Don't hide output contents on resize

Shiny 1.7.2 on CRAN

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: shiny
 Type: Package
 Title: Web Application Framework for R
-Version: 1.7.1.9003
+Version: 1.7.2.9000
 Authors@R: c(
     person("Winston", "Chang", role = c("aut", "cre"), email = "winston@rstudio.com", comment = c(ORCID = "0000-0002-1576-2126")),
     person("Joe", "Cheng", role = "aut", email = "joe@rstudio.com"),
@@ -201,7 +201,7 @@ Collate:
     'version_selectize.R'
     'version_strftime.R'
     'viewer.R'
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RdMacros: lifecycle

NEWS.md

@@ -1,42 +1,59 @@
-shiny development
+shiny 1.7.2.9000
 ================
 
+
+
+shiny 1.7.2
+===========
+
 ## Full changelog
 
 ### Breaking changes
 
-### Minor new features and improvements
+* Closed #3626: `renderPlot()` (and `plotPNG()`) now uses `ragg::agg_png()` by default when the [`{ragg}` package](https://github.com/r-lib/ragg) is installed. To restore the previous behavior, set `options(shiny.useragg = FALSE)`. (#3654)
+
+### New features and improvements
+
+* Closed #1545: `insertUI()` now executes `<script>` tags. (#3630)
+
+* `fileInput()` can set the `capture` attribute to facilitates user access to a device's media capture mechanism, such as a camera, or microphone, from within a file upload control ([W3C HTML Media Capture](https://www.w3.org/TR/html-media-capture/)). (Thanks to khaled-alshamaa, #3481)
+
+* Closed tidyverse/dplyr#5552: Compatibility of dplyr 1.0 (and rlang chained errors in general) with `req()`, `validate()`, and friends.
+
+* Closed tidyverse/dplyr#6154: Values from an `actionButton()` had S3 classes in the incorrect order.
+
+* Closed #3346: Default for `ref` input in `runGithub()` changed from `"master"` to `"HEAD"`. (#3564)
+
+* Closed #3619: In R 4.2, `splitLayout()` no longer raises warnings about incorrect length in an `if` statement. (Thanks to @dmenne, #3625)
+
+### Bug fixes
+
+* Closed #3250:`{rlang}`/`{tidyeval}` conditions (i.e., warnings and errors) are no longer filtered from stack traces. (#3602)
+
+* Closed #3581: Errors in throttled/debounced reactive expressions no longer cause the session to exit. (#3624)
+
+* Closed #3657: `throttle.ts` and the `Throttler` typescript objects it provides now function as intended. (Thanks gto @dvg-p4, #3659)
+
+* The auto-reload feature (`options(shiny.autoreload=TRUE)`) was not being activated by `devmode(TRUE)`, despite a console message asserting that it was. (#3620)
+
+* Closed #2297: If an error occurred in parsing a value in a bookmark query string, an error would be thrown and nothing would be restored. Now a message is displayed and that value is ignored. (Thanks to @daattali, #3385)
+
+* Restored the previous behavior of automatically guessing the `Content-Type` header for `downloadHandler` functions when no explicit `contentType` argument is supplied. (#3393)
+
+* Previously, updating an input value without a corresponding Input binding element did not trigger a JavaScript `shiny:inputchanged` event. Now, if no Input binding element is found, the `shiny:inputchanged` event is triggered on `window.document`. (#3584)
+
+* Closed #2955: Input and output bindings previously attempted to use `el['data-input-id']`, but that never worked. They now use `el.getAttribute('data-input-id')` instead. (#3538)
+
+### Minor improvements
+
+* When taking a test snapshot, the sort order of the json keys of the `input`, `output`, and `export` fields is currently sorted using the locale of the machine. This can lead to inconsistent test snapshot results. To opt-in to a consistent ordering of snapshot fields with `{shinytest}`, please set the global option `options(shiny.snapshotsortc = TRUE)`. `{shinytest2}` users do not need to set this value. (#3515)
+
+* Closed rstudio/shinytest2#222: When restoring a context (i.e., bookmarking) from a URL, Shiny now better handles a trailing `=` after `_inputs_` and `_values_`. (#3648)
 
 * Shiny's internal HTML dependencies are now mounted dynamically instead of statically. (#3537)
 
 * HTML dependencies that are sent to dynamic UI now have better type checking, and no longer require a `dep.src.href` field. (#3537)
 
-* Default for `ref` input in `runGithub()` changed from `"master"` to `"HEAD"`. (#3346)
-
-* When taking a test snapshot, the sort order of the json keys of the `input`, `output`, and `export` fields is currently sorted using the locale of the machine. This can lead to inconsistent test snapshot results. To opt-in to a consistent ordering of snapshot fields with `{shinytest}`, please set the global option `options(shiny.snapshotsortc = TRUE)`. `{shinytest2}` users do not need to set this value. (#3515)
-
-* The auto-reload feature (`options(shiny.autoreload=TRUE)`) was not being activated by `devmode(TRUE)`, despite a console message asserting that it was. (#3620)
-
-* Add `shiny.mathjax.url` and `shiny.mathjax.config` options for configuring the MathJax URL used by `withMathJax`. Thanks, @Neutron3529! (#3639)
-
-### Bug fixes
-
-* Closed tidyverse/dplyr#5552: Compatibility of dplyr 1.0 (and rlang chained errors in general) with `req()`, `validate()`, and friends.
-
-* Closed #1545: `insertUI()` now executes `<script>` tags. (#3630)
-
-* Closed #2955: Input and output bindings previously attempted to use `el['data-input-id']`, but that never worked. They now use `el.getAttribute('data-input-id')` instead. (#3538)
-
-* Closed tidyverse/dplyr#6154: Values from an `actionButton()` had S3 classes in the incorrect order.
-
-* Fixed a bug where updating an input value without a corresponding Input binding element did not trigger a JavaScript `shiny:inputchanged` event. Now, if no Input binding element is found, the `shiny:inputchanged` event is triggered on `window.document`. (#3584)
-
-* Restored the previous behavior of automatically guessing the `Content-Type` header for `downloadHandler` functions when no explicit `contentType` argument is supplied. (#3393)
-
-* Closed #3619: In R 4.2, `splitLayout()` raised warnings about incorrect length in an `if` statement. (Thanks to @dmenne, #3625)
-
-* Closed #2297: If an error occurred in parsing a value in a bookmark query string, an error would be thrown and nothing would be restored. Now a message is displayed and that value is ignored. (Thanks to @daattali, #3385)
-
 
 shiny 1.7.1
 ===========
@@ -78,8 +95,6 @@ shiny 1.7.0
 
 * Addressed #2521: Updated the list of TCP ports that will be rejected by default in runapp.R, adding 5060, 5061 and 6566. Added documentation describing the port range (3000:8000) and which ports are rejected. (#3456)
 
-* `fileInput()` can set the `capture` attribute to facilitates user access to a device's media capture mechanism, such as a camera, or microphone, from within a file upload control ([W3C HTML Media Capture](https://www.w3.org/TR/html-media-capture/)). (Thanks to khaled-alshamaa, #3481)
-
 ### Other improvements
 
 * Shiny's core JavaScript code was converted to TypeScript. For the latest development information, please see the [README.md in `./srcts`](https://github.com/rstudio/shiny/tree/v1.7.0/srcts). (#3296)
@@ -503,7 +518,7 @@ This is a significant release for Shiny, with a major new feature that was nearl
 
 * Removed the (ridiculously outdated) "experimental feature" tag from the reference documentation for `renderUI`. (#2036)
 
-* Addressed #1907: the `ignoreInit` argument was first added only to `observeEvent`. Later, we also added it to `eventReactive`, but forgot to update the documentation. Now done, thanks [@flo12392](https://github.com/flo12392)! (#2036)
+* Addressed #1907: the `ignoreInit` argument was first added only to `observeEvent`. Later, we also added it to `eventReactive`, but forgot to update the documentation. Now done, thanks @flo12392! (#2036)
 
 ### Bug fixes
 
@@ -517,7 +532,7 @@ This is a significant release for Shiny, with a major new feature that was nearl
 
 * Fixed #1600: URL-encoded bookmarking did not work with sliders that had dates or date-times. (#1961)
 
-* Fixed #1962: [File dragging and dropping](https://blog.rstudio.com/2017/08/15/shiny-1-0-4/) broke in the presence of jQuery version 3.0 as introduced by the [rhandsontable](https://jrowen.github.io/rhandsontable/) [htmlwidget](https://www.htmlwidgets.org/). (#2005)
+* Fixed #1962: [File dragging and dropping](https://www.rstudio.com/blog/shiny-1-0-4/) broke in the presence of jQuery version 3.0 as introduced by the [rhandsontable](https://jrowen.github.io/rhandsontable/) [htmlwidget](https://www.htmlwidgets.org/). (#2005)
 
 * Improved the error handling inside the `addResourcePath()` function, to give end users more informative error messages when the `directoryPath` argument cannot be normalized. This is especially useful for `runtime: shiny_prerendered` Rmd documents, like `learnr` tutorials. (#1968)
 

R/bookmark-state.R

@@ -370,7 +370,7 @@ RestoreContext <- R6Class("RestoreContext",
               safeFromJSON(value),
               error = function(e) {
                 varsUnparsed <<- c(varsUnparsed, name)
-                message("Failed to parse URL parameter \"", name, "\"")
+                warning("Failed to parse URL parameter \"", name, "\"")
               }
             )
           }

R/conditions.R

@@ -421,8 +421,17 @@ pruneStackTrace <- function(parents) {
   # Loop over the parent indices. Anything that is not parented by current_node
   # (a.k.a. last-known-good node), or is a dupe, can be discarded. Anything that
   # is kept becomes the new current_node.
+  #
+  # jcheng 2022-03-18: Two more reasons a node can be kept:
+  #   1. parent is 0
+  #   2. parent is i
+  # Not sure why either of these situations happen, but they're common when
+  # interacting with rlang/dplyr errors. See issue rstudio/shiny#3250 for repro
+  # cases.
   include <- vapply(seq_along(parents), function(i) {
-    if (!is_dupe[[i]] && parents[[i]] == current_node) {
+    if ((!is_dupe[[i]] && parents[[i]] == current_node) ||
+        parents[[i]] == 0 ||
+        parents[[i]] == i) {
       current_node <<- i
       TRUE
     } else {

R/imageutils.R

@@ -1,19 +1,14 @@
 startPNG <- function(filename, width, height, res, ...) {
-  # shiny.useragg is an experimental option that isn't officially supported or
-  # documented. It's here in the off chance that someone really wants
-  # to use ragg (say, instead of showtext, for custom font rendering).
-  # In the next shiny release, this option will likely be superseded in
-  # favor of a fully customizable graphics device option
-  if ((getOption('shiny.useragg') %||% FALSE) && is_installed("ragg")) {
-    pngfun <- ragg::agg_png
+  pngfun <- if ((getOption('shiny.useragg') %||% TRUE) && is_installed("ragg")) {
+    ragg::agg_png
   } else if (capabilities("aqua")) {
     # i.e., png(type = 'quartz')
-    pngfun <- grDevices::png
+    grDevices::png
   } else if ((getOption('shiny.usecairo') %||% TRUE) && is_installed("Cairo")) {
-    pngfun <- Cairo::CairoPNG
+    Cairo::CairoPNG
   } else {
     # i.e., png(type = 'cairo')
-    pngfun <- grDevices::png
+    grDevices::png
   }
 
   args <- rlang::list2(filename=filename, width=width, height=height, res=res, ...)
@@ -57,33 +52,31 @@ startPNG <- function(filename, width, height, res, ...) {
   grDevices::dev.cur()
 }
 
-#' Run a plotting function and save the output as a PNG
+#' Capture a plot as a PNG file.
 #'
-#' This function returns the name of the PNG file that it generates. In
-#' essence, it calls `png()`, then `func()`, then `dev.off()`.
-#' So `func` must be a function that will generate a plot when used this
-#' way.
-#'
-#' For output, it will try to use the following devices, in this order:
-#' quartz (via [grDevices::png()]), then [Cairo::CairoPNG()],
-#' and finally [grDevices::png()]. This is in order of quality of
-#' output. Notably, plain `png` output on Linux and Windows may not
-#' antialias some point shapes, resulting in poor quality output.
-#'
-#' In some cases, `Cairo()` provides output that looks worse than
-#' `png()`. To disable Cairo output for an app, use
-#' `options(shiny.usecairo=FALSE)`.
+#' The PNG graphics device used is determined in the following order:
+#'   * If the ragg package is installed (and the `shiny.useragg` is not
+#'    set to `FALSE`), then use [ragg::agg_png()].
+#'   * If a quartz device is available (i.e., `capabilities("aqua")` is
+#'    `TRUE`), then use `png(type = "quartz")`.
+#'   * If the Cairo package is installed (and the `shiny.usecairo` option
+#'    is not set to `FALSE`), then use [Cairo::CairoPNG()].
+#'   * Otherwise, use [grDevices::png()]. In this case, Linux and Windows
+#'    may not antialias some point shapes, resulting in poor quality output.
 #'
 #' @param func A function that generates a plot.
 #' @param filename The name of the output file. Defaults to a temp file with
 #'   extension `.png`.
 #' @param width Width in pixels.
 #' @param height Height in pixels.
-#' @param res Resolution in pixels per inch. This value is passed to
-#'   [grDevices::png()]. Note that this affects the resolution of PNG rendering in
+#' @param res Resolution in pixels per inch. This value is passed to the
+#'   graphics device. Note that this affects the resolution of PNG rendering in
 #'   R; it won't change the actual ppi of the browser.
-#' @param ... Arguments to be passed through to [grDevices::png()].
-#'   These can be used to set the width, height, background color, etc.
+#' @param ... Arguments to be passed through to the graphics device. These can
+#'   be used to set the width, height, background color, etc.
+#'
+#' @return A path to the newly generated PNG file.
+#'
 #' @export
 plotPNG <- function(func, filename=tempfile(fileext='.png'),
                     width=400, height=400, res=72, ...) {

R/reactives.R

@@ -2472,11 +2472,11 @@ debounce <- function(r, millis, priority = 100, domain = getDefaultReactiveDomai
 
       # Ensure r() is called only after setting firstRun to FALSE since r()
       # may throw an error
-      r()
+      try(r(), silent = TRUE)
       return()
     }
     # This ensures r() is still tracked after firstRun
-    r()
+    try(r(), silent = TRUE)
 
     # The value (or possibly millis) changed. Start or reset the timer.
     v$when <- getDomainTimeMs(domain) + millis()
@@ -2509,7 +2509,7 @@ debounce <- function(r, millis, priority = 100, domain = getDefaultReactiveDomai
   # commenting it out and studying the unit test failure that results.
   primer <- observe({
     primer$destroy()
-    er()
+    try(er(), silent = TRUE)
   }, label = "debounce primer", domain = domain, priority = priority)
 
   er
@@ -2551,7 +2551,7 @@ throttle <- function(r, millis, priority = 100, domain = getDefaultReactiveDomai
   }
 
   # Responsible for tracking when f() changes.
-  observeEvent(r(), {
+  observeEvent(try(r(), silent = TRUE), {
     if (v$pending) {
       # In a blackout period and someone already scheduled; do nothing
     } else if (blackoutMillisLeft() > 0) {

R/render-plot.R

@@ -34,7 +34,7 @@
 #'   When rendering an inline plot, you must provide numeric values (in pixels)
 #'   to both \code{width} and \code{height}.
 #' @param res Resolution of resulting plot, in pixels per inch. This value is
-#'   passed to [grDevices::png()]. Note that this affects the resolution of PNG
+#'   passed to [plotPNG()]. Note that this affects the resolution of PNG
 #'   rendering in R; it won't change the actual ppi of the browser.
 #' @param alt Alternate text for the HTML `<img>` tag if it cannot be displayed
 #'   or viewed (i.e., the user uses a screen reader). In addition to a character
@@ -44,7 +44,7 @@
 #'   ggplot objects; for other plots, `NA` results in alt text of "Plot object".
 #'   `NULL` or `""` is not recommended because those should be limited to
 #'   decorative images.
-#' @param ... Arguments to be passed through to [grDevices::png()].
+#' @param ... Arguments to be passed through to [plotPNG()].
 #'   These can be used to set the width, height, background color, etc.
 #' @inheritParams renderUI
 #' @param execOnResize If `FALSE` (the default), then when a plot is

R/server.R

@@ -49,7 +49,7 @@ registerClient <- function(client) {
 #' optional `session` parameter, which is used when greater control is
 #' needed.
 #'
-#' See the [tutorial](https://rstudio.github.io/shiny/tutorial/) for more
+#' See the [tutorial](https://shiny.rstudio.com/tutorial/) for more
 #' on how to write a server function.
 #'
 #' @param func The server function for this application. See the details section
@@ -331,7 +331,7 @@ argsForServerFunc <- function(serverFunc, session) {
 getEffectiveBody <- function(func) {
   if (is.null(func))
     NULL
-  else if (isS4(func) && class(func) == "functionWithTrace")
+  else if (isS4(func) && inherits(func, "functionWithTrace"))
     body(func@original)
   else
     body(func)

R/shiny-options.R

@@ -140,9 +140,10 @@ getShinyOption <- function(name, default = NULL) {
 #'   messages).}
 #' \item{shiny.autoload.r (defaults to `TRUE`)}{If `TRUE`, then the R/
 #'   of a shiny app will automatically be sourced.}
-#' \item{shiny.usecairo (defaults to `TRUE`)}{This is used to disable graphical rendering by the
-#'   Cairo package, if it is installed. See [plotPNG()] for more
-#'   information.}
+#' \item{shiny.useragg (defaults to `TRUE`)}{Set to `FALSE` to prevent PNG rendering via the
+#'   ragg package. See [plotPNG()] for more information.}
+#' \item{shiny.usecairo (defaults to `TRUE`)}{Set to `FALSE` to prevent PNG rendering via the
+#'   Cairo package. See [plotPNG()] for more information.}
 #' \item{shiny.devmode (defaults to `NULL`)}{Option to enable Shiny Developer Mode. When set,
 #'   different default `getOption(key)` values will be returned. See [devmode()] for more details.}
 ### Not documenting as 'shiny.devmode.verbose' is for niche use only

README.md

@@ -16,7 +16,7 @@ Easily build rich and productive interactive web apps in R — no HTML/CSS/J
 * A prebuilt set of highly sophisticated, customizable, and easy-to-use widgets (e.g., plots, tables, sliders, dropdowns, date pickers, and more).
 * An attractive default look based on [Bootstrap](https://getbootstrap.com/) which can also be easily customized with the [bslib](https://github.com/rstudio/bslib) package or avoided entirely with more direct R bindings to HTML/CSS/JavaScript.
 * Seamless integration with [R Markdown](https://shiny.rstudio.com/articles/interactive-docs.html), making it easy to embed numerous applications natively within a larger dynamic document.
-* Tools for improving and monitoring performance, including native support for [async programming](https://blog.rstudio.com/2018/06/26/shiny-1-1-0/), [caching](https://talks.cpsievert.me/20201117), [load testing](https://rstudio.github.io/shinyloadtest/), and [more](https://support.rstudio.com/hc/en-us/articles/231874748-Scaling-and-Performance-Tuning-in-RStudio-Connect).
+* Tools for improving and monitoring performance, including native support for [async programming](https://www.rstudio.com/blog/shiny-1-1-0/), [caching](https://talks.cpsievert.me/20201117), [load testing](https://rstudio.github.io/shinyloadtest/), and more.
 * [Modules](https://shiny.rstudio.com/articles/modules.html): a framework for reducing code duplication and complexity.
 * An ability to [bookmark application state](https://shiny.rstudio.com/articles/bookmarking-state.html) and/or [generate code to reproduce output(s)](https://github.com/rstudio/shinymeta).
 * A rich ecosystem of extension packages for more [custom widgets](http://www.htmlwidgets.org/), [input validation](https://github.com/rstudio/shinyvalidate), [unit testing](https://github.com/rstudio/shinytest), and more.

inst/www/shared/shiny-showcase.css

@@ -1,2 +1,2 @@
-/*! shiny 1.7.1.9003 | (c) 2012-2022 RStudio, PBC. | License: GPL-3 | file LICENSE */
+/*! shiny 1.7.2.9000 | (c) 2012-2022 RStudio, PBC. | License: GPL-3 | file LICENSE */
 #showcase-well{border-radius:0}.shiny-code{background-color:#fff;margin-bottom:0}.shiny-code code{font-family:Menlo,Consolas,"Courier New",monospace}.shiny-code-container{margin-top:20px;clear:both}.shiny-code-container h3{display:inline;margin-right:15px}.showcase-header{font-size:16px;font-weight:normal}.showcase-code-link{text-align:right;padding:15px}#showcase-app-container{vertical-align:top}#showcase-code-tabs{margin-right:15px}#showcase-code-tabs pre{border:none;line-height:1em}#showcase-code-tabs .nav{margin-bottom:0}#showcase-code-tabs ul{margin-bottom:0}#showcase-code-tabs .tab-content{border-style:solid;border-color:#e5e5e5;border-width:0px 1px 1px 1px;overflow:auto;border-bottom-right-radius:4px;border-bottom-left-radius:4px}#showcase-app-code{width:100%}#showcase-code-position-toggle{float:right}#showcase-sxs-code{padding-top:20px;vertical-align:top}.showcase-code-license{display:block;text-align:right}#showcase-code-content pre{background-color:#fff}

inst/www/shared/shiny-testmode.js

@@ -1,3 +1,3 @@
-/*! shiny 1.7.1.9003 | (c) 2012-2022 RStudio, PBC. | License: GPL-3 | file LICENSE */
+/*! shiny 1.7.2.9000 | (c) 2012-2022 RStudio, PBC. | License: GPL-3 | file LICENSE */
 (function(){var a=eval;window.addEventListener("message",function(i){var e=i.data;e.code&&a(e.code)});})();
 //# sourceMappingURL=shiny-testmode.js.map

man/bindCache.Rd

@@ -42,7 +42,7 @@ In the example here, the \code{bindCache()} key consists of \code{input$x} and
 \code{input$y} combined, and the value is \code{input$x * input$y}. In this simple
 example, for any given key, there is only one possible returned value.
 
-\if{html}{\out{<div class="sourceCode NA">}}\preformatted{r <- reactive(\{ input$x * input$y \}) \%>\%
+\if{html}{\out{<div class="sourceCode">}}\preformatted{r <- reactive(\{ input$x * input$y \}) \%>\%
   bindCache(input$x, input$y)
 }\if{html}{\out{</div>}}
 
@@ -67,7 +67,7 @@ have a large data set with timestamps, it might make sense to extract the
 most recent timestamp and return that. Then, instead of hashing the entire
 data object, the cached reactive only needs to hash the timestamp.
 
-\if{html}{\out{<div class="sourceCode NA">}}\preformatted{r <- reactive(\{ compute(bigdata()) \} \%>\%
+\if{html}{\out{<div class="sourceCode">}}\preformatted{r <- reactive(\{ compute(bigdata()) \} \%>\%
   bindCache(\{ extract_most_recent_time(bigdata()) \})
 }\if{html}{\out{</div>}}
 
@@ -111,7 +111,7 @@ time that someone accesses the cached reactive. It is only re-executed if
 it has been invalidated by one of the reactives it depends on. For
 example, suppose we have this cached reactive:
 
-\if{html}{\out{<div class="sourceCode NA">}}\preformatted{r <- reactive(\{ input$x * input$y \}) \%>\%
+\if{html}{\out{<div class="sourceCode">}}\preformatted{r <- reactive(\{ input$x * input$y \}) \%>\%
  bindCache(input$x, input$y)
 }\if{html}{\out{</div>}}
 
@@ -276,7 +276,7 @@ cache key, in addition to the one passed to \code{bindCache()} by the user. The
 cache hint can be viewed by calling the internal Shiny function
 \code{extractCacheHint()}:
 
-\if{html}{\out{<div class="sourceCode NA">}}\preformatted{r <- renderText(\{ input$x \})
+\if{html}{\out{<div class="sourceCode">}}\preformatted{r <- renderText(\{ input$x \})
 shiny:::extractCacheHint(r)
 }\if{html}{\out{</div>}}
 

man/bindEvent.Rd

@@ -173,7 +173,7 @@ user sets both \code{x} and \code{y}, and then clicks on an \link{actionButton}
 To use both caching and events, the object should first be passed to
 \code{bindCache()}, then \code{bindEvent()}. For example:
 
-\if{html}{\out{<div class="sourceCode NA">}}\preformatted{r <- reactive(\{
+\if{html}{\out{<div class="sourceCode">}}\preformatted{r <- reactive(\{
    Sys.sleep(2)  # Pretend this is an expensive computation
    input$x * input$y
  \}) \%>\%

man/createRenderFunction.Rd

@@ -125,12 +125,12 @@ function.
 }
 \section{Functions}{
 \itemize{
-\item \code{quoToFunction}: convert a quosure to a function.
+\item \code{quoToFunction()}: convert a quosure to a function.
 
-\item \code{installExprFunction}: converts a user's reactive \code{expr} into a
+\item \code{installExprFunction()}: converts a user's reactive \code{expr} into a
 function that's assigned to a \code{name} in the \code{assign.env}.
-}}
 
+}}
 \examples{
 # A custom render function that repeats the supplied value 3 times
 renderTriple <- function(expr) {

man/devmode.Rd

@@ -84,20 +84,20 @@ Please see the function descriptions for more details.
 }
 \section{Functions}{
 \itemize{
-\item \code{devmode}: Function to set two options to enable/disable Shiny
+\item \code{devmode()}: Function to set two options to enable/disable Shiny
 Developer Mode and Developer messages
 
-\item \code{in_devmode}: Determines if Shiny is in Developer Mode. If the
+\item \code{in_devmode()}: Determines if Shiny is in Developer Mode. If the
 \code{getOption("shiny.devmode")} is set to \code{TRUE} and not in testing inside
 \code{testthat}, then Shiny Developer Mode is enabled.
 
-\item \code{with_devmode}: Temporarily set Shiny Developer Mode and Developer
+\item \code{with_devmode()}: Temporarily set Shiny Developer Mode and Developer
 message verbosity
 
-\item \code{devmode_inform}: If Shiny Developer Mode and verbosity are enabled,
+\item \code{devmode_inform()}: If Shiny Developer Mode and verbosity are enabled,
 displays a message once every 8 hrs (by default)
 
-\item \code{register_devmode_option}: Registers a Shiny Developer Mode option with an updated
+\item \code{register_devmode_option()}: Registers a Shiny Developer Mode option with an updated
 value and Developer message. This registration method allows package
 authors to write one message in a single location.
 
@@ -138,7 +138,7 @@ register_devmode_option(
 )
 }\if{html}{\out{</div>}}
 
-\item \code{get_devmode_option}: Provides a consistent way to change the expected
+\item \code{get_devmode_option()}: Provides a consistent way to change the expected
 \code{\link[=getOption]{getOption()}} behavior when Developer Mode is enabled. This method is very
 similar to \code{\link[=getOption]{getOption()}} where the globally set option takes precedence.
 See section "Avoiding direct dependency on shiny" for
@@ -148,8 +148,8 @@ See section "Avoiding direct dependency on shiny" for
 \code{register_devmode_option()} to avoid supplying the same \code{devmode_default}
 and \code{devmode_message} values throughout your package. (This requires a
 \pkg{shiny} dependency.)
-}}
 
+}}
 \section{Avoiding direct dependency on shiny}{
 
 

man/plotPNG.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/imageutils.R
 \name{plotPNG}
 \alias{plotPNG}
-\title{Run a plotting function and save the output as a PNG}
+\title{Capture a plot as a PNG file.}
 \usage{
 plotPNG(
   func,
@@ -23,27 +23,26 @@ extension \code{.png}.}
 
 \item{height}{Height in pixels.}
 
-\item{res}{Resolution in pixels per inch. This value is passed to
-\code{\link[grDevices:png]{grDevices::png()}}. Note that this affects the resolution of PNG rendering in
+\item{res}{Resolution in pixels per inch. This value is passed to the
+graphics device. Note that this affects the resolution of PNG rendering in
 R; it won't change the actual ppi of the browser.}
 
-\item{...}{Arguments to be passed through to \code{\link[grDevices:png]{grDevices::png()}}.
-These can be used to set the width, height, background color, etc.}
+\item{...}{Arguments to be passed through to the graphics device. These can
+be used to set the width, height, background color, etc.}
+}
+\value{
+A path to the newly generated PNG file.
 }
 \description{
-This function returns the name of the PNG file that it generates. In
-essence, it calls \code{png()}, then \code{func()}, then \code{dev.off()}.
-So \code{func} must be a function that will generate a plot when used this
-way.
+The PNG graphics device used is determined in the following order:
+\itemize{
+\item If the ragg package is installed (and the \code{shiny.useragg} is not
+set to \code{FALSE}), then use \code{\link[ragg:agg_png]{ragg::agg_png()}}.
+\item If a quartz device is available (i.e., \code{capabilities("aqua")} is
+\code{TRUE}), then use \code{png(type = "quartz")}.
+\item If the Cairo package is installed (and the \code{shiny.usecairo} option
+is not set to \code{FALSE}), then use \code{\link[Cairo:Cairo]{Cairo::CairoPNG()}}.
+\item Otherwise, use \code{\link[grDevices:png]{grDevices::png()}}. In this case, Linux and Windows
+may not antialias some point shapes, resulting in poor quality output.
 }
-\details{
-For output, it will try to use the following devices, in this order:
-quartz (via \code{\link[grDevices:png]{grDevices::png()}}), then \code{\link[Cairo:Cairo]{Cairo::CairoPNG()}},
-and finally \code{\link[grDevices:png]{grDevices::png()}}. This is in order of quality of
-output. Notably, plain \code{png} output on Linux and Windows may not
-antialias some point shapes, resulting in poor quality output.
-
-In some cases, \code{Cairo()} provides output that looks worse than
-\code{png()}. To disable Cairo output for an app, use
-\code{options(shiny.usecairo=FALSE)}.
 }

man/reactlog.Rd

@@ -51,11 +51,11 @@ of the source code of your reactive expressions and observers.
 }
 \section{Functions}{
 \itemize{
-\item \code{reactlog}: Return a list of reactive information.  Can be used in conjunction with
+\item \code{reactlog()}: Return a list of reactive information.  Can be used in conjunction with
 \link[reactlog:reactlog_show]{reactlog::reactlog_show} to later display the reactlog graph.
 
-\item \code{reactlogShow}: Display a full reactlog graph for all sessions.
+\item \code{reactlogShow()}: Display a full reactlog graph for all sessions.
+
+\item \code{reactlogReset()}: Resets the entire reactlog stack.  Useful for debugging and removing all prior reactive history.
 
-\item \code{reactlogReset}: Resets the entire reactlog stack.  Useful for debugging and removing all prior reactive history.
 }}
-

man/renderCachedPlot.Rd

@@ -37,7 +37,7 @@ information on the default sizing policy.}
 (the default), \code{"session"}, or a cache object like a
 \code{\link[cachem:cache_disk]{cachem::cache_disk()}}. See the Cache Scoping section for more information.}
 
-\item{...}{Arguments to be passed through to \code{\link[grDevices:png]{grDevices::png()}}.
+\item{...}{Arguments to be passed through to \code{\link[=plotPNG]{plotPNG()}}.
 These can be used to set the width, height, background color, etc.}
 
 \item{alt}{Alternate text for the HTML \verb{<img>} tag if it cannot be displayed

man/renderPlot.Rd

@@ -35,10 +35,10 @@ When rendering an inline plot, you must provide numeric values (in pixels)
 to both \code{width} and \code{height}.}
 
 \item{res}{Resolution of resulting plot, in pixels per inch. This value is
-passed to \code{\link[grDevices:png]{grDevices::png()}}. Note that this affects the resolution of PNG
+passed to \code{\link[=plotPNG]{plotPNG()}}. Note that this affects the resolution of PNG
 rendering in R; it won't change the actual ppi of the browser.}
 
-\item{...}{Arguments to be passed through to \code{\link[grDevices:png]{grDevices::png()}}.
+\item{...}{Arguments to be passed through to \code{\link[=plotPNG]{plotPNG()}}.
 These can be used to set the width, height, background color, etc.}
 
 \item{alt}{Alternate text for the HTML \verb{<img>} tag if it cannot be displayed

man/shinyOptions.Rd

@@ -119,9 +119,10 @@ values are \code{"send"} (only print messages sent to the client),
 messages).}
 \item{shiny.autoload.r (defaults to \code{TRUE})}{If \code{TRUE}, then the R/
 of a shiny app will automatically be sourced.}
-\item{shiny.usecairo (defaults to \code{TRUE})}{This is used to disable graphical rendering by the
-Cairo package, if it is installed. See \code{\link[=plotPNG]{plotPNG()}} for more
-information.}
+\item{shiny.useragg (defaults to \code{TRUE})}{Set to \code{FALSE} to prevent PNG rendering via the
+ragg package. See \code{\link[=plotPNG]{plotPNG()}} for more information.}
+\item{shiny.usecairo (defaults to \code{TRUE})}{Set to \code{FALSE} to prevent PNG rendering via the
+Cairo package. See \code{\link[=plotPNG]{plotPNG()}} for more information.}
 \item{shiny.devmode (defaults to \code{NULL})}{Option to enable Shiny Developer Mode. When set,
 different default \code{getOption(key)} values will be returned. See \code{\link[=devmode]{devmode()}} for more details.}
 }

man/shinyServer.Rd

@@ -31,7 +31,7 @@ the Shiny application's page. It must take an \code{input} and an
 optional \code{session} parameter, which is used when greater control is
 needed.
 
-See the \href{https://rstudio.github.io/shiny/tutorial/}{tutorial} for more
+See the \href{https://shiny.rstudio.com/tutorial/}{tutorial} for more
 on how to write a server function.
 }
 \examples{

man/tabPanel.Rd

@@ -29,12 +29,12 @@ Create a tab panel
 }
 \section{Functions}{
 \itemize{
-\item \code{tabPanel}: Create a tab panel that can be included within a \code{\link[=tabsetPanel]{tabsetPanel()}} or a \code{\link[=navbarPage]{navbarPage()}}.
+\item \code{tabPanel()}: Create a tab panel that can be included within a \code{\link[=tabsetPanel]{tabsetPanel()}} or a \code{\link[=navbarPage]{navbarPage()}}.
 
-\item \code{tabPanelBody}: Create a tab panel that drops the title argument.
+\item \code{tabPanelBody()}: Create a tab panel that drops the title argument.
 This function should be used within \code{tabsetPanel(type = "hidden")}. See \code{\link[=tabsetPanel]{tabsetPanel()}} for example usage.
-}}
 
+}}
 \examples{
 # Show a tabset that includes a plot, summary, and
 # table view of the generated distribution

package.json

@@ -3,7 +3,7 @@
   "homepage": "https://shiny.rstudio.com",
   "repository": "github:rstudio/shiny",
   "name": "@types/rstudio-shiny",
-  "version": "1.7.1-alpha.9003",
+  "version": "1.7.2-alpha.9000",
   "license": "GPL-3.0-only",
   "main": "",
   "browser": "",
@@ -24,6 +24,7 @@
     "@types/datatables.net": "^1.10.19",
     "@types/ion-rangeslider": "2.3.0",
     "@types/jquery": "patch:@types/jquery@3.5.5#./srcts/patch/types-jquery.patch",
+    "@types/resize-observer-browser": "^0.1.7",
     "@types/selectize": "0.12.34"
   },
   "devDependencies": {

revdep/README.md

@@ -1,944 +1,12 @@
-# Platform
-
-|field    |value                        |
-|:--------|:----------------------------|
-|version  |R version 4.0.0 (2020-04-24) |
-|os       |macOS Catalina 10.15.5       |
-|system   |x86_64, darwin17.0           |
-|ui       |X11                          |
-|language |(EN)                         |
-|collate  |en_US.UTF-8                  |
-|ctype    |en_US.UTF-8                  |
-|tz       |America/New_York             |
-|date     |2020-06-19                   |
-
-# Dependencies
-
-|package |old     |new   |Δ  |
-|:-------|:-------|:-----|:--|
-|shiny   |1.4.0.2 |1.5.0 |*  |
-
 # Revdeps
 
-## Failed to check (3)
+## Failed to check (5)
 
-|package                                |version |error |warning |note |
-|:--------------------------------------|:-------|:-----|:-------|:----|
-|[frailtypack](failures.md#frailtypack) |3.3.0   |1     |        |     |
-|[Rariant](failures.md#rariant)         |1.24.0  |1     |        |     |
-|[skeleSim](failures.md#skelesim)       |0.9.8   |1     |        |     |
-
-## New problems (2)
-
-|package                                      |version |error  |warning |note     |
-|:--------------------------------------------|:-------|:------|:-------|:--------|
-|[bsplus](problems.md#bsplus)                 |0.1.1   |__+1__ |        |1        |
-|[RforProteomics](problems.md#rforproteomics) |1.26.0  |       |1       |2 __+1__ |
-
-## All (902)
-
-|package                                                                  |version    |error  |warning |note     |
-|:------------------------------------------------------------------------|:----------|:------|:-------|:--------|
-|[aaSEA](problems.md#aasea)                                               |1.1.0      |       |        |1        |
-|ABACUS                                                                   |1.0.0      |       |        |         |
-|abstractr                                                                |0.1.0      |       |        |         |
-|[ADAMgui](problems.md#adamgui)                                           |1.4.0      |       |        |2        |
-|[adapr](problems.md#adapr)                                               |2.0.0      |       |        |1        |
-|AdaptGauss                                                               |1.5.6      |       |        |         |
-|adaptiveGPCA                                                             |0.1.2      |       |        |         |
-|addinslist                                                               |0.3        |       |        |         |
-|addinsOutline                                                            |0.1.6      |       |        |         |
-|[adegenet](problems.md#adegenet)                                         |2.1.3      |       |        |1        |
-|[adepro](problems.md#adepro)                                             |3.0.0      |       |        |1        |
-|adespatial                                                               |0.3-8      |       |        |         |
-|[AdhereRViz](problems.md#adhererviz)                                     |0.1.0      |       |        |1        |
-|AFheritability                                                           |0.1.0      |       |        |         |
-|AFM                                                                      |1.2.6      |       |        |         |
-|ahp                                                                      |0.2.12     |       |        |         |
-|airGRteaching                                                            |0.2.8.69   |       |        |         |
-|[alevinQC](problems.md#alevinqc)                                         |1.4.0      |       |        |1        |
-|AMModels                                                                 |0.1.4      |       |        |         |
-|AmpGram                                                                  |1.0        |       |        |         |
-|[AMPLE](problems.md#ample)                                               |0.0.2      |       |        |1        |
-|AmyloGram                                                                |1.1        |       |        |         |
-|[analysisPipelines](problems.md#analysispipelines)                       |1.0.2      |       |        |1        |
-|[animalcules](problems.md#animalcules)                                   |1.4.0      |-1     |        |4        |
-|[animaltracker](problems.md#animaltracker)                               |0.1.0      |       |        |1        |
-|[animint2](problems.md#animint2)                                         |2019.7.3   |2      |        |2        |
-|aniview                                                                  |0.1.0      |       |        |         |
-|[ANOVAIREVA](problems.md#anovaireva)                                     |0.1.0      |       |        |1        |
-|ANOVAreplication                                                         |1.1.4      |       |        |         |
-|[ANOVAShiny](problems.md#anovashiny)                                     |0.1.0      |       |        |1        |
-|antaresRead                                                              |2.2.5      |       |        |         |
-|antaresViz                                                               |0.15.2     |       |        |         |
-|AnthropMMD                                                               |3.0.1      |       |        |         |
-|[antitrust](problems.md#antitrust)                                       |0.99.11    |       |        |1        |
-|aos                                                                      |0.1.0      |       |        |         |
-|[apexcharter](problems.md#apexcharter)                                   |0.1.4      |       |        |1        |
-|[appreci8R](problems.md#appreci8r)                                       |1.6.0      |1      |        |         |
-|[ArchaeoPhases](problems.md#archaeophases)                               |1.4.5      |       |        |1        |
-|archivist                                                                |2.3.4      |       |        |         |
-|[arena2r](problems.md#arena2r)                                           |1.0.0      |       |        |1        |
-|argonDash                                                                |0.2.0      |       |        |         |
-|argonR                                                                   |0.2.0      |       |        |         |
-|ARPobservation                                                           |1.2.0      |       |        |         |
-|arulesViz                                                                |1.3-3      |       |        |         |
-|asciiSetupReader                                                         |2.3.1      |       |        |         |
-|[ASSOCShiny](problems.md#assocshiny)                                     |0.1.0      |       |        |1        |
-|[AUCell](problems.md#aucell)                                             |1.10.0     |       |        |4        |
-|auth0                                                                    |0.2.1      |       |        |         |
-|AutoDeskR                                                                |0.1.3      |       |        |         |
-|autoshiny                                                                |0.0.2      |       |        |         |
-|[autoTS](problems.md#autots)                                             |0.9.11     |       |        |1        |
-|AzureAuth                                                                |1.2.4      |       |        |         |
-|azuremlsdk                                                               |0.6.85     |       |        |         |
-|backpipe                                                                 |0.2.3      |       |        |         |
-|bairt                                                                    |0.1.2      |       |        |         |
-|baRcodeR                                                                 |0.1.5      |       |        |         |
-|[BARIS](problems.md#baris)                                               |1.1.1      |       |        |1        |
-|basictabler                                                              |0.3.1      |       |        |         |
-|[BatchQC](problems.md#batchqc)                                           |1.16.0     |1      |        |1        |
-|[BayesBD](problems.md#bayesbd)                                           |1.2        |1      |        |         |
-|BayesianFROC                                                             |0.2.3      |       |        |         |
-|[BayesianNetwork](problems.md#bayesiannetwork)                           |0.1.5      |       |        |1        |
-|[BayesNetBP](problems.md#bayesnetbp)                                     |1.5.2      |       |        |1        |
-|[BBEST](problems.md#bbest)                                               |0.1-6      |1      |        |         |
-|[BCEA](problems.md#bcea)                                                 |2.3-1.1    |       |        |1        |
-|[bdchecks](problems.md#bdchecks)                                         |0.1.7      |       |        |1        |
-|[bdclean](problems.md#bdclean)                                           |0.1.15     |       |        |1        |
-|bdDwC                                                                    |0.1.15     |       |        |         |
-|[bde](problems.md#bde)                                                   |1.0.1      |       |        |1        |
-|BDEsize                                                                  |1.2        |       |        |         |
-|BDP2                                                                     |0.1.3      |       |        |         |
-|[bea.R](problems.md#bear)                                                |1.0.6      |       |        |1        |
-|BEACH                                                                    |1.3.1      |       |        |         |
-|[beanz](problems.md#beanz)                                               |2.4        |       |        |3        |
-|beats                                                                    |0.1.1      |       |        |         |
-|[bestSDP](problems.md#bestsdp)                                           |0.1.2      |       |        |1        |
-|[BETS](problems.md#bets)                                                 |0.4.9      |       |2       |1        |
-|[bibliometrix](problems.md#bibliometrix)                                 |3.0.2      |       |        |1        |
-|BIGL                                                                     |1.4.3      |       |        |         |
-|[bigPint](problems.md#bigpint)                                           |1.4.0      |       |        |1        |
-|[bigQueryR](problems.md#bigqueryr)                                       |0.5.0      |       |        |1        |
-|[billboarder](problems.md#billboarder)                                   |0.2.8      |       |        |1        |
-|[binovisualfields](problems.md#binovisualfields)                         |0.1.1      |       |        |1        |
-|[bioCancer](problems.md#biocancer)                                       |1.16.0     |       |1       |2        |
-|[BiocOncoTK](problems.md#bioconcotk)                                     |1.8.0      |1      |        |3        |
-|[BioInstaller](problems.md#bioinstaller)                                 |0.3.7      |       |        |1        |
-|[BioNetStat](problems.md#bionetstat)                                     |1.8.4      |       |        |4        |
-|[BIRDS](problems.md#birds)                                               |0.1        |       |        |2        |
-|[biva](problems.md#biva)                                                 |0.1.0      |       |        |1        |
-|[blkbox](problems.md#blkbox)                                             |1.0        |       |        |2        |
-|[blockCV](problems.md#blockcv)                                           |2.1.1      |       |        |1        |
-|blogdown                                                                 |0.19       |       |        |         |
-|[BLRShiny](problems.md#blrshiny)                                         |0.1.0      |       |        |1        |
-|bookdown                                                                 |0.19       |       |        |         |
-|bpbounds                                                                 |0.1.4      |       |        |         |
-|bridger2                                                                 |0.1.0      |       |        |         |
-|bs4Dash                                                                  |0.5.0      |       |        |         |
-|bSims                                                                    |0.2-1      |       |        |         |
-|[bsplus](problems.md#bsplus)                                             |0.1.1      |__+1__ |        |1        |
-|bullwhipgame                                                             |0.1.0      |       |        |         |
-|bunchr                                                                   |1.2.0      |       |        |         |
-|bupaR                                                                    |0.4.4      |       |        |         |
-|[caffsim](problems.md#caffsim)                                           |0.2.2      |       |        |1        |
-|CamelUp                                                                  |0.1.1      |       |        |         |
-|[canvasXpress](problems.md#canvasxpress)                                 |1.27.6-1   |       |        |1        |
-|[CaPO4Sim](problems.md#capo4sim)                                         |0.1.0      |       |        |1        |
-|[cartools](problems.md#cartools)                                         |0.1.0      |       |        |1        |
-|causaloptim                                                              |0.7.1      |       |        |         |
-|cbsodataR                                                                |0.4.1      |       |        |         |
-|[ChAMP](problems.md#champ)                                               |2.18.2     |1      |        |         |
-|ChannelAttributionApp                                                    |1.2        |       |        |         |
-|cheatR                                                                   |1.2.1      |       |        |         |
-|[CHETAH](problems.md#chetah)                                             |1.4.0      |       |        |2        |
-|[chipPCR](problems.md#chippcr)                                           |0.0.8-10   |       |        |1        |
-|[chromoMap](problems.md#chromomap)                                       |0.2        |       |        |1        |
-|chromVAR                                                                 |1.10.0     |       |        |         |
-|[cicerone](problems.md#cicerone)                                         |1.0.1      |       |        |1        |
-|Cite                                                                     |0.1.0      |       |        |         |
-|citr                                                                     |0.3.2      |       |        |         |
-|[cjoint](problems.md#cjoint)                                             |2.1.0      |       |        |2        |
-|CLME                                                                     |2.0-12     |       |        |         |
-|[clustDRM](problems.md#clustdrm)                                         |0.1-0      |       |        |1        |
-|[CLUSTShiny](problems.md#clustshiny)                                     |0.1.0      |       |        |1        |
-|cmsaf                                                                    |2.0.1      |-1     |        |         |
-|[CMShiny](problems.md#cmshiny)                                           |0.1.0      |       |        |1        |
-|cNORM                                                                    |1.2.3      |       |        |         |
-|[CNVPanelizer](problems.md#cnvpanelizer)                                 |1.20.0     |       |        |1        |
-|CNVScope                                                                 |3.0.9      |       |        |         |
-|[cocktailApp](problems.md#cocktailapp)                                   |0.2.1      |       |        |1        |
-|[codebook](problems.md#codebook)                                         |0.9.2      |       |        |2        |
-|[cognitoR](problems.md#cognitor)                                         |1.0.1      |       |        |1        |
-|colocr                                                                   |0.1.1      |       |        |         |
-|colorspace                                                               |1.4-1      |       |        |         |
-|colourpicker                                                             |1.0        |       |        |         |
-|compareGroups                                                            |4.4.1      |       |        |         |
-|[COMPASS](problems.md#compass)                                           |1.26.0     |       |        |3        |
-|[competitiontoolbox](problems.md#competitiontoolbox)                     |0.1.2      |       |        |1        |
-|complexity                                                               |1.1.1      |       |        |         |
-|condformat                                                               |0.9.0      |       |        |         |
-|condir                                                                   |0.1.2      |       |        |         |
-|condvis                                                                  |0.5-1      |       |        |         |
-|condvis2                                                                 |0.1.0      |       |        |         |
-|[conflr](problems.md#conflr)                                             |0.1.1      |       |        |1        |
-|convertr                                                                 |0.1        |       |        |         |
-|[CoRegNet](problems.md#coregnet)                                         |1.26.0     |       |1       |2        |
-|[corporaexplorer](problems.md#corporaexplorer)                           |0.8.2      |       |        |1        |
-|[cosinor](problems.md#cosinor)                                           |1.1        |       |        |1        |
-|countfitteR                                                              |1.0        |       |        |         |
-|[coveffectsplot](problems.md#coveffectsplot)                             |0.0.9      |       |        |1        |
-|[CRANsearcher](problems.md#cransearcher)                                 |1.0.0      |       |        |1        |
-|[crawl](problems.md#crawl)                                               |2.2.1      |       |        |1        |
-|credsubs                                                                 |1.1.0      |       |        |         |
-|[crispRdesignR](problems.md#crisprdesignr)                               |1.1.5      |       |        |1        |
-|[crisprseekplus](problems.md#crisprseekplus)                             |1.14.0     |       |        |1        |
-|cromwellDashboard                                                        |0.5.1      |       |        |         |
-|cronR                                                                    |0.4.0      |       |        |         |
-|[CrossICC](problems.md#crossicc)                                         |1.2.0      |       |        |1        |
-|[crossmeta](problems.md#crossmeta)                                       |1.14.0     |       |1       |2        |
-|crosstalk                                                                |1.1.0.1    |       |        |         |
-|crunchy                                                                  |0.3.1      |       |        |         |
-|[CSUV](problems.md#csuv)                                                 |0.1.0      |1      |        |         |
-|[CTAShiny](problems.md#ctashiny)                                         |0.1.0      |       |        |1        |
-|[ctsem](problems.md#ctsem)                                               |3.2.1      |       |        |3        |
-|ctsGE                                                                    |1.14.0     |       |        |         |
-|[CTShiny](problems.md#ctshiny)                                           |0.1.0      |       |        |1        |
-|CTTinShiny                                                               |0.1.0      |       |        |         |
-|CTTShiny                                                                 |0.1        |       |        |         |
-|cubeview                                                                 |0.2.0      |       |        |         |
-|[CVE](problems.md#cve)                                                   |1.11.2     |1      |1       |2        |
-|cydar                                                                    |1.12.0     |       |        |         |
-|CytobankAPIstats                                                         |2.0        |       |        |         |
-|d3heatmap                                                                |0.6.1.2    |       |        |         |
-|[d3Tree](problems.md#d3tree)                                             |0.2.0      |       |        |1        |
-|daqapo                                                                   |0.3.0      |       |        |         |
-|[datacheck](problems.md#datacheck)                                       |1.2.2      |       |        |2        |
-|[datadigest](problems.md#datadigest)                                     |1.0.2      |       |        |1        |
-|[dataesgobr](problems.md#dataesgobr)                                     |1.0.0      |       |        |1        |
-|datamaps                                                                 |0.0.3      |       |        |         |
-|datasets.load                                                            |1.4.0      |       |        |         |
-|daterangepicker                                                          |0.1.0      |       |        |         |
-|dccvalidator                                                             |0.2.0      |       |        |         |
-|ddpcr                                                                    |1.15       |       |        |         |
-|[debrowser](problems.md#debrowser)                                       |1.16.1     |       |        |1        |
-|deepdep                                                                  |0.2.1      |       |        |         |
-|deisotoper                                                               |0.0.7      |       |        |         |
-|[delayed](problems.md#delayed)                                           |0.3.0      |       |        |1        |
-|demoShiny                                                                |0.1        |       |        |         |
-|[DEP](problems.md#dep)                                                   |1.10.0     |       |        |1        |
-|[detzrcr](problems.md#detzrcr)                                           |0.3.0      |       |        |1        |
-|dextergui                                                                |0.2.2      |       |        |         |
-|diffr                                                                    |0.1        |       |        |         |
-|dipsaus                                                                  |0.0.7      |       |        |         |
-|[DiscoRhythm](problems.md#discorhythm)                                   |1.4.0      |       |        |2        |
-|discoveR                                                                 |1.2.4      |       |        |         |
-|disk.frame                                                               |0.3.6      |       |        |         |
-|distcomp                                                                 |1.1        |       |        |         |
-|distill                                                                  |0.8        |       |        |         |
-|distreg.vis                                                              |1.7.0      |       |        |         |
-|Distributacalcul                                                         |0.2.2      |       |        |         |
-|[diveRsity](problems.md#diversity)                                       |1.9.90     |       |        |1        |
-|DIZutils                                                                 |0.0.4      |       |        |         |
-|[DLMtool](problems.md#dlmtool)                                           |5.4.5      |       |        |1        |
-|dmdScheme                                                                |1.2        |       |        |         |
-|[Doscheda](problems.md#doscheda)                                         |1.10.0     |       |        |1        |
-|[dosedesignR](problems.md#dosedesignr)                                   |0.2.4      |       |        |1        |
-|dpcR                                                                     |0.5        |       |        |         |
-|[dplyrAssist](problems.md#dplyrassist)                                   |0.1.0      |       |        |1        |
-|dqshiny                                                                  |0.0.4      |       |        |         |
-|[dragon](problems.md#dragon)                                             |0.2.1      |       |        |1        |
-|dragulaR                                                                 |0.3.1      |       |        |         |
-|DRomics                                                                  |2.0-1      |       |        |         |
-|[dropR](problems.md#dropr)                                               |0.1        |       |        |1        |
-|DSAIDE                                                                   |0.8.3      |       |        |         |
-|DSAIRM                                                                   |0.8.2      |       |        |         |
-|DT                                                                       |0.13       |       |        |         |
-|DTAT                                                                     |0.3-4      |       |        |         |
-|[dtwclust](problems.md#dtwclust)                                         |5.5.6      |       |        |1        |
-|[DVHmetrics](problems.md#dvhmetrics)                                     |0.3.10     |       |        |1        |
-|[dynamichazard](problems.md#dynamichazard)                               |0.6.6      |       |        |1        |
-|DynNom                                                                   |5.0.1      |       |        |         |
-|Eagle                                                                    |2.2        |       |        |         |
-|eAnalytics                                                               |0.1.4      |       |        |         |
-|easySdcTable                                                             |0.5.0      |       |        |         |
-|[EBImage](problems.md#ebimage)                                           |4.30.0     |       |1       |1        |
-|ECharts2Shiny                                                            |0.2.13     |       |        |         |
-|echarts4r                                                                |0.3.2      |       |        |         |
-|edeaR                                                                    |0.8.5      |       |        |         |
-|edgebundleR                                                              |0.1.4      |       |        |         |
-|editData                                                                 |0.1.2      |       |        |         |
-|eechidna                                                                 |1.4.0      |       |        |         |
-|eemR                                                                     |1.0.1      |       |        |         |
-|EffectLiteR                                                              |0.4-4      |       |        |         |
-|[effectR](problems.md#effectr)                                           |1.0.2      |       |        |1        |
-|egor                                                                     |0.20.06    |       |        |         |
-|einet                                                                    |0.1.0      |       |        |         |
-|elaborator                                                               |1.0        |       |        |         |
-|[elementR](problems.md#elementr)                                         |1.3.6      |1      |        |         |
-|[embryogrowth](problems.md#embryogrowth)                                 |7.6        |       |        |1        |
-|[EML](problems.md#eml)                                                   |2.0.2      |       |        |1        |
-|EMMAgeo                                                                  |0.9.7      |       |        |         |
-|EMSaov                                                                   |2.3        |       |        |         |
-|emuR                                                                     |2.1.0      |       |        |         |
-|[ENCODExplorer](problems.md#encodexplorer)                               |2.14.0     |       |        |1        |
-|[enviGCMS](problems.md#envigcms)                                         |0.6.6      |       |        |1        |
-|enviPick                                                                 |1.5        |       |        |         |
-|[epicontacts](problems.md#epicontacts)                                   |1.1.0      |       |        |1        |
-|epimdr                                                                   |0.6-5      |       |        |         |
-|EpiModel                                                                 |1.8.0      |       |        |         |
-|[EpiSignalDetection](problems.md#episignaldetection)                     |0.1.1      |       |        |1        |
-|[epivizrChart](problems.md#epivizrchart)                                 |1.10.0     |       |        |2        |
-|eq5d                                                                     |0.7.1      |       |        |         |
-|[erma](problems.md#erma)                                                 |1.4.0      |       |        |2        |
-|ERSA                                                                     |0.1.1      |       |        |         |
-|eSDM                                                                     |0.3.4      |       |        |         |
-|eseis                                                                    |0.5.0      |       |        |         |
-|esquisse                                                                 |0.3.0      |       |        |         |
-|EurosarcBayes                                                            |1.1        |       |        |         |
-|evaluator                                                                |0.4.2      |       |        |         |
-|EventDetectGUI                                                           |0.3.0      |       |        |         |
-|[EventStudy](problems.md#eventstudy)                                     |0.36       |       |        |2        |
-|evobiR                                                                   |1.1        |       |        |         |
-|excelR                                                                   |0.4.0      |       |        |         |
-|ExPanDaR                                                                 |0.5.1      |       |        |         |
-|explor                                                                   |0.3.6      |       |        |         |
-|explore                                                                  |0.5.5      |       |        |         |
-|ExploreModelMatrix                                                       |1.0.1      |       |        |         |
-|[ezplot](problems.md#ezplot)                                             |0.6.1      |       |        |1        |
-|Factoshiny                                                               |2.2        |       |        |         |
-|fanplot                                                                  |3.4.2      |       |        |         |
-|[farrell](problems.md#farrell)                                           |0.2.0      |       |        |1        |
-|[FastqCleaner](problems.md#fastqcleaner)                                 |1.6.0      |       |        |2        |
-|[FELLA](problems.md#fella)                                               |1.8.0      |1      |        |1        |
-|findviews                                                                |0.1.3      |       |        |         |
-|fingertipsR                                                              |1.0.4      |       |        |         |
-|[firebase](problems.md#firebase)                                         |0.1.0      |       |        |1        |
-|[fitteR](problems.md#fitter)                                             |0.1.0      |       |        |1        |
-|[fitur](problems.md#fitur)                                               |0.6.1      |       |        |1        |
-|flacco                                                                   |1.8        |       |        |         |
-|[flair](problems.md#flair)                                               |0.0.2      |       |        |1        |
-|flexdashboard                                                            |0.5.1.1    |       |        |         |
-|[flora](problems.md#flora)                                               |0.3.4      |       |        |1        |
-|[flowAI](problems.md#flowai)                                             |1.18.2     |       |        |1        |
-|[flowcatchR](problems.md#flowcatchr)                                     |1.22.0     |       |        |2        |
-|flowPloidy                                                               |1.14.0     |       |        |         |
-|formatR                                                                  |1.7        |       |        |         |
-|formattable                                                              |0.2.0.1    |       |        |         |
-|[frailtypack](failures.md#frailtypack)                                   |3.3.0      |1      |        |         |
-|FreqProf                                                                 |0.0.1      |       |        |         |
-|frequency                                                                |0.4.0      |       |        |         |
-|fresh                                                                    |0.2.0      |       |        |         |
-|[FSK2R](problems.md#fsk2r)                                               |0.1.1      |1      |        |         |
-|[FunChIP](problems.md#funchip)                                           |1.14.0     |1      |        |         |
-|FuzzyR                                                                   |2.3        |       |        |         |
-|G2Sd                                                                     |2.1.5      |       |        |         |
-|[g3viz](problems.md#g3viz)                                               |1.1.2      |       |        |1        |
-|[GA4GHshiny](problems.md#ga4ghshiny)                                     |1.10.0     |1      |        |1        |
-|[gamesGA](problems.md#gamesga)                                           |1.1.3.7    |       |        |1        |
-|[gastempt](problems.md#gastempt)                                         |0.5.0      |       |        |3        |
-|gazepath                                                                 |1.3        |       |        |         |
-|[GDCRNATools](problems.md#gdcrnatools)                                   |1.8.0      |       |        |3        |
-|GDINA                                                                    |2.8.0      |       |        |         |
-|genBaRcode                                                               |1.2.3      |       |        |         |
-|[genBart](problems.md#genbart)                                           |1.0.1      |       |        |1        |
-|[GeneNetworkBuilder](problems.md#genenetworkbuilder)                     |1.30.0     |       |        |1        |
-|GeneralizedUmatrix                                                       |1.1.9      |       |        |         |
-|[GenEst](problems.md#genest)                                             |1.4.4      |       |        |1        |
-|[GeneTonic](problems.md#genetonic)                                       |1.0.1      |       |        |2        |
-|genogeographer                                                           |0.1.19     |       |        |         |
-|[GenomicScores](problems.md#genomicscores)                               |2.0.0      |1      |        |4        |
-|genTS                                                                    |0.1.3      |       |        |         |
-|geodrawr                                                                 |1.0.1      |       |        |         |
-|[GerminaR](problems.md#germinar)                                         |1.4.2      |       |        |1        |
-|gestate                                                                  |1.4.0      |       |        |         |
-|getTBinR                                                                 |0.7.1      |       |        |         |
-|gfonts                                                                   |0.1.1      |       |        |         |
-|[ggedit](problems.md#ggedit)                                             |0.3.1      |       |        |1        |
-|[ggExtra](problems.md#ggextra)                                           |0.9        |       |        |1        |
-|ggiraph                                                                  |0.7.0      |       |        |         |
-|[ggplotAssist](problems.md#ggplotassist)                                 |0.1.3      |       |        |1        |
-|ggplotgui                                                                |1.0.0      |       |        |         |
-|[ggquickeda](problems.md#ggquickeda)                                     |0.1.6      |       |        |1        |
-|ggraptR                                                                  |1.2        |       |        |         |
-|ggThemeAssist                                                            |0.1.5      |       |        |         |
-|ggvis                                                                    |0.4.5      |       |        |         |
-|gimmeTools                                                               |0.1        |       |        |         |
-|giphyr                                                                   |0.2.0      |       |        |         |
-|gitgadget                                                                |0.5.2      |       |        |         |
-|gitlabr                                                                  |1.1.6      |       |        |         |
-|gitlink                                                                  |0.1.3      |       |        |         |
-|glmaag                                                                   |0.0.6      |       |        |         |
-|GMCM                                                                     |1.4        |       |        |         |
-|[gmDatabase](problems.md#gmdatabase)                                     |0.5.0      |       |2       |1        |
-|[GmicR](problems.md#gmicr)                                               |1.2.0      |       |        |3        |
-|GMSE                                                                     |0.6.0.4    |       |        |         |
-|[GOFShiny](problems.md#gofshiny)                                         |0.1.0      |       |        |1        |
-|golem                                                                    |0.2.1      |       |        |         |
-|googleAnalyticsR                                                         |0.7.1      |       |        |         |
-|googleAuthR                                                              |1.3.0      |       |        |         |
-|googleCloudRunner                                                        |0.2.0      |       |        |         |
-|googleLanguageR                                                          |0.3.0      |       |        |         |
-|googleVis                                                                |0.6.5      |       |        |         |
-|googleway                                                                |2.7.1      |       |        |         |
-|[GPA](problems.md#gpa)                                                   |1.0.0      |       |        |1        |
-|GPoM.FDLyapu                                                             |1.0        |       |        |         |
-|[gQTLstats](problems.md#gqtlstats)                                       |1.20.0     |       |        |4        |
-|gradientPickerD3                                                         |0.1.0.0    |       |        |         |
-|[gravitas](problems.md#gravitas)                                         |0.1.2      |2      |        |         |
-|[gridsampler](problems.md#gridsampler)                                   |0.6        |       |        |1        |
-|[GSCA](problems.md#gsca)                                                 |2.17.0     |       |        |3        |
-|GSVA                                                                     |1.36.2     |       |        |         |
-|[gt](problems.md#gt)                                                     |0.2.1      |       |        |2        |
-|guiplot                                                                  |0.1.0      |       |        |         |
-|[gwdegree](problems.md#gwdegree)                                         |0.1.1      |       |        |1        |
-|GWSDAT                                                                   |3.0.3      |       |        |         |
-|[HaDeX](problems.md#hadex)                                               |1.2.1      |       |        |2        |
-|HARtools                                                                 |0.0.5      |       |        |         |
-|[hchinamap](problems.md#hchinamap)                                       |0.1.0      |       |        |1        |
-|HelpersMG                                                                |4.2        |       |        |         |
-|HH                                                                       |3.1-40     |       |        |         |
-|[highcharter](problems.md#highcharter)                                   |0.7.0      |       |        |1        |
-|highlightHTML                                                            |0.2.5      |       |        |         |
-|hpackedbubble                                                            |0.1.0      |       |        |         |
-|hR                                                                       |0.2.1      |       |        |         |
-|[HumanTranscriptomeCompendium](problems.md#humantranscriptomecompendium) |1.4.0      |2      |        |         |
-|[hwordcloud](problems.md#hwordcloud)                                     |0.1.0      |       |        |1        |
-|iAdapt                                                                   |0.1.0      |       |        |         |
-|iCellR                                                                   |1.5.1      |       |        |         |
-|iCOBRA                                                                   |1.16.0     |       |        |         |
-|ICSShiny                                                                 |0.5        |       |        |         |
-|[ideal](problems.md#ideal)                                               |1.12.1     |       |        |1        |
-|[idefix](problems.md#idefix)                                             |0.4.3      |       |        |1        |
-|[idem](problems.md#idem)                                                 |5.0        |       |        |2        |
-|ifaTools                                                                 |0.21       |       |        |         |
-|igraphinshiny                                                            |0.1        |       |        |         |
-|iheatmapr                                                                |0.4.12     |       |        |         |
-|imagefluency                                                             |0.2.3      |       |        |         |
-|Imetagene                                                                |1.18.0     |       |        |         |
-|[immunarch](problems.md#immunarch)                                       |0.6.5      |       |        |2        |
-|IMP                                                                      |1.1        |       |        |         |
-|ImportExport                                                             |1.1        |       |        |         |
-|[IMWatson](problems.md#imwatson)                                         |0.5.0      |       |        |1        |
-|[IncucyteDRC](problems.md#incucytedrc)                                   |0.5.4      |1      |        |         |
-|[INDperform](problems.md#indperform)                                     |0.2.2      |2      |        |1        |
-|inferr                                                                   |0.3.0      |       |        |         |
-|[inlabru](problems.md#inlabru)                                           |2.1.13     |       |        |2        |
-|[INSPEcT](problems.md#inspect)                                           |1.18.0     |       |        |2        |
-|[interactiveDisplay](problems.md#interactivedisplay)                     |1.26.0     |       |1       |2        |
-|interactiveDisplayBase                                                   |1.26.3     |       |        |         |
-|[interAdapt](problems.md#interadapt)                                     |0.1        |       |        |2        |
-|interimApp                                                               |0.0.1      |       |        |         |
-|[IOHanalyzer](problems.md#iohanalyzer)                                   |0.1.3      |       |        |2        |
-|ioncopy                                                                  |2.1.1      |       |        |         |
-|ipc                                                                      |0.1.3      |       |        |         |
-|ipumsr                                                                   |0.4.4      |       |        |         |
-|irtDemo                                                                  |0.1.4      |       |        |         |
-|IRTShiny                                                                 |1.2        |       |        |         |
-|[iSEE](problems.md#isee)                                                 |2.0.0      |2      |        |2        |
-|[iSEEu](problems.md#iseeu)                                               |1.0.1      |2      |        |         |
-|[iSTATS](problems.md#istats)                                             |1.4        |       |        |1        |
-|[ivygapSE](problems.md#ivygapse)                                         |1.10.0     |       |        |2        |
-|JMbayes                                                                  |0.8-85     |       |        |         |
-|JointNets                                                                |2.0.1      |       |        |         |
-|[jpmesh](problems.md#jpmesh)                                             |1.2.1      |       |        |1        |
-|[jpndistrict](problems.md#jpndistrict)                                   |0.3.7      |       |        |1        |
-|[jsmodule](problems.md#jsmodule)                                         |1.0.8      |       |        |1        |
-|KappaGUI                                                                 |2.0.2      |       |        |         |
-|KCSKNNShiny                                                              |0.1.0      |       |        |         |
-|KCSNBShiny                                                               |0.1.0      |       |        |         |
-|kgc                                                                      |1.0.0.2    |       |        |         |
-|kgschart                                                                 |1.3.5      |       |        |         |
-|[KNNShiny](problems.md#knnshiny)                                         |0.1.0      |       |        |1        |
-|[kokudosuuchi](problems.md#kokudosuuchi)                                 |0.4.2      |       |        |1        |
-|[koRpus](problems.md#korpus)                                             |0.11-5     |       |        |1        |
-|lavaan.shiny                                                             |1.2        |       |        |         |
-|LBSPR                                                                    |0.1.5      |       |        |         |
-|lcars                                                                    |0.3.1      |       |        |         |
-|lcsm                                                                     |0.1.1      |       |        |         |
-|LDAvis                                                                   |0.3.2      |       |        |         |
-|leaflet                                                                  |2.0.3      |       |        |         |
-|[leaflet.extras2](problems.md#leafletextras2)                            |1.0.0      |       |        |1        |
-|leaflet.minicharts                                                       |0.6.0      |       |        |         |
-|learnr                                                                   |0.10.1     |       |        |         |
-|[learnstats](problems.md#learnstats)                                     |0.1.1      |       |        |1        |
-|[levi](problems.md#levi)                                                 |1.6.0      |       |        |2        |
-|lifelogr                                                                 |0.1.0      |       |        |         |
-|lightsout                                                                |0.3        |       |        |         |
-|[likert](problems.md#likert)                                             |1.3.5      |       |        |1        |
-|lime                                                                     |0.5.1      |       |        |         |
-|linguisticsdown                                                          |1.2.0      |       |        |         |
-|linkspotter                                                              |1.2.0      |       |        |         |
-|linpk                                                                    |1.0        |       |        |         |
-|listviewer                                                               |3.0.0      |       |        |         |
-|[live](problems.md#live)                                                 |1.5.13     |       |        |1        |
-|[lmviz](problems.md#lmviz)                                               |0.1.2      |       |        |1        |
-|manipulateWidget                                                         |0.10.1     |       |        |         |
-|[mapdeck](problems.md#mapdeck)                                           |0.3.3      |       |        |1        |
-|[mapedit](problems.md#mapedit)                                           |0.6.0      |       |        |1        |
-|markdownInput                                                            |0.1.2      |       |        |         |
-|matman                                                                   |1.1.0      |       |        |         |
-|MAVIS                                                                    |1.1.3      |       |        |         |
-|MazamaSpatialUtils                                                       |0.6.4      |       |        |         |
-|MCPModPack                                                               |0.2        |-1     |        |         |
-|mcvis                                                                    |1.0.4      |       |        |         |
-|[MDSPCAShiny](problems.md#mdspcashiny)                                   |0.1.0      |       |        |1        |
-|meltt                                                                    |0.4.1      |       |        |         |
-|[memapp](problems.md#memapp)                                             |2.13       |       |        |1        |
-|[memery](problems.md#memery)                                             |0.5.2      |       |        |1        |
-|merTools                                                                 |0.5.0      |       |        |         |
-|[meta4diag](problems.md#meta4diag)                                       |2.0.8      |       |        |1        |
-|MetaAnalyser                                                             |0.2.1      |       |        |         |
-|metamer                                                                  |0.2.0      |       |        |         |
-|metathis                                                                 |1.0.2      |       |        |         |
-|[MetCirc](problems.md#metcirc)                                           |1.18.0     |       |        |2        |
-|[MethylAid](problems.md#methylaid)                                       |1.22.0     |2      |        |1        |
-|[methylGSA](problems.md#methylgsa)                                       |1.6.1      |       |        |1        |
-|metricsgraphics                                                          |0.9.0      |       |        |         |
-|[mgcViz](problems.md#mgcviz)                                             |0.1.6      |       |        |1        |
-|[microhaplot](problems.md#microhaplot)                                   |1.0.1      |       |        |1        |
-|microsamplingDesign                                                      |1.0.7      |       |        |         |
-|midas                                                                    |1.0.1      |       |        |         |
-|MIMSunit                                                                 |0.9.1      |       |        |         |
-|[miniMeta](problems.md#minimeta)                                         |0.2        |       |        |1        |
-|miniUI                                                                   |0.1.1.1    |       |        |         |
-|[miRcomp](problems.md#mircomp)                                           |1.18.0     |       |1       |         |
-|mirt                                                                     |1.32.1     |       |        |         |
-|mirtCAT                                                                  |1.9.3      |       |        |         |
-|[MLDAShiny](problems.md#mldashiny)                                       |0.1.0      |       |        |1        |
-|mldr                                                                     |0.4.3      |       |        |         |
-|[MLInterfaces](problems.md#mlinterfaces)                                 |1.68.0     |       |        |5        |
-|[mlr3shiny](problems.md#mlr3shiny)                                       |0.1.1      |       |        |1        |
-|[MLRShiny](problems.md#mlrshiny)                                         |0.1.0      |       |        |1        |
-|[MLRShiny2](problems.md#mlrshiny2)                                       |0.1.0      |       |        |1        |
-|mlxR                                                                     |4.1.3      |       |        |         |
-|[MMDiff2](problems.md#mmdiff2)                                           |1.16.0     |       |        |4        |
-|[MNLR](problems.md#mnlr)                                                 |0.1.0      |       |        |1        |
-|modest                                                                   |0.3-1      |       |        |         |
-|MODIStsp                                                                 |1.4.0      |       |        |         |
-|Mondrian                                                                 |1.1.0      |       |        |         |
-|mplot                                                                    |1.0.4      |       |        |         |
-|mrMLM.GUI                                                                |4.0        |       |        |         |
-|[MSEtool](problems.md#msetool)                                           |1.6.0      |       |        |1        |
-|[MSGFgui](problems.md#msgfgui)                                           |1.22.0     |1      |        |         |
-|[MSnbase](problems.md#msnbase)                                           |2.14.2     |       |        |3        |
-|MSstatsQCgui                                                             |1.8.0      |       |        |         |
-|[mstrio](problems.md#mstrio)                                             |11.2.1     |       |        |1        |
-|MtreeRing                                                                |1.4.2      |       |        |         |
-|[MuChPoint](problems.md#muchpoint)                                       |0.6.1      |       |        |1        |
-|multichull                                                               |1.0.0      |       |        |         |
-|mwaved                                                                   |1.1.7      |       |        |         |
-|mwshiny                                                                  |2.1.0      |       |        |         |
-|NACHO                                                                    |1.0.1      |       |        |         |
-|[nbc4va](problems.md#nbc4va)                                             |1.1        |1      |        |1        |
-|[NBShiny](problems.md#nbshiny)                                           |0.1.0      |       |        |1        |
-|[NBShiny2](problems.md#nbshiny2)                                         |0.1.0      |       |        |1        |
-|[NDP](problems.md#ndp)                                                   |0.1.0      |       |        |1        |
-|[neo4r](problems.md#neo4r)                                               |0.1.1      |       |        |1        |
-|netCoin                                                                  |1.1.25     |       |        |         |
-|netrankr                                                                 |0.2.1      |       |        |         |
-|nlgeocoder                                                               |0.1.3      |       |        |         |
-|NNTbiomarker                                                             |0.29.11    |       |        |         |
-|normalr                                                                  |1.0.0      |       |        |         |
-|nph                                                                      |2.0        |       |        |         |
-|[nprcgenekeepr](problems.md#nprcgenekeepr)                               |1.0.3      |       |        |1        |
-|npregfast                                                                |1.5.1      |       |        |         |
-|nse2r                                                                    |0.1.2      |       |        |         |
-|objectremover                                                            |0.7.0      |       |        |         |
-|[oceanis](problems.md#oceanis)                                           |1.7.3      |       |        |2        |
-|[omicplotR](problems.md#omicplotr)                                       |1.8.0      |       |        |2        |
-|[oneSENSE](problems.md#onesense)                                         |1.10.0     |       |1       |1        |
-|[ontoProc](problems.md#ontoproc)                                         |1.10.0     |1      |        |3        |
-|[oolong](problems.md#oolong)                                             |0.3.4      |       |        |1        |
-|OpenImageR                                                               |1.1.7      |       |        |         |
-|[openmetrics](problems.md#openmetrics)                                   |0.1.1      |       |        |1        |
-|[openPrimeRui](problems.md#openprimerui)                                 |1.10.0     |       |        |2        |
-|[oppr](problems.md#oppr)                                                 |1.0.2      |       |        |1        |
-|optimStrat                                                               |2.1        |       |        |         |
-|OWEA                                                                     |0.1.1      |       |        |         |
-|[pairsD3](problems.md#pairsd3)                                           |0.1.0      |       |        |1        |
-|[PanVizGenerator](problems.md#panvizgenerator)                           |1.16.0     |       |        |1        |
-|ParallelLogger                                                           |2.0.0      |       |        |         |
-|paramGUI                                                                 |2.1.4      |       |        |         |
-|parcoords                                                                |1.0.0      |       |        |         |
-|[PathoStat](problems.md#pathostat)                                       |1.14.0     |       |        |1        |
-|pcadapt                                                                  |4.3.3      |       |        |         |
-|[pcaExplorer](problems.md#pcaexplorer)                                   |2.14.2     |       |        |2        |
-|[pcFactorStan](problems.md#pcfactorstan)                                 |1.5.1      |       |        |2        |
-|PCRedux                                                                  |1.0-6      |       |        |         |
-|pdfsearch                                                                |0.3.0      |       |        |         |
-|PDShiny                                                                  |0.1.0      |       |        |         |
-|PELVIS                                                                   |2.0.1      |       |        |         |
-|[pepStat](problems.md#pepstat)                                           |1.22.0     |       |        |3        |
-|periscope                                                                |0.4.10-1   |       |        |         |
-|[phenocamr](problems.md#phenocamr)                                       |1.1.4      |       |        |1        |
-|phenofit                                                                 |0.2.7      |       |        |         |
-|phenology                                                                |7.3        |       |        |         |
-|phuse                                                                    |0.2.2      |       |        |         |
-|PhyloProfile                                                             |1.2.5      |       |        |         |
-|[piano](problems.md#piano)                                               |2.4.0      |       |        |2        |
-|pipe.design                                                              |0.5.1      |       |        |         |
-|pipefittr                                                                |0.1.2      |       |        |         |
-|[pitchRx](problems.md#pitchrx)                                           |1.8.2      |       |        |1        |
-|PivotalR                                                                 |0.1.18.3.1 |       |        |         |
-|[pivottabler](problems.md#pivottabler)                                   |1.5.0      |       |        |1        |
-|pixels                                                                   |0.1.0      |       |        |         |
-|PKconverter                                                              |1.5        |       |        |         |
-|pkgsearch                                                                |3.0.2      |       |        |         |
-|plainview                                                                |0.1.0      |       |        |         |
-|[plethem](problems.md#plethem)                                           |0.1.7      |1      |        |1        |
-|[plotGrouper](problems.md#plotgrouper)                                   |1.6.0      |       |        |1        |
-|[plotly](problems.md#plotly)                                             |4.9.2.1    |       |        |1        |
-|plotROC                                                                  |2.2.1      |       |        |         |
-|plotSEMM                                                                 |2.4        |       |        |         |
-|plsr                                                                     |0.0.1      |       |        |         |
-|[pmd](problems.md#pmd)                                                   |0.1.9      |       |        |1        |
-|[pogos](problems.md#pogos)                                               |1.8.0      |       |        |1        |
-|[polaroid](problems.md#polaroid)                                         |0.0.1      |       |        |1        |
-|[polmineR](problems.md#polminer)                                         |0.8.0      |       |        |1        |
-|PopED                                                                    |0.5.0      |       |        |         |
-|poppr                                                                    |2.8.6      |       |        |         |
-|populationPDXdesign                                                      |1.0.3      |       |        |         |
-|powdR                                                                    |1.2.2      |       |        |         |
-|powerlmm                                                                 |0.4.0      |       |        |         |
-|ppcSpatial                                                               |0.2.0      |       |        |         |
-|pqantimalarials                                                          |0.2        |       |        |         |
-|[precisely](problems.md#precisely)                                       |0.1.0      |       |        |1        |
-|[PrecisionTrialDrawer](problems.md#precisiontrialdrawer)                 |1.4.0      |1      |        |         |
-|[predictoR](problems.md#predictor)                                       |1.1.0      |       |        |1        |
-|[PREPShiny](problems.md#prepshiny)                                       |0.1.0      |       |        |1        |
-|[primirTSS](problems.md#primirtss)                                       |1.6.1      |       |1       |1        |
-|[prioritizr](problems.md#prioritizr)                                     |5.0.1      |       |        |2        |
-|ProbBayes                                                                |1.1        |       |        |         |
-|[PROBShiny](problems.md#probshiny)                                       |0.1.0      |       |        |1        |
-|[processanimateR](problems.md#processanimater)                           |1.0.3      |       |        |1        |
-|processmapR                                                              |0.3.4      |       |        |         |
-|processmonitR                                                            |0.1.0      |       |        |         |
-|processR                                                                 |0.2.3      |       |        |         |
-|profvis                                                                  |0.3.6      |       |        |         |
-|progressr                                                                |0.6.0      |       |        |         |
-|ProjectionBasedClustering                                                |1.1.1      |       |        |         |
-|pRolocGUI                                                                |1.22.0     |       |        |         |
-|Prostar                                                                  |1.20.0     |       |        |         |
-|[psichomics](problems.md#psichomics)                                     |1.14.1     |       |        |1        |
-|PupilPre                                                                 |0.6.2      |       |        |         |
-|pushbar                                                                  |0.1.0      |       |        |         |
-|[pwrEWAS](problems.md#pwrewas)                                           |1.2.0      |2      |        |         |
-|[QCA](problems.md#qca)                                                   |3.8.2      |       |        |2        |
-|qgam                                                                     |1.3.2      |       |        |         |
-|[qlcData](problems.md#qlcdata)                                           |0.2.1      |       |        |1        |
-|[qqplotr](problems.md#qqplotr)                                           |0.0.4      |       |        |1        |
-|qqvases                                                                  |1.0.0      |       |        |         |
-|QRAGadget                                                                |0.1.0      |       |        |         |
-|qrage                                                                    |1.0        |       |        |         |
-|QTL.gCIMapping.GUI                                                       |2.1        |       |        |         |
-|[questionr](problems.md#questionr)                                       |0.7.1      |       |        |2        |
-|R.SamBada                                                                |0.1.2      |       |        |         |
-|r2d3                                                                     |0.2.3      |       |        |         |
-|[R3CPET](problems.md#r3cpet)                                             |1.20.0     |1      |        |         |
-|r4ss                                                                     |1.36.1     |       |        |         |
-|rabi                                                                     |1.0.2      |       |        |         |
-|radarchart                                                               |0.3.1      |       |        |         |
-|radiant                                                                  |1.3.2      |       |        |         |
-|radiant.basics                                                           |1.3.4      |       |        |         |
-|radiant.data                                                             |1.3.9      |       |        |         |
-|radiant.design                                                           |1.3.5      |       |        |         |
-|radiant.model                                                            |1.3.10     |       |        |         |
-|radiant.multivariate                                                     |1.3.5      |       |        |         |
-|radix                                                                    |0.6        |       |        |         |
-|[RagGrid](problems.md#raggrid)                                           |0.2.0      |       |        |1        |
-|rainette                                                                 |0.1.1      |       |        |         |
-|[rAmCharts](problems.md#ramcharts)                                       |2.1.13     |       |        |1        |
-|rangeMapper                                                              |0.3-7      |       |        |         |
-|[rangeModelMetadata](problems.md#rangemodelmetadata)                     |0.1.3      |       |        |1        |
-|RanglaPunjab                                                             |2.3.4      |       |        |         |
-|[rapbase](problems.md#rapbase)                                           |1.10.0     |       |        |1        |
-|[Rariant](failures.md#rariant)                                           |1.24.0     |1      |        |         |
-|rbin                                                                     |0.2.0      |       |        |         |
-|rblt                                                                     |0.2.4.5    |       |        |         |
-|[rcellminer](problems.md#rcellminer)                                     |2.10.0     |       |1       |3        |
-|[rCGH](problems.md#rcgh)                                                 |1.18.0     |       |        |2        |
-|rclipboard                                                               |0.1.2      |       |        |         |
-|rco                                                                      |1.0.1      |       |        |         |
-|rcrossref                                                                |1.0.0      |       |        |         |
-|[Rcwl](problems.md#rcwl)                                                 |1.4.2      |1      |4       |5        |
-|[rddapp](problems.md#rddapp)                                             |1.2.1      |1      |        |2        |
-|RDML                                                                     |1.0        |       |        |         |
-|reactable                                                                |0.2.0      |       |        |         |
-|reactlog                                                                 |1.0.0      |       |        |         |
-|reactR                                                                   |0.4.2      |       |        |         |
-|[recmap](problems.md#recmap)                                             |1.0.7      |       |        |1        |
-|[ReDaMoR](problems.md#redamor)                                           |0.4.2      |       |        |1        |
-|[RefNet](problems.md#refnet)                                             |1.24.0     |       |1       |         |
-|refund.shiny                                                             |0.3.0      |       |        |         |
-|regexSelect                                                              |1.0.0      |       |        |         |
-|[regressoR](problems.md#regressor)                                       |1.1.8      |       |        |1        |
-|Repliscope                                                               |1.1.0      |       |        |         |
-|repo                                                                     |2.1.5      |       |        |         |
-|[ReportingTools](problems.md#reportingtools)                             |2.28.0     |       |        |1        |
-|reprex                                                                   |0.3.0      |       |        |         |
-|[reverseR](problems.md#reverser)                                         |0.1        |       |        |1        |
-|revtools                                                                 |0.4.1      |       |        |         |
-|[RforProteomics](problems.md#rforproteomics)                             |1.26.0     |       |1       |2 __+1__ |
-|[Rfssa](problems.md#rfssa)                                               |1.0.0      |       |        |1        |
-|RGA                                                                      |0.4.2      |       |        |         |
-|[rgl](problems.md#rgl)                                                   |0.100.54   |       |        |2        |
-|[rhandsontable](problems.md#rhandsontable)                               |0.3.7      |       |        |1        |
-|Rilostat                                                                 |1.1        |       |        |         |
-|rintrojs                                                                 |0.2.2      |       |        |         |
-|rivr                                                                     |1.2-2      |       |        |         |
-|[RLumShiny](problems.md#rlumshiny)                                       |0.2.2      |       |        |1        |
-|[rmarkdown](problems.md#rmarkdown)                                       |2.3        |       |        |1        |
-|[rmd](problems.md#rmd)                                                   |0.1.5      |       |        |1        |
-|[RnBeads](problems.md#rnbeads)                                           |2.6.0      |       |        |7        |
-|rnn                                                                      |0.9.8      |       |        |         |
-|roadoi                                                                   |0.6        |       |        |         |
-|robmed                                                                   |0.7.0      |       |        |         |
-|[RobStatTM](problems.md#robstattm)                                       |1.0.2      |       |        |1        |
-|[rosr](problems.md#rosr)                                                 |0.0.10     |       |        |1        |
-|rPackedBar                                                               |0.2.2      |       |        |         |
-|[rpostgisLT](problems.md#rpostgislt)                                     |0.6.0      |       |        |1        |
-|rpredictit                                                               |0.0.2      |       |        |         |
-|[Rqc](problems.md#rqc)                                                   |1.22.0     |       |        |2        |
-|[RQuantLib](problems.md#rquantlib)                                       |0.4.12     |2      |1       |         |
-|rrtable                                                                  |0.2.1      |       |        |         |
-|[rrvgo](problems.md#rrvgo)                                               |1.0.0      |       |        |3        |
-|RSCAT                                                                    |1.1.0      |       |        |         |
-|rsconnect                                                                |0.8.16     |       |        |         |
-|[rtimicropem](problems.md#rtimicropem)                                   |1.4.0      |       |        |1        |
-|rTRMui                                                                   |1.26.0     |       |        |         |
-|[RtutoR](problems.md#rtutor)                                             |1.2        |       |        |1        |
-|rusk                                                                     |0.1.1      |       |        |         |
-|ruv                                                                      |0.9.7.1    |       |        |         |
-|rwalkr                                                                   |0.5.2      |       |        |         |
-|[RxODE](problems.md#rxode)                                               |0.9.2-0    |       |        |1        |
-|sadists                                                                  |0.2.3      |       |        |         |
-|[safetyGraphics](problems.md#safetygraphics)                             |1.1.0      |       |        |1        |
-|samr                                                                     |3.0        |       |        |         |
-|[sangerseqR](problems.md#sangerseqr)                                     |1.24.0     |       |        |1        |
-|sankeywheel                                                              |0.1.0      |       |        |         |
-|[santaR](problems.md#santar)                                             |1.0        |       |        |1        |
-|[SC3](problems.md#sc3)                                                   |1.16.0     |       |        |3        |
-|scdhlm                                                                   |0.3.2      |       |        |         |
-|schex                                                                    |1.2.0      |       |        |         |
-|[scone](problems.md#scone)                                               |1.12.0     |       |        |1        |
-|sdcHierarchies                                                           |0.18.2     |       |        |         |
-|sdcMicro                                                                 |5.5.1      |       |        |         |
-|[SDEFSR](problems.md#sdefsr)                                             |0.7.21     |       |        |1        |
-|sdm                                                                      |1.0-89     |       |        |         |
-|[SEA](problems.md#sea)                                                   |1.0        |       |        |1        |
-|searchConsoleR                                                           |0.4.0      |       |        |         |
-|seasonalview                                                             |0.3        |       |        |         |
-|semantic.dashboard                                                       |0.1.5      |       |        |         |
-|[semdrw](problems.md#semdrw)                                             |0.1.0      |       |        |1        |
-|[SemNeT](problems.md#semnet)                                             |1.3.0      |       |        |2        |
-|sen2r                                                                    |1.3.6      |       |        |         |
-|[seqplots](problems.md#seqplots)                                         |1.26.0     |       |        |4        |
-|serieslcb                                                                |0.4.0      |       |        |         |
-|[sglr](problems.md#sglr)                                                 |0.7        |       |        |2        |
-|SHELF                                                                    |1.7.0      |       |        |         |
-|shiny.info                                                               |0.2.0      |       |        |         |
-|[shiny.router](problems.md#shinyrouter)                                  |0.1.1      |       |        |1        |
-|[shiny.semantic](problems.md#shinysemantic)                              |0.3.0      |       |        |1        |
-|[shinyAce](problems.md#shinyace)                                         |0.4.1      |       |        |1        |
-|[shinyaframe](problems.md#shinyaframe)                                   |1.0.1      |       |        |1        |
-|shinyalert                                                               |1.1        |       |        |         |
-|shinyanimate                                                             |0.3.0      |       |        |         |
-|shinybootstrap2                                                          |0.2.1      |       |        |         |
-|[shinybrms](problems.md#shinybrms)                                       |1.1.0      |       |        |1        |
-|[shinyBS](problems.md#shinybs)                                           |0.61       |       |        |1        |
-|shinybusy                                                                |0.2.0      |       |        |         |
-|shinycssloaders                                                          |0.3        |       |        |         |
-|shinycustomloader                                                        |0.9.0      |       |        |         |
-|shinydashboard                                                           |0.7.1      |       |        |         |
-|shinydashboardPlus                                                       |0.7.0      |       |        |         |
-|shinyDND                                                                 |0.1.0      |       |        |         |
-|[shinyEffects](problems.md#shinyeffects)                                 |0.1.0      |       |        |1        |
-|shinyEventLogger                                                         |0.1.1      |       |        |         |
-|shinyFeedback                                                            |0.2.0      |       |        |         |
-|shinyFiles                                                               |0.8.0      |       |        |         |
-|shinyglide                                                               |0.1.2      |       |        |         |
-|shinyHeatmaply                                                           |0.2.0      |       |        |         |
-|[shinyhelper](problems.md#shinyhelper)                                   |0.3.2      |       |        |1        |
-|ShinyImage                                                               |0.1.0      |       |        |         |
-|[ShinyItemAnalysis](problems.md#shinyitemanalysis)                       |1.3.3      |       |        |2        |
-|shinyjqui                                                                |0.3.3      |       |        |         |
-|[shinyjs](problems.md#shinyjs)                                           |1.1        |       |        |1        |
-|[shinyKGode](problems.md#shinykgode)                                     |1.0.5      |       |        |1        |
-|shinyKnobs                                                               |0.1.3      |       |        |         |
-|shinylogs                                                                |0.1.7      |       |        |         |
-|shinyLP                                                                  |1.1.2      |       |        |         |
-|shinymanager                                                             |1.0.200    |       |        |         |
-|shinymaterial                                                            |1.1.0      |       |        |         |
-|shinyMatrix                                                              |0.3.0      |       |        |         |
-|[shinyMethyl](problems.md#shinymethyl)                                   |1.24.0     |1      |        |         |
-|shinyML                                                                  |0.2.0      |       |        |         |
-|shinyMobile                                                              |0.7.0      |       |        |         |
-|shinyMolBio                                                              |0.2        |       |        |         |
-|shinyNotes                                                               |0.0.1      |       |        |         |
-|shinyobjects                                                             |0.1.0      |       |        |         |
-|[shinypanels](problems.md#shinypanels)                                   |0.5.0      |       |        |1        |
-|[shinyr](problems.md#shinyr)                                             |0.2.6      |       |        |1        |
-|[shinyrecap](problems.md#shinyrecap)                                     |0.1.0      |       |        |1        |
-|shinyrecipes                                                             |0.1.0      |       |        |         |
-|shinyreforms                                                             |0.0.1      |       |        |         |
-|shinyRGL                                                                 |0.1.0      |       |        |         |
-|shinySearchbar                                                           |1.0.0      |       |        |         |
-|shinySIR                                                                 |0.1.1      |       |        |         |
-|shinystan                                                                |2.5.0      |       |        |         |
-|[shinyTANDEM](problems.md#shinytandem)                                   |1.26.0     |1      |        |         |
-|shinytest                                                                |1.4.0      |       |        |         |
-|shinythemes                                                              |1.1.2      |       |        |         |
-|shinyTime                                                                |1.0.1      |       |        |         |
-|shinytoastr                                                              |2.1.1      |       |        |         |
-|shinyTree                                                                |0.2.7      |       |        |         |
-|shinyWidgets                                                             |0.5.3      |       |        |         |
-|shinyypr                                                                 |0.0.2      |       |        |         |
-|shotGroups                                                               |0.7.5.1    |       |        |         |
-|[sigmajs](problems.md#sigmajs)                                           |0.1.5      |       |        |1        |
-|sigmaNet                                                                 |1.1.0      |       |        |         |
-|signalHsmm                                                               |1.5        |       |        |         |
-|[SimDesign](problems.md#simdesign)                                       |2.0.1      |       |        |1        |
-|simglm                                                                   |0.8.0      |       |        |         |
-|simPATHy                                                                 |0.4        |       |        |         |
-|[simplevis](problems.md#simplevis)                                       |1.3.0      |       |        |1        |
-|simrel                                                                   |2.0.2      |       |        |         |
-|sinew                                                                    |0.3.8      |       |        |         |
-|SingleCaseES                                                             |0.4.3      |       |        |         |
-|[singleCellTK](problems.md#singlecelltk)                                 |1.8.0      |       |        |3        |
-|sistec                                                                   |0.1.0      |       |        |         |
-|[skeleSim](failures.md#skelesim)                                         |0.9.8      |1      |        |         |
-|[skpr](problems.md#skpr)                                                 |0.64.2     |       |        |2        |
-|SMITIDvisu                                                               |0.0.6      |       |        |         |
-|snahelper                                                                |1.1.0      |       |        |         |
-|snotelr                                                                  |1.0.4      |       |        |         |
-|[soc.ca](problems.md#socca)                                              |0.7.3      |       |        |1        |
-|Sofi                                                                     |0.16.4.8   |       |        |         |
-|[soilcarbon](problems.md#soilcarbon)                                     |1.2.0      |       |        |2        |
-|[sojourner](problems.md#sojourner)                                       |1.2.1      |1      |        |         |
-|solvebio                                                                 |2.7.2      |       |        |         |
-|SOMbrero                                                                 |1.3        |       |        |         |
-|sortable                                                                 |0.4.2      |       |        |         |
-|[soundgen](problems.md#soundgen)                                         |1.7.0      |       |        |1        |
-|[SpaDES.addins](problems.md#spadesaddins)                                |0.1.2      |       |        |1        |
-|Spaniel                                                                  |1.2.0      |       |        |         |
-|spANOVA                                                                  |0.99.2     |       |        |         |
-|[spant](problems.md#spant)                                               |1.6.0      |       |        |1        |
-|sparkline                                                                |2.0        |       |        |         |
-|[sparklyr](problems.md#sparklyr)                                         |1.2.0      |       |        |1        |
-|[sparkTable](problems.md#sparktable)                                     |1.3.0      |       |        |1        |
-|SpatialCPie                                                              |1.4.0      |       |        |         |
-|[SpatialEpiApp](problems.md#spatialepiapp)                               |0.3        |       |        |2        |
-|[spatialLIBD](problems.md#spatiallibd)                                   |1.0.0      |1      |        |1        |
-|[spectrolab](problems.md#spectrolab)                                     |0.0.9      |       |        |1        |
-|spinifex                                                                 |0.2.0      |       |        |         |
-|SpNetPrep                                                                |1.1        |       |        |         |
-|spotGUI                                                                  |0.2.1      |       |        |         |
-|SqlRender                                                                |1.6.6      |       |        |         |
-|squid                                                                    |0.1.2      |       |        |         |
-|[SSDM](problems.md#ssdm)                                                 |0.2.8      |       |        |1        |
-|[ssrch](problems.md#ssrch)                                               |1.4.0      |       |        |2        |
-|[sstModel](problems.md#sstmodel)                                         |1.0.0      |       |        |1        |
-|[STAT](problems.md#stat)                                                 |0.1.0      |       |        |1        |
-|statnetWeb                                                               |0.5.5      |       |        |         |
-|statsr                                                                   |0.2.0      |       |        |         |
-|[steemr](problems.md#steemr)                                             |0.1.3      |       |        |1        |
-|StereoMorph                                                              |1.6.3      |       |        |         |
-|stmgui                                                                   |0.1.6      |       |        |         |
-|[stminsights](problems.md#stminsights)                                   |0.3.0      |       |        |1        |
-|[STMotif](problems.md#stmotif)                                           |2.0.0      |       |        |1        |
-|[strand](problems.md#strand)                                             |0.1.3      |       |        |1        |
-|StratigrapheR                                                            |1.1.0      |       |        |         |
-|[subscreen](problems.md#subscreen)                                       |2.0.1      |       |        |1        |
-|SubVis                                                                   |2.0.2      |       |        |         |
-|swirlify                                                                 |0.5.3      |       |        |         |
-|[tableHTML](problems.md#tablehtml)                                       |2.0.0      |       |        |2        |
-|[tablerDash](problems.md#tablerdash)                                     |0.1.0      |       |        |1        |
-|tabulizer                                                                |0.2.2      |       |        |         |
-|taipan                                                                   |0.1.2      |       |        |         |
-|target                                                                   |1.2.0      |       |        |         |
-|[TAShiny](problems.md#tashiny)                                           |0.1.0      |       |        |1        |
-|[TBSignatureProfiler](problems.md#tbsignatureprofiler)                   |1.0.0      |       |        |1        |
-|[TCGAbiolinksGUI](problems.md#tcgabiolinksgui)                           |1.14.0     |       |        |3        |
-|[TeachBayes](problems.md#teachbayes)                                     |1.0        |       |1       |         |
-|teachingApps                                                             |1.0.8      |       |        |         |
-|[tenXplore](problems.md#tenxplore)                                       |1.10.0     |       |        |1        |
-|[TestDesign](problems.md#testdesign)                                     |1.0.2      |       |        |1        |
-|[testextra](problems.md#testextra)                                       |0.1.0.1    |       |        |1        |
-|[texPreview](problems.md#texpreview)                                     |1.4.4      |       |        |1        |
-|[TFutils](problems.md#tfutils)                                           |1.8.0      |1      |1       |4        |
-|themetagenomics                                                          |1.0.2      |       |        |         |
-|threeBrain                                                               |0.1.7      |       |        |         |
-|[tidycells](problems.md#tidycells)                                       |0.2.2      |2      |        |         |
-|tidycwl                                                                  |1.0.4      |       |        |         |
-|tidyvpc                                                                  |1.0.0      |       |        |         |
-|tigerstats                                                               |0.3.2      |       |        |         |
-|[timeline](problems.md#timeline)                                         |0.9        |       |        |2        |
-|[TimerQuant](problems.md#timerquant)                                     |1.18.0     |       |        |1        |
-|[timeseriesdb](problems.md#timeseriesdb)                                 |0.4.1      |       |        |1        |
-|[timevis](problems.md#timevis)                                           |0.5        |       |        |1        |
-|tippy                                                                    |0.0.1      |       |        |         |
-|tmap                                                                     |3.0        |       |        |         |
-|[tmaptools](problems.md#tmaptools)                                       |3.0        |       |        |1        |
-|TnT                                                                      |1.10.0     |       |        |         |
-|toxEval                                                                  |1.1.0      |       |        |         |
-|[TR8](problems.md#tr8)                                                   |0.9.21     |       |        |1        |
-|trackdem                                                                 |0.5.2      |       |        |         |
-|[trackeRapp](problems.md#trackerapp)                                     |1.1        |       |        |1        |
-|trackr                                                                   |0.10.6     |       |        |         |
-|trade                                                                    |0.5.4      |       |        |         |
-|treemap                                                                  |2.4-2      |       |        |         |
-|TreeSearch                                                               |0.4.1      |       |        |         |
-|[treespace](problems.md#treespace)                                       |1.1.3.2    |       |        |1        |
-|TreeTools                                                                |1.0.0      |       |        |         |
-|Trendy                                                                   |1.10.0     |       |        |         |
-|tricolore                                                                |1.2.2      |       |        |         |
-|[TSCAN](problems.md#tscan)                                               |1.26.0     |       |        |1        |
-|tsviz                                                                    |0.1.0      |       |        |         |
-|[ttestshiny](problems.md#ttestshiny)                                     |0.1.0      |       |        |1        |
-|[TVTB](problems.md#tvtb)                                                 |1.14.0     |       |        |1        |
-|[twoddpcr](problems.md#twoddpcr)                                         |1.12.0     |       |        |1        |
-|[TxRegInfra](problems.md#txreginfra)                                     |1.8.0      |       |        |5        |
-|[ubiquity](problems.md#ubiquity)                                         |1.0.1      |       |        |1        |
-|[UCSCXenaShiny](problems.md#ucscxenashiny)                               |0.5.0      |       |        |2        |
-|UCSCXenaTools                                                            |1.3.1      |       |        |         |
-|[Ularcirc](problems.md#ularcirc)                                         |1.6.0      |1      |        |         |
-|Umatrix                                                                  |3.3        |       |        |         |
-|[ursa](problems.md#ursa)                                                 |3.8.20     |       |        |1        |
-|[VariantFiltering](problems.md#variantfiltering)                         |1.24.0     |1      |        |3        |
-|[VarSelLCM](problems.md#varsellcm)                                       |2.1.3      |       |        |1        |
-|[vdiffr](problems.md#vdiffr)                                             |0.3.2      |       |        |1        |
-|vegawidget                                                               |0.3.1      |       |        |         |
-|vici                                                                     |0.5.2      |       |        |         |
-|VineCopula                                                               |2.3.0      |       |        |         |
-|[viromeBrowser](problems.md#viromebrowser)                               |1.0.0      |       |        |1        |
-|[visit](problems.md#visit)                                               |2.1        |       |        |2        |
-|[visNetwork](problems.md#visnetwork)                                     |2.0.9      |       |        |1        |
-|vistributions                                                            |0.1.1      |       |        |         |
-|visvow                                                                   |0.9.0      |       |        |         |
-|voronoiTreemap                                                           |0.2.0      |       |        |         |
-|VOSONDash                                                                |0.5.4      |       |        |         |
-|vov                                                                      |0.1.0      |       |        |         |
-|vtree                                                                    |4.0.0      |       |        |         |
-|[VTShiny](problems.md#vtshiny)                                           |0.1.0      |       |        |1        |
-|VWPre                                                                    |1.2.3      |       |        |         |
-|[waiter](problems.md#waiter)                                             |0.1.0      |       |        |1        |
-|[wallace](problems.md#wallace)                                           |1.0.6.2    |       |        |1        |
-|[webr](problems.md#webr)                                                 |0.1.5      |       |        |1        |
-|webshot                                                                  |0.5.2      |       |        |         |
-|weco                                                                     |1.2        |       |        |         |
-|weightr                                                                  |2.0.2      |       |        |         |
-|wilson                                                                   |2.4.0      |       |        |         |
-|wiqid                                                                    |0.3.0      |       |        |         |
-|[wiseR](problems.md#wiser)                                               |1.0.1      |       |        |2        |
-|workflowr                                                                |1.6.2      |       |        |         |
-|wppExplorer                                                              |2.3-4      |       |        |         |
-|[wTO](problems.md#wto)                                                   |1.6.3      |       |        |1        |
-|xplorerr                                                                 |0.1.1      |       |        |         |
-|[xROI](problems.md#xroi)                                                 |0.9.13     |       |1       |         |
-|[ymlthis](problems.md#ymlthis)                                           |0.1.2      |       |        |1        |
-|yonder                                                                   |0.2.0      |       |        |         |
-|[yuimaGUI](problems.md#yuimagui)                                         |1.3.0      |       |        |1        |
-|zooimage                                                                 |5.5.2      |       |        |         |
-|zscorer                                                                  |0.3.1      |       |        |         |
+|package    |version |error |warning |note |
+|:----------|:-------|:-----|:-------|:----|
+|ctsem      |3.6.0   |1     |        |     |
+|diveR      |?       |      |        |     |
+|loon.shiny |?       |      |        |     |
+|NA         |?       |      |        |     |
+|SSVS       |?       |      |        |     |
 

revdep/cran.md

@@ -0,0 +1,15 @@
+## revdepcheck results
+
+We checked 1039 reverse dependencies (1038 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 4 packages
+
+Issues with CRAN packages are summarised below.
+
+### Failed to check
+
+* ctsem      (NA)
+* diveR      (NA)
+* loon.shiny (NA)
+* SSVS       (NA)

srcts/src/bindings/output/image.ts

@@ -290,10 +290,12 @@ class ImageOutputBinding extends OutputBinding {
     width: number | string,
     height: number | string
   ): void {
-    $(el).find("img").trigger("resize");
-    return;
-    width;
-    height;
+    const img = $(el).find("img");
+
+    img.attr("width", width);
+    img.attr("height", height);
+
+    img.trigger("resize");
   }
 }
 

srcts/src/shiny/bind.ts

@@ -7,7 +7,7 @@ import type {
   InputValidateDecorator,
 } from "../inputPolicies";
 import { shinyAppBindOutput, shinyAppUnbindOutput } from "./initedMethods";
-import { sendImageSizeFns } from "./sendImageSize";
+import { sendOutputInfoFns } from "./sendOutputInfo";
 
 const boundInputs = {};
 
@@ -38,8 +38,6 @@ type BindInputsCtx = {
   inputsRate: InputRateDecorator;
   inputBindings: BindingRegistry<InputBinding>;
   outputBindings: BindingRegistry<OutputBinding>;
-  sendOutputHiddenState: () => void;
-  maybeAddThemeObserver: (el: HTMLElement) => void;
   initDeferredIframes: () => void;
 };
 function bindInputs(
@@ -120,11 +118,7 @@ function bindInputs(
 }
 
 function bindOutputs(
-  {
-    sendOutputHiddenState,
-    maybeAddThemeObserver,
-    outputBindings,
-  }: BindInputsCtx,
+  { outputBindings }: BindInputsCtx,
   scope: BindScope = document.documentElement
 ): void {
   const $scope = $(scope);
@@ -155,12 +149,6 @@ function bindOutputs(
         continue;
       }
 
-      // If this element reports its CSS styles to getCurrentOutputInfo()
-      // then it should have a MutationObserver() to resend CSS if its
-      // style/class attributes change. This observer should already exist
-      // for _static_ UI, but not yet for _dynamic_ UI
-      maybeAddThemeObserver(el);
-
       const bindingAdapter = new OutputBindingAdapter(el, binding);
 
       shinyAppBindOutput(id, bindingAdapter);
@@ -177,8 +165,7 @@ function bindOutputs(
   }
 
   // Send later in case DOM layout isn't final yet.
-  setTimeout(sendImageSizeFns.regular, 0);
-  setTimeout(sendOutputHiddenState, 0);
+  setTimeout(sendOutputInfoFns.regular, 0);
 }
 
 function unbindInputs(
@@ -212,7 +199,6 @@ function unbindInputs(
   }
 }
 function unbindOutputs(
-  { sendOutputHiddenState }: BindInputsCtx,
   scope: BindScope = document.documentElement,
   includeSelf = false
 ) {
@@ -243,8 +229,7 @@ function unbindOutputs(
   }
 
   // Send later in case DOM layout isn't final yet.
-  setTimeout(sendImageSizeFns.regular, 0);
-  setTimeout(sendOutputHiddenState, 0);
+  setTimeout(sendOutputInfoFns.regular, 0);
 }
 
 // (Named used before TS conversion)
@@ -256,13 +241,9 @@ function _bindAll(
   bindOutputs(shinyCtx, scope);
   return bindInputs(shinyCtx, scope);
 }
-function unbindAll(
-  shinyCtx: BindInputsCtx,
-  scope: BindScope,
-  includeSelf = false
-): void {
+function unbindAll(scope: BindScope, includeSelf = false): void {
   unbindInputs(scope, includeSelf);
-  unbindOutputs(shinyCtx, scope, includeSelf);
+  unbindOutputs(scope, includeSelf);
 }
 function bindAll(shinyCtx: BindInputsCtx, scope: BindScope): void {
   // _bindAll returns input values; it doesn't send them to the server.

srcts/src/shiny/init.ts

@@ -10,11 +10,11 @@ import {
 } from "../inputPolicies";
 import type { InputPolicy } from "../inputPolicies";
 import { addDefaultInputOpts } from "../inputPolicies/inputValidateDecorator";
-import { debounce, Debouncer } from "../time";
+import { debounce } from "../time";
 import {
   getComputedLinkColor,
   getStyle,
-  hasOwnProperty,
+  isHidden,
   mapValues,
   pixelRatio,
 } from "../utils";
@@ -22,7 +22,7 @@ import { bindAll, unbindAll, _bindAll } from "./bind";
 import type { BindInputsCtx, BindScope } from "./bind";
 import { setShinyObj } from "./initedMethods";
 import { registerDependency } from "./render";
-import { sendImageSizeFns } from "./sendImageSize";
+import { sendOutputInfoFns } from "./sendOutputInfo";
 import { ShinyApp } from "./shinyapp";
 import { registerNames as singletonsRegisterNames } from "./singletons";
 import type { InputPolicyOpts } from "../inputPolicies/inputPolicy";
@@ -87,8 +87,6 @@ function initShiny(windowShiny: Shiny): void {
     return {
       inputs,
       inputsRate,
-      sendOutputHiddenState,
-      maybeAddThemeObserver,
       inputBindings,
       outputBindings,
       initDeferredIframes,
@@ -99,7 +97,7 @@ function initShiny(windowShiny: Shiny): void {
     bindAll(shinyBindCtx(), scope);
   };
   windowShiny.unbindAll = function (scope: BindScope, includeSelf = false) {
-    unbindAll(shinyBindCtx(), scope, includeSelf);
+    unbindAll(scope, includeSelf);
   };
 
   // Calls .initialize() for all of the input objects in all input bindings,
@@ -127,12 +125,11 @@ function initShiny(windowShiny: Shiny): void {
   }
   windowShiny.initializeInputs = initializeInputs;
 
-  function getIdFromEl(el: HTMLElement) {
+  function getIdFromEl(el: HTMLElement): string | null {
     const $el = $(el);
     const bindingAdapter = $el.data("shiny-output-binding");
 
-    if (!bindingAdapter) return null;
-    else return bindingAdapter.getId();
+    return bindingAdapter ? bindingAdapter.getId() : null;
   }
 
   // Initialize all input objects in the document, before binding
@@ -150,306 +147,204 @@ function initShiny(windowShiny: Shiny): void {
     (x) => x.value
   );
 
-  // The server needs to know the size of each image and plot output element,
-  // in case it is auto-sizing
-  $(".shiny-image-output, .shiny-plot-output, .shiny-report-size").each(
-    function () {
-      const id = getIdFromEl(this);
-
-      if (this.offsetWidth !== 0 || this.offsetHeight !== 0) {
-        initialValues[".clientdata_output_" + id + "_width"] = this.offsetWidth;
-        initialValues[".clientdata_output_" + id + "_height"] =
-          this.offsetHeight;
-      }
+  // Helper function for both initializing and updating input values
+  function setInput(name: string, value: unknown, initial = false): void {
+    if (initial) {
+      initialValues[name] = value;
+    } else {
+      inputs.setInput(name, value);
     }
-  );
-
-  function getComputedBgColor(el) {
-    if (!el) {
-      // Top of document, can't recurse further
-      return null;
-    }
-
-    const bgColor = getStyle(el, "background-color");
-    const m = bgColor.match(
-      /^rgba\(\s*([\d.]+)\s*,\s*([\d.]+)\s*,\s*([\d.]+)\s*,\s*([\d.]+)\s*\)$/
-    );
-
-    if (bgColor === "transparent" || (m && parseFloat(m[4]) === 0)) {
-      // No background color on this element. See if it has a background image.
-      const bgImage = getStyle(el, "background-image");
-
-      if (bgImage && bgImage !== "none") {
-        // Failed to detect background color, since it has a background image
-        return null;
-      } else {
-        // Recurse
-        return getComputedBgColor(el.parentElement);
-      }
-    }
-    return bgColor;
   }
 
-  function getComputedFont(el) {
-    const fontFamily = getStyle(el, "font-family");
-    const fontSize = getStyle(el, "font-size");
+  function doSendSize(el: HTMLElement, initial = false): void {
+    const id = getIdFromEl(el);
 
-    return {
-      families: fontFamily.replace(/"/g, "").split(", "),
-      size: fontSize,
-    };
+    if (el.offsetWidth !== 0 || el.offsetHeight !== 0) {
+      setInput(".clientdata_output_" + id + "_width", el.offsetWidth, initial);
+      setInput(
+        ".clientdata_output_" + id + "_height",
+        el.offsetHeight,
+        initial
+      );
+    }
   }
 
-  $(".shiny-image-output, .shiny-plot-output, .shiny-report-theme").each(
-    function () {
-      // eslint-disable-next-line @typescript-eslint/no-this-alias
-      const el = this;
-      const id = getIdFromEl(el);
+  function doTriggerResize(el: HTMLElement): void {
+    const $el = $(el),
+      binding = $el.data("shiny-output-binding");
 
-      initialValues[".clientdata_output_" + id + "_bg"] =
-        getComputedBgColor(el);
-      initialValues[".clientdata_output_" + id + "_fg"] = getStyle(el, "color");
-      initialValues[".clientdata_output_" + id + "_accent"] =
-        getComputedLinkColor(el);
-      initialValues[".clientdata_output_" + id + "_font"] = getComputedFont(el);
-      maybeAddThemeObserver(el);
-    }
-  );
-
-  // Resend computed styles if *an output element's* class or style attribute changes.
-  // This gives us some level of confidence that getCurrentOutputInfo() will be
-  // properly invalidated if output container is mutated; but unfortunately,
-  // we don't have a reasonable way to detect change in *inherited* styles
-  // (other than session$setCurrentTheme())
-  // https://github.com/rstudio/shiny/issues/3196
-  // https://github.com/rstudio/shiny/issues/2998
-  function maybeAddThemeObserver(el: HTMLElement): void {
-    if (!window.MutationObserver) {
-      return; // IE10 and lower
-    }
-
-    const cl = el.classList;
-    const reportTheme =
-      cl.contains("shiny-image-output") ||
-      cl.contains("shiny-plot-output") ||
-      cl.contains("shiny-report-theme");
-
-    if (!reportTheme) {
-      return;
-    }
-
-    const $el = $(el);
-
-    if ($el.data("shiny-theme-observer")) {
-      return; // i.e., observer is already observing
-    }
-
-    const observerCallback = new Debouncer(null, () => doSendTheme(el), 100);
-    const observer = new MutationObserver(() => observerCallback.normalCall());
-    const config = { attributes: true, attributeFilter: ["style", "class"] };
-
-    observer.observe(el, config);
-    $el.data("shiny-theme-observer", observer);
+    $el.trigger({
+      type: "shiny:visualchange",
+      // @ts-expect-error; Can not remove info on a established, malformed Event object
+      visible: !isHidden(el),
+      binding: binding,
+    });
+    binding.onResize();
   }
 
-  function doSendTheme(el) {
+  function doSendTheme(el: HTMLElement, initial = false): void {
     // Sending theme info on error isn't necessary (it'd add an unnecessary additional round-trip)
     if (el.classList.contains("shiny-output-error")) {
       return;
     }
-    const id = getIdFromEl(el);
 
-    inputs.setInput(".clientdata_output_" + id + "_bg", getComputedBgColor(el));
-    inputs.setInput(".clientdata_output_" + id + "_fg", getStyle(el, "color"));
-    inputs.setInput(
-      ".clientdata_output_" + id + "_accent",
-      getComputedLinkColor(el)
-    );
-    inputs.setInput(".clientdata_output_" + id + "_font", getComputedFont(el));
-  }
+    function getComputedBgColor(el: HTMLElement): string {
+      if (!el) {
+        // Top of document, can't recurse further
+        return null;
+      }
 
-  function doSendImageSize() {
-    $(".shiny-image-output, .shiny-plot-output, .shiny-report-size").each(
-      function () {
-        const id = getIdFromEl(this);
+      const bgColor = getStyle(el, "background-color");
+      const m = bgColor.match(
+        /^rgba\(\s*([\d.]+)\s*,\s*([\d.]+)\s*,\s*([\d.]+)\s*,\s*([\d.]+)\s*\)$/
+      );
 
-        if (this.offsetWidth !== 0 || this.offsetHeight !== 0) {
-          inputs.setInput(
-            ".clientdata_output_" + id + "_width",
-            this.offsetWidth
-          );
-          inputs.setInput(
-            ".clientdata_output_" + id + "_height",
-            this.offsetHeight
-          );
+      if (bgColor === "transparent" || (m && parseFloat(m[4]) === 0)) {
+        // No background color on this element. See if it has a background image.
+        const bgImage = getStyle(el, "background-image");
+
+        if (bgImage && bgImage !== "none") {
+          // Failed to detect background color, since it has a background image
+          return null;
+        } else {
+          // Recurse
+          return getComputedBgColor(el.parentElement);
         }
       }
-    );
+      return bgColor;
+    }
 
-    $(".shiny-image-output, .shiny-plot-output, .shiny-report-theme").each(
-      function () {
-        doSendTheme(this);
-      }
-    );
+    function getComputedFont(el: HTMLElement): {
+      families: string[];
+      size: string;
+    } {
+      const fontFamily = getStyle(el, "font-family");
+      const fontSize = getStyle(el, "font-size");
 
+      return {
+        families: fontFamily.replace(/"/g, "").split(", "),
+        size: fontSize,
+      };
+    }
+
+    const id = getIdFromEl(el);
+
+    setInput(
+      ".clientdata_output_" + id + "_bg",
+      getComputedBgColor(el),
+      initial
+    );
+    setInput(
+      ".clientdata_output_" + id + "_fg",
+      getStyle(el, "color"),
+      initial
+    );
+    setInput(
+      ".clientdata_output_" + id + "_accent",
+      getComputedLinkColor(el),
+      initial
+    );
+    setInput(
+      ".clientdata_output_" + id + "_font",
+      getComputedFont(el),
+      initial
+    );
+  }
+
+  // eslint-disable-next-line prefer-const
+  let visibleOutputs = new Set();
+
+  function doSendHiddenState(el: HTMLElement, initial = false): void {
+    const id = getIdFromEl(el);
+    const hidden = isHidden(el);
+
+    if (!hidden) visibleOutputs.add(id);
+    setInput(".clientdata_output_" + id + "_hidden", hidden, initial);
+  }
+
+  function doSendOutputInfo(initial = false) {
+    const outputIds = new Set();
+
+    // TODO: can we always rely on this class existing when we're calling this (especially initially)?
     $(".shiny-bound-output").each(function () {
-      const $this = $(this),
-        binding = $this.data("shiny-output-binding");
+      // eslint-disable-next-line @typescript-eslint/no-this-alias
+      const el = this,
+        id = getIdFromEl(el),
+        isPlot =
+          el.classList.contains("shiny-image-output") ||
+          el.classList.contains("shiny-plot-output");
 
-      $this.trigger({
-        type: "shiny:visualchange",
-        // @ts-expect-error; Can not remove info on a established, malformed Event object
-        visible: !isHidden(this),
-        binding: binding,
-      });
-      binding.onResize();
+      outputIds.add(id);
+
+      function handleResize(initial = false) {
+        doTriggerResize(el);
+        doSendHiddenState(el, initial);
+        if (isPlot || el.classList.contains("shiny-report-size")) {
+          doSendSize(el, initial);
+        }
+      }
+
+      // TODO: do we need a polyfill for ResizeObserver?
+      if (!$(el).data("shiny-resize-observer")) {
+        const onResize = debounce(100, handleResize);
+        const ro = new ResizeObserver(() => onResize(false));
+
+        ro.observe(el);
+        $(el).data("shiny-resize-observer", ro);
+      }
+
+      function handleIntersect(entries) {
+        entries.forEach(() => {
+          handleResize(false);
+        });
+      }
+
+      // TODO: do we need a polyfill for IntersectionObserver?
+      if (!$(el).data("shiny-intersection-observer")) {
+        const onIntersect = debounce(100, handleIntersect);
+        const io = new IntersectionObserver(onIntersect);
+
+        io.observe(el);
+        $(el).data("shiny-intersection-observer", io);
+      }
+
+      function handleMutate(initial = false) {
+        if (isPlot || el.classList.contains("shiny-report-theme")) {
+          doSendTheme(el, initial);
+        }
+      }
+
+      // TODO: do we need a polyfill for MutationObserver?
+      if (!$(el).data("shiny-mutate-observer")) {
+        const onMutate = debounce(100, handleMutate);
+        const mo = new MutationObserver(() => onMutate(false));
+
+        mo.observe(el, {
+          attributes: true,
+          attributeFilter: ["style", "class"],
+        });
+
+        $(el).data("shiny-mutate-observer", mo);
+      }
+
+      handleResize(initial);
+      handleMutate(initial);
+    });
+
+    // It could be that previously visible outputs have been removed from the DOM,
+    // in that case, consider them hidden.
+    visibleOutputs.forEach((id) => {
+      if (!outputIds.has(id)) {
+        visibleOutputs.delete(id);
+        setInput(".clientdata_output_" + id + "_hidden", true, initial);
+      }
     });
   }
 
-  sendImageSizeFns.setImageSend(inputBatchSender, doSendImageSize);
-
-  // Return true if the object or one of its ancestors in the DOM tree has
-  // style='display:none'; otherwise return false.
-  function isHidden(obj) {
-    // null means we've hit the top of the tree. If width or height is
-    // non-zero, then we know that no ancestor has display:none.
-    if (obj === null || obj.offsetWidth !== 0 || obj.offsetHeight !== 0) {
-      return false;
-    } else if (getStyle(obj, "display") === "none") {
-      return true;
-    } else {
-      return isHidden(obj.parentNode);
-    }
-  }
-  let lastKnownVisibleOutputs = {};
-  // Set initial state of outputs to hidden, if needed
-
-  $(".shiny-bound-output").each(function () {
-    const id = getIdFromEl(this);
-
-    if (isHidden(this)) {
-      initialValues[".clientdata_output_" + id + "_hidden"] = true;
-    } else {
-      lastKnownVisibleOutputs[id] = true;
-      initialValues[".clientdata_output_" + id + "_hidden"] = false;
-    }
-  });
-  // Send update when hidden state changes
-  function doSendOutputHiddenState() {
-    const visibleOutputs = {};
-
-    $(".shiny-bound-output").each(function () {
-      const id = getIdFromEl(this);
-
-      delete lastKnownVisibleOutputs[id];
-      // Assume that the object is hidden when width and height are 0
-      const hidden = isHidden(this),
-        evt = {
-          type: "shiny:visualchange",
-          visible: !hidden,
-        };
-
-      if (hidden) {
-        inputs.setInput(".clientdata_output_" + id + "_hidden", true);
-      } else {
-        visibleOutputs[id] = true;
-        inputs.setInput(".clientdata_output_" + id + "_hidden", false);
-      }
-      const $this = $(this);
-
-      // @ts-expect-error; Can not remove info on a established, malformed Event object
-      evt.binding = $this.data("shiny-output-binding");
-      // @ts-expect-error; Can not remove info on a established, malformed Event object
-      $this.trigger(evt);
-    });
-    // Anything left in lastKnownVisibleOutputs is orphaned
-    for (const name in lastKnownVisibleOutputs) {
-      if (hasOwnProperty(lastKnownVisibleOutputs, name))
-        inputs.setInput(".clientdata_output_" + name + "_hidden", true);
-    }
-    // Update the visible outputs for next time
-    lastKnownVisibleOutputs = visibleOutputs;
-  }
-  // sendOutputHiddenState gets called each time DOM elements are shown or
-  // hidden. This can be in the hundreds or thousands of times at startup.
-  // We'll debounce it, so that we do the actual work once per tick.
-  const sendOutputHiddenStateDebouncer = new Debouncer(
-    null,
-    doSendOutputHiddenState,
-    0
-  );
-
-  function sendOutputHiddenState() {
-    sendOutputHiddenStateDebouncer.normalCall();
-  }
-  // We need to make sure doSendOutputHiddenState actually gets called before
-  // the inputBatchSender sends data to the server. The lastChanceCallback
-  // here does that - if the debouncer has a pending call, flush it.
-  inputBatchSender.lastChanceCallback.push(function () {
-    if (sendOutputHiddenStateDebouncer.isPending())
-      sendOutputHiddenStateDebouncer.immediateCall();
-  });
-
-  // Given a namespace and a handler function, return a function that invokes
-  // the handler only when e's namespace matches. For example, if the
-  // namespace is "bs", it would match when e.namespace is "bs" or "bs.tab".
-  // If the namespace is "bs.tab", it would match for "bs.tab", but not "bs".
-  function filterEventsByNamespace(namespace, handler, ...args) {
-    namespace = namespace.split(".");
-
-    return function (e) {
-      const eventNamespace = e.namespace.split(".");
-
-      // If any of the namespace strings aren't present in this event, quit.
-      for (let i = 0; i < namespace.length; i++) {
-        if (eventNamespace.indexOf(namespace[i]) === -1) return;
-      }
-
-      handler.apply(this, [namespace, handler, ...args]);
-    };
-  }
-
-  // The size of each image may change either because the browser window was
-  // resized, or because a tab was shown/hidden (hidden elements report size
-  // of 0x0). It's OK to over-report sizes because the input pipeline will
-  // filter out values that haven't changed.
-  $(window).resize(debounce(500, sendImageSizeFns.regular));
-  // Need to register callbacks for each Bootstrap 3 class.
-  const bs3classes = [
-    "modal",
-    "dropdown",
-    "tab",
-    "tooltip",
-    "popover",
-    "collapse",
-  ];
-
-  $.each(bs3classes, function (idx, classname) {
-    $(document.body).on(
-      "shown.bs." + classname + ".sendImageSize",
-      "*",
-      filterEventsByNamespace("bs", sendImageSizeFns.regular)
-    );
-    $(document.body).on(
-      "shown.bs." +
-        classname +
-        ".sendOutputHiddenState " +
-        "hidden.bs." +
-        classname +
-        ".sendOutputHiddenState",
-      "*",
-      filterEventsByNamespace("bs", sendOutputHiddenState)
-    );
-  });
-
-  // This is needed for Bootstrap 2 compatibility and for non-Bootstrap
-  // related shown/hidden events (like conditionalPanel)
-  $(document.body).on("shown.sendImageSize", "*", sendImageSizeFns.regular);
-  $(document.body).on(
-    "shown.sendOutputHiddenState hidden.sendOutputHiddenState",
-    "*",
-    sendOutputHiddenState
-  );
+  // Send initial input values to the server and also register a callback
+  // to send updated input values whenever we receive new UI, etc.
+  doSendOutputInfo(true);
+  sendOutputInfoFns.setSendMethod(inputBatchSender, doSendOutputInfo);
 
   // Send initial pixel ratio, and update it if it changes
   initialValues[".clientdata_pixelratio"] = pixelRatio();

srcts/src/shiny/render.ts

@@ -7,7 +7,7 @@ import {
   shinyInitializeInputs,
   shinyUnbindAll,
 } from "./initedMethods";
-import { sendImageSizeFns } from "./sendImageSize";
+import { sendOutputInfoFns } from "./sendOutputInfo";
 
 import { renderHtml as singletonsRenderHtml } from "./singletons";
 import type { WherePosition } from "./singletons";
@@ -250,7 +250,7 @@ function addStylesheetsAndRestyle(links: HTMLLinkElement[]): void {
       // should have been applied synchronously.
       oldStyle.remove();
       removeSheet(oldSheet);
-      sendImageSizeFns.transitioned();
+      sendOutputInfoFns.transitioned();
     };
     xhr.send();
   };
@@ -310,7 +310,7 @@ function addStylesheetsAndRestyle(links: HTMLLinkElement[]): void {
       // base64-encoded and inlined into the href. We also add a dummy DOM
       // element that the CSS applies to. The dummy CSS includes a
       // transition, and when the `transitionend` event happens, we call
-      // sendImageSizeFns.transitioned() and remove the old sheet. We also remove the
+      // sendOutputInfoFns.transitioned() and remove the old sheet. We also remove the
       // dummy DOM element and dummy CSS content.
       //
       // The reason this works is because (we assume) that if multiple
@@ -320,7 +320,7 @@ function addStylesheetsAndRestyle(links: HTMLLinkElement[]): void {
       //
       // Because it is common for multiple stylesheets to arrive close
       // together, but not on exactly the same tick, we call
-      // sendImageSizeFns.transitioned(), which is debounced. Otherwise, it can result in
+      // sendOutputInfoFns.transitioned(), which is debounced. Otherwise, it can result in
       // the same plot being redrawn multiple times with different
       // styling.
       $link.attr("onload", () => {
@@ -333,7 +333,7 @@ function addStylesheetsAndRestyle(links: HTMLLinkElement[]): void {
         $dummyEl.one("transitionend", () => {
           $dummyEl.remove();
           removeSheet(oldSheet);
-          sendImageSizeFns.transitioned();
+          sendOutputInfoFns.transitioned();
         });
         $(document.body).append($dummyEl);
 

srcts/src/shiny/sendImageSize.ts

@@ -1,36 +0,0 @@
-import type { InputBatchSender } from "../inputPolicies";
-import { debounce, Debouncer } from "../time";
-
-class SendImageSize {
-  // This function gets defined in initShiny() and 'hoisted' so it can be reused
-  // (to send CSS info) inside of Shiny.renderDependencies()
-  regular: () => void;
-  transitioned: () => void;
-
-  setImageSend(
-    inputBatchSender: InputBatchSender,
-    doSendImageSize: () => void
-  ): Debouncer<typeof doSendImageSize> {
-    const sendImageSizeDebouncer = new Debouncer(null, doSendImageSize, 0);
-
-    this.regular = function () {
-      sendImageSizeDebouncer.normalCall();
-    };
-
-    // Make sure sendImageSize actually gets called before the inputBatchSender
-    // sends data to the server.
-    inputBatchSender.lastChanceCallback.push(function () {
-      if (sendImageSizeDebouncer.isPending())
-        sendImageSizeDebouncer.immediateCall();
-    });
-
-    // A version of sendImageSize which debounces for longer.
-    this.transitioned = debounce(200, this.regular);
-
-    return sendImageSizeDebouncer;
-  }
-}
-
-const sendImageSizeFns = new SendImageSize();
-
-export { sendImageSizeFns };

srcts/src/shiny/sendOutputInfo.ts

@@ -0,0 +1,36 @@
+import type { InputBatchSender } from "../inputPolicies";
+import { debounce, Debouncer } from "../time";
+
+class SendOutputInfo {
+  // This function gets defined in initShiny() and 'hoisted' so it can be reused
+  // (to send CSS info) inside of Shiny.renderDependencies()
+  regular: () => void;
+  transitioned: () => void;
+
+  setSendMethod(
+    inputBatchSender: InputBatchSender,
+    doSendOutputInfo: () => void
+  ): Debouncer<typeof doSendOutputInfo> {
+    const sendOutputInfoDebouncer = new Debouncer(null, doSendOutputInfo, 0);
+
+    this.regular = function () {
+      sendOutputInfoDebouncer.normalCall();
+    };
+
+    // Make sure sendOutputInfo actually gets called before the inputBatchSender
+    // sends data to the server.
+    inputBatchSender.lastChanceCallback.push(function () {
+      if (sendOutputInfoDebouncer.isPending())
+        sendOutputInfoDebouncer.immediateCall();
+    });
+
+    // A version of sendOutputInfo which debounces for longer.
+    this.transitioned = debounce(200, this.regular);
+
+    return sendOutputInfoDebouncer;
+  }
+}
+
+const sendOutputInfoFns = new SendOutputInfo();
+
+export { sendOutputInfoFns };

srcts/src/time/throttle.ts

@@ -19,40 +19,67 @@ class Throttler<X extends AnyVoidFunction> implements InputRatePolicy<X> {
     this.args = null;
   }
 
+  // If no timer is currently running, immediately call the function and set the
+  // timer; if a timer is running out, just queue up the args for the call when
+  // the timer runs out. Later calls during the same timeout will overwrite
+  // earlier ones.
   normalCall(...args: Parameters<X>): void {
+    // This will be an empty array (not null) if called without arguments, and
+    // `[null]` if called with `null`.
     this.args = args;
+
+    // Only invoke immediately if there isn't a timer running.
     if (this.timerId === null) {
       this.$invoke();
-      this.timerId = setTimeout(() => {
-        // IE8 doesn't reliably clear timeout, so this additional
-        // check is needed
-        if (this.timerId === null) return;
-        this.$clearTimer();
-        if (args.length > 0) this.normalCall(...args);
-      }, this.delayMs);
     }
   }
+
+  // Reset the timer if active and call immediately
   immediateCall(...args: Parameters<X>): void {
     this.$clearTimer();
     this.args = args;
     this.$invoke();
   }
+
+  // Is there a call waiting to send?
   isPending(): boolean {
-    return this.timerId !== null;
+    return this.args !== null;
   }
+
   $clearTimer(): void {
     if (this.timerId !== null) {
       clearTimeout(this.timerId);
       this.timerId = null;
     }
   }
+
+  // Invoke the throttled function with the currently-stored args and start the
+  // timer.
   $invoke(): void {
-    if (this.args && this.args.length > 0) {
-      this.func.apply(this.target, this.args);
-    } else {
-      this.func.apply(this.target);
+    if (this.args === null) {
+      // Shouldn't get here, because $invoke should only be called right after
+      // setting this.args. But just in case.
+      return;
     }
+
+    this.func.apply(this.target, this.args);
+
+    // Clear the stored args. This is used to track if a call is pending.
     this.args = null;
+
+    // Set this.timerId to a newly-created timer, which will invoke a call with
+    // the most recently called args (if any) when it expires.
+    this.timerId = setTimeout(() => {
+      // IE8 doesn't reliably clear timeout, so this additional check is needed
+      if (this.timerId === null) return;
+
+      this.$clearTimer();
+      // Do we have a call queued up?
+      if (this.isPending()) {
+        // If so, invoke the call with queued args and reset timer.
+        this.$invoke();
+      }
+    }, this.delayMs);
   }
 }
 

srcts/src/utils/index.ts

@@ -9,7 +9,7 @@ function escapeHTML(str: string): string {
     "<": "&lt;",
     ">": "&gt;",
     // eslint-disable-next-line prettier/prettier
-    "\"": "&quot;",
+    '"': "&quot;",
     "'": "&#039;",
     "/": "&#x2F;",
   };
@@ -54,6 +54,20 @@ function getStyle(el: Element, styleProp: string): string | undefined {
   return x;
 }
 
+// Return true if the object or one of its ancestors in the DOM tree has
+// style='display:none'; otherwise return false.
+function isHidden(obj: HTMLElement): boolean {
+  // null means we've hit the top of the tree. If width or height is
+  // non-zero, then we know that no ancestor has display:none.
+  if (obj === null || obj.offsetWidth !== 0 || obj.offsetHeight !== 0) {
+    return false;
+  } else if (getStyle(obj, "display") === "none") {
+    return true;
+  } else {
+    return isHidden(obj.parentElement);
+  }
+}
+
 // Convert a number to a string with leading zeros
 function padZeros(n: number, digits: number): string {
   let str = n.toString();
@@ -384,6 +398,7 @@ export {
   randomId,
   strToBool,
   getStyle,
+  isHidden,
   padZeros,
   roundSignif,
   parseDate,

srcts/types/src/shiny/bind.d.ts

@@ -7,8 +7,6 @@ declare type BindInputsCtx = {
     inputsRate: InputRateDecorator;
     inputBindings: BindingRegistry<InputBinding>;
     outputBindings: BindingRegistry<OutputBinding>;
-    sendOutputHiddenState: () => void;
-    maybeAddThemeObserver: (el: HTMLElement) => void;
     initDeferredIframes: () => void;
 };
 declare function bindInputs(shinyCtx: BindInputsCtx, scope?: BindScope): {
@@ -22,7 +20,7 @@ declare function bindInputs(shinyCtx: BindInputsCtx, scope?: BindScope): {
     };
 };
 declare function _bindAll(shinyCtx: BindInputsCtx, scope: BindScope): ReturnType<typeof bindInputs>;
-declare function unbindAll(shinyCtx: BindInputsCtx, scope: BindScope, includeSelf?: boolean): void;
+declare function unbindAll(scope: BindScope, includeSelf?: boolean): void;
 declare function bindAll(shinyCtx: BindInputsCtx, scope: BindScope): void;
 export { unbindAll, bindAll, _bindAll };
 export type { BindScope, BindInputsCtx };

srcts/types/src/shiny/sendImageSize.d.ts

@@ -1,9 +0,0 @@
-import type { InputBatchSender } from "../inputPolicies";
-import { Debouncer } from "../time";
-declare class SendImageSize {
-    regular: () => void;
-    transitioned: () => void;
-    setImageSend(inputBatchSender: InputBatchSender, doSendImageSize: () => void): Debouncer<typeof doSendImageSize>;
-}
-declare const sendImageSizeFns: SendImageSize;
-export { sendImageSizeFns };

srcts/types/src/shiny/sendOutputInfo.d.ts

@@ -0,0 +1,9 @@
+import type { InputBatchSender } from "../inputPolicies";
+import { Debouncer } from "../time";
+declare class SendOutputInfo {
+    regular: () => void;
+    transitioned: () => void;
+    setSendMethod(inputBatchSender: InputBatchSender, doSendOutputInfo: () => void): Debouncer<typeof doSendOutputInfo>;
+}
+declare const sendOutputInfoFns: SendOutputInfo;
+export { sendOutputInfoFns };

srcts/types/src/utils/index.d.ts

@@ -4,6 +4,7 @@ declare function escapeHTML(str: string): string;
 declare function randomId(): string;
 declare function strToBool(str: string): boolean | undefined;
 declare function getStyle(el: Element, styleProp: string): string | undefined;
+declare function isHidden(obj: HTMLElement): boolean;
 declare function padZeros(n: number, digits: number): string;
 declare function roundSignif(x: number, digits?: number): number;
 declare function parseDate(dateString: string): Date;
@@ -29,4 +30,4 @@ declare function updateLabel(labelTxt: string | undefined, labelNode: JQuery<HTM
 declare function getComputedLinkColor(el: HTMLElement): string;
 declare function isBS3(): boolean;
 declare function toLowerCase<T extends string>(str: T): Lowercase<T>;
-export { escapeHTML, randomId, strToBool, getStyle, padZeros, roundSignif, parseDate, formatDateUTC, makeResizeFilter, pixelRatio, scopeExprToFunc, asArray, mergeSort, $escape, mapValues, isnan, _equal, equal, compareVersion, updateLabel, getComputedLinkColor, makeBlob, hasOwnProperty, isBS3, toLowerCase, };
+export { escapeHTML, randomId, strToBool, getStyle, isHidden, padZeros, roundSignif, parseDate, formatDateUTC, makeResizeFilter, pixelRatio, scopeExprToFunc, asArray, mergeSort, $escape, mapValues, isnan, _equal, equal, compareVersion, updateLabel, getComputedLinkColor, makeBlob, hasOwnProperty, isBS3, toLowerCase, };

tests/testthat/test-bookmarking.R

@@ -45,12 +45,12 @@ test_that("Inputs and values in query string", {
   suppress_stacktrace(expect_warning(expect_warning(RestoreContext$new("?_inputs_&a=1&_inputs_&b=2"))))
   suppress_stacktrace(expect_warning(expect_warning(RestoreContext$new("?_inputs_&a=1&_values_&b=2&_inputs_&"))))
   suppress_stacktrace(expect_warning(expect_warning(RestoreContext$new("?_values_&a=1&_values_"))))
-  suppress_stacktrace(expect_warning(expect_warning(RestoreContext$new("?_inputs_&a=1&_values_&_values&b=2"))))
+  suppress_stacktrace(expect_warning(RestoreContext$new("?_inputs_&a=1&_values_&_values&b=2")))
 
   # If there's an error in the conversion from query string, should have
   # blank values.
-  suppress_stacktrace(expect_warning(expect_warning(rc <- RestoreContext$new("?_inputs_&a=[x&b=1"))))
-  expect_identical(rc$input$asList(), list())
+  suppress_stacktrace(expect_warning(rc <- RestoreContext$new("?_inputs_&a=[x&b=1")))
+  expect_identical(rc$input$asList(), list(b=1L))
   expect_identical(as.list(rc$values), list())
   expect_identical(rc$dir, NULL)
 

tests/testthat/test-reactives.R

@@ -13,3 +13,28 @@ test_that("can access reactive values directly", {
   y <- reactive(x1() + x2$a)
   expect_equal(y(), 4)
 })
+
+test_that("errors in throttled/debounced reactives are catchable", {
+  reactiveConsole(TRUE)
+  on.exit(reactiveConsole(FALSE))
+
+  # In Shiny 1.7 and earlier, if a throttled/debounced reactive threw an error,
+  # it would cause internal observers used by the implementations of
+  # debounce/throttle to error, which would kill the session. The correct
+  # behavior is to only expose the error to consumers of the throttled/debounced
+  # reactive.
+
+  r <- reactive({
+    stop("boom")
+  })
+
+  rd <- r %>% debounce(1000)
+  rt <- r %>% throttle(1000)
+
+  observe({
+    try(rd(), silent = TRUE)
+    try(rt(), silent = TRUE)
+  })
+
+  expect_silent(flushReact())
+})

tests/testthat/test-stacks-pruning.R

@@ -1,30 +1,33 @@
-capture <- function() {
-  list(
-    calls = sys.calls(),
-    parents = sys.parents()
+foo <- function() {
+  capture <- function() {
+    list(
+      calls = sys.calls(),
+      parents = sys.parents()
+    )
+  }
+
+  capture_1 <- function() {
+    capture()
+  }
+
+  capture_2 <- function() {
+    capture_1()
+  }
+
+  do.call(
+    identity,
+    list(
+      identity(capture_2())
+    )
   )
 }
-
-capture_1 <- function() {
-  capture()
-}
-
-capture_2 <- function() {
-  capture_1()
-}
-
-res <- do.call(
-  identity,
-  list(
-    identity(capture_2())
-  )
-)
-res$calls <- tail(res$calls, 5)
-res$parents <- tail(res$parents - (length(res$parents) - 5), 5)
+res <- foo()
+res$calls <- tail(res$calls, 6)
+res$parents <- tail(res$parents - (length(res$parents) - 6), 6)
 
 describe("stack pruning", {
   it("passes basic example", {
-    expect_equal(pruneStackTrace(res$parents), c(F, F, T, T, T))
-    expect_equal(lapply(list(res$parents), pruneStackTrace), list(c(F, F, T, T, T)))
+    expect_equal(pruneStackTrace(res$parents), c(T, F, F, T, T, T))
+    expect_equal(lapply(list(res$parents), pruneStackTrace), list(c(T, F, F, T, T, T)))
   })
 })

tsconfig.json

@@ -2,6 +2,7 @@
   "declaration": true,
   "compilerOptions": {
     "target": "ES5",
+    "lib": ["dom"],
     "isolatedModules": true,
     "esModuleInterop": true,
     "declaration": true,

yarn.lock

@@ -1935,6 +1935,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@types/resize-observer-browser@npm:^0.1.7":
+  version: 0.1.7
+  resolution: "@types/resize-observer-browser@npm:0.1.7"
+  checksum: eef8c82c9d3f9f4c57cad6134e795f4eebfcf11a8790d21636539e4314bf0e0c140e525c4a8cb440dd42788855daddb2c52c18f93e1c59bed20e9be6e65de290
+  languageName: node
+  linkType: hard
+
 "@types/rstudio-shiny@workspace:.":
   version: 0.0.0-use.local
   resolution: "@types/rstudio-shiny@workspace:."
@@ -1958,6 +1965,7 @@ __metadata:
     "@types/jqueryui": 1.12.15
     "@types/lodash": ^4.14.170
     "@types/node": ^15.6.1
+    "@types/resize-observer-browser": ^0.1.7
     "@types/selectize": 0.12.34
     "@types/showdown": ^1.9.3
     "@typescript-eslint/eslint-plugin": ^4.25.0