Merge branch 'master' into htmltools-figures

.github/ISSUE_TEMPLATE.md

@@ -1,23 +1,12 @@
-For general questions, please ask them on StackOverflow first, using the tags `r` and `knitr`: http://stackoverflow.com/questions/ask Please come back here only if nobody answers your question there, and let me know the URL of your StackOverflow post. It is a better idea to use the wisdom of the community than the limited time of a single person.
-
-For bug reports, please provide a minimal, self-contained, and reproducible example by reducing your example as much as possible right before the problem goes away. By doing this, you may be able to figure out what the problem really is before reporting to me. You can attach your example as a zip file here along with `devtools::session_info('knitr')`, and screenshots are often very helpful to illustrate your issues.
-
-To include a verbatim chunk of arbitrary text, wrap it in a pair of three backticks. When any line of your text contains N backticks (N >= 3), use N + 1 backticks to wrap the text, e.g. use four backticks to wrap three:
-
-````
-A sample document.
-
-```{r}
-1 + 1  # a line of code
-```
-
-Another paragraph.
-````
-
-If it is just a chunk of R code (or other languages) and you want syntax highlighting, you may use three backticks to format it, e.g.
-
-```r
-rnorm(10)
-```
-
-Usually your issue will be closed after it is fixed, but sometimes it is closed only because I'm not able to offer any help. It does not mean your issue is not real or bad. You can propose a fix by yourself through a pull request. Your constructive feedback is always appreciated.
+By filing an issue to this repo, I promise that
+
+- [ ] I have fully read the isse guide at https://yihui.name/issue/.
+- [ ] I have provided the necessary information about my issue.
+    - If I'm asking a question, I have already asked it on Stack Overflow or RStudio Community, waited for at least 24 hours, and included a link to my question there.
+    - If I'm filing a bug report, I have included a minimal, self-contained, and reproducible example, and have also included `xfun::session_info('knitr')`. I have upgraded all my packages to their latest versions (e.g., R, RStudio, and R packages), and also tried the development version: `remotes::install_github('yihui/knitr')`.
+    - If I have posted the same issue elsewhere, I have also mentioned it in this issue.
+- [ ] I have learned the Github Markdown syntax, and formatted my issue correctly.
+
+<!--
+Pleaes keep the above portion in your issue and delete the portion below. Your issue will be closed if any of the above boxes is not checked. In certain (rare) cases, you may be exempted if you give a brief explanation (e.g., you are only making a suggestion for improvement). Thanks!
+-->

.travis.yml

@@ -1,7 +1,5 @@
 language: r
 
-sudo: false
-
 # environment variables
 env:
   matrix:
@@ -37,6 +35,8 @@ addons:
     - qpdf
     - texinfo
     - cargo
+    - libmagick++-dev
+    - libpoppler-cpp-dev
 
 repos:
   XRAN: https://xran.yihui.name

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: knitr
 Type: Package
 Title: A General-Purpose Package for Dynamic Report Generation in R
-Version: 1.21.5
+Version: 1.22.4
 Authors@R: c(
     person("Yihui", "Xie", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-0645-5666")),
     person("Adam", "Vogt", role = "ctb"),
@@ -22,6 +22,7 @@ Authors@R: c(
     person("Doug", "Hemken", role = "ctb"),
     person("Duncan", "Murdoch", role = "ctb"),
     person("Elio", "Campitelli", role = "ctb"),
+    person("Emily", "Riederer", role = "ctb"),
     person("Fabian", "Hirschmann", role = "ctb"),
     person("Fitch", "Simeon", role = "ctb"),
     person("Forest", "Fang", role = "ctb"),
@@ -122,6 +123,7 @@ Suggests:
     tinytex,
     reticulate (>= 1.4),
     JuliaCall (>= 0.11.1),
+    magick,
     png,
     jpeg,
     gifski,

NEWS.md

@@ -1,17 +1,65 @@
+# CHANGES IN knitr VERSION 1.23
+
+## NEW FEATURES 
+
+- It is possible to customize the sign `\times` used for the scientific notation of inline numeric output via a global option, e.g., `options(knitr.inline.times = '\\cdot ')` (thanks, @wuffi @trentks, #1563).
+
+## BUG FIXES
+
+- For R Markdown documents, inline numeric output that is formatted with the scientific notation will be wrapped in `\ensuremath{}`. This will fix the LaTeX error `! Missing $ inserted.`. However, you are still recommended to add a pair of dollar signs around the inline output when it is formatted with the scientific notation (e.g., `` $`r 1.234e12`$``), otherwise it will not work with other R Markdown output formats such as HTML or Word (thanks, @billdenney and many who have suffered from this issue, rstudio/rmarkdown#1527).
+
+- For an input file that contains no code chunks or inline R code expressions, `purl()` should return an empty string instead of the original text from the input (thanks, @jrnold, #1660).
+
+- `purl()` might trigger a warning for non-R code chunks (thanks, @adamcagle, rstudio/rmarkdown#1528).
+
+## MAJOR CHANGES
+
+- `knitr::knit()` will try to read the input file with the UTF-8 encoding first. If UTF-8 doesn't work, it will try to read with the system native encoding instead (with a warning). The `encoding` argument of `knitr::knit()` is completely ignored. In the future, only UTF-8 will be supported, and we will stop retrying with the system native encoding. The output file from `knitr::knit()` is always encoded in UTF-8.
+
 # CHANGES IN knitr VERSION 1.22
 
+## NEW FEATURES 
+
+- Added chunk options `class.error`, `class.warning`, and `class.message` to customize the CSS classes for errors, warnings, and messages in R Markdown output, respectively (thanks, @gadenbuie, #1676).
+
+- Added a new engine `sass`/`scss` to convert Sass/SCSS to CSS using either the **sass** [R package](https://github.com/rstudio/sass) (LibSass) or Dart Sass [executable](https://sass-lang.com/install) (when R package not found, the engine option `engine.opts = list(package = FALSE)`, or `engine.path` to executable is provided). After conversion, resulting CSS is treated as in the CSS engine (thanks, @emilyriederer, #1666).
+
+- The `cat` engine supports the chunk option `eval = FALSE` now (thanks, @HanOostdijk, #1618).
+
+- The chunk option `out.extra` can be used to include extra attributes for the `<iframe>` generated from `knitr::include_url()` or `knitr::include_app()` (thanks, @jvcasillas, #1648).
+
 ## BUG FIXES
 
+- `knit_meta_add()` could exhaust the system's memory because of a wrong method of vectorization (thanks, @kevinushey @nikkoc, rstudio/rmarkdown#1538).
+
 - The output path should be quoted in `pandoc()` (thanks, @antoine-sachet, #1644).
 
+- When there are multiple figures with multiple captions in a code chunk, **bookdown**'s figure numbering is incorrect (thanks, Catherine Peng, https://stackoverflow.com/q/53880195/559676).
+
+- Added an argument `label` to `kable()` so that users can manually specify a label (thanks, @Inferrator, #1655).
+
+- The chunk option `fig.show='hide'` doesn't work for `knitr::include_graphics()` (thanks, @vincentarelbundock, #1675).
+
+- The `tikz` engine doesn't work on Windows (thanks, Andry, https://stackoverflow.com/q/54839403/559676).
+
+- `kable()` now generates a table for R Markdown documents even when the data has 0 rows (thanks, @yutannihilation, #1677).
+
+- The chunk options `dev = 'tikz'` and `external = FALSE` didn't work in R Markdown (thanks, @martinschmelzer, #1649).
+
 ## MAJOR CHANGES
 
 - `knitr::knit()` starts to warn against non-UTF8 encodings ([Why?](https://yihui.name/en/2018/11/biggest-regret-knitr/)). In the future, we will only support UTF-8 input. If your input file is not encoded in UTF-8, we strongly recommend that you re-save it with UTF-8.
 
-- Removed the `encoding` arguments in `knitr::pandoc()`, `knitr::knit2pandoc()`, `knitr::knit2pdf()`, `knitr2wp()`, and `knitr::Sweave2knitr()`. The input files must be encoded in UTF-8.
+- Removed the `encoding` arguments in `knitr::pandoc()`, `knitr::knit2pdf()`, `knitr2wp()`, and `knitr::Sweave2knitr()`. The input files must be encoded in UTF-8.
 
 - `knitr::knit2html()` still has the `encoding` argument, but it only supports UTF-8 internally.
 
+## MINOR CHANGES
+
+- Changed `tools::texi2dvi()` to `tinytex::latexmk()` for the `tikz` engine to compile TikZ graphics to other foramts (e.g., `svg` or `png`). This requires the **tinytex** package >= v0.10.10: https://github.com/yihui/tinytex.
+
+- Empty lines are no longer removed in the output of `purl()` (thanks, Marius Hofert).
+
 # CHANGES IN knitr VERSION 1.21
 
 ## NEW FEATURES

R/block.R

@@ -38,7 +38,7 @@ call_block = function(block) {
     )
     if (!params$eval) return('')
     cmds = lapply(sc_split(params$child), knit_child, options = block$params)
-    out = paste(unlist(cmds), collapse = '\n')
+    out = one_string(unlist(cmds))
     return(out)
   }
 
@@ -161,7 +161,7 @@ block_exec = function(options) {
   # only evaluate certain lines
   if (is.numeric(ev <- options$eval)) {
     # group source code into syntactically complete expressions
-    if (isFALSE(options$tidy)) code = sapply(highr:::group_src(code), paste, collapse = '\n')
+    if (isFALSE(options$tidy)) code = sapply(highr:::group_src(code), one_string)
     iss = seq_along(code)
     code = comment_out(code, '##', setdiff(iss, iss[ev]), newline = FALSE)
   }
@@ -464,25 +464,25 @@ process_tangle.block = function(x) {
   }
   if (isFALSE(params$purl)) return('')
   label = params$label; ev = params$eval
-  if (params$engine != 'R') return(comment_out(knit_code$get(label)))
+  if (params$engine != 'R') return(one_string(comment_out(knit_code$get(label))))
   code = if (!isFALSE(ev) && !is.null(params$child)) {
     cmds = lapply(sc_split(params$child), knit_child)
-    paste(unlist(cmds), collapse = '\n')
+    one_string(unlist(cmds))
   } else knit_code$get(label)
   # read external code if exists
   if (!isFALSE(ev) && length(code) && any(grepl('read_chunk\\(.+\\)', code))) {
     eval(parse_only(unlist(stringr::str_extract_all(code, 'read_chunk\\(([^)]+)\\)'))))
   }
   code = parse_chunk(code)
   if (isFALSE(ev)) code = comment_out(code, params$comment, newline = FALSE)
-  if (opts_knit$get('documentation') == 0L) return(paste(code, collapse = '\n'))
+  if (opts_knit$get('documentation') == 0L) return(one_string(code))
   label_code(code, x$params.src)
 }
 #' @export
 process_tangle.inline = function(x) {
 
   output = if (opts_knit$get('documentation') == 2L) {
-    output = paste(line_prompt(x$input.src, "#' ", "#' "), collapse = '\n')
+    output = one_string(line_prompt(x$input.src, "#' ", "#' "))
   } else ''
 
   code = x$code
@@ -496,13 +496,13 @@ process_tangle.inline = function(x) {
     output = c(output, cout, '')
   }
 
-  paste(output, collapse = '\n')
+  one_string(output)
 }
 
 
 # add a label [and extra chunk options] to a code chunk
 label_code = function(code, label) {
-  code = paste(c('', code, ''), collapse = '\n')
+  code = one_string(c('', code, ''))
   paste0('## ----', stringr::str_pad(label, max(getOption('width') - 11L, 0L), 'right', '-'),
          '----', code)
 }

R/cache.R

@@ -317,6 +317,6 @@ clean_cache = function(clean = FALSE, path = opts_chunk$get('cache.path')) {
   if (p1 != '') i = i & (substr(base, 1, nchar(p1)) == p1)
   if (!any(i)) return()
   if (clean) unlink(files[i]) else message(
-    'Clean these cache files?\n\n', paste(files[i], collapse = '\n'), '\n'
+    'Clean these cache files?\n\n', one_string(files[i]), '\n'
   )
 }

R/defaults.R

@@ -54,9 +54,10 @@ new_defaults = function(value = list()) {
 #'
 #'   A list of available options:
 #'   \url{https://yihui.name/knitr/options/#chunk_options}
-#' @note \code{opts_current} is read-only in the sense that it does nothing if
-#'   you call \code{opts_current$set()}; you can only query the options via
-#'   \code{opts_current$get()}.
+#' @note \code{opts_current} should be treated as read-only and you are supposed
+#'   to only query its values via \code{opts_current$get()}. Technically you
+#'   could also call \code{opts_current$set()} to change the values, but you are
+#'   not recommended to do so unless you understand the consequences.
 #' @export
 #' @examples opts_chunk$get('prompt'); opts_chunk$get('fig.keep')
 opts_chunk = new_defaults(list(