Upstream changes:
CHANGES IN knitr VERSION 1.15.1
@yihui yihui released this on 23 Nov 2016 · 49 commits to master since this release
NEW FEATURES
added a new hook function hook_pngquant() that can call pngquant to optimize PNG images (thanks, @slowkow, #1320)
BUG FIXES
not really a knitr bug, but knit_params() should be better at dealing with multibyte characters now due to the bug fix in the yaml package viking/r-yaml#6
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v1.15
b08a7bc
CHANGES IN knitr VERSION 1.15
@yihui yihui released this on 10 Nov 2016 · 63 commits to master since this release
NEW FEATURES
NA values can be displayed using different characters (including empty strings) in kable(); you can set the option knitr.kable.NA, e.g. options(knitr.kable.NA = '') to hide NA values (#1283)
added a fortran95 engine (thanks, @stefanedwards, #1282)
added a block2 engine for R Markdown documents as an alternative to the block engine; it should be faster and supports arbitrary Pandoc's Markdown syntax, but it is essentially a hack; note when the output format is LaTeX/PDF, you have to define \let\BeginKnitrBlock\begin \let\EndKnitrBlock\end in the LaTeX preamble
figure captions specified in the chunk option fig.cap are also applied to HTML widgets (thanks, @byzheng, rstudio/bookdown#118)
when the chunk option fig.show = 'animate' and ffmpeg.format = 'gif', a GIF animation of the plots in the chunk will be generated for HTML output (https://twitter.com/thomasp85/status/785800003436421120)
added a width argument to write_bib() so long lines in bib entries can be wrapped
the inline syntax r#code is also supported besides r code; this can make sure the inline expression is not split when the line is wrapped (thanks, Dave Jarvis)
provided a global R option knitr.use.cwd so users can choose to evaluate the R code chunks in the current working directory after setting options(knitr.use.cwd = TRUE); the default is to evaluate code in the directory of the input document, unless the knitr option opts_knit$set(root.dir = ...) has been set
if options(knitr.digits.signif = TRUE), numbers from inline expressions will be formatted using getOption('digits') as the number of significant digits, otherwise (the default behavior) getOption('digits') is treated as the number of decimal places (thanks, @numatt, #1053)
the chunk option engine.path can also be a list of paths to the engine executables now, e.g., you can set knitr::opts_chunk$set(engine.path = list(python = '/anaconda/bin/python', perl = '/usr/local/bin/perl')), then when a python code chunk is executed, /anaconda/bin/python will be called instead of the system default (rstudio/rmarkdown#812)
introduced a mechanism to protect text output in the sense that it will not be touched by Pandoc during the conversion from R Markdown to another format; this is primarily for package developers to extend R Markdown; see ?raw_output for details (which also shows new functions extract_raw_output() and restore_raw_output())
MAJOR CHANGES
the minimal version of R required for knitr is 3.1.0 now (#1269)
the formatR package is an optional package since the default chunk option tidy = FALSE has been there for a long time; if you use tidy = TRUE, you need to install formatR separately if it is not installed
:set +m is no longer automatically added to haskell code chunks (#1274)
MINOR CHANGES
the package option opts_knit$get('stop_on_error') has been removed
the confusing warning message about knitr::knit2html() when buiding package vignettes using the knitr::rmarkdown engine without pandoc/pandoc-citeproc has been removed (#1286)
the default value of the quiet argument of plot_crop() was changed from !opts_knit$get('progress') to TRUE, i.e., by default the messages from cropping images are suppressed
BUG FIXES
the chunk option cache.vars did not really behave like what was documented (thanks, @simonkth, #1280)
asis_output() should not be merged with normal character output when results='hold' (thanks, @kevinushey, #1310)
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v1.14
b34be0d
CHANGES IN knitr VERSION 1.14
@yihui yihui released this on 12 Aug 2016 · 845 commits to master since this release
NEW FEATURES
improved caching for Rcpp code chunks: the shared library built from the C++ code will be preserved on disk and reloaded the next time if caching is enabled (chunk option cache = TRUE), so that the exported R functions are still usable in later R code chunks; note this feature requires Rcpp >= 0.12.5.6 (thanks, @jjallaire, #1239)
added a helper function all_rcpp_labels(), which is simply all_labels(engine == 'Rcpp') and can be used to extract all chunk lables of Rcpp chunks
added a new engine named sql that uses the DBI package to execute SQL queries, and optionally assign the result to a variable in the knitr session; see http://rmarkdown.rstudio.com/authoring_knitr_engines.html for details (#1241)
fig.keep now accepts numeric values to index low-level plots to keep (#1265)
BUG FIXES
fixed#1211: pandoc('foo.md') generates foo_utf8.html instead of foo.html by default
fixed#1236: include = FALSE for code chunks inside blockquotes did not work (should return > instead of a blank line) (thanks, @fmichonneau)
fixed#1217: define the command \hlipl for syntax highlighting for Rnw documents (thanks, @conjugateprior)
fixed#1215: restoring par() settings might fail when the plot window is partitioned, e.g. par(mfrow = c(1, 2)) (thanks, @jrwishart @jmichaelgilbert)
fixed#1250: in the quiet mode, knit() should not emit the message "processing file ..." when processing child documents (thanks, @KZARCA)
MAJOR CHANGES
knitr will no longer generate screenshots automatically for HTML widgets if the webshot package or PhantomJS is not installed
MINOR CHANGES
if dev = 'cairo_pdf', the cairo_pdf device will be used to record plots (previously the pdf device was used) (#1235)
LaTeX short captions now go up to the first ., : or ; character followed by a space or newline (thanks, @knokknok, #1249)
Upstream changes:
CHANGES IN knitr VERSION 1.13
NEW FEATURES
code chunks that generate metadata may be cached now; it requires htmlwidgets >= v0.6 and htmltools >= 0.3.3 if you cache code chunks that contain HTML widgets or Shiny inputs/outputs (#1158)
when the output format is not HTML, HTML widgets used to fail to render; now knitr will try to generate static screenshots for HTML widgets automatically using the webshot package; you can specify alternative screenshots via the chunk option screenshot.alt (which takes a character vector of image paths), and pass more options to webshot::webshot() via the chunk option screenshot.opts, e.g. list(delay = 3, cliprect = 'viewport')
added two functions include_url() and include_app() to embed URLs in the output (the latter is for Shiny app URLs); when the output format is HTML, iframe will be used; otherwise screenshots of the URLs will be used
screenshotting for HTML widgets and URLs can be forced for all output formats via the chunk option screenshot.force = TRUE; if you set the chunk option screenshot.force = FALSE, knitr will just render these content normally and not take screenshots
added a new chunk option fig.link, which can be used to attach hyperlinks on figures, e.g. you can add a link to a screenshot of a Shiny app so that readers can check out the actual live app after clicking on the static screenshot (this chunk option currently only works for Markdown and LaTeX output)
syntactical errors in code chunks will be allowed when the chunk option error = TRUE and the package version of evaluate is at least 0.8.4; previously knitr would just stop on parsing errors (hadley/evaluate#65)
PNG/JPEG images included via include_graphics() also respects the chunk option dpi now; if it is numeric and the chunk option out.width is not set, the output width (in inches) of an image will be automatically calculated from the actual width (in pixels) divided by dpi; note this feature requires the packages png and/or jpeg to be installed, and you can disable the feature using dpi = NA (thanks, @hadley, rstudio/bookdown#38)
added a new hook function named evaluate in knit_hooks so that users can redefine a evaluator to evaluate the code chunk; the default is evaluate::evaluate(), and your custom evaluator must be compatible with evaluate::evaluate() in terms of the argument names and the data structure of the returned value (a list of values with special classes)
added a new function combine_words() to combine multiple words / phrases into a single string, which may be useful in inline R expressions, e.g. combine_words(c('a', 'b', 'c')) returns a, b, and c
render_markdown() gained a new argument fence_char to customize the character to be used as the code blocks fence, e.g. it can be a backtick, or a tilde, depending on the Markdown rendering engine (thanks, @tinyheero, #1161)
the pandoc() function no longer assumes Markdown input (thanks, @scls19fr, #1170)
added a new function knit_meta_add() so that users can manually inject metadata into the current knitr session
for the tikz engine, if fig.ext = 'svg', dvisvgm will be called to convert the DVI output of TikZ to SVG; you need to install dvisvgm, and Windows users have to install GhostScript as well (thanks, @dkilfoyle, #1177)
new js and css engines which surround their content with <script> and <style> tags respecitvely, and print no output when not in an HTML document
for LaTeX tables, kable() supports short captions now via the caption.short argument, e.g. kable(..., caption = 'A long caption', caption.short = 'A short caption') (thanks, @ismayc, #1199)
added three global R options knitr.sanitize.errors, knitr.sanitize.warnings, and knitr.sanitize.messages to mask or change the messages, e.g. if options(knitr.sanitize.errors = TRUE) and the chunk option error = TRUE, the actual error message will be replaced by a character string like "An error occurred"; these options can also accept character values so you can customize the messages to be displayed, e.g. options(knitr.sanitize.warnings = 'You had a warning from the code'); see rstudio/shiny#1123 for the motivation of these options
BUG FIXES
when the chunk option cache.rebuild = TRUE, the cache database should be rewritten (thanks, Oleg Mayba)
include_graphics() did not work in inline R expressions (thanks, @WastlM, #1166)
the cex parameter was not correctly restored in the case of opts_knit$set(global.par = TRUE) (http://stackoverflow.com/q/35606445/559676)
for Rnw documents, when there are two instances of \documentclass{}, knitr might mistakenly treats the second instance as the the actual command to declare the document class (thanks, #1180, @ekstroem)
corrected the environment for evaluating R scripts in stitch_rhtml() and stitch_rmd() (thanks, @Hughan, #1207)
MAJOR CHANGES
the default value of the package option eval.after is changed from NULL to fig.cap, i.e. the figure caption will always be evaluated after a code chunk is evaluated (thanks, @JoshOBrien, #1165)
the function eclipse_theme() has been removed since the website eclipsecolorthemes.org has been down for a long time
Problems found locating distfiles:
Package acroread7: missing distfile AdobeReader_enu-7.0.9-1.i386.tar.gz
Package acroread8: missing distfile AdobeReader_enu-8.1.7-1.sparc.tar.gz
Package cups-filters: missing distfile cups-filters-1.1.0.tar.xz
Package dvidvi: missing distfile dvidvi-1.0.tar.gz
Package lgrind: missing distfile lgrind.tar.bz2
Otherwise, existing SHA1 digests verified and found to be the same on
the machine holding the existing distfiles (morden). All existing
SHA1 digests retained for now as an audit trail.
This package provides a general-purpose tool for dynamic report
generation in R, which can be used to deal with any type of (plain
text) files, including Sweave, HTML, Markdown, reStructuredText,
AsciiDoc, and Textile. R code is evaluated as if it were copied and
pasted in an R terminal thanks to the evaluate package (e.g., we do
not need to explicitly print() plots from ggplot2 or lattice). R code
can be reformatted by the formatR package so that long lines are
automatically wrapped, with indent and spaces added, and comments
preserved. A simple caching mechanism is provided to cache results
from computations for the first time and the computations will be
skipped the next time. Almost all common graphics devices, including
those in base R and add-on packages like Cairo, cairoDevice and
tikzDevice, are built-in with this package and it is straightforward
to switch between devices without writing any special functions. The
width and height as well as alignment of plots in the output document
can be specified in chunk options (the size of plots for graphics
devices is also supported). Multiple plots can be recorded in a single
code chunk, and it is also allowed to rearrange plots to the end of a
chunk or just keep the last plot. Warnings, messages and errors are
written in the output document by default (can be turned off). The
language in code chunks is not restricted to R (there is simple
support to Python and shell scripts, etc). Many features are borrowed
from or inspired by Sweave, cacheSweave, pgfSweave, brew and decumar.
Note: this commit is part of reorganizing some of the recently
imported R packages, which are being reimported into more appropriate
categories (and removed from math) as a result of a recent discussion
on tech-pkg and privately with wiz@. See the thread starting with:
http://mail-index.netbsd.org/tech-pkg/2014/09/05/msg013558.html
wen
agc
brook