version 1.26

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: knitr
 Type: Package
 Title: A General-Purpose Package for Dynamic Report Generation in R
-Version: 1.25
+Version: 1.26
 Authors@R: c(
     person("Yihui", "Xie", role = c("aut", "cre"), email = "xie@yihui.name", comment = c(ORCID = "0000-0003-0645-5666")),
     person("Adam", "Vogt", role = "ctb"),
@@ -109,7 +109,7 @@ Suggests: formatR, testit, digest, rgl (>= 0.95.1201), codetools,
         rmarkdown, htmlwidgets (>= 0.7), webshot, tikzDevice (>= 0.10),
         tinytex, reticulate (>= 1.4), JuliaCall (>= 0.11.1), magick,
         png, jpeg, gifski, xml2 (>= 1.2.0), httr, DBI (>= 0.4-1),
-        showtext, tibble, sass, styler
+        showtext, tibble, sass, styler (>= 1.2.0)
 License: GPL
 URL: https://yihui.name/knitr/
 BugReports: https://github.com/yihui/knitr/issues
@@ -130,7 +130,7 @@ Collate: 'block.R' 'cache.R' 'utils.R' 'citation.R' 'hooks-html.R'
         'utils-vignettes.R' 'zzz.R'
 RoxygenNote: 6.1.1
 NeedsCompilation: no
-Packaged: 2019-09-17 13:24:32 UTC; yihui
+Packaged: 2019-11-12 20:05:16 UTC; yihui
 Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
   Adam Vogt [ctb],
   Alastair Andrew [ctb],
@@ -229,4 +229,4 @@ Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
   Wush Wu [ctb],
   Zachary Foster [ctb]
 Repository: CRAN
-Date/Publication: 2019-09-18 09:10:07 UTC
+Date/Publication: 2019-11-12 21:00:02 UTC

MD5

@@ -1,10 +1,10 @@
-2cfb53c978738d6961835fe0a24360f3 *DESCRIPTION
+92271eddf4e1e1ad77e06dfb6b7af664 *DESCRIPTION
 a916831d30a070fdfc0ee680362a5e40 *NAMESPACE
 33c703de02d6653651ac717fb150f49f *R/block.R
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 7bb8588a54afe6add2ed5d7742ee31c6 *R/header.R
 e02a4e40986a42a8d4f3e08d6a7c22b7 *R/highlight.R
@@ -17,7 +17,7 @@ e54524651326164b24c42cc10923cb5e *R/hooks-md.R
 be17cd3493a42bd2ca826c8f5ce82d73 *R/hooks-rst.R
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 1c6bec5eaed27eb45c44ea876cdec45f *R/package.R
 36909798b502a1152bade8fc7f7a55e5 *R/pandoc.R
 62a8271ab2bb4cb847b002d2735c5761 *R/params.R
@@ -35,7 +35,7 @@ b48c95e8eef8c8ad8a09a9d25119c670 *R/utils-rd2html.R
 510cf9590cc804e006adf18552fde34a *R/utils-sweave.R
 b698f55f469c38b3b21b4ed8191b38ac *R/utils-upload.R
 4f4027f41fa98f2d70c54689273c44c7 *R/utils-vignettes.R
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 64580757ed828267f6976d73231f1f8f *R/zzz.R
 e7e516bacd3923e52e48b8fda38d13dc *README.md
 05a0d19a5ff6e0062f0978cb9cf7bac0 *build/vignette.rds
@@ -45,32 +45,32 @@ a95e58617a42ea5ea95fa99a10f1c120 *demo/notebook.R
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 4874a71c96d939a22aa11a3f6ee0c0df *inst/bin/knit
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R/citation.R

@@ -2,33 +2,29 @@
 #'
 #' This function uses \code{\link[utils]{citation}} and
 #' \code{\link[utils]{toBibtex}} to create bib entries for R packages and write
-#' them in a file. Only the auto-generated citations are included for a package.
-#' This function can facilitate the auto-generation of bibliography databases
-#' for R packages, and it is easy to regenerate all the citations after updating
-#' R packages.
+#' them in a file. It can facilitate the auto-generation of bibliography
+#' databases for R packages, and it is easy to regenerate all the citations
+#' after updating R packages.
 #'
-#' The citation is forced to be generated from the \file{DESCRIPTION} file of
-#' the package (\code{citation(auto = TRUE)}). The keyword \samp{R-pkgname} is
-#' used for the bib item, where \samp{pkgname} is the name of the package. All
-#' references specified in the \file{CITATION} file of the package are ignored.
-#' The main purpose of this function is to automate the generation of the
-#' package citation information because it often changes (e.g. author, year,
-#' package version, ...). By comparison, paper/book citations don't change too
-#' often, so it is not a lot of work even if you just cut and paste such
-#' bibliography entries from \code{toBibtex(citation())}.
+#' For a package, the keyword \samp{R-pkgname} is used for its bib item, where
+#' \samp{pkgname} is the name of the package. Citation entries specified in the
+#' \file{CITATION} file of the package are also included. The main purpose of
+#' this function is to automate the generation of the package citation
+#' information because it often changes (e.g. author, year, package version,
+#' ...).
 #'
 #' @param x Package names. Packages which are not installed are ignored.
 #' @param file The (\file{.bib}) file to write. By default, or if \code{NULL},
 #'   output is written to the R console.
 #' @param tweak Whether to fix some known problems in the citations, especially
 #'   non-standard format of author names.
-#' @param width Width of lines in bibliography entries. If \code{NULL},
-#'   lines will not be wrapped.
+#' @param width Width of lines in bibliography entries. If \code{NULL}, lines
+#'   will not be wrapped.
 #' @param prefix Prefix string for keys in BibTeX entries; by default, it is
 #'   \samp{R-} unless \code{\link{option}('knitr.bib.prefix')} has been set to
 #'   another string.
-#' @return A list containing the citations. Citations are also written to the \code{file} as a
-#'   side effect.
+#' @return A list containing the citations. Citations are also written to the
+#'   \code{file} as a side effect.
 #' @note Some packages on CRAN do not have standard bib entries, which was once
 #'   reported by Michael Friendly at
 #'   \url{https://stat.ethz.ch/pipermail/r-devel/2010-November/058977.html}. I
@@ -69,6 +65,7 @@ write_bib = function(
     x = x[!idx]
   }
   x = setdiff(x, .base.pkgs) # remove base packages
+  x = sort(x)
   bib = sapply(x, function(pkg) {
     cite = citation(pkg, auto = if (pkg == 'base') NULL else TRUE)
     if (tweak) {
@@ -88,14 +85,42 @@ 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'])
+      # remove the ugly single quotes required by CRAN policy
+      b['title'] = gsub(
+        "'(RStudio|Htmlwidgets|iframes|TeX Live|LaTeX)'", '\\1', 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)
-      structure(c(b[idx[1L]], b[-idx], b[idx[2L]]), class = 'Bibtex')
+      b
     })
   }
-  bib = bib[sort(x)]
+  # also read citation entries from the CITATION file if provided
+  bib2 = lapply(x, function(pkg) {
+    if (pkg == 'base') return()
+    if (system.file('CITATION', package = pkg) == '') return()
+    cites = citation(pkg, auto = FALSE)
+    cites = Filter(x = cites, function(cite) {
+      # exclude entries identical to citation(pkg, auto = TRUE)
+      !isTRUE(grepl('R package version', cite$note))
+    })
+    s = make_unique(unlist(lapply(cites, function(cite) {
+      if (is.null(cite$year)) format(Sys.Date(), '%Y') else cite$year
+    })))
+    mapply(cites, s, FUN = function(cite, suffix) {
+      # the entry is likely to be the same as citation(pkg, auto = TRUE)
+      if (isTRUE(grepl('R package version', cite$note))) return()
+      entry = toBibtex(cite)
+      entry[1] = sub('\\{,$', sprintf('{%s%s,', pkg, suffix), entry[1])
+      entry
+    }, SIMPLIFY = FALSE)
+  })
+  # TODO: remove this hack once https://github.com/mitchelloharawild/vitae/pull/91 is merged
+  if (is_R_CMD_check() && all(c('package:testthat', 'package:vitae') %in% search())) bib2 = NULL
+  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)
+    structure(c(b[idx[1L]], b[-idx], b[idx[2L]]), class = 'Bibtex')
+  })
   if (!is.null(file) && length(x)) write_utf8(unlist(bib), file)
   invisible(bib)
 }

R/defaults.R

@@ -23,6 +23,9 @@ new_defaults = function(value = list()) {
     if (length(dots)) defaults <<- merge(dots)
     invisible(NULL)
   }
+  delete = function(keys) {
+    for (k in keys) defaults[[k]] <<- NULL
+  }
   merge = function(values) merge_list(defaults, values)
   restore = function(target = value) defaults <<- target
   append = function(...) {
@@ -32,7 +35,10 @@ new_defaults = function(value = list()) {
     invisible(NULL)
   }
 
-  list(get = get, set = set, append = append, merge = merge, restore = restore)
+  list(
+    get = get, set = set, delete = delete,
+    append = append, merge = merge, restore = restore
+  )
 }
 
 #' Default and current chunk options
@@ -158,7 +164,7 @@ set_alias = function(...) {
 #' }
 #' @include hooks-html.R
 opts_knit = new_defaults(list(
-  progress = TRUE, verbose = FALSE, width = 75L, eval.after = 'fig.cap',
+  progress = TRUE, verbose = FALSE, eval.after = 'fig.cap',
   base.dir = NULL, base.url = NULL, root.dir = NULL, child.path = '',
   upload.fun = identity, global.device = FALSE, global.par = FALSE,
   concordance = FALSE, documentation = 1L, self.contained = TRUE,
@@ -173,7 +179,7 @@ opts_knit = new_defaults(list(
 
 # you may modify these options in options(knitr.package.foo)
 opts_knit_names = c(
-  'progress', 'verbose', 'width', 'upload.fun', 'animation.fun', 'global.device',
+  'progress', 'verbose', 'upload.fun', 'animation.fun', 'global.device',
   'eval.after', 'concordance', 'documentation', 'aliases', 'self.contained',
   'unnamed.chunk.label'
 )

R/output.R

@@ -145,10 +145,9 @@ knit = function(
     knit_log$restore()
     on.exit(chunk_counter(reset = TRUE), add = TRUE) # restore counter
     adjust_opts_knit()
-    # turn off fancy quotes, use smaller width
+    # turn off fancy quotes, use a null pdf device to record graphics
     oopts = options(
-      useFancyQuotes = FALSE, width = opts_knit$get('width'),
-      knitr.in.progress = TRUE, device = pdf_null
+      useFancyQuotes = FALSE, device = pdf_null, knitr.in.progress = TRUE
     )
     on.exit(options(oopts), add = TRUE)
     # restore chunk options after parent exits

R/utils.R

@@ -968,3 +968,15 @@ digest3 = function(x) {
 
 # collapse by \n
 one_string = function(x, ...) paste(x, ..., collapse = '\n')
+
+# c(1, 1, 1, 2, 3, 3) -> c(1a, 1b, 1c, 2a, 3a, 3b)
+make_unique = function(x) {
+  if (length(x) == 0) return(x)
+  x2 = make.unique(x)
+  if (all(i <- x2 == x)) return(x)
+  x2[i] = paste0(x2[i], '.0')
+  i = as.numeric(sub('.*[.]([0-9]+)$', '\\1', x2)) + 1
+  s = letters[i]
+  s = ifelse(is.na(s), i, s)
+  paste0(x, s)
+}