knitr 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).

• The environment in which code chunks are evaluated can be changed by passing a custom environment to knit_global() now (thanks, @abhsarma, #2358).

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).

• The chunk option autodep = TRUE stopped working due to a regression from #2321 (thanks, @heavywatal #2344, @atusy #2377).

• 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

• If a character value is passed to the chunk option message or warning, it will be coerced by as.logical(), e.g., a character string "NA" will be coerced to NA (thanks, @cderv, #2375).

• Issue a warning when the chunk option dependson receives an invalid value (thanks, @otoomet, #2376).

• 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.

knitr 1.48

BUG FIXES

• Fix regression from 1.46 with collapse = TRUE option not correctly collapsing source code and output into one when code chunk returns multiple outputs (thanks, @jennybc, @florisvdh, tidyverse/reprex#463).

• hook_purl() should not write the path of the R script to the output document (thanks, @fenguoerbian, #2348).

knitr 1.47

NEW FEATURES

• For kable(), you can set the global option knitr.kable.max_rows to limit the number of rows to show in the table, e.g., options(knitr.kable.max_rows = 30). This is a way to prevent kable() from generating a huge table from a large data object by accident.

• write_bib() now escapes all non-escaped "&" in the bibliography by default. Previously, it only escaped the title field of the package citation. You can disable the escape with the argument tweak = FALSE (thanks, @HedvigS #2335, @atusy #2342).

BUG FIXES

• Fixed a bug that write_bib() fails to use the first URL of a package when multiple URLs are provided in DESCRIPTION and separated by \n (thanks, @bastistician, #2343).

MINOR CHANGES

• The syntax highlighting LaTeX commands for Rnw documents, \hlstr and \hlstd, were renamed to \hlsng and \hldef, respectively, to maintain consistency with Andrew Simon's highlight package (thanks, @dcser123, #2341).

knitr 1.46

NEW FEATURES

• Added a new chunk option tab.cap to specify the table caption for kable() (thanks, @ulyngs, #1679). Previously, the caption could only be specified via the caption argument of kable(). Now you can set it in the chunk header if you want. Please note that this chunk option only works with a single kable() in each code chunk, and its value must be of length 1.

• spin() now recognizes # %% as a valid code chunk delimiter (thanks, @kylebutts, #2307).

• spin() also recognizes #| comments as code chunks now (thanks, @kylebutts, #2320).

• Chunk hooks can have the ... argument now. Previously, only arguments before, options, envir, and name are accepted. If a chunk hook function has the ... argument, all the aforementioned four arguments are passed to the hook. This means the hook function no longer has to have the four arguments explicitly in its signature, e.g., function(before, ...) is also valid if only the before argument is used inside the hook. See https://yihui.org/knitr/hooks/#chunk-hooks for more information.

• For package vignettes, PNG plots will be optimized by optipng and pngquant if they are installed and can be found from the system PATH variable. This can help reduce the package size if vignettes contain PNG plots (thanks, @nanxstats, https://nanx.me/blog/post/rpkgs-pngquant-ragg/).

BUG FIXES

• spin() stopped working with input that cannot be parsed as R code due to #1605. Now it works again (thanks, @Hemken, #1773).

• write_bib() generated empty entries for packages without URLs (thanks, @bastistician, #2304).

• The family argument was not passed to the pdf device (thanks, @sebkopf, rstudio/rmarkdown#2526).

• Trailing spaces escaped by \ should not be trimmed in kable() (thanks, @mjsmith037, #2308).

• kable() fails when the value of the caption argument is of length > 1 (thanks, @LeeMendelowitz, #2312).

• include_graphics() may provide an incorrect plot width to LaTeX when the locale setting for LC_NUMERIC is not C because the decimal separator may not be a dot (thanks, @tdhock, rstudio/rmarkdown#2525).

• When TinyTeX and the LaTeX package pdfcrop are installed, knitr::pdf_crop() is unable to find pdfcrop (thanks, @dmkaplan2000, rstudio/tinytex#435).

MAJOR CHANGES

• Unbalanced chunk delimiters (fences) in R Markdown documents are no longer allowed, as announced two years ago at https://yihui.org/en/2021/10/unbalanced-delimiters/ (#2306). This means the opening delimiter must strictly match the closing delimiter, e.g., if a code chunk starts with four backticks, it must also end with four; or if a chunk header is indented by two spaces, the closing fence must be indented by exactly two spaces. For authors who cannot update their R Markdown documents for any reason at the moment, setting options(knitr.unbalanced.chunk = TRUE) (e.g., in .Rprofile) can temporarily prevent knitr from throwing an error, but it is strongly recommended that you fix the problems as soon as possible, because this workaround will be removed in future.

• Package vignettes are tangled by default during R CMD check, per request from CRAN maintainers (d0d1b47). The consequence is that R CMD check will check R scripts tangled from vignettes by default, unless you set the environment variable _R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true. Previously, knitr would skip tangling vignettes during R CMD check, because R scripts tangled from vignettes are not guaranteed to valid. With the skip undone, R CMD check may fail in places other than CRAN (because CRAN has set the environment variable).

MINOR CHANGES

• Fixed broken vignettes, improved CSS for HTML vignettes, and reduced the file sizes.

• SQL code chunks that run ALTER statements are only executed and not tried to fecth a result (thanks, @maxschmi, #2330).

• The function imgur_upload() has been moved to (and enhanced in) the xfun package as xfun::upload_imgur() so it is no longer tied to knitr and can be reused by other pakages. Now knitr::imgur_upload() is only a wrapper function of xfun::upload_imgur(). You are recommended to use the latter (#2325).

• spin() dropped support for #- as the chunk delimiter token. Please use #+ or # %% or #| instead.

• Faster processing of cache dependencies in dep_auto() (thanks, @knokknok, #2318).

• Removed some S3 methods that are used internally and changed them to normal functions: print.block -> print_block, print.inline -> print_inline, process_group.block/process_group.inline -> process_group, and process_tangle.block/process_tangle.inline -> process_tangle.

knitr 1.45

NEW FEATURES

• Improved the error message to contain more specific information when YAML chunk options could not be parsed (thanks, @pedropark99, #2294).

BUG FIXES

• Special characters in the chunk option fig.alt are properly escaped now (thanks, @jay-sf, #2290).

• Negative numbers returned from inline R expressions lost their minus signs when formatted in the scientific notation (thanks, @fkohrt, #2288).

• convert_chunk_header(type = 'yaml') will now use dash option name for known knitr options, and numeric option are kept with same significant digits, e.g fig.width = 10 is converted to fig-width: 10.

• Add the necessary \newline to the last subfigure (thanks, @slrellison, rstudio/rmarkdown#2518).

• Percent signs (%) in LaTeX figure captions and short captions are properly escaped now (thanks, @s-u, #2302).

MAJOR CHANGES

• The object opts_current will be restored after each code chunk has finished executing. Previously, it would not be restored, which means even for inline R expressions, opts_current$get() will inherit chunk options from a previous code chunk (thanks, @rundel, #1988). Besides, opts_current$get('label') will return a unique label for inline expressions. One possible application is to construct unique figure paths via fig_path() (e.g., ropensci/magick#310).

• opts_current$set() without opts_current$lock(FALSE) will trigger a warning instead of an error for now and it will become an error in future (#2296).

knitr 1.44

NEW FEATURES

• kable() can generate Emacs org-mode tables now via kable(..., format = 'org') (thanks, @xvrdm #1372, @maxecharel #2258).

• Added support for the qmd (Quarto) output format to spin(), e.g., spin('script.R', format = 'qmd') (thanks, @cderv, #2284).

• write_bib() has a new argument packageURL to control whether to use a URL from the DESCRIPTION file or the one generated by utils::citation() (thanks, @dmurdoch, #2264).

• Updated the package vignette vignette('knit_print', 'knitr') to mention that package authors no longer have to make knitr a hard dependency if they want to define S3 methods for knitr::knit_print with R >= 3.6.0 (thanks, @cderv, #1929).

• Added a new function download_image() to download an image from a URL and include it via include_graphics(). This is mainly for including online images when the output format is not HTML (e.g., LaTeX), because the URL will not work as the image path, and it has to be downloaded beforehand (thanks, @bayeslearner, #2274).

BUG FIXES

• Make the internal function add_html_caption() work with Quarto <= v1.3.353 (thanks, @giabaio, #2261).

• Fixed a bug in spin(format = 'Rnw') reported by @Tarious14 at yihui/yihui.org#769 (reply in thread)

• When the chunk option dev = 'svglite', the svglite device should be used to record plots (thanks, @Darxor, #2272).

• Figure captions are no longer escaped for reStructuredText output, and the alt text can also be specified via the fig.alt chunk option now (thanks, @trevorld, #2023).

• Use the correct type of progress bar when rendering Quarto documents in RStudio, which takes place in RStudio's background jobs pane or build pane (thanks, @hadley, #2271).

• The opts_current object can no longer be modified within code chunks via its $set() method (thanks, @AshesITR, #1798).

• The argument col.names of kable() can be used to specify the column name of row names now, e.g., kable(head(mtcars), col.names = c("car", names(mtcars))) ("car" will be the column name of row names in the first column) (thanks, @iago-pssjd, #1933).

MAJOR CHANGES

• Dashes (-) in the names of all chunk options are normalized to dots (.) now, e.g., fig-height will be converted to fig.height. This is to make knitr more compatible with Quarto since Quarto always use dashes in chunk option names (#2282).

MINOR CHANGES

• In-body chunk options (#|) are now preserved when extracting code from a document via purl() (thanks, @LuisLauM, #2268).

• A warning message will be issued when taking PDF screenshots for HTML widgets with the webshot2 package, because webshot2 doesn't use the correct figure size at the moment (thanks, @icejean, #2276).

• If the title argument of knit2wp() is omitted and a title field is specified in the YAML metadata of the input document, the YAML title will be used (thanks, @arencambre, #1924).

knitr 1.43

NEW FEATURES

• Progress bar includes the chunk location (chunk-name @ file:line) when options(knitr.progress.linenums = TRUE) is set (thanks, @zeehio, #2232).

• The global option knitr.progress.simple can be used to decide whether to output the bar in the progress. When set to FALSE, only the step numbers and chunk labels will be printed, and the progress bar is omitted. This can be more useful for logging purposes since the bar itself is not useful (thanks, @hadley, #2221). By default, the simple progress output is used when the progress is not written to a connection such as stdout or stderr (e.g., written to a file instead), or the output connection is not a "terminal".

• HTML Widgets can now support alt text by specifying an attribute aria-labelledby="<label>" in their first HTML tag. The text will be obtained from the fig.alt or fig.cap chunk option in the usual way (thanks, @dmurdoch, #2243).

• Added a new argument newline to kable() to handle newlines in data when the table output format is Markdown-based (simple, pipe, rst, or jira). By default, newlines are not processed, which can result in broken tables. To substitute newlines with spaces, use kable(..., newline = ' '). To remove newlines, use kable(..., newline = '') (thanks, @aronatkins, #2255).

BUG FIXES

• The chunk option collapse = TRUE works with HTML widgets now (thanks, @dmurdoch, #2212).

• Option hooks should be run before child documents are processed (thanks, @richarddmorey, #2247).

• For .Rnw documents, is_latex_output() returns TRUE for output formats sweave (render_sweave()) and listings (render_listings()) now (thanks, @DavisVaughan, #2231).

• write_bib() does not fail anymore if an empty string is passed as package name (thanks, @phargarten2, #2240).

• Fix an issue with using cache = TRUE on sql engine chunk not defining a output.var (thanks, @mfherman, @eitsupi, #1842).

• plot_crop() correctly checks the required tools (pdfcrop and ghostscript) on Windows when the LaTeX is distribution is TeX Live or TinyTeX (thanks, @remlapmot, #2246). An external installation of ghostscript is no longer required on Windows, since TeX Live's built-in ghostscript will be used.

• The chunk option dev.args was not recognized in certain cases (thanks, @petrbouchal, #2238).

MINOR CHANGES

• The css and js engines work for the markdown output format now. Previous these engines will not output anything when the output format is markdown. If you still want to disable them for markdown output, you may use the chunk option eval = FALSE or eval = knitr::is_html_output(excludes = 'markdown').

• is_html_output() recognizes R Markdown v1 documents now (.Rmd documents compiled via the markdown package).

• For .Rnw documents, dots in figure file paths are no longer sanitized to underscores (thanks, @otoomet, #2213). Other special characters are still sanitized, but this feature can be turned off via options(knitr.sanitize.paths = FALSE).

• imgur_upload() now recognizes a global option knitr.imgur.key or an environment variable R_KNITR_IMGUR_KEY for a custom client ID (thanks, @jonthegeek, #2233).

• imgur_upload() requires fewer package dependencies now. It only requires the curl package; httr is no longer required, and xml2 has become optional.

knitr 1.42

NEW FEATURES

• Better .qmd (Quarto) file support:

  • purl() will keep the in-chunk YAML syntax for options in the tangled R file
  • knit() will produce a .md file instead of .txt

• 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().

• Allow concordances to be embedded in HTML output (thanks, @dmurdoch, #2200).

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, yihui/yihui.org#1458).

• The stringr dependency has been removed. All string operations are done with base R now (thanks, @HughParsonage #1549 #1552, @rich-iannone #2174 #2177 #2186 #2187 #2195 #2202 #2205).

MINOR CHANGES

• Improved the error message when inline R code cannot be parsed (thanks, @hadley #2173, @rich-iannone #2198).

• 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).

BUG FIXES

• The sql engine now correctly prints tables with NA in the first column (thanks, @mariusbommert, #2207).

knitr 1.41

NEW FEATURES

• Added support for generating Jira tables via kable(, format = 'jira') (thanks, @pedropark99 #2180, @mruessler #2024).

• Added a new chunk option fig.id. When it is TRUE, the chunk option out.extra will gain an id attribute for each image from a code chunk in R Markdown (thanks, @jooyoungseo, #2169). By default, the attribute consists of a prefix, the chunk label, and the figure number. See https://yihui.org/knitr/options/ for detailed documentation of fig.id.

• Added an argument exact to pandoc_to() and pandoc_from() to decide whether to use/return the exact Pandoc output/input format name. If not (default), Pandoc extensions will be removed from the format name, e.g., latex-smart will be treated as latex.

BUG FIXES

• Plot created outside of knit() could sneak into knit_child() results (thanks, @niklaswillrich, #2166).

• User-provided background colors for code chunks in .Rnw documents may fail (thanks, @nielsrhansen, #2167).

• tabularx and xltabular tables should work without captions (thanks, @amarakon, #2188).

knitr 1.40

NEW FEATURES

• Added a function convert_chunk_header() to convert the old in-header chunk options to the new in-body chunk options (#2149 #2151).

• Added a new "graphics device", dev = "gridSVG", which uses gridSVG::grid.export() to export grid graphics to SVG (thanks, @jooyoungseo, #2152).

• Added a new engine eviews, which calls the EviewsR package to execute EViews code (thanks, @sagirumati, #2158).

• Added support for a php engine like other engines for interpreted languages. It will call php -r <code>, with <code> being the chunk content (thanks, @ralmond, #2144).

• Per suggestion of @jakubkaczor (#2116) and discussion with @pedropark99 (#2140), the chunk option fig.sep can also be used to add LaTeX code before the first sub-figure now. Previously this option can only be used for adding LaTeX code after each sub-figure.

• knitr::kable() supports tabularx and xltabular environments now for LaTeX tables, e.g., knitr::kable(head(iris), format = 'latex', tabular = 'tabularx') (thanks, @amarakon, #2138).

• For HTML output formats of R Markdown, SVG plots (e.g., in case of chunk option dev = 'svg' or dev = 'gridSVG') can be embedded differently now when options(knitr.svg.object = TRUE): if the HTML output is self-contained, the raw SVG code will be embedded directly in HTML, otherwise the .svg file is embedded in the <object> tag. By default, this feature is not enabled, i.e., the default is options(knitr.svg.object = FALSE) for backward-compatibility, which means the <img> tag is used for SVG plots just like other plot formats. This new feature will make assistive technology agents, such as screen readers, interact with SVG plots (thanks, @jooyoungseo, #2152).

BUG FIXES

• Fixed epub2 output not being considered as HTML format (thanks, @flipacholas, #2145).

• kable(format = 'pipe') calculates column widths correctly now if any text columns contain Markdown hyperlinks (thanks, @jacobbien, #2148).

• dev.args = list(engine = ...) was ignored by dev = 'tikz' when the tikz plot is compiled to PDF (thanks, @fkohrt, #2150).

MINOR CHANGES

• When the inline R code cannot be correctly parsed, the error message will show the original code in addition to the parsing error, which can make it easier to identify the code error in the source document (thanks, @AlbertLei, #2141).

• The internal function knitr:::wrap() has been removed from this package. If you rely on this function, you will have to use the exported function knitr::sew() instead.

• Duplicate chunk label error will now be thrown with code chunks using code or file chunk options (thanks, @mine-cetinkaya-rundel, #2126).

• Simplified R Markdown's inline code parser (thanks, @atusy, #2143).