Merge pull request #399 from dmurdoch/markdown

Use markdown::html_format vignettes

.github/workflows/R-CMD-check.yaml

@@ -33,8 +33,6 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install dependencies on MacOS
         if: runner.os == 'macOS'

.github/workflows/R-CMD-fullcheck.yaml

@@ -43,8 +43,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}

.github/workflows/R-CMD-nosoft-check.yml

@@ -40,8 +40,6 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           rtools-version: ${{ matrix.config.rtools-version }}
-
-      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install automake
         if: runner.os == 'macOS'

.github/workflows/R-CMD-oldwincheck.yml

@@ -36,8 +36,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}

.github/workflows/pkgdown.yaml

@@ -23,8 +23,6 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: rgl
-Version: 1.2.8
+Version: 1.2.9
 Title: 3D Visualization Using OpenGL
 Authors@R: c(person("Duncan", "Murdoch", role = c("aut", "cre"),
                      email = "[email protected]"),
@@ -26,10 +26,11 @@ Authors@R: c(person("Duncan", "Murdoch", role = c("aut", "cre"),
               person("Michael", "Sumner", role = "ctb"),
               person("Mike", "Stein", role = "ctb"))
 Depends: R (>= 3.3.0)
-Suggests: MASS, rmarkdown (>= 2.16), deldir (>= 1.0-4), orientlib, lattice, misc3d,
+Suggests: MASS, markdown (>= 1.12), 
+          rmarkdown (>= 2.16), deldir (>= 1.0-4), orientlib, lattice, misc3d,
           magick, plotrix (>= 3.7-3), tripack, interp, alphashape3d, tcltk,
           js (>= 1.2), webshot2 (>= 0.1.0), downlit (>= 0.4.0), pkgdown (>= 2.0.0), extrafont,
-          shiny, manipulateWidget (>= 0.9.0), testthat, markdown,
+          shiny, manipulateWidget (>= 0.9.0), testthat,
           crosstalk, V8, chromote, jpeg, png
 Imports: graphics, grDevices, stats, utils, 
          htmlwidgets (>= 1.6.0), htmltools, knitr (>= 1.33), jsonlite (>= 0.9.20),
@@ -46,10 +47,9 @@ URL: https://github.com/dmurdoch/rgl,
 SystemRequirements: OpenGL and GLU Library (Required for
     display in R.  See "Installing OpenGL support" in README.md.  
     Not needed if only browser displays using rglwidget() are wanted.),
-    zlib (optional), libpng (>=1.2.9, optional), FreeType (optional),
-    pandoc (>=1.14, needed for vignettes)
+    zlib (optional), libpng (>=1.2.9, optional), FreeType (optional)
 BugReports: https://github.com/dmurdoch/rgl/issues
-VignetteBuilder: knitr, rmarkdown
+VignetteBuilder: knitr
 Biarch: true
-RoxygenNote: 7.2.2.9000
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,8 +1,11 @@
-# rgl 1.2.8
+# rgl 1.2.9
 
 ## Minor changes
 
 * ARIA support now declares `rgl` scenes with `role = "img"`.
+* The vignettes in this package now use
+`markdown::html_format`, so they no longer require Pandoc
+(though Pandoc-using output formats like `html_document` will still be supported).
 
 ## Bug fixes
 

R/knitr.R

@@ -69,9 +69,9 @@ hook_rgl <- function(before, options, envir) {
     margin <- options$rgl.margin
     if (is.null(margin)) margin <- 100
     par3d(windowRect = margin + options$dpi * 
-                                c(0, 0, options$fig.width, options$fig.height))
+            c(0, 0, options$fig.width, options$fig.height))
     Sys.sleep(.05) # need time to respond to window size change
-
+    
     dir <- knitr::opts_knit$get("base_dir")
     if (is.character(dir)) {
       if (!file_test("-d", dir)) dir.create(dir, recursive = TRUE)
@@ -114,9 +114,9 @@ save_rgl <- function(name, devices) {
 # Evaluate an expression using our own private stream of
 # randomness (not affected by set.seed).
 withPrivateSeed <- local({
-
+  
   ownSeed <- NULL
-
+  
   function(expr) {
     # Save the old seed if present.
     if (exists(".Random.seed", envir = .GlobalEnv, inherits = FALSE)) {
@@ -125,7 +125,7 @@ withPrivateSeed <- local({
     } else {
       hasOrigSeed <- FALSE
     }
-
+    
     # Swap in the private seed.
     if (is.null(ownSeed)) {
       if (hasOrigSeed) {
@@ -135,11 +135,11 @@ withPrivateSeed <- local({
     } else {
       .GlobalEnv$.Random.seed <- ownSeed
     }
-
+    
     # On exit, save the modified private seed, and put the old seed back.
     on.exit({
       ownSeed <<- .GlobalEnv$.Random.seed
-
+      
       if (hasOrigSeed) {
         .GlobalEnv$.Random.seed <- origSeed
       } else {
@@ -149,7 +149,7 @@ withPrivateSeed <- local({
       # commented it out.
       # Need to call this to make sure that the value of .Random.seed gets put
       # into R's internal RNG state. (Issue #1763)
-
+      
       # httpuv::getRNGState() # nolint
     })
 
@@ -177,32 +177,20 @@ fns <- local({
   setupKnitr <- function(autoprint = FALSE, 
                          rgl.newwindow = autoprint,
                          rgl.closewindows = autoprint) {
+
+    # R produces multiple vignettes in the same session.
+    # Watch out for leftovers
+
     if (!is.null(setupDone)) {
-      if (setupDone$autoprint) {
-        message("undoing setup")
-        options(saveopts)
-        saveopts <<- NULL
-        setupDone <<- NULL
-      }
-    }
-
-      if (!is.null(setupDone)) {
-        if (setupDone$autoprint != autoprint ||
-            setupDone$rgl.newwindow != rgl.newwindow ||
-            setupDone$rgl.closewindows != rgl.closewindows) {
-          warning("Already set autoprint = ", setupDone$autoprint,
-                  ", rgl.newwindow = ", setupDone$rgl.newwindow,
-                  ", rgl.closewindows = ", setupDone$rgl.closewindows)
-        }
-        return()
-      }
+      options(saveopts)
+      saveopts <<- NULL
       counter <<- 0L
+    }
 
     setupDone <<- list(autoprint = autoprint,
                        rgl.newwindow = rgl.newwindow,
                        rgl.closewindows = rgl.closewindows)
 
-    # R produces multiple vignettes in the same session.
     knitr::opts_chunk$set(rgl.newwindow = rgl.newwindow, 
                           rgl.closewindows = rgl.closewindows,
                           rgl.chunk = TRUE)
@@ -239,49 +227,49 @@ fns <- local({
     } else
       invisible(x)
   }
-
-    sew.rglRecordedplot <- function(x, options = list(), ...)  {
-      latex <- identical(opts_knit$get("out.format"), "latex") || identical(opts_knit$get("rmarkdown.pandoc.to"), "latex")
-      scene <- x$scene
-      doSnapshot <- knitrNeedsSnapshot(options)
-      content <- rglwidget(scene,
-                           width = x$width,
-                           height = x$height,
-                           webgl = !doSnapshot)
-      if (inherits(content, "knit_image_paths")) {
-        # # We've done a snapshot, put it in the right place.
-        name <- fig_path("-rgl.png", options, rgl_counter())
-        if (!file_test("-d", dirname(name)))
-          dir.create(dirname(name), recursive = TRUE)
-        file.copy(content, name, overwrite = TRUE)
-        unlink(content)
-        content <- structure(list(file = name,
-                                  extension = "png"),
-                             class = "html_screenshot")
-      }
-      fig.align <- options$fig.align
-      if (length(fig.align) ==  1 && fig.align != "default")
-        content <- prependContent(content,
-                                  tags$style(sprintf(
-                                    "#%s {%s}",
-                                    content$elementId,
-                                    switch(fig.align,
-                                           center = "margin:auto;",
-                                           left   = "margin-left:0;margin-right:auto;",
-                                           right  = "margin-left:auto;margin-right:0;",
-                                           ""))))
-      result <- do.call("knit_print", c(list(content, options), x$args))
-      if (!latex)
-        class(result) <- c(class(result), "knit_asis_htmlwidget")
-
-      sew(result, options)
+
+  sew.rglRecordedplot <- function(x, options = list(), ...)  {
+    latex <- identical(opts_knit$get("out.format"), "latex") || identical(opts_knit$get("rmarkdown.pandoc.to"), "latex")
+    scene <- x$scene
+    doSnapshot <- knitrNeedsSnapshot(options)
+    content <- rglwidget(scene,
+                         width = x$width,
+                         height = x$height,
+                         webgl = !doSnapshot)
+    if (inherits(content, "knit_image_paths")) {
+      # # We've done a snapshot, put it in the right place.
+      name <- fig_path("-rgl.png", options, rgl_counter())
+      if (!file_test("-d", dirname(name)))
+        dir.create(dirname(name), recursive = TRUE)
+      file.copy(content, name, overwrite = TRUE)
+      unlink(content)
+      content <- structure(list(file = name,
+                                extension = "png"),
+                           class = "html_screenshot")
     }
+    fig.align <- options$fig.align
+    if (length(fig.align) ==  1 && fig.align != "default")
+      content <- prependContent(content,
+                                tags$style(sprintf(
+                                  "#%s {%s}",
+                                  content$elementId,
+                                  switch(fig.align,
+                                         center = "margin:auto;",
+                                         left   = "margin-left:0;margin-right:auto;",
+                                         right  = "margin-left:auto;margin-right:0;",
+                                         ""))))
+    result <- do.call("knit_print", c(list(content, options), x$args))
+    if (!latex)
+      class(result) <- c(class(result), "knit_asis_htmlwidget")
 
-    list(
-      setupKnitr = setupKnitr,
-      knit_print.rglOpen3d = knit_print.rglOpen3d,
-      knit_print.rglId = knit_print.rglId,
-      sew.rglRecordedplot = sew.rglRecordedplot)
+    sew(result, options)
+  }
+
+  list(
+    setupKnitr = setupKnitr,
+    knit_print.rglOpen3d = knit_print.rglOpen3d,
+    knit_print.rglId = knit_print.rglId,
+    sew.rglRecordedplot = sew.rglRecordedplot)
 })
 
 setupKnitr <- fns[["setupKnitr"]]

R/r3d.rgl.R

@@ -1079,8 +1079,9 @@ snapshot3d <- function(filename = tempfile(fileext = ".png"),
                          elementId = "webshot",
                          width = width,
                          height = height,
-                         webgl = TRUE), 
-               f1)
+                         webgl = TRUE),
+               f1,
+               selfcontained = FALSE)
     unlink(filename)
     res <- try(capture.output(webshot2::webshot(f1, file = filename, selector = "#webshot",
                         vwidth = width + 100, vheight = height, ...),

README.Rmd

@@ -1,5 +1,6 @@
 ---
-output: github_document
+output: 
+  markdown::html_format
 ---
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
@@ -16,9 +17,8 @@ knitr::opts_chunk$set(
 options(rgl.useNULL=TRUE)
 suppressPackageStartupMessages(library(rgl))
 
-if (!requireNamespace("rmarkdown", quietly = TRUE) ||
-    !rmarkdown::pandoc_available("1.14")) {
-  warning(call. = FALSE, "These vignettes assume rmarkdown and pandoc version 1.14.  These were not found. Older versions will not work.")
+if (!requireNamespace("rmarkdown", quietly = TRUE)) {
+  warning(call. = FALSE, "These vignettes assume rmarkdown.  This was not found.")
   knitr::knit_exit()
 }
 setupKnitr(autoprint = TRUE)

man/setupKnitr.Rd

@@ -42,11 +42,6 @@ or \code{\link{highlevel}} functions.  All RGL functions that
 produce graphics do this, but functions in other packages that
 call them may not return values appropriately.
 
-If you have multiple calls to \code{setupKnitr()}, all
-should have the same arguments.  If any differ, a 
-warning will be issued, and the first set of arguments
-will be used.
-
 Mixing explicit calls
 to \code{\link{rglwidget}} with auto-printing is likely to lead to failure of some
 scenes to display.  To avoid this, set \code{options(rgl.printRglwidget = FALSE)} before using such explicit calls.  Similarly,

vignettes/WebGL.Rmd

@@ -3,13 +3,16 @@ title: "User Interaction in WebGL (updated)"
 author: "Duncan Murdoch"
 date: "`r format(Sys.time(), '%B %d, %Y')`"
 output:
+  markdown::html_format:
+    options:
+      toc: true
   rmarkdown::html_vignette:
     toc: yes
     fig_width: 5
     fig_height: 5
 vignette: >
   %\VignetteIndexEntry{User Interaction in WebGL (updated)} 
-  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEngine{knitr::knitr}
   %\VignetteDepends{crosstalk}
 ---
 

vignettes/demos.Rmd

@@ -2,11 +2,12 @@
 title: "rgl Demos"
 date: "`r Sys.Date()`"
 output: 
-  rmarkdown::html_vignette:
-    toc: true
+  markdown::html_format:
+    options:
+      toc: true
 vignette: >
   %\VignetteIndexEntry{rgl Demos}
-  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---
 

vignettes/deprecation.Rmd

@@ -3,11 +3,14 @@ title: "Deprecating the `rgl.*` interface"
 author: "Duncan Murdoch"
 date: "`r Sys.Date()`"
 output: 
+  markdown::html_format:
+    options:
+      toc: true
   rmarkdown::html_vignette:
     toc: true
 vignette: >
   %\VignetteIndexEntry{Deprecating the `rgl.*` interface}
-  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEngine{knitr::knitr}
   %\VignetteEncoding{UTF-8}
 ---