version 1.15.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: knitr
 Type: Package
 Title: A General-Purpose Package for Dynamic Report Generation in R
-Version: 1.15
-Date: 2016-11-09
+Version: 1.15.1
+Date: 2016-11-22
 Authors@R: c(
     person("Yihui", "Xie", email = "xie@yihui.name", role = c("aut", "cre")),
     person("Adam", "Vogt", role = "ctb"),
@@ -45,6 +45,7 @@ Authors@R: c(
     person("Joseph", "Larmarange", role = "ctb"),
     person("Julien", "Barnier", role = "ctb"),
     person("Kaiyin", "Zhong", role = "ctb"),
+    person("Kamil", "Slowikowski", role = "ctb"),
     person(c("Kevin", "K."), "Smith", role = "ctb"),
     person("Kirill", "Mueller", role = "ctb"),
     person("Kohske", "Takahashi", role = "ctb"),
@@ -79,7 +80,7 @@ Description: Provides a general-purpose tool for dynamic report generation in R
     using Literate Programming techniques.
 Depends: R (>= 3.1.0)
 Imports: evaluate (>= 0.10), digest, highr, markdown, stringr (>= 0.6),
-        yaml (>= 2.1.5), methods, tools
+        yaml, methods, tools
 Suggests: formatR, testit, rgl (>= 0.95.1201), codetools, rmarkdown,
         htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10), png, jpeg,
         XML, RCurl, DBI (>= 0.4-1), tibble
@@ -102,7 +103,7 @@ Collate: 'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R'
         'utils-vignettes.R' 'zzz.R'
 RoxygenNote: 5.0.1
 NeedsCompilation: no
-Packaged: 2016-11-08 23:46:37 UTC; yihui
+Packaged: 2016-11-22 05:33:02 UTC; yihui
 Author: Yihui Xie [aut, cre],
   Adam Vogt [ctb],
   Alastair Andrew [ctb],
@@ -146,6 +147,7 @@ Author: Yihui Xie [aut, cre],
   Joseph Larmarange [ctb],
   Julien Barnier [ctb],
   Kaiyin Zhong [ctb],
+  Kamil Slowikowski [ctb],
   Kevin K. Smith [ctb],
   Kirill Mueller [ctb],
   Kohske Takahashi [ctb],
@@ -175,4 +177,4 @@ Author: Yihui Xie [aut, cre],
   Wush Wu [ctb],
   Zachary Foster [ctb]
 Repository: CRAN
-Date/Publication: 2016-11-09 18:28:52
+Date/Publication: 2016-11-22 09:36:46

MD5

@@ -1,16 +1,16 @@
-6c01175105eb2c5db4b4efc56826b710 *DESCRIPTION
-54b1c3f9e6b195d59baf287211d779af *NAMESPACE
-2a6b600badb2dc10730df2a1efec9f18 *R/block.R
+b0acd6b4402bebffe304e38ea3eb80e9 *DESCRIPTION
+37621070683a68a4bc227566e0a03721 *NAMESPACE
+2020a5be55f21396e99866ad276388cb *R/block.R
 397799b33f6c92366eb231e7064b368b *R/cache.R
-6da551afb249af398702fec5ff4e537c *R/citation.R
+f4de17ed656fa9124cce2e7429e27d6a *R/citation.R
 d3066cdaec8d60368dfa30093222ac88 *R/concordance.R
 dcd2c08d9ce1917ce089d8578cb40457 *R/defaults.R
-1b2ae89a5a503c719b93d7fc00866471 *R/engine.R
+77b340611c485589d7441d395852defe *R/engine.R
 44370920d24fd560ceeb3f5985c83215 *R/header.R
 e36c54d9b272ea1245ab8e0bcba9c8a1 *R/highlight.R
 ef19e925acc44824076bc6eb2dfc50aa *R/hooks-asciidoc.R
 ad8783b17b5906fc6c07f09f4d296f7b *R/hooks-chunk.R
-22921f2a49542ae19e31e742f9a7392b *R/hooks-extra.R
+be602dec68f60269d7d9bb0c06c2d3a7 *R/hooks-extra.R
 e4ada63ee08edeb85d8989d51407edad *R/hooks-html.R
 209d5b0c6fcf3e44d6bff450f3d3662f *R/hooks-latex.R
 692badbd7b542004c8d6f23618bc7d3a *R/hooks-md.R
@@ -20,7 +20,7 @@ e4ada63ee08edeb85d8989d51407edad *R/hooks-html.R
 e257dc01156580249316cb45eed9018e *R/output.R
 21ce69e8540725f8206050bc4e71ea3c *R/package.R
 dbfc00595b8621af0cb83c20274ed99f *R/pandoc.R
-4f2a820f12d00290dc4977bc0539ba9c *R/params.R
+bfffd7d37228dba6fc19745f53a7a608 *R/params.R
 1eea1417232ec06100f9c58fefc10622 *R/parser.R
 40a3f7837f7cceecd189b0fb2a396152 *R/pattern.R
 d4246a8aa0b1e2ebdea43123149a1f3a *R/plot.R
@@ -37,8 +37,8 @@ cef5bab6cd92a77e0dbe91d5f8235098 *R/utils-base64.R
 18927d3734faccb549ae7a93c038f664 *R/utils-vignettes.R
 70a9b341689125a0de4c2c0edb887329 *R/utils.R
 64580757ed828267f6976d73231f1f8f *R/zzz.R
-d651706f6a72d80af95501d5d3ca6c68 *README.md
-c7a70576b151bb14f645d053c262bed1 *build/knitr.pdf
+d341508952d70b263d2c079e2b9e4424 *README.md
+5df8c6a245231c66b4543f6c82d34bb0 *build/knitr.pdf
 c5617fe42ca44b01644e6da5e63774cd *build/vignette.rds
 5320cec79c972798fe0eb5579eb51927 *demo/00Index
 a0d48f6ce89f9e1d39ee7248ff8c5511 *demo/gwidgets.R
@@ -57,21 +57,21 @@ b47c340c4060c759ed158eeb0c258560 *inst/doc/docco-classic.Rmd
 0a3c5c8a96824d354a8573aa1e5a7e75 *inst/doc/docco-linear.html
 d060cc6329c3b03347a61d5240cbb527 *inst/doc/knit_expand.R
 45dec121925f328760fee414d1890168 *inst/doc/knit_expand.Rmd
-d52aedfffc7ae585ada632f5bcc35cee *inst/doc/knit_expand.html
+d16dc4b606ff71296097a82cd2b58455 *inst/doc/knit_expand.html
 4eea99d3bf4431c606eacdf79713ded6 *inst/doc/knit_print.R
 c90ac685808dfe85c05d21191dfe36a8 *inst/doc/knit_print.Rmd
-a170fcfc48598cf0e163e1647ab8eb86 *inst/doc/knit_print.html
+e6f43dfed1f856b04612e1b31a292ec9 *inst/doc/knit_print.html
 7c333d10e4255222789dda55dad958d8 *inst/doc/knitr-html.R
 824b923dd4a500fb460a2366aabfb19c *inst/doc/knitr-html.Rhtml
 8a8a2edbfa2ae3c06f8a335fd22d1c2e *inst/doc/knitr-html.html
 97b83b9e94f5690f0dcce82bda0eef48 *inst/doc/knitr-intro.R
 fa0189ffab9ee6f23ebf599740a16ddb *inst/doc/knitr-intro.Rmd
-3ef6e0359ea52a0f7700ae75749eef79 *inst/doc/knitr-intro.html
+a004b0626171a81e690ebce02eebe371 *inst/doc/knitr-intro.html
 aa3f1c19ae5b4ba70df72922f67996dc *inst/doc/knitr-markdown.R
 3d047ff09d3b18b13466241cda178c57 *inst/doc/knitr-markdown.Rmd
-4be2b0349f6a8c65564bc26b4d695eae *inst/doc/knitr-markdown.html
+d61323ff5fbf6706eb21c9aec6bfa29c *inst/doc/knitr-markdown.html
 b41a48fcc33fd13fcb30ff44bb644b03 *inst/doc/knitr-refcard.Rmd
-86131bc39933175e6c519c8da9f8d11e *inst/doc/knitr-refcard.pdf
+7e989013fd52f274aa3160ed0cd0c62f *inst/doc/knitr-refcard.pdf
 f16d37ed927336b920c67ce2e958ffc5 *inst/examples/README.md
 80d81165446ea535b4368b5f6375d7a1 *inst/examples/Sweavel.sty
 5cc86725bad53543ab7cc881a2783269 *inst/examples/child/knitr-child-a.Rnw
@@ -224,7 +224,7 @@ c2abe08ea4638d3c157c8df34a621e47 *inst/themes/zmrok.css
 85e96631ee501c9741b3b3c6872f88b8 *man/all_labels.Rd
 0d0e0d50e323fe0b63fdddd90bd904dc *man/all_patterns.Rd
 c66a982c680ce38bcad35e31d5ff5b8e *man/asis_output.Rd
-8ba9a74eb42f834127d9a8a7012a4d32 *man/chunk_hook.Rd
+27fd66bb85a5a21262f49cbae16a8bae *man/chunk_hook.Rd
 f61d44236133b9dae05c6754e3e97e17 *man/clean_cache.Rd
 e867bbdfee1ee5f5396acf32b43f6f34 *man/combine_words.Rd
 0dc6684ce1d6e71acd2a3d93402b8f37 *man/current_input.Rd

NAMESPACE

@@ -44,6 +44,7 @@ export(hook_plot_md)
 export(hook_plot_rst)
 export(hook_plot_tex)
 export(hook_plot_textile)
+export(hook_pngquant)
 export(hook_purl)
 export(hook_r2swf)
 export(hook_scianimator)

R/block.R

@@ -476,6 +476,6 @@ label_code = function(code, label) {
          '----', code)
 }
 
-as.source <- function(code) {
+as.source = function(code) {
   list(structure(list(src = code), class = 'source'))
 }

R/citation.R

@@ -86,6 +86,7 @@ write_bib = function(
     }
     bib = lapply(bib, function(b) {
       b['author'] = sub('Duncan Temple Lang', 'Duncan {Temple Lang}', b['author'])
+      b['title'] = sub("'RStudio'", 'RStudio', b['title'])
       if (!('year' %in% names(b))) b['year'] = .this.year
       idx = which(names(b) == '')
       if (!is.null(width)) b[-idx] = stringr::str_wrap(b[-idx], width, 2, 4)

R/engine.R

@@ -106,8 +106,8 @@ eng_interpreted = function(options) {
     )
   } else paste(switch(
     engine, bash = '-c', coffee = '-e', groovy = '-e', lein = 'exec -e',
-    mysql = '-e', node = '-e', perl = '-e', psql = '-c', python = '-c',
-    ruby = '-e', scala = '-e', sh = '-c', zsh = '-c', NULL
+    mysql = '-e', node = '-e', octave = '--eval', perl = '-e', psql = '-c',
+    python = '-c', ruby = '-e', scala = '-e', sh = '-c', zsh = '-c', NULL
   ), shQuote(paste(options$code, collapse = '\n')))
 
   # FIXME: for these engines, the correct order is options + code + file
@@ -543,8 +543,8 @@ eng_sql = function(options) {
 local({
   for (i in c(
     'awk', 'bash', 'coffee', 'gawk', 'groovy', 'haskell', 'lein', 'mysql',
-    'node', 'perl', 'psql', 'python', 'Rscript', 'ruby', 'sas', 'scala', 'sed',
-    'sh', 'stata', 'zsh'
+    'node', 'octave', 'perl', 'psql', 'python', 'Rscript', 'ruby', 'sas',
+    'scala', 'sed', 'sh', 'stata', 'zsh'
   )) knit_engines$set(setNames(list(eng_interpreted), i))
 })
 

R/hooks-extra.R

@@ -21,6 +21,11 @@
 #' provide additional parameters to the program \command{optipng}, e.g.
 #' \code{optipng = '-o7'}.
 #'
+#' The function \code{hook_pngquant()} calls the program \command{pngquant} to
+#' optimize PNG images. Note the chunk option \code{pngquant} can be used to
+#' provide additional parameters to the program \command{pngquant}, e.g.
+#' \code{pngquant = '--speed=1 --quality=0-50'}.
+#'
 #' When the plots are not recordable via \code{\link[grDevices]{recordPlot}} and
 #' we save the plots to files manually via other functions (e.g. \pkg{rgl}
 #' plots), we can use the chunk hook \code{hook_plot_custom} to help write code
@@ -62,26 +67,46 @@ hook_pdfcrop = function(before, options, envir) {
 #' @export
 #' @rdname chunk_hook
 hook_optipng = function(before, options, envir) {
+  hook_png(before, options, envir, 'optipng')
+}
+
+hook_png = function(
+  before, options, envir, cmd = c('optipng', 'pngquant'), post_process = identity
+) {
   if (before) return()
   ext = tolower(options$fig.ext)
   if (ext != 'png') {
     warning('this hook only works with PNG at the moment'); return()
   }
-  if (!nzchar(Sys.which('optipng'))) {
-    warning('cannot find optipng; please install and put it in PATH'); return()
+  cmd = match.arg(cmd)
+  if (!nzchar(Sys.which(cmd))) {
+    warning('cannot find ', cmd, '; please install and put it in PATH'); return()
   }
   paths = all_figs(options, ext)
 
   in_base_dir(
     lapply(paths, function(x) {
       message('optimizing ', x)
-      x = shQuote(x)
-      cmd = paste('optipng', if (is.character(options$optipng)) options$optipng, x)
+      cmd = paste(cmd, if (is.character(options[[cmd]])) options[[cmd]], shQuote(x))
       (if (is_windows()) shell else system)(cmd)
+      post_process(x)
     })
   )
   return()
 }
+
+#' @export
+#' @rdname chunk_hook
+hook_pngquant = function(before, options, envir) {
+  if (is.null(options[['pngquant']])) options$pngquant = '--skip-if-larger'
+  options[['pngquant']] = paste(options[['pngquant']], '--ext -fs8.png')
+  hook_png(before, options, envir, 'pngquant', function(x) {
+    # pngquant creates an output file with '-fs8.png' as the extension.
+    x2 = sub("\\.png$", "-fs8.png", x)
+    if (file.exists(x2)) file.rename(x2, x)
+  })
+}
+
 #' @export
 #' @rdname chunk_hook
 hook_plot_custom = function(before, options, envir){

R/params.R

@@ -79,8 +79,7 @@ knit_params = function(text, evaluate = TRUE) {
   yaml = yaml_front_matter(text)
   if (is.null(yaml)) return(list())
 
-  yaml = enc2utf8(yaml)
-  knit_params_yaml(yaml, evaluate = evaluate)
+  knit_params_yaml(enc2utf8(yaml), evaluate = evaluate)
 }
 
 #' Extract knit parameters from YAML text
@@ -106,7 +105,7 @@ knit_params_yaml = function(yaml, evaluate = TRUE) {
 
   # if we found paramters then resolve and return them
   if (is.list(parsed_yaml) && !is.null(parsed_yaml$params)) {
-    resolve_params(mark_utf8(parsed_yaml$params), evaluate = evaluate)
+    resolve_params(parsed_yaml$params, evaluate = evaluate)
   } else {
     list()
   }
@@ -119,19 +118,6 @@ flatten_params = function(params) {
   res
 }
 
-# copied from rmarkdown:::mark_utf8
-mark_utf8 = function(x) {
-  if (is.character(x)) {
-    Encoding(x) = 'UTF-8'
-    return(x)
-  }
-  if (!is.list(x)) return(x)
-  attrs = attributes(x)
-  res = lapply(x, mark_utf8)
-  attributes(res) = attrs
-  res
-}
-
 # Extract the yaml front matter (if any) from the passed lines. The front
 # matter is returned as a single-element character vector (with newlines
 # delimited by \n) suitable for passing to yaml::load. This code is based on
@@ -161,14 +147,12 @@ yaml_front_matter = function(lines) {
 
   front_matter = front_matter_lines
   front_matter = front_matter[2:(length(front_matter) - 1)]
-  # FIXME: this is only for apex on CRAN (https://github.com/thibautjombart/apex/pull/15)
-  if (length(grep('^params:', front_matter)) == 0) return()
+  if (length(grep('^params:', front_matter)) == 0) return()  # no params in YAML
   front_matter = paste(front_matter, collapse = "\n")
 
   # ensure that the front-matter doesn't terminate with ':', so it won't cause a
   # crash when passed to yaml::load
   if (!grepl(":\\s*$", front_matter)) front_matter
-
 }
 
 

README.md

@@ -2,7 +2,7 @@
 
 [![Build Status](https://travis-ci.org/yihui/knitr.svg)](https://travis-ci.org/yihui/knitr)
 [![Coverage Status](https://coveralls.io/repos/yihui/knitr/badge.svg?branch=master&service=github)](https://coveralls.io/github/yihui/knitr?branch=master)
-[![Downloads from the RStudio CRAN mirror](http://cranlogs.r-pkg.org/badges/knitr)](https://cran.r-project.org/package=knitr)
+[![Downloads from the RStudio CRAN mirror](http://cranlogs.r-pkg.org/badges/knitr)](https://cran.rstudio.org/package=knitr)
 
 The R package **knitr** is a general-purpose literate programming engine,
 with lightweight API's designed to give users full control of the output
@@ -15,7 +15,7 @@ frequently asked questions (including where to ask questions).
 ## Installation
 
 You can install the stable version on
-[CRAN](https://cran.r-project.org/package=knitr):
+[CRAN](https://cran.rstudio.org/package=knitr):
 
 ```r
 install.packages('knitr', dependencies = TRUE)
@@ -39,8 +39,8 @@ devtools::install_github('yihui/knitr', build_vignettes = TRUE)
 ## Motivation
 
 While Sweave and related add-on packages like
-[**cacheSweave**](https://cran.r-project.org/package=cacheSweave) and
-[**pgfSweave**](https://cran.r-project.org/package=pgfSweave) are fairly good
+[**cacheSweave**](https://cran.rstudio.org/package=cacheSweave) and
+[**pgfSweave**](https://cran.rstudio.org/package=pgfSweave) are fairly good
 engines for literate programming in R, but I often feel my hands are tied,
 for example:
 
@@ -60,15 +60,15 @@ for example:
 - I wished there was a way to round the numbers in `\Sexpr{}` other than
   writing expressions like `\Sexpr{round(x, 3)}` for *each single* `\Sexpr{}`
 - I wished I did not have to `print()` plots from
-  [**ggplot2**](https://cran.r-project.org/package=ggplot2) and a simple
+  [**ggplot2**](https://cran.rstudio.org/package=ggplot2) and a simple
   `qplot(x, y)` would just give me a plot in Sweave
 - I wished users would never need instructions on `Sweave.sty` or run into
   troubles due to the fact that LaTeX cannot find `Sweave.sty`
 - I wished **cacheSweave** could print the results of a code chunk even if
   it was cached
-- I wished [**brew**](https://cran.r-project.org/package=brew) could support
+- I wished [**brew**](https://cran.rstudio.org/package=brew) could support
   graphics
-- I wished [**R2HTML**](https://cran.r-project.org/package=R2HTML) could
+- I wished [**R2HTML**](https://cran.rstudio.org/package=R2HTML) could
   support R code syntax highlighting
 - ...
 

inst/doc/knit_expand.html

@@ -220,7 +220,7 @@ <h1>Demos of <code>knit_expand()</code></h1>
 <pre><code class="r">knit_expand(text = &quot;The value of a is {{a}}, so a + 1 is {{a+1}}.&quot;, a = rnorm(1))
 </code></pre>
 
-<pre><code>## [1] &quot;The value of a is -0.420789961861209, so a + 1 is 0.579210038138791.&quot;
+<pre><code>## [1] &quot;The value of a is 0.703623490875254, so a + 1 is 1.70362349087525.&quot;
 </code></pre>
 
 <pre><code class="r">knit_expand(text = &quot;The area of a circle with radius {{r}} is {{pi*r^2}}&quot;, r = 5)
@@ -260,7 +260,7 @@ <h1>Demos of <code>knit_expand()</code></h1>
 <pre><code class="r">knit_expand(text = &quot;you cannot see the value of x {{x=rnorm(1)}}but it is indeed created: x = {{x}}&quot;)
 </code></pre>
 
-<pre><code>## [1] &quot;you cannot see the value of x but it is indeed created: x = -1.52347367655193&quot;
+<pre><code>## [1] &quot;you cannot see the value of x but it is indeed created: x = 1.53456091566555&quot;
 </code></pre>
 
 <pre><code class="r">res = knit_expand(text = c(&quot; x | x^2&quot;, &quot;{{x=1:5;paste(sprintf(\&quot;%2d | %3d\&quot;, x, x^2), collapse = \&quot;\n\&quot;)}}&quot;))

inst/doc/knit_print.html

@@ -12,7 +12,7 @@
 
 <meta name="author" content="Yihui Xie" />
 
-<meta name="date" content="2016-11-08" />
+<meta name="date" content="2016-11-21" />
 
 <title>Custom Print Methods</title>
 
@@ -70,7 +70,7 @@
 
 <h1 class="title toc-ignore">Custom Print Methods</h1>
 <h4 class="author"><em>Yihui Xie</em></h4>
-<h4 class="date"><em>2016-11-08</em></h4>
+<h4 class="date"><em>2016-11-21</em></h4>
 
 
 <div id="TOC">
@@ -110,10 +110,11 @@ <h2>Customize Printing</h2>
 ## }
 ## &lt;environment: namespace:knitr&gt;</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">methods</span>(knit_print)</code></pre></div>
-<pre><code>## [1] knit_print.data.frame*     knit_print.default*       
-## [3] knit_print.html*           knit_print.knit_asis*     
-## [5] knit_print.knitr_kable*    knit_print.shiny.tag*     
-## [7] knit_print.shiny.tag.list*
+<pre><code>##  [1] knit_print.data.frame*     knit_print.default*       
+##  [3] knit_print.grouped_df*     knit_print.html*          
+##  [5] knit_print.knit_asis*      knit_print.knitr_kable*   
+##  [7] knit_print.rowwise_df*     knit_print.shiny.tag*     
+##  [9] knit_print.shiny.tag.list* knit_print.tbl_sql*       
 ## see '?methods' for accessing help and source code</code></pre>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">getS3method</span>(<span class="st">&quot;knit_print&quot;</span>, <span class="st">&quot;default&quot;</span>)  <span class="co"># the default method</span></code></pre></div>
 <pre><code>## function (x, ..., inline = FALSE)