
 - `knit()` no longer prints out chunk options beneath the text progress bar while knitting a document (thanks, @hadley, #1880).
 
+- Due to a change in the **evaluate** package, the chunk options `message = FALSE` and `warning = FALSE` will completely suppress the messages/warnings now, instead of sending them to the console. To get back to the old behavior, you can use `NA` instead of `FALSE` (thanks, @gadenbuie, https://github.com/yihui/yihui.org/discussions/1458).
+
 ## MINOR CHANGES
 
 - If the chunk option `child` is used for a code chunk but the chunk is not empty, you will get a warning indicating that this non-empty code will not be executed when you knit the document. Now this warning can be silenced by `options(knitr.child.warning = FALSE)` (thanks, @jwijffels, #2191).
 
+- Devices from the package **cairoDevice** (`Cairo_pdf`, `Cairo_png`, `Cairo_ps`, `Cairo_svg`) are no longer supported since the package has been archived on CRAN for more than a year (thanks, @jessekps, #2204).
+
 # CHANGES IN knitr VERSION 1.41
 
 ## NEW FEATURES

R/block.R

@@ -256,8 +256,8 @@ eng_r = function(options) {
   } else in_input_dir(
     evaluate(
       code, envir = env, new_device = FALSE,
-      keep_warning = !isFALSE(options$warning),
-      keep_message = !isFALSE(options$message),
+      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
       },
@@ -364,7 +364,7 @@ purge_cache = function(options) {
 
 cache_globals = function(option, code) {
   if (is.character(option)) option else {
-    (if (xfun::isFALSE(option)) find_symbols else find_globals)(code)
+    (if (isFALSE(option)) find_symbols else find_globals)(code)
   }
 }
 
@@ -616,7 +616,7 @@ process_tangle.inline = function(x) {
 # add a label [and extra chunk options] to a code chunk
 label_code = function(code, label) {
   code = one_string(c('', code, ''))
-  paste0('## ----', stringr::str_pad(label, max(getOption('width') - 11L, 0L), 'right', '-'),
+  paste0('## ----', label, strrep('-', max(getOption('width') - 11L - nchar(label), 0L)),
          '----', code)
 }
 

R/citation.R

@@ -132,7 +132,7 @@ write_bib = function(
   bib = c(bib, unlist(bib2, recursive = FALSE))
   bib = lapply(bib, function(b) {
     idx = which(names(b) == '')
-    if (!is.null(width)) b[-idx] = stringr::str_wrap(b[-idx], width, 2, 4)
+    if (!is.null(width)) b[-idx] = str_wrap(b[-idx], width, 2, 4)
     structure(c(b[idx[1L]], b[-idx], b[idx[2L]], ''), class = 'Bibtex')
   })
   if (!is.null(file) && length(x)) write_utf8(unlist(bib), file)

R/output.R

@@ -289,8 +289,9 @@ process_file = function(text, output) {
     labels = unlist(lapply(groups, function(g) {
       if (is.list(g$params)) g[[c('params', 'label')]] else ''
     }))
-    pb = txtProgressBar(0, n, char = '.', style = 3)
-    on.exit(close(pb), add = TRUE)
+    pb_fun = getOption('knitr.progress.fun', txt_pb)
+    pb = if (is.function(pb_fun)) pb_fun(n, labels)
+    on.exit(if (!is.null(pb)) pb$done(), add = TRUE)
   }
   wd = getwd()
   for (i in 1:n) {
@@ -302,7 +303,7 @@ process_file = function(text, output) {
       }
       break  # must have called knit_exit(), so exit early
     }
-    if (progress) setTxtProgressBar(pb, i)
+    if (progress && !is.null(pb)) pb$update(i)
     group = groups[[i]]
     res[i] = withCallingHandlers(
       if (tangle) process_tangle(group) else process_group(group),
@@ -495,7 +496,7 @@ sew.source = function(x, options, ...) {
 msg_wrap = function(message, type, options) {
   # when the output format is LaTeX, do not wrap messages (let LaTeX deal with wrapping)
   if (!length(grep('\n', message)) && !out_format(c('latex', 'listings', 'sweave')))
-    message = stringr::str_wrap(message, width = getOption('width'))
+    message = str_wrap(message, width = getOption('width'))
   knit_log$set(setNames(
     list(c(knit_log$get(type), paste0('Chunk ', options$label, ':\n  ', message))),
     type

R/package.R

@@ -25,7 +25,7 @@
 #'   \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 isFALSE is_windows loadable parse_only
+#' @importFrom xfun attr file_ext is_windows loadable parse_only
 #'   sans_ext try_silent with_ext read_utf8 write_utf8 file_string
 #'   is_R_CMD_check is_abs_path
 NULL

R/parser.R

@@ -333,7 +333,6 @@ get_option_comment = function(engine) {
 
 print.block = function(x, ...) {
   params = x$params
-  cat(' chunk:', params$label, '\n')
   if (opts_knit$get('verbose')) {
     code = knit_code$get(params$label)
     if (length(code) && !is_blank(code)) {

R/pattern.R

@@ -152,7 +152,7 @@ detect_pattern = function(text, ext) {
   for (p in names(all_patterns)) {
     for (i in c('chunk.begin', 'inline.code')) {
       pat = all_patterns[[p]][[i]]
-      if (length(pat) && any(stringr::str_detect(text, pat))) return(p)
+      if (length(pat) && any(grepl(pat, text, perl = TRUE))) return(p)
     }
   }
   # *.Rtex indicates the tex syntax in knitr, but Rnw syntax in traditional

R/plot.R

@@ -1,4 +1,4 @@
-# graphics devices in base R, plus those in Cairo, cairoDevice, tikzDevice
+# graphics devices in base R, plus those in Cairo, tikzDevice
 auto_exts = c(
   bmp = 'bmp', postscript = 'eps', pdf = 'pdf', png = 'png', svg = 'svg',
   jpeg = 'jpeg', pictex = 'tex', tiff = 'tiff', win.metafile = 'wmf',
@@ -11,8 +11,6 @@ auto_exts = c(
   CairoJPEG = 'jpeg', CairoPNG = 'png', CairoPS = 'eps', CairoPDF = 'pdf',
   CairoSVG = 'svg', CairoTIFF = 'tiff',
 
-  Cairo_pdf = 'pdf', Cairo_png = 'png', Cairo_ps = 'eps', Cairo_svg = 'svg',
-
   svglite = 'svg', gridSVG = 'svg',
 
   ragg_png = 'png',
@@ -88,11 +86,6 @@ dev_get = function(dev, options = opts_current$get(), dpi = options$dpi[1]) {
     CairoPDF = load_device('CairoPDF', 'Cairo'),
     CairoSVG = load_device('CairoSVG', 'Cairo'),
 
-    Cairo_pdf = load_device('Cairo_pdf', 'cairoDevice'),
-    Cairo_png = load_device('Cairo_png', 'cairoDevice'),
-    Cairo_ps = load_device('Cairo_ps', 'cairoDevice'),
-    Cairo_svg = load_device('Cairo_svg', 'cairoDevice'),
-
     svglite = load_device('svglite', 'svglite'),
 
     # similar to load_device(), but the `dpi` argument is named `res`
@@ -217,7 +210,7 @@ get_dargs = function(dargs, dev) {
   dargs
 }
 
-# this is mainly for Cairo and cairoDevice
+# this is mainly for Cairo
 load_device = function(name, package, dpi = NULL) {
   dev = getFromNamespace(name, package)
   # dpi is for bitmap devices; units must be inches!

R/spin.R

@@ -140,8 +140,8 @@ spin = function(
   l = attr(gregexpr('`+', x)[[1]], 'match.length')
   l = max(l, 0)
   if (length(l) > 0) {
-    i = highr:::spaces(l + 1, '`')
-    b = highr:::spaces(max(l + 1, 3), '`')
+    i = strrep('`', l + 1)
+    b = strrep('`', max(l + 1, 3))
   } else {
     i = '`'
     b = '```'

R/table.R

@@ -490,12 +490,7 @@ pad_width = function(x, width, side) {
     stop("'side' must be 'left', 'right', or 'both'")
   w = width - nchar(x, 'width')
   w1 = floor(w / 2)  # the left half of spaces when side = 'both'
-  s1 = v_spaces(w * (side == 'left') + w1 * (side == 'both'))
-  s2 = v_spaces(w * (side == 'right') + (w - w1) * (side == 'both'))
+  s1 = strrep(' ', pmax(0, w * (side == 'left') + w1 * (side == 'both')))
+  s2 = strrep(' ', pmax(0, w * (side == 'right') + (w - w1) * (side == 'both')))
   paste0(s1, x, s2)
 }
-
-# vectorized over n to generate sequences of spaces
-v_spaces = function(n) {
-  unlist(lapply(n, highr:::spaces))
-}

R/utils-string.R

@@ -8,3 +8,11 @@ str_replace = function(x, pos, value) {
   y = substring(x, m[1, ], m[2, ])
   paste(rbind(y, c(value, '')), collapse = '')
 }
+
+# a wrapper function to make strwrap() return a character vector of the same
+# length as the input vector; each element of the output vector is a string
+# formed by concatenating wrapped strings by \n
+str_wrap = function(...) {
+  res = strwrap(..., simplify = FALSE)
+  unlist(lapply(res, one_string))
+}

R/utils.R

@@ -44,6 +44,9 @@ comment_to_var = function(x, varname, pattern, envir) {
   FALSE
 }
 
+# TODO: remove this when we don't support R < 3.5.0
+if (getRversion() < '3.5.0') isFALSE = function(x) identical(x, FALSE)
+
 is_blank = function(x) {
   if (length(x)) all(grepl('^\\s*$', x)) else TRUE
 }
@@ -577,7 +580,13 @@ print_knitlog = function() {
 }
 
 # count the number of lines
-line_count = function(x) stringr::str_count(x, '\n') + 1L
+line_count = function(x) {
+  n = lengths(strsplit(x, '\n', fixed = TRUE))
+  i = grep('\n$', x)
+  n[i] = n[i] + 1L  # add an extra count for lines ending with \n
+  n[n == 0] = 1L  # should be at least one line
+  n
+}
 
 has_package = function(pkg) loadable(pkg, FALSE)
 has_packages = function(pkgs) {
@@ -1085,3 +1094,30 @@ str_split = function(x, split, ...) {
   y[x == ''] = list('')
   y
 }
+
+# default progress bar function in knitr: create a text progress bar, and return
+# methods to update/close it
+txt_pb = function(total, labels) {
+  s = ifelse(labels == '', '', sprintf(' (%s)', labels))  # chunk labels in ()
+  w = nchar(s)  # widths of labels
+  n = max(w)
+  # right-pad spaces for same width of all labels so a wider label of the
+  # progress bar in a previous step could be completely wiped (by spaces)
+  s = paste0(s, strrep(' ', n - w))
+  w2 = getOption('width')
+  con = getOption('knitr.progress.output', '')
+  pb = txtProgressBar(
+    0, total, 0, '.', width = max(w2 - 10 - n, 10), style = 3, file = con
+  )
+  list(
+    update = function(i) {
+      setTxtProgressBar(pb, i)
+      cat(s[i], file = con)  # append chunk label to the progress bar
+    },
+    done = function() {
+      # wipe the progress bar
+      cat(paste0('\r', strrep(' ', max(w2, 10) + 10 + n)), file = con)
+      close(pb)
+    }
+  )
+}