Bump version

IE8/9 file upload

.gitattributes

@@ -0,0 +1 @@
+/NEWS merge=union

.travis.yml

@@ -10,11 +10,14 @@ install:
   - sudo apt-add-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu `lsb_release -cs`/"
   - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
   - sudo apt-add-repository -y ppa:marutter/c2d4u
-  - sudo apt-get update
-  - sudo apt-get install r-base-dev r-cran-shiny r-cran-cairo r-cran-markdown
+  - sudo apt-get -qq update
+  - sudo apt-get -qq install r-base r-cran-shiny r-cran-cairo r-cran-markdown r-cran-knitr
   - "[ ! -d ~/R ] && mkdir ~/R"
-  - Rscript -e "install.packages(c('xtable', 'knitr', 'htmltools'), repos = 'http://cran.rstudio.org')"
-  - Rscript -e "install.packages('$R_MY_PKG', dep = TRUE, repos = 'http://cran.rstudio.org')"
+  - echo "options(repos = c(CRAN = 'http://cran.rstudio.com'))" > ~/.Rprofile
+  - Rscript -e "install.packages(c('mime'), quiet = TRUE, repos = 'http://rforge.net')"
+  - Rscript -e "install.packages(c('xtable', 'R6'), quiet = TRUE)"
+  - Rscript -e "update.packages(instlib = '~/R', ask = FALSE, quiet = TRUE)"
+  - Rscript -e "install.packages('$R_MY_PKG', dep = TRUE, quiet = TRUE)"
 
 # run tests
 script:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shiny
 Type: Package
 Title: Web Application Framework for R
-Version: 0.10.0.9000
-Date: 2014-06-13
+Version: 0.10.2.2
+Date: 2014-08-19
 Author: RStudio, Inc.
 Maintainer: Winston Chang <winston@rstudio.com>
 Description: Shiny makes it incredibly easy to build interactive web
@@ -11,26 +11,25 @@ Description: Shiny makes it incredibly easy to build interactive web
     beautiful, responsive, and powerful applications with minimal effort.
 License: GPL-3
 Depends:
-    R (>= 2.14.1),
-    methods
+    R (>= 3.0.0)
 Imports:
     tools,
     utils,
-    httpuv (>= 1.2.0),
-    caTools,
+    httpuv (>= 1.2.2),
+    mime (>= 0.1.3),
     RJSONIO,
     xtable,
     digest,
-    htmltools (>= 0.2.4)
+    htmltools (>= 0.2.6),
+    R6 (>= 2.0)
 Suggests:
     datasets,
     Cairo (>= 1.5-5),
     testthat,
     knitr (>= 1.6),
     markdown
-URL: http://www.rstudio.com/shiny/
+URL: http://shiny.rstudio.com
 BugReports: https://github.com/rstudio/shiny/issues
-Roxygen: list(wrap = FALSE)
 Collate:
     'app.R'
     'bootstrap-layout.R'
@@ -40,6 +39,7 @@ Collate:
     'bootstrap.R'
     'cache.R'
     'fileupload.R'
+    'stack.R'
     'graph.R'
     'hooks.R'
     'html-deps.R'
@@ -49,6 +49,7 @@ Collate:
     'middleware-shiny.R'
     'middleware.R'
     'priorityqueue.R'
+    'progress.R'
     'react.R'
     'reactive-domains.R'
     'reactives.R'

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.0.1): do not edit by hand
+# Generated by roxygen2 (4.0.2): do not edit by hand
 
 S3method("$",reactivevalues)
 S3method("$",shinyoutput)
@@ -24,6 +24,7 @@ S3method(print,reactive)
 S3method(print,shiny.appobj)
 S3method(str,reactivevalues)
 export(HTML)
+export(Progress)
 export(a)
 export(absolutePanel)
 export(actionButton)
@@ -39,6 +40,7 @@ export(checkboxInput)
 export(code)
 export(column)
 export(conditionalPanel)
+export(createWebDependency)
 export(dataTableOutput)
 export(dateInput)
 export(dateRangeInput)
@@ -69,6 +71,7 @@ export(htmlOutput)
 export(icon)
 export(imageOutput)
 export(img)
+export(incProgress)
 export(includeCSS)
 export(includeHTML)
 export(includeMarkdown)
@@ -79,6 +82,7 @@ export(installExprFunction)
 export(invalidateLater)
 export(is.reactive)
 export(is.reactivevalues)
+export(is.shiny.appobj)
 export(is.singleton)
 export(isolate)
 export(knit_print.html)
@@ -134,6 +138,7 @@ export(runUrl)
 export(selectInput)
 export(selectizeInput)
 export(serverInfo)
+export(setProgress)
 export(shinyApp)
 export(shinyAppDir)
 export(shinyServer)
@@ -179,12 +184,13 @@ export(verbatimTextOutput)
 export(verticalLayout)
 export(wellPanel)
 export(withMathJax)
+export(withProgress)
 export(withReactiveDomain)
 export(withTags)
-import(RJSONIO)
-import(caTools)
+import(R6)
 import(digest)
 import(htmltools)
 import(httpuv)
-import(methods)
+import(mime)
 import(xtable)
+importFrom(RJSONIO,fromJSON)

NEWS

@@ -1,3 +1,83 @@
+shiny 0.10.2.2
+--------------------------------------------------------------------------------
+
+* Remove use of `rstudio::viewer` in a code example, for R CMD check.
+
+shiny 0.10.2.1
+--------------------------------------------------------------------------------
+
+* Changed some examples to use \donttest instead of \dontrun.
+
+shiny 0.10.2
+--------------------------------------------------------------------------------
+
+* The minimal version of R required for the shiny package is 3.0.0 now.
+
+* Shiny apps can now consist of a single file, app.R, instead of ui.R and
+  server.R.
+
+* Upgraded DataTables from 1.9.4 to 1.10.2. This might be a breaking change if
+  you have customized the DataTables options in your apps. (More info:
+  https://github.com/rstudio/shiny/pull/558)
+
+* File uploading via `fileInput()` works for Internet Explorer 8 and 9 now. Note
+  IE8/9 do not support multiple files from a single file input. If you need to
+  upload multiple files, you have to use one file input for each file.
+
+* Switched away from reference classes to R6.
+
+* Reactive log performance has been greatly improved.
+
+* Added `Progress` and `withProgress`, to display the progress of computation
+  on the client browser.
+
+* Fixed #557: updateSelectizeInput(choices, server = TRUE) did not work when
+  `choices` is a character vector.
+
+* Searching in DataTables is case-insensitive and the search strings are not
+  treated as regular expressions by default now. If you want case-sensitive
+  searching or regular expressions, you can use the configuration options
+  `search$caseInsensitive` and `search$regex`, e.g. `renderDataTable(...,
+  options = list(search = list(caseInsensitve = FALSE, regex = TRUE)))`.
+
+* Added support for `htmltools::htmlDependency`'s new `attachment` parameter to
+  `renderUI`/`uiOutput`.
+
+* Exported `createWebDependency`. It takes an `htmltools::htmlDependency` object
+  and makes it available over Shiny's built-in web server.
+
+* Custom output bindings can now render `htmltools::htmlDependency` objects at
+  runtime using `Shiny.renderDependencies()`.
+
+* Fixes to rounding behavior of sliderInput. (#301, #502)
+
+shiny 0.10.1
+--------------------------------------------------------------------------------
+
+* Added Unicode support for Windows. Shiny apps running on Windows must use the
+  UTF-8 encoding for ui.R and server.R (also the optional global.R) if they
+  contain non-ASCII characters. See this article for details and examples:
+  http://shiny.rstudio.com/gallery/unicode-characters.html (#516)
+
+* `runGitHub()` also allows the 'username/repo' syntax now, which is equivalent
+  to `runGitHub('repo', 'username')`. (#427)
+
+* `navbarPage()` now accepts a `windowTitle` parameter to set the web browser
+  page title to something other than the title displayed in the navbar.
+
+* Added an `inline` argument to `textOutput()`, `imageOutput()`, `plotOutput()`,
+  and `htmlOutput()`. When `inline = TRUE`, these outputs will be put in
+  `span()` instead of the default `div()`. This occurs automatically when these
+  outputs are created via the inline expressions (e.g. `r renderText(expr)`) in
+  R Markdown documents. See an R Markdown example at
+  http://shiny.rstudio.com/gallery/inline-output.html (#512)
+
+* Added support for option groups in the select/selectize inputs. When the
+  `choices` argument for `selectInput()`/`selectizeInput()` is a list of
+  sub-lists and any sub-list is of length greater than 1, the HTML tag
+  `<optgroup>` will be used. See an example at
+  http://shiny.rstudio.com/gallery/option-groups-for-selectize-input.html (#542)
+
 shiny 0.10.0
 --------------------------------------------------------------------------------
 
@@ -64,6 +144,10 @@ shiny 0.10.0
 * Fixed #220: the zip file for a directory created by some programs may not have
   the directory name as its first entry, in which case runUrl() can fail. (#220)
 
+* `runGitHub()` can also take a value of the form "username/repo" in its first
+  argument, e.g. both runGitHub("shiny_example", "rstudio") and
+  runGitHub("rstudio/shiny_example") are valid ways to run the GitHub repo.
+
 shiny 0.9.1
 --------------------------------------------------------------------------------
 

R/app.R

@@ -26,7 +26,7 @@
 #'   app.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' shinyApp(
 #'   ui = fluidPage(
 #'     numericInput("n", "n", 1),
@@ -34,43 +34,23 @@
 #'   ),
 #'   server = function(input, output) {
 #'     output$plot <- renderPlot( plot(head(cars, input$n)) )
-#'   },
-#'   options=list(launch.browser = rstudio::viewer)
+#'   }
 #' )
 #'
 #' shinyAppDir(system.file("examples/01_hello", package="shiny"))
 #' }
 #'
 #' @export
-shinyApp <- function(ui, server, onStart=NULL, options=list(), uiPattern="/") {
+shinyApp <- function(ui=NULL, server=NULL, onStart=NULL, options=list(),
+                     uiPattern="/") {
+  if (is.null(server)) {
+    stop("`server` missing from shinyApp")
+  }
+
   # Ensure that the entire path is a match
   uiPattern <- sprintf("^%s$", uiPattern)
 
-  httpHandler <- function(req) {
-    if (!identical(req$REQUEST_METHOD, 'GET'))
-      return(NULL)
-
-    if (!isTRUE(grepl(uiPattern, req$PATH_INFO)))
-      return(NULL)
-
-    textConn <- textConnection(NULL, "w")
-    on.exit(close(textConn))
-
-    uiValue <- if (is.function(ui)) {
-      if (length(formals(ui)) > 0)
-        ui(req)
-      else
-        ui()
-    } else {
-      ui
-    }
-    if (is.null(uiValue))
-      return(NULL)
-
-    renderPage(uiValue, textConn)
-    html <- paste(textConnectionValue(textConn), collapse='\n')
-    return(httpResponse(200, content=html))
-  }
+  httpHandler <- uiHttpHandler(ui, uiPattern)
 
   serverFuncSource <- function() {
     server
@@ -91,10 +71,7 @@ shinyApp <- function(ui, server, onStart=NULL, options=list(), uiPattern="/") {
 #'   file and either ui.R or www/index.html)
 #' @export
 shinyAppDir <- function(appDir, options=list()) {
-  # Most of the complexity here comes from needing to hot-reload if the .R files
-  # change on disk, or are created, or are removed.
-
-  if (!file.exists(appDir)) {
+  if (!file_test('-d', appDir)) {
     stop("No Shiny application exists at the path \"", appDir, "\"")
   }
 
@@ -102,6 +79,21 @@ shinyAppDir <- function(appDir, options=list()) {
   # affected by future changes to the path)
   appDir <- normalizePath(appDir, mustWork = TRUE)
 
+  if (file.exists.ci(appDir, "server.R")) {
+    shinyAppDir_serverR(appDir, options = options)
+  } else if (file.exists.ci(appDir, "app.R")) {
+    shinyAppDir_appR(appDir, options = options)
+  } else {
+    stop("App dir must contain either app.R or server.R.")
+  }
+}
+
+# This reads in an app dir in the case that there's a server.R (and ui.R/www)
+# present, and returns a shiny.appobj.
+shinyAppDir_serverR <- function(appDir, options=list()) {
+  # Most of the complexity here comes from needing to hot-reload if the .R files
+  # change on disk, or are created, or are removed.
+
   # uiHandlerSource is a function that returns an HTTP handler for serving up
   # ui.R as a webpage. The "cachedFuncWithFile" call makes sure that the closure
   # we're creating here only gets executed when ui.R's contents change.
@@ -112,9 +104,7 @@ shinyAppDir <- function(appDir, options=list()) {
         # If not, then take the last expression that's returned from ui.R.
         .globals$ui <- NULL
         on.exit(.globals$ui <- NULL, add = FALSE)
-        ui <- source(uiR,
-          local = new.env(parent = globalenv()),
-          keep.source = TRUE)$value
+        ui <- sourceUTF8(uiR, local = new.env(parent = globalenv()))$value
         if (!is.null(.globals$ui)) {
           ui <- .globals$ui[[1]]
         }
@@ -137,11 +127,7 @@ shinyAppDir <- function(appDir, options=list()) {
       # server.R.
       .globals$server <- NULL
       on.exit(.globals$server <- NULL, add = TRUE)
-      result <- source(
-        serverR,
-        local = new.env(parent = globalenv()),
-        keep.source = TRUE
-      )$value
+      result <- sourceUTF8(serverR, local = new.env(parent = globalenv()))$value
       if (!is.null(.globals$server)) {
         result <- .globals$server[[1]]
       }
@@ -169,7 +155,7 @@ shinyAppDir <- function(appDir, options=list()) {
     oldwd <<- getwd()
     setwd(appDir)
     if (file.exists(file.path.ci(appDir, "global.R")))
-      source(file.path.ci(appDir, "global.R"), keep.source = TRUE)
+      sourceUTF8(file.path.ci(appDir, "global.R"))
   }
   onEnd <- function() {
     setwd(oldwd)
@@ -186,6 +172,60 @@ shinyAppDir <- function(appDir, options=list()) {
   )
 }
 
+# This reads in an app dir in the case that there's a app.R present, and returns
+# a shiny.appobj.
+shinyAppDir_appR <- function(appDir, options=list()) {
+  fullpath <- file.path.ci(appDir, "app.R")
+
+  # This sources app.R and caches the content. When appObj() is called but
+  # app.R hasn't changed, it won't re-source the file. But if called and
+  # app.R has changed, it'll re-source the file and return the result.
+  appObj <- cachedFuncWithFile(appDir, "app.R", case.sensitive = FALSE,
+    function(appR) {
+      result <- sourceUTF8(fullpath, local = new.env(parent = globalenv()))$value
+
+      if (!is.shiny.appobj(result))
+        stop("app.R did not return a shiny.appobj object.")
+
+      return(result)
+    }
+  )
+
+  # A function that invokes the http handler from the appObj in app.R, but
+  # since this uses appObj(), it only re-sources the file when it changes.
+  dynHttpHandler <- function(...) {
+    appObj()$httpHandler(...)
+  }
+
+  dynServerFuncSource <- function(...) {
+    appObj()$serverFuncSource(...)
+  }
+
+  wwwDir <- file.path.ci(appDir, "www")
+  fallbackWWWDir <- system.file("www-dir", package = "shiny")
+
+  oldwd <- NULL
+  onStart <- function() {
+    oldwd <<- getwd()
+    setwd(appDir)
+  }
+  onEnd <- function() {
+    setwd(oldwd)
+  }
+
+  structure(
+    list(
+      httpHandler = joinHandlers(c(dynHttpHandler, wwwDir, fallbackWWWDir)),
+      serverFuncSource = dynServerFuncSource,
+      onStart = onStart,
+      onEnd = onEnd,
+      options = options
+    ),
+    class = "shiny.appobj"
+  )
+}
+
+
 #' @rdname shinyApp
 #' @param x Object to convert to a Shiny app.
 #' @export
@@ -211,6 +251,12 @@ as.shiny.appobj.character <- function(x) {
   shinyAppDir(x)
 }
 
+#' @rdname shinyApp
+#' @export
+is.shiny.appobj <- function(x) {
+  inherits(x, "shiny.appobj")
+}
+
 #' @rdname shinyApp
 #' @param ... Additional parameters to be passed to print.
 #' @export
@@ -249,26 +295,33 @@ as.tags.shiny.appobj <- function(x, ...) {
 #' @param ... Additional knit_print arguments
 NULL
 
+# If there's an R Markdown runtime option set but it isn't set to Shiny, then
+# return a warning indicating the runtime is inappropriate for this object.
+# Returns NULL in all other cases.
+shiny_rmd_warning <- function() {
+  runtime <- knitr::opts_knit$get("rmarkdown.runtime")
+  if (!is.null(runtime) && runtime != "shiny")
+    # note that the RStudio IDE checks for this specific string to detect Shiny
+    # applications in static document
+    list(structure(
+      "Shiny application in a static R Markdown document",
+      class = "rmd_warning"))
+  else
+    NULL
+}
+
 #' @rdname knitr_methods
 #' @export
 knit_print.shiny.appobj <- function(x, ...) {
   opts <- x$options %OR% list()
   width <- if (is.null(opts$width)) "100%" else opts$width
   height <- if (is.null(opts$height)) "400" else opts$height
-  shiny_warning <- NULL
-  # if there's an R Markdown runtime option set but it isn't set to Shiny, then
-  # emit a warning indicating the runtime is inappropriate for this object
+
   runtime <- knitr::opts_knit$get("rmarkdown.runtime")
   if (!is.null(runtime) && runtime != "shiny") {
-    # note that the RStudio IDE checks for this specific string to detect Shiny
-    # applications in static document
-    shiny_warning <- list(structure(
-      "Shiny application in a static R Markdown document",
-      class = "rmd_warning"))
-
-    # create a box exactly the same dimensions as the Shiny app would have had
-    # (so the document continues to flow as it would have with the app), and
-    # display a diagnostic message
+    # If not rendering to a Shiny document, create a box exactly the same
+    # dimensions as the Shiny app would have had (so the document continues to
+    # flow as it would have with the app), and display a diagnostic message
     width <- validateCssUnit(width)
     height <- validateCssUnit(height)
     output <- tags$div(
@@ -289,15 +342,19 @@ knit_print.shiny.appobj <- function(x, ...) {
   # for now it's not an issue, so just return the HTML and warning.
 
   knitr::asis_output(htmlPreserve(format(output, indent=FALSE)),
-                     meta = shiny_warning, cacheable = FALSE)
+                     meta = shiny_rmd_warning(), cacheable = FALSE)
 }
 
-# Lets us use a nicer syntax in knitr chunks than literally
+# Let us use a nicer syntax in knitr chunks than literally
 # calling output$value <- renderFoo(...) and fooOutput().
 #' @rdname knitr_methods
+#' @param inline Whether the object is printed inline.
 #' @export
-knit_print.shiny.render.function <- function(x, ...) {
+knit_print.shiny.render.function <- function(x, ..., inline = FALSE) {
+  x <- htmltools::as.tags(x, inline = inline)
   output <- knitr::knit_print(tagList(x))
   attr(output, "knit_cacheable") <- FALSE
+  attr(output, "knit_meta") <- append(attr(output, "knit_meta"),
+                                      shiny_rmd_warning())
   output
 }

R/bootstrap.R

@@ -160,6 +160,8 @@ pageWithSidebar <- function(headerPanel,
 #' @param theme Alternative Bootstrap stylesheet (normally a css file within the
 #'   www directory). For example, to use the theme located at
 #'   \code{www/bootstrap.css} you would use \code{theme = "bootstrap.css"}.
+#' @param windowTitle The title that should be displayed by the browser window.
+#'   Useful if \code{title} is not a string.
 #' @param icon Optional icon to appear on a \code{navbarMenu} tab.
 #'
 #' @return A UI defintion that can be passed to the \link{shinyUI} function.
@@ -194,7 +196,8 @@ navbarPage <- function(title,
                        collapsable = FALSE,
                        fluid = TRUE,
                        responsive = TRUE,
-                       theme = NULL) {
+                       theme = NULL,
+                       windowTitle = title) {
 
   # alias title so we can avoid conflicts w/ title in withTags
   pageTitle <- title
@@ -259,7 +262,7 @@ navbarPage <- function(title,
 
   # build the page
   bootstrapPage(
-    title = title,
+    title = windowTitle,
     responsive = responsive,
     theme = theme,
     div(class=navbarClass,
@@ -381,6 +384,11 @@ mainPanel <- function(..., width = 8) {
 #'   determine whether the panel should be displayed.
 #' @param ... Elements to include in the panel.
 #'
+#' @note You are not recommended to use special JavaScript characters such as a
+#'   period \code{.} in the input id's, but if you do use them anyway, for
+#'   example, \code{inputId = "foo.bar"}, you will have to use
+#'   \code{input["foo.bar"]} instead of \code{input.foo.bar} to read the input
+#'   value.
 #' @examples
 #' sidebarPanel(
 #'    selectInput(
@@ -473,8 +481,6 @@ numericInput <- function(inputId, label, value, min = NA, max = NA, step = NA) {
 #' File Upload Control
 #'
 #' Create a file upload control that can be used to upload one or more files.
-#' \bold{Does not work on older browsers, including Internet Explorer 9 and
-#' earlier.}
 #'
 #' Whenever a file upload completes, the corresponding input variable is set
 #' to a dataframe. This dataframe contains one row for each selected file, and
@@ -498,13 +504,14 @@ numericInput <- function(inputId, label, value, min = NA, max = NA, step = NA) {
 #' @param inputId Input variable to assign the control's value to.
 #' @param label Display label for the control.
 #' @param multiple Whether the user should be allowed to select and upload
-#'   multiple files at once.
+#'   multiple files at once. \bold{Does not work on older browsers, including
+#'   Internet Explorer 9 and earlier.}
 #' @param accept A character vector of MIME types; gives the browser a hint of
 #'   what kind of files the server is expecting.
 #'
 #' @export
 fileInput <- function(inputId, label, multiple = FALSE, accept = NULL) {
-  inputTag <- tags$input(id = inputId, type = "file")
+  inputTag <- tags$input(id = inputId, name = inputId, type = "file")
   if (multiple)
     inputTag$attribs$multiple <- "multiple"
   if (length(accept) > 0)
@@ -576,31 +583,13 @@ checkboxGroupInput <- function(inputId, label, choices, selected = NULL, inline
   if (!is.null(selected))
     selected <- validateSelected(selected, choices, inputId)
 
-  # Create tags for each of the options
-  ids <- paste0(inputId, seq_along(choices))
-
-  checkboxes <- mapply(ids, choices, names(choices),
-    SIMPLIFY = FALSE, USE.NAMES = FALSE,
-    FUN = function(id, value, name) {
-      inputTag <- tags$input(type = "checkbox",
-                             name = inputId,
-                             id = id,
-                             value = value)
-
-    if (value %in% selected)
-      inputTag$attribs$checked <- "checked"
-
-    tags$label(class = if (inline) "checkbox inline" else "checkbox",
-               inputTag,
-               tags$span(name))
-    }
-  )
+  options <- generateOptions(inputId, choices, selected, inline)
 
   # return label and select tag
   tags$div(id = inputId,
            class = "control-group shiny-input-checkboxgroup",
            controlLabel(inputId, label),
-           checkboxes)
+           options)
 }
 
 # Before shiny 0.9, `selected` refers to names/labels of `choices`; now it
@@ -608,11 +597,12 @@ checkboxGroupInput <- function(inputId, label, choices, selected = NULL, inline
 validateSelected <- function(selected, choices, inputId) {
   # drop names, otherwise toJSON() keeps them too
   selected <- unname(selected)
-  if (is.list(choices)) {
-    # <optgroup> is not there yet
-    if (any(sapply(choices, length) > 1)) return(selected)
-    choices <- unlist(choices)
-  }
+  # if you are using optgroups, you're using shiny > 0.10.0, and you should
+  # already know that `selected` must be a value instead of a label
+  if (needOptgroup(choices)) return(selected)
+
+  if (is.list(choices)) choices <- unlist(choices)
+
   nms <- names(choices)
   # labels and values are identical, no need to validate
   if (identical(nms, unname(choices))) return(selected)
@@ -630,6 +620,29 @@ validateSelected <- function(selected, choices, inputId) {
   selected
 }
 
+# generate options for radio buttons and checkbox groups (type = 'checkbox' or
+# 'radio')
+generateOptions <- function(inputId, choices, selected, inline, type = 'checkbox') {
+  # create tags for each of the options
+  ids <- paste0(inputId, seq_along(choices))
+  # generate a list of <input type=? [checked] />
+  mapply(
+    ids, choices, names(choices),
+    FUN = function(id, value, name) {
+      inputTag <- tags$input(
+        type = type, name = inputId, id = id, value = value
+      )
+      if (value %in% selected)
+        inputTag$attribs$checked <- "checked"
+      tags$label(
+        class = paste(type, if (inline) "inline"),
+        inputTag, tags$span(name)
+      )
+    },
+    SIMPLIFY = FALSE, USE.NAMES = FALSE
+  )
+}
+
 #' Create a help text element
 #'
 #' Create help text which can be added to an input form to provide additional
@@ -654,20 +667,43 @@ controlLabel <- function(controlName, label) {
 # Takes a vector or list, and adds names (same as the value) to any entries
 # without names.
 choicesWithNames <- function(choices) {
-  if (is.null(choices)) return(choices)  # ignore NULL
+  # Take a vector or list, and convert to list. Also, if any children are
+  # vectors with length > 1, convert those to list. If the list is unnamed,
+  # convert it to a named list with blank names.
+  listify <- function(obj) {
+    # If a list/vector is unnamed, give it blank names
+    makeNamed <- function(x) {
+      if (is.null(names(x))) names(x) <- character(length(x))
+      x
+    }
 
-  # get choice names
-  choiceNames <- names(choices)
-  if (is.null(choiceNames))
-    choiceNames <- character(length(choices))
+    res <- lapply(obj, function(val) {
+      if (is.list(val))
+        listify(val)
+      else if (length(val) == 1 && is.null(names(val)))
+        val
+      else
+        makeNamed(as.list(val))
+    })
+
+    makeNamed(res)
+  }
+
+  choices <- listify(choices)
+  if (length(choices) == 0) return(choices)
+
+  # Recurse into any subgroups
+  choices <- mapply(choices, names(choices), FUN = function(choice, name) {
+    if (!is.list(choice)) return(choice)
+    if (name == "") stop('All sub-lists in "choices" must be named.')
+    choicesWithNames(choice)
+  }, SIMPLIFY = FALSE)
 
   # default missing names to choice values
-  missingNames <- choiceNames == ""
-  choiceNames[missingNames] <- paste(choices)[missingNames]
-  names(choices) <- choiceNames
+  missing <- names(choices) == ""
+  names(choices)[missing] <- as.character(choices)[missing]
 
-  # return choices
-  return (choices)
+  choices
 }
 
 #' Create a select list input control
@@ -707,21 +743,11 @@ selectInput <- function(inputId, label, choices, selected = NULL,
 
   # default value if it's not specified
   if (is.null(selected)) {
-    if (!multiple) selected <- choices[[1]]
+    if (!multiple) selected <- firstChoice(choices)
   } else selected <- validateSelected(selected, choices, inputId)
 
-  # Create tags for each of the options
-  options <- HTML(paste("<option value=\"",
-    htmlEscape(choices),
-    "\"",
-    ifelse(choices %in% selected, " selected", ""),
-    ">",
-    htmlEscape(names(choices)),
-    "</option>",
-    sep = "", collapse = "\n"));
-
   # create select tag and add options
-  selectTag <- tags$select(id = inputId, options)
+  selectTag <- tags$select(id = inputId, selectOptions(choices, selected))
   if (multiple)
     selectTag$attribs$multiple <- "multiple"
 
@@ -731,6 +757,44 @@ selectInput <- function(inputId, label, choices, selected = NULL,
   selectizeIt(inputId, res, NULL, width, nonempty = !multiple && !("" %in% choices))
 }
 
+firstChoice <- function(choices) {
+  if (length(choices) == 0L) return()
+  choice <- choices[[1]]
+  if (is.list(choice)) firstChoice(choice) else choice
+}
+
+# Create tags for each of the options; use <optgroup> if necessary.
+# This returns a HTML string instead of tags, because of the 'selected'
+# attribute.
+selectOptions <- function(choices, selected = NULL) {
+  html <- mapply(choices, names(choices), FUN = function(choice, label) {
+    if (is.list(choice)) {
+      # If sub-list, create an optgroup and recurse into the sublist
+      sprintf(
+        '<optgroup label="%s">\n%s\n</optgroup>',
+        htmlEscape(label),
+        selectOptions(choice, selected)
+      )
+
+    } else {
+      # If single item, just return option string
+      sprintf(
+        '<option value="%s"%s>%s</option>',
+        htmlEscape(choice),
+        if (choice %in% selected) ' selected' else '',
+        htmlEscape(label)
+      )
+    }
+  })
+
+  HTML(paste(html, collapse = '\n'))
+}
+
+# need <optgroup> when choices contains sub-lists
+needOptgroup <- function(choices) {
+  any(vapply(choices, is.list, logical(1)))
+}
+
 #' @rdname selectInput
 #' @param ... Arguments passed to \code{selectInput()}.
 #' @param options A list of options. See the documentation of \pkg{selectize.js}
@@ -812,33 +876,14 @@ radioButtons <- function(inputId, label, choices, selected = NULL, inline = FALS
   selected <- if (is.null(selected)) choices[[1]] else {
     validateSelected(selected, choices, inputId)
   }
+  if (length(selected) > 1) stop("The 'selected' argument must be of length 1")
 
-  # Create tags for each of the options
-  ids <- paste0(inputId, seq_along(choices))
-
-  inputTags <- mapply(ids, choices, names(choices),
-    SIMPLIFY = FALSE, USE.NAMES = FALSE,
-    FUN = function(id, value, name) {
-      inputTag <- tags$input(type = "radio",
-                             name = inputId,
-                             id = id,
-                             value = value)
-
-      if (identical(value, selected))
-        inputTag$attribs$checked = "checked"
-
-      # Put the label text in a span
-      tags$label(class = if (inline) "radio inline" else "radio",
-                inputTag,
-                tags$span(name)
-      )
-    }
-  )
+  options <- generateOptions(inputId, choices, selected, inline, type = 'radio')
 
   tags$div(id = inputId,
     class = 'control-group shiny-input-radiogroup',
     label %AND% tags$label(class = "control-label", `for` = inputId, label),
-    inputTags)
+    options)
 }
 
 #' Create a submit button
@@ -1490,13 +1535,15 @@ buildTabset <- function(tabs,
 #' text will be included within an HTML \code{div} tag by default.
 #' @param outputId output variable to read the value from
 #' @param container a function to generate an HTML element to contain the text
+#' @param inline use an inline (\code{span()}) or block container (\code{div()})
+#'   for the output
 #' @return A text output element that can be included in a panel
 #' @details Text is HTML-escaped prior to rendering. This element is often used
-#' to display \link{renderText} output variables.
+#'   to display \link{renderText} output variables.
 #' @examples
 #' h3(textOutput("caption"))
 #' @export
-textOutput <- function(outputId, container = div) {
+textOutput <- function(outputId, container = if (inline) span else div, inline = FALSE) {
   container(id = outputId, class = "shiny-text-output")
 }
 
@@ -1530,6 +1577,7 @@ verbatimTextOutput <- function(outputId) {
 #'   \code{"400px"}, \code{"auto"}) or a number, which will be coerced to a
 #'   string and have \code{"px"} appended.
 #' @param height Image height
+#' @inheritParams textOutput
 #' @return An image output element that can be included in a panel
 #' @examples
 #' # Show an image
@@ -1537,38 +1585,45 @@ verbatimTextOutput <- function(outputId) {
 #'   imageOutput("dataImage")
 #' )
 #' @export
-imageOutput <- function(outputId, width = "100%", height="400px") {
+imageOutput <- function(outputId, width = "100%", height="400px", inline=FALSE) {
   style <- paste("width:", validateCssUnit(width), ";",
     "height:", validateCssUnit(height))
-  div(id = outputId, class = "shiny-image-output", style = style)
+  container <- if (inline) span else div
+  container(id = outputId, class = "shiny-image-output", style = style)
 }
 
 #' Create an plot output element
 #'
 #' Render a \link{renderPlot} within an application page.
 #' @param outputId output variable to read the plot from
-#' @param width Plot width. Must be a valid CSS unit (like \code{"100\%"},
-#'   \code{"400px"}, \code{"auto"}) or a number, which will be coerced to a
-#'   string and have \code{"px"} appended.
-#' @param height Plot height
+#' @param width,height Plot width/height. Must be a valid CSS unit (like
+#'   \code{"100\%"}, \code{"400px"}, \code{"auto"}) or a number, which will be
+#'   coerced to a string and have \code{"px"} appended. These two arguments are
+#'   ignored when \code{inline = TRUE}, in which case the width/height of a plot
+#'   must be specified in \code{renderPlot()}.
 #' @param clickId If not \code{NULL}, the plot will send coordinates to the
 #'   server whenever it is clicked. This information will be accessible on the
-#'   \code{input} object using \code{input$}\emph{\code{clickId}}. The value will be a
-#'   named list or vector with \code{x} and \code{y} elements indicating the
-#'   mouse position in user units.
+#'   \code{input} object using \code{input$}\emph{\code{clickId}}. The value
+#'   will be a named list or vector with \code{x} and \code{y} elements
+#'   indicating the mouse position in user units.
 #' @param hoverId If not \code{NULL}, the plot will send coordinates to the
 #'   server whenever the mouse pauses on the plot for more than the number of
 #'   milliseconds determined by \code{hoverTimeout}. This information will be
-#    accessible on the \code{input} object using \code{input$}\emph{\code{clickId}}.
-#'   The value will be \code{NULL} if the user is not hovering, and a named
-#'   list or vector with \code{x} and \code{y} elements indicating the mouse
-#'   position in user units.
+#'   accessible on the \code{input} object using
+#'   \code{input$}\emph{\code{clickId}}. The value will be \code{NULL} if the
+#'   user is not hovering, and a named list or vector with \code{x} and \code{y}
+#'   elements indicating the mouse position in user units.
 #' @param hoverDelay The delay for hovering, in milliseconds.
 #' @param hoverDelayType The type of algorithm for limiting the number of hover
 #'   events. Use \code{"throttle"} to limit the number of hover events to one
 #'   every \code{hoverDelay} milliseconds. Use \code{"debounce"} to suspend
 #'   events while the cursor is moving, and wait until the cursor has been at
 #'   rest for \code{hoverDelay} milliseconds before sending an event.
+#' @inheritParams textOutput
+#' @note The arguments \code{clickId} and \code{hoverId} only work for R base
+#'   graphics (see the \pkg{\link{graphics}} package). They do not work for
+#'   \pkg{\link[grid:grid-package]{grid}}-based graphics, such as \pkg{ggplot2},
+#'   \pkg{lattice}, and so on.
 #' @return A plot output element that can be included in a panel
 #' @examples
 #' # Show a plot of the generated distribution
@@ -1578,7 +1633,7 @@ imageOutput <- function(outputId, width = "100%", height="400px") {
 #' @export
 plotOutput <- function(outputId, width = "100%", height="400px",
                        clickId = NULL, hoverId = NULL, hoverDelay = 300,
-                       hoverDelayType = c("debounce", "throttle")) {
+                       hoverDelayType = c("debounce", "throttle"), inline = FALSE) {
   if (is.null(clickId) && is.null(hoverId)) {
     hoverDelay <- NULL
     hoverDelayType <- NULL
@@ -1586,9 +1641,12 @@ plotOutput <- function(outputId, width = "100%", height="400px",
     hoverDelayType <- match.arg(hoverDelayType)[[1]]
   }
 
-  style <- paste("width:", validateCssUnit(width), ";",
-    "height:", validateCssUnit(height))
-  div(id = outputId, class = "shiny-plot-output", style = style,
+  style <- if (!inline) {
+    paste("width:", validateCssUnit(width), ";", "height:", validateCssUnit(height))
+  }
+
+  container <- if (inline) span else div
+  container(id = outputId, class = "shiny-plot-output", style = style,
       `data-click-id` = clickId,
       `data-hover-id` = hoverId,
       `data-hover-delay` = hoverDelay,
@@ -1611,13 +1669,13 @@ tableOutput <- function(outputId) {
 
 dataTableDependency <- list(
   htmlDependency(
-    "datatables", "1.9.4", c(href = "shared/datatables"),
+    "datatables", "1.10.2", c(href = "shared/datatables"),
     script = "js/jquery.dataTables.min.js"
   ),
   htmlDependency(
-    "datatables-bootstrap", "1.9.4", c(href = "shared/datatables"),
-    stylesheet = "css/DT_bootstrap.css",
-    script = "js/DT_bootstrap.js"
+    "datatables-bootstrap", "1.10.2", c(href = "shared/datatables"),
+    stylesheet = c("css/dataTables.bootstrap.css", "css/dataTables.extra.css"),
+    script = "js/dataTables.bootstrap.js"
   )
 )
 
@@ -1640,19 +1698,19 @@ dataTableOutput <- function(outputId) {
 #' server side. It is currently just an alias for \code{htmlOutput}.
 #'
 #' @param outputId output variable to read the value from
+#' @inheritParams textOutput
 #' @return An HTML output element that can be included in a panel
 #' @examples
 #' htmlOutput("summary")
 #' @export
-htmlOutput <- function(outputId) {
-  div(id = outputId, class="shiny-html-output")
+htmlOutput <- function(outputId, inline = FALSE) {
+  container <- if (inline) span else div
+  container(id = outputId, class="shiny-html-output")
 }
 
 #' @rdname htmlOutput
 #' @export
-uiOutput <- function(outputId) {
-  htmlOutput(outputId)
-}
+uiOutput <- htmlOutput
 
 #' Create a download button or link
 #'

R/cache.R

@@ -2,18 +2,15 @@
 # files changes on disk. Each time the cache is dirtied, the set of files is
 # cleared. Therefore, the set of files needs to be re-built each time the cached
 # code executes. This approach allows for dynamic dependency graphs.
-CacheContext <- setRefClass(
+CacheContext <- R6Class(
   'CacheContext',
-  fields = list(
-    .dirty = 'logical',
-    .tests = 'list'
-  ),
-  methods = list(
-    initialize = function() {
-      .dirty <<- TRUE
-      # List of functions that return TRUE if dirty
-      .tests <<- list()
-    },
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .dirty = TRUE,
+    # List of functions that return TRUE if dirty
+    .tests = list(),
+
     addDependencyFile = function(file) {
       if (.dirty)
         return()
@@ -53,7 +50,7 @@ CacheContext <- setRefClass(
     },
     with = function(func) {
       oldCC <- .currentCacheContext$cc
-      .currentCacheContext$cc <- .self
+      .currentCacheContext$cc <- self
       on.exit(.currentCacheContext$cc <- oldCC)
 
       return(func())

R/fileupload.R

@@ -20,18 +20,19 @@
 # form upload, i.e. traditional HTTP POST-based file upload) doesn't work with
 # the websockets package's HTTP server at the moment.
 
-FileUploadOperation <- setRefClass(
+FileUploadOperation <- R6Class(
   'FileUploadOperation',
-  fields = list(
-    .parent = 'ANY',
-    .id = 'character',
-    .files = 'data.frame',
-    .dir = 'character',
-    .currentFileInfo = 'list',
-    .currentFileData = 'ANY',
-    .pendingFileInfos = 'list'
-  ),
-  methods = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .parent = NULL,
+    .id = character(0),
+    .files = data.frame(),
+    .dir = character(0),
+    .currentFileInfo = list(),
+    .currentFileData = NULL,
+    .pendingFileInfos = list(),
+
     initialize = function(parent, id, dir, fileInfos) {
       .parent <<- parent
       .id <<- id
@@ -78,15 +79,17 @@ FileUploadOperation <- setRefClass(
 )
 
 #' @include map.R
-FileUploadContext <- setRefClass(
+FileUploadContext <- R6Class(
   'FileUploadContext',
-  fields = list(
-    .basedir = 'character',
-    .operations = 'Map'
-  ),
-  methods = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .basedir = character(0),
+    .operations = 'Map',
+
     initialize = function(dir=tempdir()) {
       .basedir <<- dir
+      .operations <<- Map$new()
     },
     createUploadOperation = function(fileInfos) {
       while (TRUE) {
@@ -95,7 +98,7 @@ FileUploadContext <- setRefClass(
         if (!dir.create(dir))
           next
 
-        op <- FileUploadOperation$new(.self, id, dir, fileInfos)
+        op <- FileUploadOperation$new(self, id, dir, fileInfos)
         .operations$set(id, op)
         return(id)
       }

R/graph.R

@@ -1,5 +1,5 @@
 writeReactLog <- function(file=stdout()) {
-  cat(RJSONIO::toJSON(.graphEnv$log, pretty=TRUE), file=file)
+  cat(RJSONIO::toJSON(.graphStack$as_list(), pretty=TRUE), file=file)
 }
 
 #' Reactive Log Visualizer
@@ -55,8 +55,8 @@ renderReactLog <- function() {
 }
 
 .graphAppend <- function(logEntry, domain = getDefaultReactiveDomain()) {
-  if (isTRUE(getOption('shiny.reactlog', FALSE)))
-    .graphEnv$log <- c(.graphEnv$log, list(logEntry))
+  if (isTRUE(getOption('shiny.reactlog')))
+    .graphStack$push(logEntry)
 
   if (!is.null(domain)) {
     domain$reactlog(logEntry)
@@ -99,5 +99,5 @@ renderReactLog <- function() {
   .graphAppend(list(action='invalidate', id=id), domain)
 }
 
-.graphEnv <- new.env()
-.graphEnv$log <- list()
+#' @include stack.R
+.graphStack <- Stack$new()

R/html-deps.R

@@ -1,3 +1,17 @@
+#' Create a web dependency
+#'
+#' Ensure that a file-based HTML dependency (from the htmltools package) can be
+#' served over Shiny's HTTP server. This function works by using
+#' \code{\link{addResourcePath}} to map the HTML dependency's directory to a
+#' URL.
+#'
+#' @param dependency A single HTML dependency object, created using
+#'   \code{\link{htmlDependency}}. If the \code{src} value is named, then
+#'   \code{href} and/or \code{file} names must be present.
+#'
+#' @return A single HTML dependency object that has an \code{href}-named element
+#'   in its \code{src}.
+#' @export
 createWebDependency <- function(dependency) {
   if (is.null(dependency))
     return(NULL)

R/imageutils.R

@@ -34,7 +34,7 @@ plotPNG <- function(func, filename=tempfile(fileext='.png'),
   # Finally, if neither quartz nor Cairo, use png().
   if (capabilities("aqua")) {
     pngfun <- png
-  } else if (getOption('shiny.usecairo', TRUE) &&
+  } else if ((getOption('shiny.usecairo') %OR% TRUE) &&
              nchar(system.file(package = "Cairo"))) {
     pngfun <- Cairo::CairoPNG
   } else {

R/map.R

@@ -9,58 +9,65 @@
 # Remove of unknown key does nothing
 # Setting a key twice always results in last-one-wins
 # /TESTS
-Map <- setRefClass(
+Map <- R6Class(
   'Map',
-  fields = list(
-    .env = 'environment'
-  ),
-  methods = list(
+  portable = FALSE,
+  public = list(
     initialize = function() {
-      .env <<- new.env(parent=emptyenv())
+      private$env <- new.env(parent=emptyenv())
     },
     get = function(key) {
-      if (.self$containsKey(key))
-        base::get(key, pos=.env, inherits=FALSE)
+      env[[key]]
     },
     set = function(key, value) {
-      assign(key, value, pos=.env, inherits=FALSE)
+      env[[key]] <- value
       value
     },
     mset = function(...) {
       args <- list(...)
-      for (key in names(args))
-        set(key, args[[key]])
+      if (length(args) == 0)
+        return()
+
+      arg_names <- names(args)
+      if (is.null(arg_names) || any(!nzchar(arg_names)))
+        stop("All elements must be named")
+
+      list2env(args, envir = env)
     },
     remove = function(key) {
-      if (.self$containsKey(key)) {
-        result <- .self$get(key)
-        rm(list = key, pos=.env, inherits=FALSE)
-        result
-      }
+      if (!self$containsKey(key))
+        return(NULL)
+
+      result <- env[[key]]
+      rm(list=key, envir=env, inherits=FALSE)
+      result
     },
     containsKey = function(key) {
-      exists(key, where=.env, inherits=FALSE)
+      exists(key, envir=env, inherits=FALSE)
     },
     keys = function() {
-      ls(envir=.env, all.names=TRUE)
+      # Sadly, this is much faster than ls(), because it doesn't sort the keys.
+      names(as.list(env, all.names=TRUE))
     },
     values = function() {
-      mget(.self$keys(), envir=.env, inherits=FALSE)
+      as.list(env, all.names=TRUE)
     },
     clear = function() {
-      .env <<- new.env(parent=emptyenv())
+      private$env <- new.env(parent=emptyenv())
       invisible(NULL)
     },
     size = function() {
-      length(.env)
+      length(env)
     }
+  ),
+
+  private = list(
+    env = 'environment'
   )
 )
 
 as.list.Map <- function(map) {
-  sapply(map$keys(),
-         map$get,
-         simplify=FALSE)
+  map$values()
 }
 length.Map <- function(map) {
   map$size()

R/middleware-shiny.R

@@ -5,7 +5,7 @@ reactLogHandler <- function(req) {
   if (!identical(req$PATH_INFO, '/reactlog'))
     return(NULL)
 
-  if (!getOption('shiny.reactlog', FALSE)) {
+  if (!isTRUE(getOption('shiny.reactlog'))) {
     return(NULL)
   }
 

R/middleware.R

@@ -222,11 +222,12 @@ staticHandler <- function(root) {
 # return value of `createHttpuvApp` to httpuv's `startServer` function.
 #
 ## ------------------------------------------------------------------------
-HandlerList <- setRefClass("HandlerList",
-  fields = list(
-    handlers = "list"
-  ),
-  methods = list(
+HandlerList <- R6Class("HandlerList",
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    handlers = list(),
+
     add = function(handler, key, tail = FALSE) {
       if (!is.null(handlers[[key]]))
         stop("Key ", key, " already in use")
@@ -256,12 +257,18 @@ HandlerList <- setRefClass("HandlerList",
   )
 )
 
-HandlerManager <- setRefClass("HandlerManager",
-  fields = list(
+HandlerManager <- R6Class("HandlerManager",
+  portable = FALSE,
+  class = FALSE,
+  public = list(
     handlers = "HandlerList",
-    wsHandlers = "HandlerList"
-  ),
-  methods = list(
+    wsHandlers = "HandlerList",
+
+    initialize = function() {
+      handlers <<- HandlerList$new()
+      wsHandlers <<- HandlerList$new()
+    },
+
     addHandler = function(handler, key, tail = FALSE) {
       handlers$add(handler, key, tail)
     },
@@ -281,7 +288,7 @@ HandlerManager <- setRefClass("HandlerManager",
     createHttpuvApp = function() {
       list(
         onHeaders = function(req) {
-          maxSize <- getOption('shiny.maxRequestSize', 5 * 1024 * 1024)
+          maxSize <- getOption('shiny.maxRequestSize') %OR% (5 * 1024 * 1024)
           if (maxSize <= 0)
             return(NULL)
 
@@ -306,7 +313,7 @@ HandlerManager <- setRefClass("HandlerManager",
           function (req) {
             return(handlers$invoke(req))
           },
-          getOption('shiny.sharedSecret', NULL)
+          getOption('shiny.sharedSecret')
         ),
         onWSOpen = function(ws) {
           return(wsHandlers$invoke(ws))
@@ -314,7 +321,7 @@ HandlerManager <- setRefClass("HandlerManager",
       )
     },
     .httpServer = function(handler, sharedSecret) {
-      filter <- getOption('shiny.http.response.filter', NULL)
+      filter <- getOption('shiny.http.response.filter')
       if (is.null(filter))
         filter <- function(req, response) response
 
@@ -329,11 +336,11 @@ HandlerManager <- setRefClass("HandlerManager",
         response <- handler(req)
         if (is.null(response))
           response <- httpResponse(404, content="<h1>Not Found</h1>")
-        
+
         if (inherits(response, "httpResponse")) {
           headers <- as.list(response$headers)
           headers$'Content-Type' <- response$content_type
-  
+
           response <- filter(req, response)
           return(list(status=response$status,
             body=response$content,

R/priorityqueue.R

@@ -4,15 +4,19 @@
 # elements have the same priority, they are served according to their order in
 # the queue." (http://en.wikipedia.org/wiki/Priority_queue)
 
-PriorityQueue <- setRefClass(
+PriorityQueue <- R6Class(
   'PriorityQueue',
-  fields = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
     # Keys are priorities, values are subqueues (implemented as list)
     .itemsByPriority = 'Map',
     # Sorted vector (largest first)
-    .priorities = 'numeric'
-  ),
-  methods = list(
+    .priorities = numeric(0),
+
+    initialize = function() {
+      .itemsByPriority <<- Map$new()
+    },
     # Enqueue an item, with the given priority level (must be integer). Higher
     # priority numbers are dequeued earlier than lower.
     enqueue = function(item, priority) {

R/progress.R

@@ -0,0 +1,276 @@
+#' Reporting progress (object-oriented API)
+#'
+#' Reports progress to the user during long-running operations.
+#'
+#' This package exposes two distinct programming APIs for working with
+#' progress. \code{\link{withProgress}} and \code{\link{setProgress}}
+#' together provide a simple function-based interface, while the
+#' \code{Progress} reference class provides an object-oriented API.
+#'
+#' Instantiating a \code{Progress} object causes a progress panel to be
+#' created, and it will be displayed the first time the \code{set}
+#' method is called. Calling \code{close} will cause the progress panel
+#' to be removed.
+#'
+#' \strong{Methods}
+#'   \describe{
+#'     \item{\code{initialize(session, min = 0, max = 1)}}{
+#'       Creates a new progress panel (but does not display it).
+#'     }
+#'     \item{\code{set(value = NULL, message = NULL, detail = NULL)}}{
+#'       Updates the progress panel. When called the first time, the
+#'       progress panel is displayed.
+#'     }
+#'     \item{\code{inc(amount = 0.1, message = NULL, detail = NULL)}}{
+#'       Like \code{set}, this updates the progress panel. The difference is
+#'       that \code{inc} increases the progress bar by \code{amount}, instead
+#'       of setting it to a specific value.
+#'     }
+#'     \item{\code{close()}}{
+#'       Removes the progress panel. Future calls to \code{set} and
+#'       \code{close} will be ignored.
+#'     }
+#'   }
+#'
+#' @param session The Shiny session object, as provided by
+#'   \code{shinyServer} to the server function.
+#' @param min The value that represents the starting point of the
+#'   progress bar. Must be less tham \code{max}.
+#' @param max The value that represents the end of the progress bar.
+#'   Must be greater than \code{min}.
+#' @param message A single-element character vector; the message to be
+#'   displayed to the user, or \code{NULL} to hide the current message
+#'   (if any).
+#' @param detail A single-element character vector; the detail message
+#'   to be displayed to the user, or \code{NULL} to hide the current
+#'   detail message (if any). The detail message will be shown with a
+#'   de-emphasized appearance relative to \code{message}.
+#' @param value A numeric value at which to set
+#'   the progress bar, relative to \code{min} and \code{max}.
+#'   \code{NULL} hides the progress bar, if it is currently visible.
+#' @param amount Single-element numeric vector; the value at which to set
+#'   the progress bar, relative to \code{min} and \code{max}.
+#'   \code{NULL} hides the progress bar, if it is currently visible.
+#' @param amount For the \code{inc()} method, a numeric value to increment the
+#'   progress bar.
+#'
+#' @examples
+#' \dontrun{
+#' # server.R
+#' shinyServer(function(input, output, session) {
+#'   output$plot <- renderPlot({
+#'     progress <- shiny::Progress$new(session, min=1, max=15)
+#'     on.exit(progress$close())
+#'
+#'     progress$set(message = 'Calculation in progress',
+#'                  detail = 'This may take a while...')
+#'
+#'     for (i in 1:15) {
+#'       progress$set(value = i)
+#'       Sys.sleep(0.5)
+#'     }
+#'     plot(cars)
+#'   })
+#' })
+#' }
+#' @seealso \code{\link{withProgress}}
+#' @format NULL
+#' @usage NULL
+#' @export
+Progress <- R6Class(
+  'Progress',
+  portable = TRUE,
+  public = list(
+
+    initialize = function(session = getDefaultReactiveDomain(), min = 0, max = 1) {
+      # A hacky check to make sure the session object is indeed a session object.
+      if (is.null(session$onFlush)) stop("'session' is not a session object.")
+
+      private$session <- session
+      private$id <- paste(as.character(as.raw(runif(8, min=0, max=255))), collapse='')
+      private$min <- min
+      private$max <- max
+      private$value <- NULL
+      private$closed <- FALSE
+
+      session$sendProgress('open', list(id = private$id))
+    },
+
+    set = function(value = NULL, message = NULL, detail = NULL) {
+      if (private$closed) {
+        warning("Attempting to set progress, but progress already closed.")
+        return()
+      }
+
+      if (is.null(value) || is.na(value)) {
+        value <- NULL
+      } else {
+        value <- min(1, max(0, (value - private$min) / (private$max - private$min)))
+      }
+
+      private$value <- value
+
+      data <- dropNulls(list(
+        id = private$id,
+        message = message,
+        detail = detail,
+        value = value
+      ))
+
+       private$session$sendProgress('update', data)
+    },
+
+    inc = function(amount = 0.1, message = NULL, detail = NULL) {
+      value <- min(private$value + amount, private$max)
+      self$set(value, message, detail)
+    },
+
+    getMin = function() private$min,
+
+    getMax = function() private$max,
+
+    getValue = function() private$value,
+
+    close = function() {
+      if (private$closed) {
+        warning("Attempting to close progress, but progress already closed.")
+        return()
+      }
+
+      private$session$sendProgress('close', list(id = private$id))
+      private$closed <- TRUE
+    }
+  ),
+
+  private = list(
+    session = 'environment',
+    id = character(0),
+    min = numeric(0),
+    max = numeric(0),
+    value = NULL,
+    closed = logical(0)
+  )
+)
+
+#' Reporting progress (functional API)
+#'
+#' Reports progress to the user during long-running operations.
+#'
+#' This package exposes two distinct programming APIs for working with progress.
+#' Using \code{withProgress} with \code{incProgress} or \code{setProgress}
+#' provide a simple function-based interface, while the \code{\link{Progress}}
+#' reference class provides an object-oriented API.
+#'
+#' Use \code{withProgress} to wrap the scope of your work; doing so will cause a
+#' new progress panel to be created, and it will be displayed the first time
+#' \code{incProgress} or \code{setProgress} are called. When \code{withProgress}
+#' exits, the corresponding progress panel will be removed.
+#'
+#' The \code{incProgress} function increments the status bar by a specified
+#' amount, whereas the \code{setProgress} function sets it to a specific value,
+#' and can also set the text displayed.
+#'
+#' Generally, \code{withProgress}/\code{incProgress}/\code{setProgress} should
+#' be sufficient; the exception is if the work to be done is asynchronous (this
+#' is not common) or otherwise cannot be encapsulated by a single scope. In that
+#' case, you can use the \code{Progress} reference class.
+#'
+#' @param session The Shiny session object, as provided by \code{shinyServer} to
+#'   the server function. The default is to automatically find the session by
+#'   using the current reactive domain.
+#' @param expr The work to be done. This expression should contain calls to
+#'   \code{setProgress}.
+#' @param min The value that represents the starting point of the progress bar.
+#'   Must be less tham \code{max}. Default is 0.
+#' @param max The value that represents the end of the progress bar. Must be
+#'   greater than \code{min}. Default is 1.
+#' @param amount For \code{incProgress}, the amount to increment the status bar.
+#'   Default is 0.1.
+#' @param env The environment in which \code{expr} should be evaluated.
+#' @param quoted Whether \code{expr} is a quoted expression (this is not
+#'   common).
+#' @param message A single-element character vector; the message to be displayed
+#'   to the user, or \code{NULL} to hide the current message (if any).
+#' @param detail A single-element character vector; the detail message to be
+#'   displayed to the user, or \code{NULL} to hide the current detail message
+#'   (if any). The detail message will be shown with a de-emphasized appearance
+#'   relative to \code{message}.
+#' @param value Single-element numeric vector; the value at which to set the
+#'   progress bar, relative to \code{min} and \code{max}. \code{NULL} hides the
+#'   progress bar, if it is currently visible.
+#'
+#' @examples
+#' \dontrun{
+#' # server.R
+#' shinyServer(function(input, output) {
+#'   output$plot <- renderPlot({
+#'     withProgress(message = 'Calculation in progress',
+#'                  detail = 'This may take a while...', value = 0, {
+#'       for (i in 1:15) {
+#'         incProgress(1/15)
+#'         Sys.sleep(0.25)
+#'       }
+#'     })
+#'     plot(cars)
+#'   })
+#' })
+#' }
+#' @seealso \code{\link{Progress}}
+#' @rdname withProgress
+#' @export
+withProgress <- function(expr, min = 0, max = 1,
+                         value = min + (max - min) * 0.1,
+                         message = NULL, detail = NULL,
+                         session = getDefaultReactiveDomain(),
+                         env = parent.frame(), quoted = FALSE) {
+
+  if (!quoted)
+    expr <- substitute(expr)
+
+  p <- Progress$new(session, min = min, max = max)
+
+  session$progressStack$push(p)
+  on.exit({
+    session$progressStack$pop()
+    p$close()
+  })
+
+  p$set(value, message, detail)
+
+  eval(expr, env)
+}
+
+#' @rdname withProgress
+#' @export
+setProgress <- function(value = NULL, message = NULL, detail = NULL,
+                        session = getDefaultReactiveDomain()) {
+
+  # A hacky check to make sure the session object is indeed a session object.
+  if (is.null(session$onFlush)) stop("'session' is not a session object.")
+
+  if (session$progressStack$size() == 0) {
+    warning('setProgress was called outside of withProgress; ignoring')
+    return()
+  }
+
+  session$progressStack$peek()$set(value, message, detail)
+  invisible()
+}
+
+#' @rdname withProgress
+#' @export
+incProgress <- function(amount = 0.1, message = NULL, detail = NULL,
+                        session = getDefaultReactiveDomain()) {
+
+  # A hacky check to make sure the session object is indeed a session object.
+  if (is.null(session$onFlush)) stop("'session' is not a session object.")
+
+  if (session$progressStack$size() == 0) {
+    warning('incProgress was called outside of withProgress; ignoring')
+    return()
+  }
+
+  p <- session$progressStack$peek()
+  p$inc(amount, message, detail)
+  invisible()
+}

R/react.R

@@ -1,19 +1,17 @@
-Context <- setRefClass(
+Context <- R6Class(
   'Context',
-  fields = list(
-    id = 'character',
-    .label = 'character',      # For debug purposes
-    .invalidated = 'logical',
-    .invalidateCallbacks = 'list',
-    .flushCallbacks = 'list',
-    .domain = 'ANY'
-  ),
-  methods = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    id = character(0),
+    .label = character(0),      # For debug purposes
+    .invalidated = FALSE,
+    .invalidateCallbacks = list(),
+    .flushCallbacks = list(),
+    .domain = NULL,
+
     initialize = function(domain, label='', type='other', prevId='') {
       id <<- .getReactiveEnvironment()$nextId()
-      .invalidated <<- FALSE
-      .invalidateCallbacks <<- list()
-      .flushCallbacks <<- list()
       .label <<- label
       .domain <<- domain
       .graphCreateContext(id, label, type, prevId, domain)
@@ -24,7 +22,7 @@ Context <- setRefClass(
         env <- .getReactiveEnvironment()
         .graphEnterContext(id)
         tryCatch(
-          env$runWith(.self, func),
+          env$runWith(self, func),
           finally = .graphExitContext(id)
         )
       })
@@ -56,7 +54,7 @@ Context <- setRefClass(
     addPendingFlush = function(priority) {
       "Tell the reactive environment that this context should be flushed the
         next time flushReact() called."
-      .getReactiveEnvironment()$addPendingFlush(.self, priority)
+      .getReactiveEnvironment()$addPendingFlush(self, priority)
     },
     onFlush = function(func) {
       "Register a function to be called when this context is flushed."
@@ -77,20 +75,18 @@ Context <- setRefClass(
   )
 )
 
-ReactiveEnvironment <- setRefClass(
+ReactiveEnvironment <- R6Class(
   'ReactiveEnvironment',
-  fields = list(
-    .currentContext = 'ANY',
-    .nextId = 'integer',
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .currentContext = NULL,
+    .nextId = 0L,
     .pendingFlush = 'PriorityQueue',
-    .inFlush = 'logical'
-  ),
-  methods = list(
+    .inFlush = FALSE,
+
     initialize = function() {
-      .currentContext <<- NULL
-      .nextId <<- 0L
       .pendingFlush <<- PriorityQueue$new()
-      .inFlush <<- FALSE
     },
     nextId = function() {
       .nextId <<- .nextId + 1L
@@ -98,7 +94,7 @@ ReactiveEnvironment <- setRefClass(
     },
     currentContext = function() {
       if (is.null(.currentContext)) {
-        if (isTRUE(getOption('shiny.suppressMissingContextError', FALSE))) {
+        if (isTRUE(getOption('shiny.suppressMissingContextError'))) {
           return(getDummyContext())
         } else {
           stop('Operation not allowed without an active reactive context. ',
@@ -138,7 +134,7 @@ ReactiveEnvironment <- setRefClass(
       reactiveEnvironment <<- ReactiveEnvironment$new()
     return(reactiveEnvironment)
   }
-}) 
+})
 
 # Causes any pending invalidations to run.
 flushReact <- function() {

R/reactive-domains.R

@@ -75,6 +75,7 @@ createMockDomain <- function() {
 #
 ## ------------------------------------------------------------------------
 
+#' @name domains
 #' @rdname domains
 #' @export
 getDefaultReactiveDomain <- function() {

R/reactives.R

@@ -1,12 +1,16 @@
 #' @include utils.R
 NULL
 
-Dependents <- setRefClass(
+Dependents <- R6Class(
   'Dependents',
-  fields = list(
-    .dependents = 'Map'
-  ),
-  methods = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .dependents = 'Map',
+
+    initialize = function() {
+      .dependents <<- Map$new()
+    },
     register = function(depId=NULL, depLabel=NULL) {
       ctx <- .getReactiveEnvironment()$currentContext()
       if (!.dependents$containsKey(ctx$id)) {
@@ -36,11 +40,12 @@ Dependents <- setRefClass(
 
 # ReactiveValues ------------------------------------------------------------
 
-ReactiveValues <- setRefClass(
+ReactiveValues <- R6Class(
   'ReactiveValues',
-  fields = list(
+  portable = FALSE,
+  public = list(
     # For debug purposes
-    .label = 'character',
+    .label = character(0),
     .values = 'environment',
     .dependents = 'environment',
     # Dependents for the list of all names, including hidden
@@ -48,15 +53,17 @@ ReactiveValues <- setRefClass(
     # Dependents for all values, including hidden
     .allValuesDeps = 'Dependents',
     # Dependents for all values
-    .valuesDeps = 'Dependents'
-  ),
-  methods = list(
+    .valuesDeps = 'Dependents',
+
     initialize = function() {
       .label <<- paste('reactiveValues',
                        p_randomInt(1000, 10000),
                        sep="")
       .values <<- new.env(parent=emptyenv())
       .dependents <<- new.env(parent=emptyenv())
+      .namesDeps <<- Dependents$new()
+      .allValuesDeps <<- Dependents$new()
+      .valuesDeps <<- Dependents$new()
     },
     get = function(key) {
       ctx <- .getReactiveEnvironment()$currentContext()
@@ -114,7 +121,7 @@ ReactiveValues <- setRefClass(
     mset = function(lst) {
       lapply(base::names(lst),
              function(name) {
-               .self$set(name, lst[[name]])
+               self$set(name, lst[[name]])
              })
     },
     names = function() {
@@ -192,9 +199,6 @@ reactiveValues <- function(...) {
   values
 }
 
-# Register the S3 class so that it can be used for a field in a Reference Class
-setOldClass("reactivevalues")
-
 # Create a reactivevalues object
 #
 # @param values A ReactiveValues object
@@ -310,21 +314,21 @@ str.reactivevalues <- function(object, indent.str = " ", ...) {
 
 # Observable ----------------------------------------------------------------
 
-Observable <- setRefClass(
+Observable <- R6Class(
   'Observable',
-  fields = list(
+  portable = FALSE,
+  public = list(
     .func = 'function',
-    .label = 'character',
-    .domain = 'ANY',
+    .label = character(0),
+    .domain = NULL,
     .dependents = 'Dependents',
-    .invalidated = 'logical',
-    .running = 'logical',
-    .value = 'ANY',
-    .visible = 'logical',
-    .execCount = 'integer',
-    .mostRecentCtxId = 'character'
-  ),
-  methods = list(
+    .invalidated = logical(0),
+    .running = logical(0),
+    .value = NULL,
+    .visible = logical(0),
+    .execCount = integer(0),
+    .mostRecentCtxId = character(0),
+
     initialize = function(func, label = deparse(substitute(func)),
                           domain = getDefaultReactiveDomain()) {
       if (length(formals(func)) > 0)
@@ -332,10 +336,11 @@ Observable <- setRefClass(
              "or more parameters; only functions without parameters can be ",
              "reactive.")
       .func <<- func
-      .invalidated <<- TRUE
-      .running <<- FALSE
       .label <<- label
       .domain <<- domain
+      .dependents <<- Dependents$new()
+      .invalidated <<- TRUE
+      .running <<- FALSE
       .execCount <<- 0L
       .mostRecentCtxId <<- ""
     },
@@ -343,7 +348,7 @@ Observable <- setRefClass(
       .dependents$register()
 
       if (.invalidated || .running) {
-        .self$.updateValue()
+        self$.updateValue()
       }
 
       .graphDependsOnId(getCurrentContext()$id, .mostRecentCtxId)
@@ -440,7 +445,7 @@ reactive <- function(x, env = parent.frame(), quoted = FALSE, label = NULL,
   attr(label, "srcfile") <- srcFileOfRef(srcref[[1]])
   o <- Observable$new(fun, label, domain)
   registerDebugHook(".func", o, "Reactive")
-  structure(o$getValue@.Data, observable = o, class = "reactive")
+  structure(o$getValue, observable = o, class = "reactive")
 }
 
 #' @export
@@ -455,8 +460,8 @@ is.reactive <- function(x) inherits(x, "reactive")
 
 # Return the number of times that a reactive expression or observer has been run
 execCount <- function(x) {
-  if (is.function(x))
-    return(environment(x)$.execCount)
+  if (is.reactive(x))
+    return(attr(x, "observable")$.execCount)
   else if (inherits(x, 'Observer'))
     return(x$.execCount)
   else
@@ -465,22 +470,22 @@ execCount <- function(x) {
 
 # Observer ------------------------------------------------------------------
 
-Observer <- setRefClass(
+Observer <- R6Class(
   'Observer',
-  fields = list(
+  portable = FALSE,
+  public = list(
     .func = 'function',
-    .label = 'character',
+    .label = character(0),
     .domain = 'ANY',
-    .priority = 'numeric',
-    .autoDestroy = 'logical',
-    .invalidateCallbacks = 'list',
-    .execCount = 'integer',
+    .priority = numeric(0),
+    .autoDestroy = logical(0),
+    .invalidateCallbacks = list(),
+    .execCount = integer(0),
     .onResume = 'function',
-    .suspended = 'logical',
-    .destroyed = 'logical',
-    .prevId = 'character'
-  ),
-  methods = list(
+    .suspended = logical(0),
+    .destroyed = logical(0),
+    .prevId = character(0),
+
     initialize = function(func, label, suspended = FALSE, priority = 0,
                           domain = getDefaultReactiveDomain(),
                           autoDestroy = TRUE) {
@@ -499,7 +504,7 @@ Observer <- setRefClass(
       .destroyed <<- FALSE
       .prevId <<- ''
 
-      onReactiveDomainEnded(.domain, .self$.onDomainEnded)
+      onReactiveDomainEnded(.domain, self$.onDomainEnded)
 
       # Defer the first running of this until flushReact is called
       .createContext()$invalidate()

R/run-url.R

@@ -1,124 +1,31 @@
-#' Run a Shiny application from https://gist.github.com
-#'
-#' Download and launch a Shiny application that is hosted on GitHub as a gist.
-#'
-#' @param gist The identifier of the gist. For example, if the gist is
-#'   https://gist.github.com/jcheng5/3239667, then \code{3239667},
-#'   \code{'3239667'}, and \code{'https://gist.github.com/jcheng5/3239667'}
-#'   are all valid values.
-#' @param port The TCP port that the application should listen on. Defaults to
-#'   choosing a random port.
-#' @param launch.browser If true, the system's default web browser will be
-#'   launched automatically after the app is started. Defaults to true in
-#'   interactive sessions only.
-#'
-#' @examples
-#' \dontrun{
-#' runGist(3239667)
-#' runGist("https://gist.github.com/jcheng5/3239667")
-#'
-#' # Old URL format without username
-#' runGist("https://gist.github.com/3239667")
-#' }
-#'
-#' @export
-runGist <- function(gist,
-                    port=NULL,
-                    launch.browser=getOption('shiny.launch.browser',
-                                             interactive())) {
-
-  gistUrl <- if (is.numeric(gist) || grepl('^[0-9a-f]+$', gist)) {
-    sprintf('https://gist.github.com/%s/download', gist)
-  } else if(grepl('^https://gist.github.com/([^/]+/)?([0-9a-f]+)$', gist)) {
-    paste(gist, '/download', sep='')
-  } else {
-    stop('Unrecognized gist identifier format')
-  }
-
-  runUrl(gistUrl, filetype=".tar.gz", subdir=NULL, port=port,
-    launch.browser=launch.browser)
-}
-
-
-#' Run a Shiny application from a GitHub repository
-#'
-#' Download and launch a Shiny application that is hosted in a GitHub repository.
-#'
-#' @param repo Name of the repository
-#' @param username GitHub username
-#' @param ref Desired git reference. Could be a commit, tag, or branch
-#'   name. Defaults to \code{"master"}.
-#' @param subdir A subdirectory in the repository that contains the app. By
-#'   default, this function will run an app from the top level of the repo, but
-#'   you can use a path such as `\code{"inst/shinyapp"}.
-#' @param port The TCP port that the application should listen on. Defaults to
-#'   choosing a random port.
-#' @param launch.browser If true, the system's default web browser will be
-#'   launched automatically after the app is started. Defaults to true in
-#'   interactive sessions only.
-#'
-#' @examples
-#' \dontrun{
-#' runGitHub("shiny_example", "rstudio")
-#'
-#' # Can run an app from a subdirectory in the repo
-#' runGitHub("shiny_example", "rstudio", subdir = "inst/shinyapp/")
-#' }
-#'
-#' @export
-runGitHub <- function(repo, username = getOption("github.user"),
-  ref = "master", subdir = NULL, port = NULL,
-  launch.browser = getOption('shiny.launch.browser', interactive())) {
-
-  if (is.null(ref)) {
-    stop("Must specify either a ref. ")
-  }
-
-  message("Downloading github repo(s) ",
-    paste(repo, ref, sep = "/", collapse = ", "),
-    " from ",
-    paste(username, collapse = ", "))
-  name <- paste(username, "-", repo, sep = "")
-
-  url <- paste("https://github.com/", username, "/", repo, "/archive/",
-    ref, ".tar.gz", sep = "")
-
-  runUrl(url, subdir=subdir, port=port, launch.browser=launch.browser)
-}
-
-
 #' Run a Shiny application from a URL
 #'
-#' Download and launch a Shiny application that is hosted at a downloadable
-#' URL. The Shiny application must be saved in a .zip, .tar, or .tar.gz file.
-#' The Shiny application files must be contained in a subdirectory in the
-#' archive. For example, the files might be \code{myapp/server.r} and
-#' \code{myapp/ui.r}.
-#'
+#' \code{runUrl()} downloads and launches a Shiny application that is hosted at
+#' a downloadable URL. The Shiny application must be saved in a .zip, .tar, or
+#' .tar.gz file. The Shiny application files must be contained in the root
+#' directory or a subdirectory in the archive. For example, the files might be
+#' \code{myapp/server.r} and \code{myapp/ui.r}. The functions \code{runGitHub()}
+#' and \code{runGist()} are based on \code{runUrl()}, using URL's from GitHub
+#' (\url{https://github.com}) and GitHub gists (\url{https://gist.github.com}),
+#' respectively.
 #' @param url URL of the application.
 #' @param filetype The file type (\code{".zip"}, \code{".tar"}, or
 #'   \code{".tar.gz"}. Defaults to the file extension taken from the url.
 #' @param subdir A subdirectory in the repository that contains the app. By
 #'   default, this function will run an app from the top level of the repo, but
 #'   you can use a path such as `\code{"inst/shinyapp"}.
-#' @param port The TCP port that the application should listen on. Defaults to
-#'   choosing a random port.
-#' @param launch.browser If true, the system's default web browser will be
-#'   launched automatically after the app is started. Defaults to true in
-#'   interactive sessions only.
-#'
+#' @param ... Other arguments to be passed to \code{\link{runApp}()}, such as
+#'   \code{port} and \code{launch.browser}.
+#' @export
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' runUrl('https://github.com/rstudio/shiny_example/archive/master.tar.gz')
 #'
 #' # Can run an app from a subdirectory in the archive
 #' runUrl("https://github.com/rstudio/shiny_example/archive/master.zip",
 #'  subdir = "inst/shinyapp/")
 #' }
-#'
-#' @export
-runUrl <- function(url, filetype = NULL, subdir = NULL, port = NULL,
-  launch.browser = getOption('shiny.launch.browser', interactive())) {
+runUrl <- function(url, filetype = NULL, subdir = NULL, ...) {
 
   if (!is.null(subdir) && ".." %in% strsplit(subdir, '/')[[1]])
     stop("'..' not allowed in subdir")
@@ -163,5 +70,65 @@ runUrl <- function(url, filetype = NULL, subdir = NULL, port = NULL,
   if (!file_test('-d', appdir)) appdir <- dirname(appdir)
 
   if (!is.null(subdir)) appdir <- file.path(appdir, subdir)
-  runApp(appdir, port=port, launch.browser=launch.browser)
+  runApp(appdir, ...)
+}
+
+#' @rdname runUrl
+#' @param gist The identifier of the gist. For example, if the gist is
+#'   https://gist.github.com/jcheng5/3239667, then \code{3239667},
+#'   \code{'3239667'}, and \code{'https://gist.github.com/jcheng5/3239667'} are
+#'   all valid values.
+#' @export
+#' @examples
+#' \donttest{
+#' runGist(3239667)
+#' runGist("https://gist.github.com/jcheng5/3239667")
+#'
+#' # Old URL format without username
+#' runGist("https://gist.github.com/3239667")
+#' }
+#'
+runGist <- function(gist, ...) {
+
+  gistUrl <- if (is.numeric(gist) || grepl('^[0-9a-f]+$', gist)) {
+    sprintf('https://gist.github.com/%s/download', gist)
+  } else if(grepl('^https://gist.github.com/([^/]+/)?([0-9a-f]+)$', gist)) {
+    paste(gist, '/download', sep='')
+  } else {
+    stop('Unrecognized gist identifier format')
+  }
+
+  runUrl(gistUrl, filetype=".tar.gz", ...)
+}
+
+
+#' @rdname runUrl
+#' @param repo Name of the repository.
+#' @param username GitHub username. If \code{repo} is of the form
+#'   \code{"username/repo"}, \code{username} will be taken from \code{repo}.
+#' @param ref Desired git reference. Could be a commit, tag, or branch name.
+#'   Defaults to \code{"master"}.
+#' @export
+#' @examples
+#' \donttest{
+#' runGitHub("shiny_example", "rstudio")
+#' # or runGitHub("rstudio/shiny_example")
+#'
+#' # Can run an app from a subdirectory in the repo
+#' runGitHub("shiny_example", "rstudio", subdir = "inst/shinyapp/")
+#' }
+runGitHub <- function(repo, username = getOption("github.user"),
+                      ref = "master", subdir = NULL, ...) {
+
+  if (grepl('/', repo)) {
+    res <- strsplit(repo, '/')[[1]]
+    if (length(res) != 2) stop("'repo' must be of the form 'username/repo'")
+    username <- res[1]
+    repo     <- res[2]
+  }
+
+  url <- paste("https://github.com/", username, "/", repo, "/archive/",
+               ref, ".tar.gz", sep = "")
+
+  runUrl(url, subdir=subdir, ...)
 }

R/server.R

@@ -169,13 +169,6 @@ addResourcePath <- function(prefix, directoryPath) {
 
   existing <- .globals$resources[[prefix]]
 
-  if (!is.null(existing)) {
-    if (!identical(existing$directoryPath, directoryPath)) {
-      warning("Overriding existing prefix ", prefix, " => ",
-              existing$directoryPath)
-    }
-  }
-
   .globals$resources[[prefix]] <- list(directoryPath=directoryPath,
                                        func=staticHandler(directoryPath))
 }
@@ -249,8 +242,11 @@ decodeMessage <- function(data) {
     packBits(rawToBits(data[pos:(pos+3)]), type='integer')
   }
 
-  if (readInt(1) != 0x01020202L)
-    return(fromJSON(rawToChar(data), asText=TRUE, simplify=FALSE))
+  if (readInt(1) != 0x01020202L) {
+    # use native encoding for the message
+    nativeData <- iconv(rawToChar(data), 'UTF-8')
+    return(fromJSON(nativeData, asText=TRUE, simplify=FALSE))
+  }
 
   i <- 5
   parts <- list()
@@ -278,7 +274,7 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
   # This value, if non-NULL, must be present on all HTTP and WebSocket
   # requests as the Shiny-Shared-Secret header or else access will be
   # denied (403 response for HTTP, and instant close for websocket).
-  sharedSecret <- getOption('shiny.sharedSecret', NULL)
+  sharedSecret <- getOption('shiny.sharedSecret')
 
   appHandlers <- list(
     http = joinHandlers(c(
@@ -303,7 +299,7 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
         if (is.character(msg))
           msg <- charToRaw(msg)
 
-        if (getOption('shiny.trace', FALSE)) {
+        if (isTRUE(getOption('shiny.trace'))) {
           if (binary)
             message("RECV ", '$$binary data$$')
           else
@@ -577,8 +573,9 @@ serviceApp <- function() {
 #'
 #' # Start app in a subdirectory called myapp
 #' runApp("myapp")
+#' }
 #'
-#'
+#' \donttest{
 #' # Apps can be run without a server.r and ui.r file
 #' runApp(list(
 #'   ui = bootstrapPage(
@@ -634,7 +631,9 @@ runApp <- function(appDir=getwd(),
   if (is.character(appDir)) {
     desc <- file.path.ci(appDir, "DESCRIPTION")
     if (file.exists(desc)) {
-      settings <- read.dcf(desc)
+      con <- file(desc, encoding = checkEncoding(desc))
+      on.exit(close(con), add = TRUE)
+      settings <- read.dcf(con)
       if ("DisplayMode" %in% colnames(settings)) {
         mode <- settings[1,"DisplayMode"]
         if (mode == "Showcase") {
@@ -760,7 +759,7 @@ stopApp <- function(returnValue = NULL) {
 #'   code or commentary.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # List all available examples
 #' runExample()
 #'

R/shiny.R

@@ -1,4 +1,4 @@
-#' @include utils.R
+#' @include utils.R stack.R
 NULL
 
 #' Web Application Framework for R
@@ -15,7 +15,8 @@ NULL
 #' @name shiny-package
 #' @aliases shiny
 #' @docType package
-#' @import htmltools httpuv caTools RJSONIO xtable digest methods
+#' @import htmltools httpuv xtable digest R6 mime
+#' @importFrom RJSONIO fromJSON
 NULL
 
 createUniqueId <- function(bytes, prefix = "", suffix = "") {
@@ -31,6 +32,10 @@ createUniqueId <- function(bytes, prefix = "", suffix = "") {
   })
 }
 
+toJSON <- function(x, ..., digits = getOption("shiny.json.digits", 16)) {
+  RJSONIO::toJSON(x, digits = digits, ...)
+}
+
 # Call the workerId func with no args to get the worker id, and with an arg to
 # set it.
 #
@@ -170,15 +175,17 @@ NULL
 
 
 #' @include utils.R
-ShinySession <- setRefClass(
+ShinySession <- R6Class(
   'ShinySession',
-  fields = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
     .websocket = 'ANY',
     .invalidatedOutputValues = 'Map',
     .invalidatedOutputErrors = 'Map',
-    .inputMessageQueue = 'list',    # A list of inputMessages to send when flushed
-    .outputs = 'list',       # Keeps track of all the output observer objects
-    .outputOptions = 'list', # Options for each of the output observer objects
+    .inputMessageQueue = list(),    # A list of inputMessages to send when flushed
+    .outputs = list(),       # Keeps track of all the output observer objects
+    .outputOptions = list(), # Options for each of the output observer objects
     .progressKeys = 'character',
     .showcase   = 'ANY',
     .fileUploadContext = 'FileUploadContext',
@@ -187,31 +194,40 @@ ShinySession <- setRefClass(
     .closedCallbacks = 'Callbacks',
     .flushCallbacks = 'Callbacks',
     .flushedCallbacks = 'Callbacks',
+    progressStack = 'Stack', # Stack of progress objects
     input       = 'reactivevalues', # Externally-usable S3 wrapper object for .input
     output      = 'ANY',    # Externally-usable S3 wrapper object for .outputs
     clientData  = 'reactivevalues', # Externally-usable S3 wrapper object for .clientData
     token = 'character',  # Used to identify this instance in URLs
     files = 'Map',        # For keeping track of files sent to client
     downloads = 'Map',
-    closed = 'logical',
+    closed = logical(0),
     session = 'environment',      # Object for the server app to access session stuff
-    singletons = 'character'  # Tracks singleton HTML fragments sent to the page
-  ),
-  methods = list(
+    singletons = character(0),  # Tracks singleton HTML fragments sent to the page
+
     initialize = function(websocket) {
       .websocket <<- websocket
       closed <<- FALSE
       # TODO: Put file upload context in user/app-specific dir if possible
 
+      .invalidatedOutputValues <<- Map$new()
+      .invalidatedOutputErrors <<- Map$new()
+      .fileUploadContext <<- FileUploadContext$new()
+      .closedCallbacks <<- Callbacks$new()
+      .flushCallbacks <<- Callbacks$new()
+      .flushedCallbacks <<- Callbacks$new()
       .input      <<- ReactiveValues$new()
       .clientData <<- ReactiveValues$new()
+      progressStack <<- Stack$new()
+      files <<- Map$new()
+      downloads <<- Map$new()
 
       input      <<- .createReactiveValues(.input,      readonly=TRUE)
       .setLabel(input, 'input')
       clientData <<- .createReactiveValues(.clientData, readonly=TRUE)
       .setLabel(clientData, 'clientData')
 
-      output     <<- .createOutputWriter(.self)
+      output     <<- .createOutputWriter(self)
 
       token <<- createUniqueId(16)
       .outputs <<- list()
@@ -219,18 +235,20 @@ ShinySession <- setRefClass(
 
       session <<- new.env(parent=emptyenv())
       session$clientData        <<- clientData
-      session$sendCustomMessage <<- .self$.sendCustomMessage
-      session$sendInputMessage  <<- .self$.sendInputMessage
-      session$onSessionEnded    <<- .self$onSessionEnded
-      session$onEnded           <<- .self$onEnded
-      session$onFlush           <<- .self$onFlush
-      session$onFlushed         <<- .self$onFlushed
-      session$isClosed          <<- .self$isClosed
-      session$input             <<- .self$input
-      session$output            <<- .self$output
-      session$reactlog          <<- .self$reactlog
-      session$registerDataObj   <<- .self$registerDataObj
-      session$.impl             <<- .self
+      session$sendCustomMessage <<- self$.sendCustomMessage
+      session$sendInputMessage  <<- self$.sendInputMessage
+      session$onSessionEnded    <<- self$onSessionEnded
+      session$onEnded           <<- self$onEnded
+      session$onFlush           <<- self$onFlush
+      session$onFlushed         <<- self$onFlushed
+      session$isClosed          <<- self$isClosed
+      session$input             <<- self$input
+      session$output            <<- self$output
+      session$reactlog          <<- self$reactlog
+      session$registerDataObj   <<- self$registerDataObj
+      session$progressStack     <<- self$progressStack
+      session$sendProgress      <<- self$sendProgress
+      session$.impl             <<- self
 
       if (!is.null(websocket$request$HTTP_SHINY_SERVER_CREDENTIALS)) {
         try({
@@ -307,7 +325,7 @@ ShinySession <- setRefClass(
         if (length(formals(func)) != 0) {
           orig <- func
           func <- function() {
-            orig(name=name, shinysession=.self)
+            orig(name=name, shinysession=self)
           }
         }
 
@@ -412,15 +430,19 @@ ShinySession <- setRefClass(
 
       .progressKeys <<- c(.progressKeys, id)
 
-      json <- toJSON(list(progress=list(id)))
-
+      sendProgress('binding', list(id = id))
+    },
+    sendProgress = function(type, message) {
+      json <- toJSON(list(
+        progress = list(type = type, message = message)
+      ))
       .write(json)
     },
     dispatch = function(msg) {
       method <- paste('@', msg$method, sep='')
       # we must use $ instead of [[ here at the moment; see
       # https://github.com/rstudio/shiny/issues/274
-      func <- try(do.call(`$`, list(.self, method)), silent=TRUE)
+      func <- try(do.call(`$`, list(self, method)), silent=TRUE)
       if (inherits(func, 'try-error')) {
         .sendErrorResponse(msg, paste('Unknown method', msg$method))
       }
@@ -488,15 +510,20 @@ ShinySession <- setRefClass(
       if (closed){
         return()
       }
-      if (getOption('shiny.trace', FALSE))
+      if (isTRUE(getOption('shiny.trace')))
         message('SEND ',
            gsub('(?m)base64,[a-zA-Z0-9+/=]+','[base64 data]',json,perl=TRUE))
-      if (getOption('shiny.transcode.json', TRUE))
-        json <- iconv(json, to='UTF-8')
+      # first convert to native encoding, then to UTF8, otherwise we may get the
+      # error in Chrome "WebSocket connection failed: Could not decode a text
+      # frame as UTF-8"
+      json <- enc2utf8(enc2native(json))
       .websocket$send(json)
     },
 
     # Public RPC methods
+    `@uploadieFinish` = function() {
+      # Do nothing; just want the side effect of flushReact, output flush, etc.
+    },
     `@uploadInit` = function(fileInfos) {
       maxSize <- getOption('shiny.maxRequestSize', 5 * 1024 * 1024)
       fileInfos <- lapply(fileInfos, function(fi) {
@@ -559,6 +586,13 @@ ShinySession <- setRefClass(
         }
       }
 
+      if (matches[2] == 'uploadie' && identical(req$REQUEST_METHOD, "POST")) {
+        id <- URLdecode(matches[3])
+        res <- mime::parse_multipart(req)
+        .input$set(id, res[[id]])
+        return(httpResponse(200, 'text/plain', 'OK'))
+      }
+
       if (matches[2] == 'download') {
 
         # A bunch of ugliness here. Filenames can be dynamically generated by
@@ -664,7 +698,7 @@ ShinySession <- setRefClass(
       fileData <- readBin(file, 'raw', n=bytes)
 
       if (isTRUE(.clientData$.values$allowDataUriScheme)) {
-        b64 <- base64encode(fileData)
+        b64 <- rawToBase64(fileData)
         return(paste('data:', contentType, ';base64,', b64, sep=''))
       } else {
         return(saveFileUrl(name, fileData, contentType))

R/shinyui.R

@@ -14,7 +14,7 @@ NULL
 #' # now we can just write "static" content without withMathJax()
 #' div("more math here $$\\sqrt{2}$$")
 withMathJax <- function(...) {
-  path <- 'https://c328740.ssl.cf1.rackcdn.com/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+  path <- 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
   tagList(
     tags$head(
       singleton(tags$script(src = path, type = 'text/javascript'))
@@ -33,6 +33,7 @@ renderPage <- function(ui, connection, showcase=0) {
 
   deps <- c(
     list(
+      htmlDependency("json2", "2014.02.04", c(href="shared"), script = "json2-min.js"),
       htmlDependency("jquery", "1.11.0", c(href="shared"), script = "jquery.js"),
       htmlDependency("shiny", packageVersion("shiny"), c(href="shared"),
         script = "shiny.js", stylesheet = "shiny.css")
@@ -98,7 +99,7 @@ shinyUI <- function(ui) {
   ui
 }
 
-uiHttpHandler <- function(ui, path = "/") {
+uiHttpHandler <- function(ui, uiPattern = "^/$") {
 
   force(ui)
 
@@ -106,7 +107,7 @@ uiHttpHandler <- function(ui, path = "/") {
     if (!identical(req$REQUEST_METHOD, 'GET'))
       return(NULL)
 
-    if (req$PATH_INFO != path)
+    if (!isTRUE(grepl(uiPattern, req$PATH_INFO)))
       return(NULL)
 
     textConn <- textConnection(NULL, "w")
@@ -123,11 +124,14 @@ uiHttpHandler <- function(ui, path = "/") {
         ui(req)
       else
         ui()
-    }
-    else
+    } else {
       ui
+    }
+    if (is.null(uiValue))
+      return(NULL)
+
     renderPage(uiValue, textConn, showcaseMode)
     html <- paste(textConnectionValue(textConn), collapse='\n')
-    return(httpResponse(200, content=html))
+    return(httpResponse(200, content=enc2utf8(html)))
   }
 }

R/shinywrappers.R

@@ -16,24 +16,26 @@ globalVariables('func')
 #'
 #' @export
 markRenderFunction <- function(uiFunc, renderFunc) {
-  class(renderFunc) <- c("shiny.render.function", "function")
-  attr(renderFunc, "outputFunc") <- uiFunc
-  renderFunc
+  structure(renderFunc,
+            class      = c("shiny.render.function", "function"),
+            outputFunc = uiFunc)
 }
 
-useRenderFunction <- function(renderFunc) {
+useRenderFunction <- function(renderFunc, inline = FALSE) {
   outputFunction <- attr(renderFunc, "outputFunc")
   id <- createUniqueId(8, "out")
   o <- getDefaultReactiveDomain()$output
   if (!is.null(o))
     o[[id]] <- renderFunc
-  return(outputFunction(id))
+  if (is.logical(formals(outputFunction)[["inline"]])) {
+    outputFunction(id, inline = inline)
+  } else outputFunction(id)
 }
 
 #' @export
 #' @method as.tags shiny.render.function
-as.tags.shiny.render.function <- function(x, ...) {
-  useRenderFunction(x)
+as.tags.shiny.render.function <- function(x, ..., inline = FALSE) {
+  useRenderFunction(x, inline = inline)
 }
 
 #' Plot Output
@@ -48,16 +50,13 @@ as.tags.shiny.render.function <- function(x, ...) {
 #'   the output, see \code{\link{plotPNG}}.
 #'
 #' @param expr An expression that generates a plot.
-#' @param width The width of the rendered plot, in pixels; or \code{'auto'} to
-#'   use the \code{offsetWidth} of the HTML element that is bound to this plot.
-#'   You can also pass in a function that returns the width in pixels or
-#'   \code{'auto'}; in the body of the function you may reference reactive
-#'   values and functions.
-#' @param height The height of the rendered plot, in pixels; or \code{'auto'} to
-#'   use the \code{offsetHeight} of the HTML element that is bound to this plot.
-#'   You can also pass in a function that returns the width in pixels or
-#'   \code{'auto'}; in the body of the function you may reference reactive
-#'   values and functions.
+#' @param width,height The width/height of the rendered plot, in pixels; or
+#'   \code{'auto'} to use the \code{offsetWidth}/\code{offsetHeight} of the HTML
+#'   element that is bound to this plot. You can also pass in a function that
+#'   returns the width/height in pixels or \code{'auto'}; in the body of the
+#'   function you may reference reactive values and functions. 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 \code{\link{png}}. Note that this affects the resolution of PNG
 #'   rendering in R; it won't change the actual ppi of the browser.
@@ -94,10 +93,8 @@ renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
   # div needs to adapt to the height of renderPlot. By default, plotOutput
   # sets the height to 400px, so to make it adapt we need to override it
   # with NULL.
-  outputFunc <- if (identical(height, 'auto'))
-    plotOutput
-  else
-    function(outputId) plotOutput(outputId, height = NULL)
+  outputFunc <- plotOutput
+  if (!identical(height, 'auto')) formals(outputFunc)['height'] <- list(NULL)
 
   return(markRenderFunction(outputFunc, function(shinysession, name, ...) {
     if (!is.null(widthWrapper))
@@ -124,9 +121,13 @@ renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
 
     coordmap <- NULL
     plotFunc <- function() {
-      # Actually perform the plotting: use capture.output() to suppress output
-      # to console, and print func() if it returns a visible value
-      capture.output(func())
+      # Actually perform the plotting
+      result <- withVisible(func())
+      if (result$visible) {
+        # Use capture.output to squelch printing to the actual console; we
+        # are only interested in plot output
+        capture.output(print(result$value))
+      }
 
       # Now capture some graphics device info before we close it
       usrCoords <- par('usr')
@@ -316,7 +317,7 @@ renderTable <- function(expr, ..., env=parent.frame(), quoted=FALSE, func=NULL)
   }
 
   markRenderFunction(tableOutput, function() {
-    classNames <- getOption('shiny.table.class', 'data table table-bordered table-condensed')
+    classNames <- getOption('shiny.table.class') %OR% 'data table table-bordered table-condensed'
     data <- func()
 
     if (is.null(data) || identical(data, data.frame()))
@@ -541,15 +542,15 @@ downloadHandler <- function(filename, content, contentType=NA) {
 #'   frequent search requests).
 #' @param callback A JavaScript function to be applied to the DataTable object.
 #'   This is useful for DataTables plug-ins, which often require the DataTable
-#'   instance to be available (\url{http://datatables.net/extras/}).
+#'   instance to be available (\url{http://datatables.net/extensions/}).
 #' @references \url{http://datatables.net}
 #' @export
 #' @inheritParams renderPlot
 #' @examples  # pass a callback function to DataTables using I()
 #' renderDataTable(iris,
 #'   options = list(
-#'     iDisplayLength = 5,
-#'     fnInitComplete = I("function(oSettings, json) {alert('Done.');}")
+#'     pageLength = 5,
+#'     initComplete = I("function(settings, json) {alert('Done.');}")
 #'   )
 #' )
 renderDataTable <- function(expr, options = NULL, searchDelay = 500,
@@ -558,7 +559,9 @@ renderDataTable <- function(expr, options = NULL, searchDelay = 500,
   installExprFunction(expr, "func", env, quoted)
 
   markRenderFunction(dataTableOutput, function(shinysession, name, ...) {
-    res <- checkAsIs(if (is.function(options)) options() else options)
+    if (is.function(options)) options <- options()
+    options <- checkDT9(options)
+    res <- checkAsIs(options)
     data <- func()
     if (length(dim(data)) != 2) return() # expects a rectangular data object
     action <- shinysession$registerDataObj(name, data, dataTablesJSON)
@@ -570,6 +573,43 @@ renderDataTable <- function(expr, options = NULL, searchDelay = 500,
   })
 }
 
+# a data frame containing the DataTables 1.9 and 1.10 names
+DT10Names <- function() {
+  rbind(
+    read.table(system.file('www/shared/datatables/upgrade1.10.txt', package = 'shiny'),
+               stringsAsFactors = FALSE),
+    c('aoColumns', 'Removed')  # looks like an omission on the upgrade guide
+  )
+}
+
+# check DataTables 1.9.x options, and give instructions for upgrading to 1.10.x
+checkDT9 <- function(options) {
+  nms <- names(options)
+  if (length(nms) == 0L) return(options)
+  DT10 <- DT10Names()
+  # e.g. the top level option name for oLanguage.sSearch should be oLanguage
+  i <- nms %in% gsub('[.].*', '', DT10[, 1])
+  if (!any(i)) return(options)  # did not see old option names, ready to go!
+  msg <- paste(
+    'shiny (>= 0.10.2) has upgraded DataTables from 1.9.4 to 1.10.2, ',
+    'and DataTables 1.10.x uses different parameter names with 1.9.x. ',
+    'Please follow the upgrade guide https://datatables.net/upgrade/1.10-convert',
+    ' to change your DataTables parameter names:\n\n',
+    paste(formatUL(nms[i]), collapse = '\n'), '\n', sep = ''
+  )
+  j <- gsub('[.].*', '', DT10[, 1]) %in% nms
+  # I cannot help you upgrade automatically in these cases, so I have to stop
+  if (any(grepl('[.]', DT10[j, 1])) || any(grepl('[.]', DT10[j, 2]))) stop(msg)
+  warning(msg)
+  nms10 <- DT10[match(nms[i], DT10[, 1]), 2]
+  if (any(nms10 == 'Removed')) stop(
+    "These parameters have been removed in DataTables 1.10.x:\n\n",
+    paste(formatUL(nms[i][nms10 == 'Removed']), collapse = '\n'),
+    "\n\n", msg
+  )
+  names(options)[i] <- nms10
+  options
+}
 
 # Deprecated functions ------------------------------------------------------
 

R/showcase.R

@@ -50,7 +50,7 @@ showcaseHead <- function() {
          href="shared/shiny-showcase.css"),
     if (file.exists(mdfile))
       script(type="text/markdown", id="showcase-markdown-content",
-        paste(readLines(mdfile, warn = FALSE), collapse="\n"))
+        paste(readUTF8(mdfile), collapse="\n"))
     else ""
   ))
 
@@ -90,7 +90,7 @@ showcaseCodeTabs <- function(codeLicense) {
       i(class="fa fa-level-up", "show with app")),
     ul(class="nav nav-tabs",
        lapply(rFiles, function(rFile) {
-         li(class=if (tolower(rFile) == "server.r") "active" else "",
+         li(class=if (tolower(rFile) %in% c("app.r", "server.r")) "active" else "",
             a(href=paste("#", gsub(".", "_", rFile, fixed=TRUE),
                          "_code", sep=""),
               "data-toggle"="tab", rFile))
@@ -98,7 +98,8 @@ showcaseCodeTabs <- function(codeLicense) {
     div(class="tab-content", id="showcase-code-content",
         lapply(rFiles, function(rFile) {
           div(class=paste("tab-pane",
-                          if (tolower(rFile) == "server.r") " active" else "",
+                          if (tolower(rFile) %in% c("app.r", "server.r")) " active"
+                          else "",
                           sep=""),
               id=paste(gsub(".", "_", rFile, fixed=TRUE),
                        "_code", sep=""),
@@ -106,8 +107,7 @@ showcaseCodeTabs <- function(codeLicense) {
                   # we need to prevent the indentation of <code> ... </code>
                   HTML(format(tags$code(
                     class="language-r",
-                    paste(readLines(file.path.ci(getwd(), rFile), warn=FALSE),
-                          collapse="\n")
+                    paste(readUTF8(file.path.ci(getwd(), rFile)), collapse="\n")
                   ), indent = FALSE))))
         })),
     codeLicense))
@@ -121,7 +121,9 @@ showcaseAppInfo <- function() {
   readmemd <- file.path.ci(getwd(), "Readme.md")
   hasReadme <- file.exists(readmemd)
   if (hasDesc) {
-    desc <- read.dcf(descfile)
+    con <- textConnection(readUTF8(descfile))
+    on.exit(close(con), add = TRUE)
+    desc <- read.dcf(con)
   }
   with(tags,
     div(class="container-fluid shiny-code-container well",

R/stack.R

@@ -0,0 +1,70 @@
+# A Stack object backed by a list. The backing list will grow or shrink as
+# the stack changes in size.
+Stack <- R6Class(
+  'Stack',
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+
+    initialize = function(init = 20L) {
+      # init is the initial size of the list. It is also used as the minimum
+      # size of the list as it shrinks.
+      private$stack <- vector("list", init)
+      private$init <- init
+    },
+
+    push = function(..., .list = NULL) {
+      args <- c(list(...), .list)
+      new_size <- count + length(args)
+
+      # Grow if needed; double in size
+      while (new_size > length(stack)) {
+        stack[length(stack) * 2] <<- list(NULL)
+      }
+      stack[count + seq_along(args)] <<- args
+      count <<- new_size
+
+      invisible(self)
+    },
+
+    pop = function() {
+      if (count == 0L)
+        return(NULL)
+
+      value <- stack[[count]]
+      stack[count] <<- list(NULL)
+      count <<- count - 1L
+
+      # Shrink list if < 1/4 of the list is used, down to a minimum size of `init`
+      len <- length(stack)
+      if (len > init && count < len/4) {
+        new_len <- max(init, ceiling(len/2))
+        stack <<- stack[seq_len(new_len)]
+      }
+
+      value
+    },
+
+    peek = function() {
+      if (count == 0L)
+        return(NULL)
+      stack[[count]]
+    },
+
+    size = function() {
+      count
+    },
+
+    # Return the entire stack as a list, where the first item in the list is the
+    # oldest item in the stack, and the last item is the most recently added.
+    as_list = function() {
+      stack[seq_len(count)]
+    }
+  ),
+
+  private = list(
+    stack = NULL,   # A list that holds the items
+    count = 0L,     # Current number of items in the stack
+    init = 20L      # Initial and minimum size of the stack
+  )
+)

R/tar.R

@@ -141,7 +141,7 @@ untar2 <- function(tarfile, files = NULL, list = FALSE, exdir = ".")
                             warning(gettextf("failed to copy %s to %s", sQuote(name2), sQuote(name)), domain = NA)
                     }
                 } else {
-                    if(.Platform$OS.type == "windows") {
+                    if(isWindows()) {
                         ## this will not work for links to dirs
                         from <- file.path(dirname(name), name2)
                         if (!file.copy(from, name))

R/timer.R

@@ -4,16 +4,17 @@ now <- function() {
   as.numeric(Sys.time()) * 1000
 }
 
-TimerCallbacks <- setRefClass(
+TimerCallbacks <- R6Class(
   'TimerCallbacks',
-  fields = list(
-    .nextId = 'integer',
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .nextId = 0L,
     .funcs = 'Map',
-    .times = 'data.frame'
-  ),
-  methods = list(
+    .times = data.frame(),
+
     initialize = function() {
-      .nextId <<- 0L
+      .funcs <<- Map$new()
     },
     clear = function() {
       .nextId <<- 0L

R/update-input.R

@@ -118,7 +118,7 @@ updateSliderInput <- updateTextInput
 #' }
 #' @export
 updateDateInput <- function(session, inputId, label = NULL, value = NULL,
-    min = NULL, max = NULL) {
+                            min = NULL, max = NULL) {
 
   # If value is a date object, convert it to a string with yyyy-mm-dd format
   # Same for min and max
@@ -163,8 +163,8 @@ updateDateInput <- function(session, inputId, label = NULL, value = NULL,
 #' }
 #' @export
 updateDateRangeInput <- function(session, inputId, label = NULL,
-    start = NULL, end = NULL, min = NULL, max = NULL) {
-
+                                 start = NULL, end = NULL, min = NULL,
+                                 max = NULL) {
   # Make sure start and end are strings, not date objects. This is for
   # consistency across different locales.
   if (inherits(start, "Date"))  start <- format(start, '%Y-%m-%d')
@@ -256,13 +256,28 @@ updateNumericInput <- function(session, inputId, label = NULL, value = NULL,
   session$sendInputMessage(inputId, message)
 }
 
+updateInputOptions <- function(session, inputId, label = NULL, choices = NULL,
+                               selected = NULL, inline = FALSE,
+                               type = 'checkbox') {
+
+  choices <- choicesWithNames(choices)
+  if (!is.null(selected))
+    selected <- validateSelected(selected, choices, inputId)
+
+  options <- if (length(choices))
+    format(tagList(
+      generateOptions(inputId, choices, selected, inline, type = type)
+    ))
+
+  message <- dropNulls(list(label = label, options = options, value = selected))
+
+  session$sendInputMessage(inputId, message)
+}
 
 #' Change the value of a checkbox group input on the client
 #'
 #' @template update-input
-#' @param choices A named vector or named list of options. For each item, the
-#'   name will be used as the label, and the value will be used as the value.
-#' @param selected A vector or list of options (values) which will be selected.
+#' @inheritParams checkboxGroupInput
 #'
 #' @seealso \code{\link{checkboxGroupInput}}
 #'
@@ -295,27 +310,16 @@ updateNumericInput <- function(session, inputId, label = NULL, value = NULL,
 #' }
 #' @export
 updateCheckboxGroupInput <- function(session, inputId, label = NULL,
-  choices = NULL, selected = NULL) {
-
-  choices <- choicesWithNames(choices)
-  if (!is.null(selected))
-    selected <- validateSelected(selected, choices, inputId)
-
-  options <- if (length(choices))
-    columnToRowData(list(value = choices, label = names(choices)))
-
-  message <- dropNulls(list(label = label, options = options, value = selected))
-
-  session$sendInputMessage(inputId, message)
+                                     choices = NULL, selected = NULL,
+                                     inline = FALSE) {
+  updateInputOptions(session, inputId, label, choices, selected, inline)
 }
 
 
 #' Change the value of a radio input on the client
 #'
 #' @template update-input
-#' @param choices A named vector or named list of options. For each item, the
-#'   name will be used as the label, and the value will be used as the value.
-#' @param selected A vector or list of options (values) which will be selected.
+#' @inheritParams radioButtons
 #'
 #' @seealso \code{\link{radioButtons}}
 #'
@@ -345,15 +349,18 @@ updateCheckboxGroupInput <- function(session, inputId, label = NULL,
 #' })
 #' }
 #' @export
-updateRadioButtons <- updateCheckboxGroupInput
+updateRadioButtons <- function(session, inputId, label = NULL, choices = NULL,
+                               selected = NULL, inline = FALSE) {
+  # you must select at least one radio button
+  if (is.null(selected) && !is.null(choices)) selected <- choices[[1]]
+  updateInputOptions(session, inputId, label, choices, selected, inline, type = 'radio')
+}
 
 
 #' Change the value of a select input on the client
 #'
 #' @template update-input
-#' @param choices A named vector or named list of options. For each item, the
-#'   name will be used as the label, and the value will be used as the value.
-#' @param selected A vector or list of options (values) which will be selected.
+#' @inheritParams selectInput
 #'
 #' @seealso \code{\link{selectInput}}
 #'
@@ -386,19 +393,26 @@ updateRadioButtons <- updateCheckboxGroupInput
 #' })
 #' }
 #' @export
-updateSelectInput <- updateCheckboxGroupInput
+updateSelectInput <- function(session, inputId, label = NULL, choices = NULL,
+                              selected = NULL) {
+  choices <- choicesWithNames(choices)
+  if (!is.null(selected))
+    selected <- validateSelected(selected, choices, inputId)
+  options <- if (length(choices)) selectOptions(choices, selected)
+  message <- dropNulls(list(label = label, options = options, value = selected))
+  session$sendInputMessage(inputId, message)
+}
 
 #' @rdname updateSelectInput
-#' @param options a list of options (see \code{\link{selectizeInput}})
+#' @inheritParams selectizeInput
 #' @param server whether to store \code{choices} on the server side, and load
 #'   the select options dynamically on searching, instead of writing all
 #'   \code{choices} into the page at once (i.e., only use the client-side
 #'   version of \pkg{selectize.js})
 #' @export
-updateSelectizeInput <- function(
-  session, inputId, label = NULL, choices = NULL, selected = NULL,
-  options = list(), server = FALSE
-) {
+updateSelectizeInput <- function(session, inputId, label = NULL, choices = NULL,
+                                 selected = NULL, options = list(),
+                                 server = FALSE) {
   if (length(options)) {
     res <- checkAsIs(options)
     cfg <- tags$script(
@@ -407,7 +421,7 @@ updateSelectizeInput <- function(
       `data-eval` = if (length(res$eval)) HTML(toJSON(res$eval)),
       HTML(toJSON(res$options))
     )
-    session$sendInputMessage(inputId, list(newOptions = as.character(cfg)))
+    session$sendInputMessage(inputId, list(config = as.character(cfg)))
   }
   if (!server) {
     return(updateSelectInput(session, inputId, label, choices, selected))
@@ -431,7 +445,7 @@ updateSelectizeInput <- function(
 selectizeJSON <- function(data, req) {
   query <- parseQueryString(req$QUERY_STRING)
   # extract the query variables, conjunction (and/or), search string, maximum options
-  var <- fromJSON(query$field)
+  var <- unlist(fromJSON(query$field, asText = TRUE))
   cjn <- if (query$conju == 'and') all else any
   # all keywords in lower-case, for case-insensitive matching
   key <- unique(strsplit(tolower(query$query), '\\s+')[[1]])
@@ -441,8 +455,8 @@ selectizeJSON <- function(data, req) {
   # convert a single vector to a data frame so it returns {label: , value: }
   # later in JSON; other objects return arbitrary JSON {x: , y: , foo: , ...}
   data <- if (is.atomic(data)) {
-    data <- choicesWithNames(data)
-    data.frame(label = names(data), value = data, stringsAsFactors = FALSE)
+    data.frame(label = names(choicesWithNames(data)), value = data,
+               stringsAsFactors = FALSE)
   } else as.data.frame(data, stringsAsFactors = FALSE)
 
   # start searching for keywords in all specified columns

R/utils.R

@@ -153,18 +153,44 @@ dropNullsOrEmpty <- function(x) {
 
 # Combine dir and (file)name into a file path. If a file already exists with a
 # name differing only by case, then use it instead.
-file.path.ci <- function(dir, name) {
-  default <- file.path(dir, name)
+file.path.ci <- function(...) {
+  result <- find.file.ci(...)
+  if (!is.null(result))
+    return(result)
+
+  # If not found, return the file path that was given to us.
+  return(file.path(...))
+}
+
+# Does a particular file exist? Case-insensitive for filename, case-sensitive
+# for path (on platforms with case-sensitive file system).
+file.exists.ci <- function(...) {
+  !is.null(find.file.ci(...))
+}
+
+# Look for a file, case-insensitive for filename, case-sensitive for path (on
+# platforms with case-sensitive filesystem). If found, return the path to the
+# file, with the correct case. If not found, return NULL.
+find.file.ci <- function(...) {
+  default <- file.path(...)
+  if (length(default) > 1)
+    stop("find.file.ci can only check for one file at a time.")
   if (file.exists(default))
     return(default)
-  if (!file.exists(dir))
-    return(default)
 
-  matches <- list.files(dir, name, ignore.case=TRUE, full.names=TRUE,
-    include.dirs=TRUE)
+  dir <- dirname(default)
+  name <- basename(default)
+
+  # If we got here, then we'll check for a directory with the exact case, and a
+  # name with any case.
+  all_files <- list.files(dir, all.files=TRUE, full.names=TRUE,
+                          include.dirs=TRUE)
+  match_idx <- tolower(name) == tolower(basename(all_files))
+  matches <- all_files[match_idx]
   if (length(matches) == 0)
-    return(default)
-  return(matches[[1]])
+    return(NULL)
+
+  return(matches[1])
 }
 
 # Attempt to join a path and relative path, and turn the result into a
@@ -185,7 +211,7 @@ resolve <- function(dir, relpath) {
   abs.path <- normalizePath(abs.path, winslash='/', mustWork=TRUE)
   dir <- normalizePath(dir, winslash='/', mustWork=TRUE)
   # trim the possible trailing slash under Windows (#306)
-  if (.Platform$OS.type == 'windows') dir <- sub('/$', '', dir)
+  if (isWindows()) dir <- sub('/$', '', dir)
   if (nchar(abs.path) <= nchar(dir) + 1)
     return(NULL)
   if (substr(abs.path, 1, nchar(dir)) != dir ||
@@ -195,6 +221,8 @@ resolve <- function(dir, relpath) {
   return(abs.path)
 }
 
+isWindows <- function() .Platform$OS.type == 'windows'
+
 # This is a wrapper for download.file and has the same interface.
 # The only difference is that, if the protocol is https, it changes the
 # download settings, depending on platform.
@@ -203,7 +231,7 @@ download <- function(url, ...) {
   if (grepl('^https?://', url)) {
 
     # If Windows, call setInternet2, then use download.file with defaults.
-    if (.Platform$OS.type == "windows") {
+    if (isWindows()) {
       # If we directly use setInternet2, R CMD CHECK gives a Note on Mac/Linux
       mySI2 <- `::`(utils, 'setInternet2')
       # Store initial settings
@@ -417,6 +445,12 @@ installExprFunction <- function(expr, name, eval.env = parent.frame(2),
 #' Returns a named character vector of key-value pairs.
 #'
 #' @param str The query string. It can have a leading \code{"?"} or not.
+#' @param nested Whether to parse the query string of as a nested list when it
+#'   contains pairs of square brackets \code{[]}. For example, the query
+#'   \samp{a[i1][j1]=x&b[i1][j1]=y&b[i2][j1]=z} will be parsed as \code{list(a =
+#'   list(i1 = list(j1 = 'x')), b = list(i1 = list(j1 = 'y'), i2 = list(j1 =
+#'   'z')))} when \code{nested = TRUE}, and \code{list(`a[i1][j1]` = 'x',
+#'   `b[i1][j1]` = 'y', `b[i2][j1]` = 'z')} when \code{nested = FALSE}.
 #' @export
 #' @examples
 #' parseQueryString("?foo=1&bar=b%20a%20r")
@@ -442,7 +476,7 @@ installExprFunction <- function(expr, name, eval.env = parent.frame(2),
 #' })
 #' }
 #'
-parseQueryString <- function(str) {
+parseQueryString <- function(str, nested = FALSE) {
   if (is.null(str) || nchar(str) == 0)
     return(list())
 
@@ -462,10 +496,29 @@ parseQueryString <- function(str) {
   keys   <- gsub('+', ' ', keys,   fixed = TRUE)
   values <- gsub('+', ' ', values, fixed = TRUE)
 
-  keys   <- vapply(keys,   function(x) URLdecode(x), FUN.VALUE = character(1))
-  values <- vapply(values, function(x) URLdecode(x), FUN.VALUE = character(1))
+  keys   <- vapply(keys,   URLdecode, character(1), USE.NAMES = FALSE)
+  values <- vapply(values, URLdecode, character(1), USE.NAMES = FALSE)
 
-  setNames(as.list(values), keys)
+  res <- setNames(as.list(values), keys)
+  if (!nested) return(res)
+
+  # Make a nested list from a query of the form ?a[1][1]=x11&a[1][2]=x12&...
+  for (i in grep('\\[.+\\]', keys)) {
+    k <- strsplit(keys[i], '[][]')[[1L]]  # split by [ or ]
+    res <- assignNestedList(res, k[k != ''], values[i])
+    res[[keys[i]]] <- NULL    # remove res[['a[1][1]']]
+  }
+  res
+}
+
+# Assign value to the bottom element of the list x using recursive indices idx
+assignNestedList <- function(x = list(), idx, value) {
+  for (i in seq_along(idx)) {
+    sub <- idx[seq_len(i)]
+    if (is.null(x[[sub]])) x[[sub]] <- list()
+  }
+  x[[idx]] <- value
+  x
 }
 
 # decide what to do in case of errors; it is customizable using the shiny.error
@@ -487,7 +540,7 @@ shinyCallingHandlers <- function(expr) {
 shinyDeprecated <- function(new=NULL, msg=NULL,
                             old=as.character(sys.call(sys.parent()))[1L]) {
 
-  if (getOption("shiny.deprecation.messages", default=TRUE) == FALSE)
+  if (getOption("shiny.deprecation.messages") %OR% TRUE == FALSE)
     return(invisible())
 
   if (is.null(msg)) {
@@ -522,15 +575,17 @@ registerDebugHook <- function(name, where, label) {
   }
 }
 
-Callbacks <- setRefClass(
+Callbacks <- R6Class(
   'Callbacks',
-  fields = list(
-    .nextId = 'integer',
-    .callbacks = 'Map'
-  ),
-  methods = list(
+  portable = FALSE,
+  class = FALSE,
+  public = list(
+    .nextId = integer(0),
+    .callbacks = 'Map',
+
     initialize = function() {
       .nextId <<- as.integer(.Machine$integer.max)
+      .callbacks <<- Map$new()
     },
     register = function(callback) {
       id <- as.character(.nextId)
@@ -557,80 +612,91 @@ Callbacks <- setRefClass(
 
 # convert a data frame to JSON as required by DataTables request
 dataTablesJSON <- function(data, req) {
-  query <- req$QUERY_STRING
   n <- nrow(data)
-  with(parseQueryString(query), {
-    useRegex <- function(j, envir = parent.frame()) {
-      # FIXME: bRegex is not part of the query string yet (DataTables 1.9.4)
-      return(TRUE)
-      ex <- getExists(
-        if (missing(j)) 'bRegex' else sprintf('bRegex_%s', j), 'character', envir
-      )
-      is.null(ex) || ex == 'true'
-    }
-    # global searching
-    i <- seq_len(n)
-    sSearch <- getExists('sSearch', 'character')
-    if (length(sSearch) && nzchar(sSearch)) {
-      bRegex <- useRegex()
-      i0 <- apply(data, 2, function(x) grep(sSearch, as.character(x), fixed = !bRegex))
-      i <- intersect(i, unique(unlist(i0)))
-    }
-    # search by columns
-    if (length(i)) for (j in seq_len(as.integer(iColumns)) - 1) {
-      if (is.null(s <- getExists(sprintf('bSearchable_%d', j), 'character')) ||
-            s == "0" || s == "false") next  # the j-th column is not searchable
-      if (is.null(k <- getExists(sprintf('sSearch_%d', j), 'character'))) next
-      if (nzchar(k)) {
-        dj <- data[, j + 1]
-        r  <- commaToRange(k)
-        ij <- if (length(r) == 2 && is.numeric(dj)) {
-          which(dj >= r[1] & dj <= r[2])
-        } else {
-          grep(k, as.character(dj), fixed = !useRegex(j))
-        }
-        i <- intersect(ij, i)
-      }
-      if (length(i) == 0) break
-    }
-    if (length(i) != n) data <- data[i, , drop = FALSE]
-    # sorting
-    oList <- list()
-    for (j in seq_len(as.integer(iSortingCols)) - 1) {
-      if (is.null(k <- getExists(sprintf('iSortCol_%d', j), 'character'))) break
-      desc <- getExists(sprintf('sSortDir_%d', j), 'character')
-      if (is.character(desc)) {
-        col <- data[, as.integer(k) + 1]
-        oList[[length(oList) + 1]] <- (if (desc == 'asc') identity else `-`)(
-          if (is.numeric(col)) col else xtfrm(col)
-        )
-      }
-    }
-    if (length(oList)) {
-      i <- do.call(order, oList)
-      data <- data[i, , drop = FALSE]
-    }
-    # paging
-    if (iDisplayLength != '-1') {
-      i <- seq(as.integer(iDisplayStart) + 1L, length.out = as.integer(iDisplayLength))
-      i <- i[i <= nrow(data)]
-      fdata <- data[i, , drop = FALSE]  # filtered data
-    } else fdata <- data
-    fdata <- unname(as.matrix(fdata))
-    # WAT: toJSON(list(x = matrix(nrow = 0, ncol = 1))) => {"x": } (#299)
-    if (nrow(fdata) == 0) fdata <- list()
-    # WAT: toJSON(list(x = matrix(1:2))) => {x: [ [1], [2] ]}, however,
-    # toJSON(list(x = matrix(1))) => {x: [ 1 ]} (loss of dimension, #429)
-    if (all(dim(fdata) == 1)) fdata <- list(list(fdata[1, 1]))
+  q <- parseQueryString(req$QUERY_STRING, nested = TRUE)
+  ci <- q$search[['caseInsensitive']] == 'true'
 
-    res <- toJSON(list(
-      sEcho = as.integer(sEcho),
-      iTotalRecords = n,
-      iTotalDisplayRecords = nrow(data),
-      aaData = fdata
-    ))
-    httpResponse(200, 'application/json', res)
-  })
+  # global searching
+  i <- seq_len(n)
+  if (q$search[['value']] != '') {
+    i0 <- apply(data, 2, function(x) {
+      grep2(q$search[['value']], as.character(x),
+            fixed = q$search[['regex']] == 'false', ignore.case = ci)
+    })
+    i <- intersect(i, unique(unlist(i0)))
+  }
+
+  # search by columns
+  if (length(i)) for (j in names(q$columns)) {
+    col <- q$columns[[j]]
+    # if the j-th column is not searchable or the search string is "", skip it
+    if (col[['searchable']] != 'true') next
+    if ((k <- col[['search']][['value']]) == '') next
+    j <- as.integer(j)
+    dj <- data[, j + 1]
+    r  <- commaToRange(k)
+    ij <- if (length(r) == 2 && is.numeric(dj)) {
+      which(dj >= r[1] & dj <= r[2])
+    } else {
+      grep2(k, as.character(dj), fixed = col[['search']][['regex']] == 'false',
+            ignore.case = ci)
+    }
+    i <- intersect(ij, i)
+    if (length(i) == 0) break
+  }
+  if (length(i) != n) data <- data[i, , drop = FALSE]
+
+  # sorting
+  oList <- list()
+  for (ord in q$order) {
+    k <- ord[['column']]  # which column to sort
+    d <- ord[['dir']]     # direction asc/desc
+    if (q$columns[[k]][['orderable']] != 'true') next
+    col <- data[, as.integer(k) + 1]
+    oList[[length(oList) + 1]] <- (if (d == 'asc') identity else `-`)(
+      if (is.numeric(col)) col else xtfrm(col)
+    )
+  }
+  if (length(oList)) {
+    i <- do.call(order, oList)
+    data <- data[i, , drop = FALSE]
+  }
+  # paging
+  if (q$length != '-1') {
+    i <- seq(as.integer(q$start) + 1L, length.out = as.integer(q$length))
+    i <- i[i <= nrow(data)]
+    fdata <- data[i, , drop = FALSE]  # filtered data
+  } else fdata <- data
+
+  fdata <- unname(as.matrix(fdata))
+  # WAT: toJSON(list(x = matrix(nrow = 0, ncol = 1))) => {"x": } (#299)
+  if (nrow(fdata) == 0) fdata <- list()
+  # WAT: toJSON(list(x = matrix(1:2))) => {x: [ [1], [2] ]}, however,
+  # toJSON(list(x = matrix(1))) => {x: [ 1 ]} (loss of dimension, #429)
+  if (length(fdata) && all(dim(fdata) == 1)) fdata <- list(list(fdata[1, 1]))
+
+  res <- toJSON(list(
+    draw = q$draw,
+    recordsTotal = n,
+    recordsFiltered = nrow(data),
+    data = fdata
+  ))
+  httpResponse(200, 'application/json', res)
+}
+
+# when both ignore.case and fixed are TRUE, we use grep(ignore.case = FALSE,
+# fixed = TRUE) to do lower-case matching of pattern on x
+grep2 <- function(pattern, x, ignore.case = FALSE, fixed = FALSE, ...) {
+  if (fixed && ignore.case) {
+    pattern <- tolower(pattern)
+    x <- tolower(x)
+    ignore.case <- FALSE
+  }
+  # when the user types in the search box, the regular expression may not be
+  # complete before it is sent to the server, in which case we do not search
+  if (!fixed && inherits(try(grep(pattern, ''), silent = TRUE), 'try-error'))
+    return(seq_along(x))
+  grep(pattern, x, ignore.case = ignore.case, fixed = fixed, ...)
 }
 
 getExists <- function(x, mode, envir = parent.frame()) {
@@ -655,6 +721,7 @@ commaToRange <- function(string) {
 checkAsIs <- function(options) {
   evalOptions <- if (length(options)) {
     nms <- names(options)
+    if (length(nms) == 0L || any(nms == '')) stop("'options' must be a named list")
     i <- unlist(lapply(options, function(x) {
       is.character(x) && inherits(x, 'AsIs')
     }))
@@ -736,18 +803,6 @@ cachedFuncWithFile <- function(dir, file, func, case.sensitive = FALSE) {
   }
 }
 
-# Returns a function that sources the file and caches the result for subsequent
-# calls, unless the file's mtime changes.
-cachedSource <- function(dir, file, case.sensitive = FALSE) {
-  dir <- normalizePath(dir, mustWork=TRUE)
-  cachedFuncWithFile(dir, file, function(fname, ...) {
-    if (file.exists(fname))
-      return(source(fname, ...))
-    else
-      return(NULL)
-  })
-}
-
 # turn column-based data to row-based data (mainly for JSON), e.g. data.frame(x
 # = 1:10, y = 10:1) ==> list(list(x = 1, y = 10), list(x = 2, y = 9), ...)
 columnToRowData <- function(data) {
@@ -915,6 +970,9 @@ stopWithCondition <- function(class, message) {
 #' its version, and whether it is the open source edition or professional
 #' edition. If the app is not served through the Shiny Server, this function
 #' just returns \code{list(shinyServer = FALSE)}.
+#'
+#' This function will only return meaningful data when using Shiny Server
+#' version 1.2.2 or later.
 #' @export
 #' @return A list of the Shiny Server information.
 serverInfo <- function() {
@@ -928,3 +986,64 @@ setServerInfo <- function(...) {
   infoOld[names(infoNew)] <- infoNew
   .globals$serverInfo <- infoOld
 }
+
+# see if the file can be read as UTF-8 on Windows, and converted from UTF-8 to
+# native encoding; if the conversion fails, it will produce NA's in the results
+checkEncoding <- function(file) {
+  # skip *nix because its locale is normally UTF-8 based (e.g. en_US.UTF-8), and
+  # *nix users have to make a conscious effort to save a file with an encoding
+  # that is not UTF-8; if they choose to do so, we cannot do much about it
+  # except sitting back and seeing them punished after they choose to escape a
+  # world of consistency (falling back to getOption('encoding') will not help
+  # because native.enc is also normally UTF-8 based on *nix)
+  if (!isWindows()) return('UTF-8')
+  # an empty file?
+  size <- file.info(file)[, 'size']
+  if (size == 0) return('UTF-8')
+
+  x <- readLines(file, encoding = 'UTF-8', warn = FALSE)
+  # if conversion is successful and there are no embedded nul's, use UTF-8
+  if (!any(is.na(iconv(x, 'UTF-8'))) &&
+        !any(readBin(file, 'raw', size) == as.raw(0))) return('UTF-8')
+
+  # check if there is a BOM character: this is also skipped on *nix, because R
+  # on *nix simply ignores this meaningless character if present, but it hurts
+  # on Windows
+  if (identical(charToRaw(readChar(file, 3L, TRUE)), charToRaw('\UFEFF'))) {
+    warning('You should not include the Byte Order Mark (BOM) in ', file, '. ',
+            'Please re-save it in UTF-8 without BOM. See ',
+            'http://shiny.rstudio.com/articles/unicode.html for more info.')
+    if (getRversion() < '3.0.0')
+      stop('R does not support UTF-8-BOM before 3.0.0. Please upgrade R.')
+    return('UTF-8-BOM')
+  }
+
+  enc <- getOption('encoding')
+  msg <- c(sprintf('The file "%s" is not encoded in UTF-8. ', file),
+           'Please convert its encoding to UTF-8 ',
+           '(e.g. use the menu `File -> Save with Encoding` in RStudio). ',
+           'See http://shiny.rstudio.com/articles/unicode.html for more info.')
+  if (enc == 'UTF-8') stop(msg)
+  # if you publish the app to ShinyApps.io, you will be in trouble
+  warning(c(msg, ' Falling back to the encoding "', enc, '".'))
+
+  enc
+}
+
+# try to read a file using UTF-8 (fall back to getOption('encoding') in case of
+# failure, which defaults to native.enc, i.e. native encoding)
+readUTF8 <- function(file) {
+  enc <- checkEncoding(file)
+  # readLines() does not support UTF-8-BOM directly; has to go through file()
+  if (enc == 'UTF-8-BOM') {
+    file <- base::file(file, encoding = enc)
+    on.exit(close(file), add = TRUE)
+  }
+  x <- readLines(file, encoding = enc, warn = FALSE)
+  enc2native(x)
+}
+
+# similarly, try to source() a file with UTF-8
+sourceUTF8 <- function(file, ...) {
+  source(file, ..., keep.source = TRUE, encoding = checkEncoding(file))
+}

README.md

@@ -4,7 +4,7 @@
 
 Shiny is a new package from RStudio that makes it incredibly easy to build interactive web applications with R.
 
-For an introduction and examples, visit the [Shiny homepage](http://www.rstudio.com/shiny/).
+For an introduction and examples, visit the [Shiny Dev Center](http://shiny.rstudio.com/).
 
 ## Features
 
@@ -37,7 +37,7 @@ devtools::install_github("shiny", "rstudio")
 
 ## Getting Started
 
-To learn more we highly recommend you check out the [Shiny Tutorial](http://rstudio.github.com/shiny/tutorial). The tutorial explains the framework in-depth, walks you through building a simple application, and includes extensive annotated examples.
+To learn more we highly recommend you check out the [Shiny Tutorial](http://shiny.rstudio.com/tutorial/). The tutorial explains the framework in-depth, walks you through building a simple application, and includes extensive annotated examples.
 
 We hope you enjoy using Shiny. If you have general questions about using Shiny, please use the Shiny [mailing list](https://groups.google.com/forum/#!forum/shiny-discuss). For bug reports, please use the [issue tracker](https://github.com/rstudio/shiny/issues).
 

inst/staticdocs/index.r

@@ -64,7 +64,9 @@ sd_section("UI Outputs",
     "tableOutput",
     "textOutput",
     "verbatimTextOutput",
-    "downloadButton"
+    "downloadButton",
+    "Progress",
+    "withProgress"
   )
 )
 sd_section("Interface builder functions",
@@ -127,8 +129,6 @@ sd_section("Running",
   c(
     "runApp",
     "runExample",
-    "runGist",
-    "runGitHub",
     "runUrl",
     "stopApp"
   )
@@ -136,6 +136,7 @@ sd_section("Running",
 sd_section("Extending Shiny",
   "Functions that are intended to be called by third-party packages that extend Shiny.",
   c(
+    "createWebDependency",
     "addResourcePath",
     "registerInputHandler",
     "removeInputHandler",
@@ -152,7 +153,8 @@ sd_section("Utility functions",
     "parseQueryString",
     "plotPNG",
     "repeatable",
-    "shinyDeprecated"
+    "shinyDeprecated",
+    "serverInfo"
   )
 )
 sd_section("Embedding",

inst/tests/test-bootstrap.r

@@ -43,3 +43,110 @@ test_that("Repeated names for selectInput and radioButtons choices", {
   expect_equal(choices[[2]][[3]]$children[[1]]$attribs$value, 'x3')
   expect_equal(choices[[2]][[3]]$children[[1]]$attribs$checked, NULL)
 })
+
+
+test_that("Choices are correctly assigned names", {
+  # Unnamed vector
+  expect_identical(
+    choicesWithNames(c("a","b","3")),
+    list(a="a", b="b", "3"="3")
+  )
+  # Unnamed list
+  expect_identical(
+    choicesWithNames(list("a","b",3)),
+    list(a="a", b="b", "3"=3)
+  )
+  # Vector, with some named, some not
+  expect_identical(
+    choicesWithNames(c(A="a", "b", C="3", "4")),
+    list(A="a", "b"="b", C="3", "4"="4")
+  )
+  # List, with some named, some not
+  expect_identical(
+    choicesWithNames(list(A="a", "b", C=3, 4)),
+    list(A="a", "b"="b", C=3, "4"=4)
+  )
+  # List, named, with a sub-vector
+  expect_identical(
+    choicesWithNames(list(A="a", B="b", C=c("d", "e"))),
+    list(A="a", B="b", C=list(d="d", e="e"))
+  )
+  # List, named, with sublist
+  expect_identical(
+    choicesWithNames(list(A="a", B="b", C=list("d", "e"))),
+    list(A="a", B="b", C=list(d="d", e="e"))
+  )
+  # List, named, with a named sub-vector of length 1
+  expect_identical(
+    choicesWithNames(list(A="a", B="b", C=c(D="d"))),
+    list(A="a", B="b", C=list(D="d"))
+  )
+  # List, some named, with sublist
+  expect_identical(
+    choicesWithNames(list(A="a", "b", C=list("d", E="e"))),
+    list(A="a", b="b", C=list(d="d", E="e"))
+  )
+  # Deeper nesting
+  expect_identical(
+    choicesWithNames(list(A="a", "b", C=list(D=list("e", "f"), G=c(H="h", "i")))),
+    list(A="a", b="b", C=list(D=list(e="e", f="f"), G=list(H="h", i="i")))
+  )
+  # Error when sublist is unnamed
+  expect_error(choicesWithNames(list(A="a", "b", list(1,2))))
+})
+
+
+test_that("selectOptions returns correct HTML", {
+  # None selected
+  expect_identical(
+    selectOptions(choicesWithNames(list("a", "b")), list()),
+    HTML("<option value=\"a\">a</option>\n<option value=\"b\">b</option>")
+  )
+  # One selected
+  expect_identical(
+    selectOptions(choicesWithNames(list("a", "b")), "a"),
+    HTML("<option value=\"a\" selected>a</option>\n<option value=\"b\">b</option>")
+  )
+  # One selected, with named items
+  expect_identical(
+    selectOptions(choicesWithNames(list(A="a", B="b")), "a"),
+    HTML("<option value=\"a\" selected>A</option>\n<option value=\"b\">B</option>")
+  )
+  # Two selected, with optgroup
+  expect_identical(
+    selectOptions(choicesWithNames(list("a", B=list("c", D="d"))), c("a", "d")),
+    HTML("<option value=\"a\" selected>a</option>\n<optgroup label=\"B\">\n<option value=\"c\">c</option>\n<option value=\"d\" selected>D</option>\n</optgroup>")
+  )
+
+  # Escape HTML in strings
+  expect_identical(
+    selectOptions(choicesWithNames(list("<A>"="a", B="b")), "a"),
+    HTML("<option value=\"a\" selected>&lt;A&gt;</option>\n<option value=\"b\">B</option>")
+  )
+})
+
+test_that("selectInput selects items by default", {
+  # None specified as selected (defaults to first)
+  expect_true(grepl(
+    '<option value="a" selected>',
+    selectInput('x', 'x', list("a", "b"))
+  ))
+
+  # Nested list (optgroup)
+  expect_true(grepl(
+    '<option value="a" selected>',
+    selectInput('x', 'x', list(A=list("a", "b"), "c"))
+  ))
+
+  # Nothing selected when choices=NULL
+  expect_identical(
+    '<select id="x"></select>',
+    format(selectInput('x', NULL, NULL, selectize = FALSE))
+  )
+
+  # None specified as selected. With multiple=TRUE, none selected by default.
+  expect_true(grepl(
+    '<option value="a">',
+    selectInput('x', 'x', list("a", "b"), multiple = TRUE)
+  ))
+})

inst/tests/test-gc.r

@@ -7,10 +7,8 @@ test_that("unreferenced observers are garbage collected", {
   obs  <- observe({ vals$A })
 
   # These are called when the objects are garbage-collected
-  reg.finalizer(attr(.subset2(vals,'impl'), ".xData"),
-                function(e) vals_removed <<- TRUE)
-  reg.finalizer(attr(obs, ".xData"),
-                function(e) obs_removed  <<- TRUE)
+  reg.finalizer(.subset2(vals,'impl'), function(e) vals_removed <<- TRUE)
+  reg.finalizer(obs, function(e) obs_removed  <<- TRUE)
 
   flushReact()
 
@@ -42,10 +40,8 @@ test_that("suspended observers are garbage collected", {
   obs  <- observe({ vals$A })
 
   # These are called when the objects are garbage-collected
-  reg.finalizer(attr(.subset2(vals,'impl'), ".xData"),
-                function(e) vals_removed <<- TRUE)
-  reg.finalizer(attr(obs, ".xData"),
-                function(e) obs_removed  <<- TRUE)
+  reg.finalizer(.subset2(vals,'impl'), function(e) vals_removed <<- TRUE)
+  reg.finalizer(obs, function(e) obs_removed <<- TRUE)
 
   flushReact()
 

inst/tests/test-stack.R

@@ -0,0 +1,40 @@
+context("Stack")
+
+test_that("Basic operations", {
+  s <- Stack$new()
+  expect_identical(s$size(), 0L)
+
+  s$push(5)$push(6)$push(NULL)$push(list(a=1,b=2))
+
+  expect_identical(s$pop(), list(a=1,b=2))
+  expect_identical(s$peek(), NULL)
+  expect_identical(s$pop(), NULL)
+  expect_identical(s$size(), 2L)
+
+  # as_list() returns in the order that they were inserted
+  expect_identical(s$as_list(), list(5, 6))
+})
+
+
+test_that("Pushing multiple", {
+  s <- Stack$new()
+  s$push(1,2,3)
+  s$push(4,5, .list=list(6,list(7,8)))
+  s$push(9,10)
+  expect_identical(s$as_list(), list(1,2,3,4,5,6,list(7,8),9,10))
+  expect_identical(s$pop(), 10)
+  expect_identical(s$pop(), 9)
+  expect_identical(s$pop(), list(7,8))
+})
+
+
+test_that("Popping from empty stack", {
+  s <- Stack$new()
+  expect_null(s$pop())
+  expect_null(s$pop())
+  expect_null(s$peek())
+  expect_identical(s$size(), 0L)
+
+  s$push(5)$push(6)
+  expect_identical(s$as_list(), list(5, 6))
+})

inst/tests/test-staticdocs.R

@@ -6,7 +6,7 @@ test_that("All man pages have an entry in staticdocs/index.r", {
     return()
   }
   # Known not to be indexed
-  known_unindexed <- c("shiny-package", "knitr_methods")
+  known_unindexed <- c("shiny-package", "knitr_methods", "knitr_methods_htmltools")
 
   indexed_topics <- local({
     result <- character(0)

inst/tests/test-url.R

@@ -17,4 +17,26 @@ test_that("Query string parsing", {
 
   # Should be the same with or without leading question mark
   expect_identical(parseQueryString("?foo=1&bar=b"), parseQueryString("foo=1&bar=b"))
+
+
+  # Nested and non-nested query strings
+  expect_identical(
+    parseQueryString("a[i1][j1]=x&b[i1][j1]=y&b[i2][j1]=z"),
+    list(
+      "a[i1][j1]" = "x",
+      "b[i1][j1]" = "y",
+      "b[i2][j1]" = "z"
+    )
+  )
+
+  expect_identical(
+    parseQueryString("a[i1][j1]=x&b[i1][j1]=y&b[i2][j1]=z", nested = TRUE),
+    list(
+      a = list(i1 = list(j1 = "x")),
+      b = list(
+        i1 = list(j1 = "y"),
+        i2 = list(j1 = "z")
+      )
+    )
+  )
 })

inst/www-dir/index.html

@@ -7,6 +7,7 @@
   <ul>
     <li><code>www/index.html</code></li>
     <li><code>ui.R</code></li>
+    <li><code>app.R</code></li>
   </ul>
 </body>
 </html>

inst/www/shared/datatables/css/DT_bootstrap.css

@@ -1,123 +0,0 @@
-
-div.dataTables_length label {
-	float: left;
-	text-align: left;
-}
-
-div.dataTables_length select {
-	width: 75px;
-}
-
-div.dataTables_filter label {
-	float: right;
-}
-
-div.dataTables_info {
-	padding-top: 8px;
-}
-
-div.dataTables_paginate {
-	float: right;
-	margin: 0;
-}
-
-table.table {
-	clear: both;
-	margin-bottom: 6px !important;
-	max-width: none !important;
-}
-
-table.table thead .sorting,
-table.table thead .sorting_asc,
-table.table thead .sorting_desc,
-table.table thead .sorting_asc_disabled,
-table.table thead .sorting_desc_disabled {
-	cursor: pointer;
-	*cursor: hand;
-}
-
-table.table thead .sorting { background: url('images/sort_both.png') no-repeat center right; }
-table.table thead .sorting_asc { background: url('images/sort_asc.png') no-repeat center right; }
-table.table thead .sorting_desc { background: url('images/sort_desc.png') no-repeat center right; }
-
-table.table thead .sorting_asc_disabled { background: url('images/sort_asc_disabled.png') no-repeat center right; }
-table.table thead .sorting_desc_disabled { background: url('images/sort_desc_disabled.png') no-repeat center right; }
-
-table.dataTable th:active {
-	outline: none;
-}
-
-table.dataTable tr.odd td.sorting_1 { background-color: #D3D6FF; }
-table.dataTable tr.odd td.sorting_2 { background-color: #DADCFF; }
-table.dataTable tr.odd td.sorting_3 { background-color: #E0E2FF; }
-table.dataTable tr.even td.sorting_1 { background-color: #EAEBFF; }
-table.dataTable tr.even td.sorting_2 { background-color: #F2F3FF; }
-table.dataTable tr.even td.sorting_3 { background-color: #F9F9FF; }
-
-/* Scrolling */
-div.dataTables_scrollHead table {
-	margin-bottom: 0 !important;
-	border-bottom-left-radius: 0;
-	border-bottom-right-radius: 0;
-}
-
-div.dataTables_scrollHead table thead tr:last-child th:first-child,
-div.dataTables_scrollHead table thead tr:last-child td:first-child {
-	border-bottom-left-radius: 0 !important;
-	border-bottom-right-radius: 0 !important;
-}
-
-div.dataTables_scrollBody table {
-	border-top: none;
-	margin-bottom: 0 !important;
-}
-
-div.dataTables_scrollBody tbody tr:first-child th,
-div.dataTables_scrollBody tbody tr:first-child td {
-	border-top: none;
-}
-
-div.dataTables_scrollFoot table {
-	border-top: none;
-}
-
-/* Active rows */
-
-.table tbody tr.active td,
-.table tbody tr.active th {
-	background-color: #08C;
-	color: white;
-}
-
-.table tbody tr.active:hover td,
-.table tbody tr.active:hover th {
-	background-color: #0075b0 !important;
-}
-
-.table-striped tbody tr.active:nth-child(odd) td,
-.table-striped tbody tr.active:nth-child(odd) th {
-	background-color: #017ebc;
-}
-
-/* Processing indicator */
-
-.dataTables_processing {
-	position: absolute;
-	top: 50%;
-	left: 50%;
-	width: 250px;
-	height: 30px;
-	margin-left: -125px;
-	margin-top: -15px;
-	padding: 14px 0 2px 0;
-	border: 1px solid #ddd;
-	text-align: center;
-	color: #999;
-	font-size: 14px;
-	background-color: white;
-}
-
-/* Search boxes in the footer */
-table tfoot input {
-  width: 100%;
-}

inst/www/shared/datatables/css/dataTables.bootstrap.css

@@ -0,0 +1,205 @@
+div.dataTables_length label {
+	float: left;
+	text-align: left;
+}
+
+div.dataTables_length select {
+	width: 75px;
+}
+
+div.dataTables_filter label {
+	float: right;
+}
+
+div.dataTables_info {
+	padding-top: 8px;
+}
+
+div.dataTables_paginate {
+	float: right;
+	margin: 0;
+}
+
+table.table {
+	clear: both;
+	margin-bottom: 6px !important;
+	max-width: none !important;
+}
+
+table.table thead .sorting,
+table.table thead .sorting_asc,
+table.table thead .sorting_desc,
+table.table thead .sorting_asc_disabled,
+table.table thead .sorting_desc_disabled {
+	cursor: pointer;
+	*cursor: hand;
+}
+
+table.table thead .sorting { background: url('../images/sort_both.png') no-repeat center right; }
+table.table thead .sorting_asc { background: url('../images/sort_asc.png') no-repeat center right; }
+table.table thead .sorting_desc { background: url('../images/sort_desc.png') no-repeat center right; }
+
+table.table thead .sorting_asc_disabled { background: url('../images/sort_asc_disabled.png') no-repeat center right; }
+table.table thead .sorting_desc_disabled { background: url('../images/sort_desc_disabled.png') no-repeat center right; }
+
+table.dataTable th:active {
+	outline: none;
+}
+
+/* Scrolling */
+div.dataTables_scrollHead table {
+	margin-bottom: 0 !important;
+	border-bottom-left-radius: 0;
+	border-bottom-right-radius: 0;
+}
+
+div.dataTables_scrollHead table thead tr:last-child th:first-child,
+div.dataTables_scrollHead table thead tr:last-child td:first-child {
+	border-bottom-left-radius: 0 !important;
+	border-bottom-right-radius: 0 !important;
+}
+
+div.dataTables_scrollBody table {
+	border-top: none;
+	margin-top: 0 !important;
+	margin-bottom: 0 !important;
+}
+
+div.dataTables_scrollBody tbody tr:first-child th,
+div.dataTables_scrollBody tbody tr:first-child td {
+	border-top: none;
+}
+
+div.dataTables_scrollFoot table {
+	margin-top: 0 !important;
+	border-top: none;
+}
+
+
+
+
+/*
+ * TableTools styles
+ */
+.table tbody tr.active td,
+.table tbody tr.active th {
+	background-color: #08C;
+	color: white;
+}
+
+.table tbody tr.active:hover td,
+.table tbody tr.active:hover th {
+	background-color: #0075b0 !important;
+}
+
+.table tbody tr.active a {
+	color: white;
+}
+
+.table-striped tbody tr.active:nth-child(odd) td,
+.table-striped tbody tr.active:nth-child(odd) th {
+	background-color: #017ebc;
+}
+
+table.DTTT_selectable tbody tr {
+	cursor: pointer;
+	*cursor: hand;
+}
+
+div.DTTT .btn {
+	color: #333 !important;
+	font-size: 12px;
+}
+
+div.DTTT .btn:hover {
+	text-decoration: none !important;
+}
+
+ul.DTTT_dropdown.dropdown-menu {
+  z-index: 2003;
+}
+
+ul.DTTT_dropdown.dropdown-menu a {
+	color: #333 !important; /* needed only when demo_page.css is included */
+}
+
+ul.DTTT_dropdown.dropdown-menu li {
+	position: relative;
+}
+
+ul.DTTT_dropdown.dropdown-menu li:hover a {
+	background-color: #0088cc;
+	color: white !important;
+}
+
+div.DTTT_collection_background {
+	z-index: 2002;	
+}
+
+/* TableTools information display */
+div.DTTT_print_info.modal {
+	height: 150px;
+	margin-top: -75px;
+	text-align: center;
+}
+
+div.DTTT_print_info h6 {
+	font-weight: normal;
+	font-size: 28px;
+	line-height: 28px;
+	margin: 1em;
+}
+
+div.DTTT_print_info p {
+	font-size: 14px;
+	line-height: 20px;
+}
+
+
+
+/*
+ * FixedColumns styles
+ */
+div.DTFC_LeftHeadWrapper table,
+div.DTFC_LeftFootWrapper table,
+div.DTFC_RightHeadWrapper table,
+div.DTFC_RightFootWrapper table,
+table.DTFC_Cloned tr.even {
+    background-color: white;
+    margin-bottom: 0;
+}
+ 
+div.DTFC_RightHeadWrapper table ,
+div.DTFC_LeftHeadWrapper table {
+    margin-bottom: 0 !important;
+    border-top-right-radius: 0 !important;
+    border-bottom-left-radius: 0 !important;
+    border-bottom-right-radius: 0 !important;
+}
+ 
+div.DTFC_RightHeadWrapper table thead tr:last-child th:first-child,
+div.DTFC_RightHeadWrapper table thead tr:last-child td:first-child,
+div.DTFC_LeftHeadWrapper table thead tr:last-child th:first-child,
+div.DTFC_LeftHeadWrapper table thead tr:last-child td:first-child {
+    border-bottom-left-radius: 0 !important;
+    border-bottom-right-radius: 0 !important;
+}
+ 
+div.DTFC_RightBodyWrapper table,
+div.DTFC_LeftBodyWrapper table {
+    border-top: none;
+    margin-bottom: 0 !important;
+}
+ 
+div.DTFC_RightBodyWrapper tbody tr:first-child th,
+div.DTFC_RightBodyWrapper tbody tr:first-child td,
+div.DTFC_LeftBodyWrapper tbody tr:first-child th,
+div.DTFC_LeftBodyWrapper tbody tr:first-child td {
+    border-top: none;
+}
+ 
+div.DTFC_RightFootWrapper table,
+div.DTFC_LeftFootWrapper table {
+    border-top: none;
+}
+

inst/www/shared/datatables/css/dataTables.extra.css

@@ -0,0 +1,47 @@
+/* Sorting */
+table.dataTable tr.odd td.sorting_1 { background-color: #D3D6FF; }
+table.dataTable tr.odd td.sorting_2 { background-color: #DADCFF; }
+table.dataTable tr.odd td.sorting_3 { background-color: #E0E2FF; }
+table.dataTable tr.even td.sorting_1 { background-color: #EAEBFF; }
+table.dataTable tr.even td.sorting_2 { background-color: #F2F3FF; }
+table.dataTable tr.even td.sorting_3 { background-color: #F9F9FF; }
+
+table.dataTable tr.odd td.sorting_1 { background-color: #D3D6FF; }
+table.dataTable tr.odd td.sorting_2 { background-color: #DADCFF; }
+table.dataTable tr.odd td.sorting_3 { background-color: #E0E2FF; }
+table.dataTable tr.even td.sorting_1 { background-color: #EAEBFF; }
+table.dataTable tr.even td.sorting_2 { background-color: #F2F3FF; }
+table.dataTable tr.even td.sorting_3 { background-color: #F9F9FF; }
+
+/* Selected rows */
+table.dataTable tbody tr.selected,
+table.dataTable tr.selected td.sorting_1,
+table.dataTable tr.selected td.sorting_2,
+table.dataTable tr.selected td.sorting_3,
+.table-striped tbody>tr.selected:nth-child(odd)>td,
+.table-striped tbody>tr.selected:nth-child(even)>td {
+  background-color: #b0bed9;
+}
+
+/* Processing indicator */
+.dataTables_processing {
+	position: absolute;
+	top: 50%;
+	left: 50%;
+	width: 250px;
+	height: 30px;
+	margin-left: -125px;
+	margin-top: -15px;
+	padding: 14px 0 2px 0;
+	border: 1px solid #ddd;
+	text-align: center;
+	color: #999;
+	font-size: 14px;
+	background-color: white;
+}
+
+/* Search boxes in the footer */
+table tfoot input {
+  width: 100%;
+}
+

inst/www/shared/datatables/js/dataTables.bootstrap.js

@@ -107,3 +107,42 @@ $.extend( $.fn.dataTableExt.oPagination, {
 		}
 	}
 } );
+
+
+/*
+ * TableTools Bootstrap compatibility
+ * Required TableTools 2.1+
+ */
+if ( $.fn.DataTable.TableTools ) {
+	// Set the classes that TableTools uses to something suitable for Bootstrap
+	$.extend( true, $.fn.DataTable.TableTools.classes, {
+		"container": "DTTT btn-group",
+		"buttons": {
+			"normal": "btn",
+			"disabled": "disabled"
+		},
+		"collection": {
+			"container": "DTTT_dropdown dropdown-menu",
+			"buttons": {
+				"normal": "",
+				"disabled": "disabled"
+			}
+		},
+		"print": {
+			"info": "DTTT_print_info modal"
+		},
+		"select": {
+			"row": "active"
+		}
+	} );
+
+	// Have the collection use a bootstrap compatible dropdown
+	$.extend( true, $.fn.DataTable.TableTools.DEFAULTS.oTags, {
+		"collection": {
+			"container": "ul",
+			"button": "li",
+			"liner": "a"
+		}
+	} );
+}
+

inst/www/shared/datatables/js/jquery.dataTables.min.js

@@ -1,155 +1,155 @@
-/*
- * File:        jquery.dataTables.min.js
- * Version:     1.9.4
- * Author:      Allan Jardine (www.sprymedia.co.uk)
- * Info:        www.datatables.net
- * 
- * Copyright 2008-2012 Allan Jardine, all rights reserved.
- *
- * This source file is free software, under either the GPL v2 license or a
- * BSD style license, available at:
- *   http://datatables.net/license_gpl2
- *   http://datatables.net/license_bsd
- * 
- * This source file is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY 
- * or FITNESS FOR A PARTICULAR PURPOSE. See the license files for details.
+/*! DataTables 1.10.2
+ * ©2008-2014 SpryMedia Ltd - datatables.net/license
  */
-(function(X,l,n){var L=function(h){var j=function(e){function o(a,b){var c=j.defaults.columns,d=a.aoColumns.length,c=h.extend({},j.models.oColumn,c,{sSortingClass:a.oClasses.sSortable,sSortingClassJUI:a.oClasses.sSortJUI,nTh:b?b:l.createElement("th"),sTitle:c.sTitle?c.sTitle:b?b.innerHTML:"",aDataSort:c.aDataSort?c.aDataSort:[d],mData:c.mData?c.oDefaults:d});a.aoColumns.push(c);if(a.aoPreSearchCols[d]===n||null===a.aoPreSearchCols[d])a.aoPreSearchCols[d]=h.extend({},j.models.oSearch);else if(c=a.aoPreSearchCols[d],
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-bDeferRender:null,bFilter:null,bInfo:null,bLengthChange:null,bPaginate:null,bProcessing:null,bServerSide:null,bSort:null,bSortClasses:null,bStateSave:null},oScroll:{bAutoCss:null,bCollapse:null,bInfinite:null,iBarWidth:0,iLoadGap:null,sX:null,sXInner:null,sY:null},oLanguage:{fnInfoCallback:null},oBrowser:{bScrollOversize:!1},aanFeatures:[],aoData:[],aiDisplay:[],aiDisplayMaster:[],aoColumns:[],aoHeader:[],aoFooter:[],asDataSearch:[],oPreviousSearch:{},aoPreSearchCols:[],aaSorting:null,aaSortingFixed:null,
-asStripeClasses:null,asDestroyStripes:[],sDestroyWidth:0,aoRowCallback:[],aoHeaderCallback:[],aoFooterCallback:[],aoDrawCallback:[],aoRowCreatedCallback:[],aoPreDrawCallback:[],aoInitComplete:[],aoStateSaveParams:[],aoStateLoadParams:[],aoStateLoaded:[],sTableId:"",nTable:null,nTHead:null,nTFoot:null,nTBody:null,nTableWrapper:null,bDeferLoading:!1,bInitialised:!1,aoOpenRows:[],sDom:null,sPaginationType:"two_button",iCookieDuration:0,sCookiePrefix:"",fnCookieCallback:null,aoStateSave:[],aoStateLoad:[],
-oLoadedState:null,sAjaxSource:null,sAjaxDataProp:null,bAjaxDataGet:!0,jqXHR:null,fnServerData:null,aoServerParams:[],sServerMethod:null,fnFormatNumber:null,aLengthMenu:null,iDraw:0,bDrawing:!1,iDrawError:-1,_iDisplayLength:10,_iDisplayStart:0,_iDisplayEnd:10,_iRecordsTotal:0,_iRecordsDisplay:0,bJUI:null,oClasses:{},bFiltered:!1,bSorted:!1,bSortCellsTop:null,oInit:null,aoDestroyCallback:[],fnRecordsTotal:function(){return this.oFeatures.bServerSide?parseInt(this._iRecordsTotal,10):this.aiDisplayMaster.length},
-fnRecordsDisplay:function(){return this.oFeatures.bServerSide?parseInt(this._iRecordsDisplay,10):this.aiDisplay.length},fnDisplayEnd:function(){return this.oFeatures.bServerSide?!1===this.oFeatures.bPaginate||-1==this._iDisplayLength?this._iDisplayStart+this.aiDisplay.length:Math.min(this._iDisplayStart+this._iDisplayLength,this._iRecordsDisplay):this._iDisplayEnd},oInstance:null,sInstance:null,iTabIndex:0,nScrollHead:null,nScrollFoot:null};j.ext=h.extend(!0,{},j.models.ext);h.extend(j.ext.oStdClasses,
-{sTable:"dataTable",sPagePrevEnabled:"paginate_enabled_previous",sPagePrevDisabled:"paginate_disabled_previous",sPageNextEnabled:"paginate_enabled_next",sPageNextDisabled:"paginate_disabled_next",sPageJUINext:"",sPageJUIPrev:"",sPageButton:"paginate_button",sPageButtonActive:"paginate_active",sPageButtonStaticDisabled:"paginate_button paginate_button_disabled",sPageFirst:"first",sPagePrevious:"previous",sPageNext:"next",sPageLast:"last",sStripeOdd:"odd",sStripeEven:"even",sRowEmpty:"dataTables_empty",
-sWrapper:"dataTables_wrapper",sFilter:"dataTables_filter",sInfo:"dataTables_info",sPaging:"dataTables_paginate paging_",sLength:"dataTables_length",sProcessing:"dataTables_processing",sSortAsc:"sorting_asc",sSortDesc:"sorting_desc",sSortable:"sorting",sSortableAsc:"sorting_asc_disabled",sSortableDesc:"sorting_desc_disabled",sSortableNone:"sorting_disabled",sSortColumn:"sorting_",sSortJUIAsc:"",sSortJUIDesc:"",sSortJUI:"",sSortJUIAscAllowed:"",sSortJUIDescAllowed:"",sSortJUIWrapper:"",sSortIcon:"",
-sScrollWrapper:"dataTables_scroll",sScrollHead:"dataTables_scrollHead",sScrollHeadInner:"dataTables_scrollHeadInner",sScrollBody:"dataTables_scrollBody",sScrollFoot:"dataTables_scrollFoot",sScrollFootInner:"dataTables_scrollFootInner",sFooterTH:"",sJUIHeader:"",sJUIFooter:""});h.extend(j.ext.oJUIClasses,j.ext.oStdClasses,{sPagePrevEnabled:"fg-button ui-button ui-state-default ui-corner-left",sPagePrevDisabled:"fg-button ui-button ui-state-default ui-corner-left ui-state-disabled",sPageNextEnabled:"fg-button ui-button ui-state-default ui-corner-right",
-sPageNextDisabled:"fg-button ui-button ui-state-default ui-corner-right ui-state-disabled",sPageJUINext:"ui-icon ui-icon-circle-arrow-e",sPageJUIPrev:"ui-icon ui-icon-circle-arrow-w",sPageButton:"fg-button ui-button ui-state-default",sPageButtonActive:"fg-button ui-button ui-state-default ui-state-disabled",sPageButtonStaticDisabled:"fg-button ui-button ui-state-default ui-state-disabled",sPageFirst:"first ui-corner-tl ui-corner-bl",sPageLast:"last ui-corner-tr ui-corner-br",sPaging:"dataTables_paginate fg-buttonset ui-buttonset fg-buttonset-multi ui-buttonset-multi paging_",
-sSortAsc:"ui-state-default",sSortDesc:"ui-state-default",sSortable:"ui-state-default",sSortableAsc:"ui-state-default",sSortableDesc:"ui-state-default",sSortableNone:"ui-state-default",sSortJUIAsc:"css_right ui-icon ui-icon-triangle-1-n",sSortJUIDesc:"css_right ui-icon ui-icon-triangle-1-s",sSortJUI:"css_right ui-icon ui-icon-carat-2-n-s",sSortJUIAscAllowed:"css_right ui-icon ui-icon-carat-1-n",sSortJUIDescAllowed:"css_right ui-icon ui-icon-carat-1-s",sSortJUIWrapper:"DataTables_sort_wrapper",sSortIcon:"DataTables_sort_icon",
-sScrollHead:"dataTables_scrollHead ui-state-default",sScrollFoot:"dataTables_scrollFoot ui-state-default",sFooterTH:"ui-state-default",sJUIHeader:"fg-toolbar ui-toolbar ui-widget-header ui-corner-tl ui-corner-tr ui-helper-clearfix",sJUIFooter:"fg-toolbar ui-toolbar ui-widget-header ui-corner-bl ui-corner-br ui-helper-clearfix"});h.extend(j.ext.oPagination,{two_button:{fnInit:function(e,j,m){var k=e.oLanguage.oPaginate,n=function(h){e.oApi._fnPageChange(e,h.data.action)&&m(e)},k=!e.bJUI?'<a class="'+
-e.oClasses.sPagePrevDisabled+'" tabindex="'+e.iTabIndex+'" role="button">'+k.sPrevious+'</a><a class="'+e.oClasses.sPageNextDisabled+'" tabindex="'+e.iTabIndex+'" role="button">'+k.sNext+"</a>":'<a class="'+e.oClasses.sPagePrevDisabled+'" tabindex="'+e.iTabIndex+'" role="button"><span class="'+e.oClasses.sPageJUIPrev+'"></span></a><a class="'+e.oClasses.sPageNextDisabled+'" tabindex="'+e.iTabIndex+'" role="button"><span class="'+e.oClasses.sPageJUINext+'"></span></a>';h(j).append(k);var l=h("a",j),
-k=l[0],l=l[1];e.oApi._fnBindAction(k,{action:"previous"},n);e.oApi._fnBindAction(l,{action:"next"},n);e.aanFeatures.p||(j.id=e.sTableId+"_paginate",k.id=e.sTableId+"_previous",l.id=e.sTableId+"_next",k.setAttribute("aria-controls",e.sTableId),l.setAttribute("aria-controls",e.sTableId))},fnUpdate:function(e){if(e.aanFeatures.p)for(var h=e.oClasses,j=e.aanFeatures.p,k,l=0,n=j.length;l<n;l++)if(k=j[l].firstChild)k.className=0===e._iDisplayStart?h.sPagePrevDisabled:h.sPagePrevEnabled,k=k.nextSibling,
-k.className=e.fnDisplayEnd()==e.fnRecordsDisplay()?h.sPageNextDisabled:h.sPageNextEnabled}},iFullNumbersShowPages:5,full_numbers:{fnInit:function(e,j,m){var k=e.oLanguage.oPaginate,l=e.oClasses,n=function(h){e.oApi._fnPageChange(e,h.data.action)&&m(e)};h(j).append('<a  tabindex="'+e.iTabIndex+'" class="'+l.sPageButton+" "+l.sPageFirst+'">'+k.sFirst+'</a><a  tabindex="'+e.iTabIndex+'" class="'+l.sPageButton+" "+l.sPagePrevious+'">'+k.sPrevious+'</a><span></span><a tabindex="'+e.iTabIndex+'" class="'+
-l.sPageButton+" "+l.sPageNext+'">'+k.sNext+'</a><a tabindex="'+e.iTabIndex+'" class="'+l.sPageButton+" "+l.sPageLast+'">'+k.sLast+"</a>");var t=h("a",j),k=t[0],l=t[1],r=t[2],t=t[3];e.oApi._fnBindAction(k,{action:"first"},n);e.oApi._fnBindAction(l,{action:"previous"},n);e.oApi._fnBindAction(r,{action:"next"},n);e.oApi._fnBindAction(t,{action:"last"},n);e.aanFeatures.p||(j.id=e.sTableId+"_paginate",k.id=e.sTableId+"_first",l.id=e.sTableId+"_previous",r.id=e.sTableId+"_next",t.id=e.sTableId+"_last")},
-fnUpdate:function(e,o){if(e.aanFeatures.p){var m=j.ext.oPagination.iFullNumbersShowPages,k=Math.floor(m/2),l=Math.ceil(e.fnRecordsDisplay()/e._iDisplayLength),n=Math.ceil(e._iDisplayStart/e._iDisplayLength)+1,t="",r,B=e.oClasses,u,M=e.aanFeatures.p,L=function(h){e.oApi._fnBindAction(this,{page:h+r-1},function(h){e.oApi._fnPageChange(e,h.data.page);o(e);h.preventDefault()})};-1===e._iDisplayLength?n=k=r=1:l<m?(r=1,k=l):n<=k?(r=1,k=m):n>=l-k?(r=l-m+1,k=l):(r=n-Math.ceil(m/2)+1,k=r+m-1);for(m=r;m<=k;m++)t+=
-n!==m?'<a tabindex="'+e.iTabIndex+'" class="'+B.sPageButton+'">'+e.fnFormatNumber(m)+"</a>":'<a tabindex="'+e.iTabIndex+'" class="'+B.sPageButtonActive+'">'+e.fnFormatNumber(m)+"</a>";m=0;for(k=M.length;m<k;m++)u=M[m],u.hasChildNodes()&&(h("span:eq(0)",u).html(t).children("a").each(L),u=u.getElementsByTagName("a"),u=[u[0],u[1],u[u.length-2],u[u.length-1]],h(u).removeClass(B.sPageButton+" "+B.sPageButtonActive+" "+B.sPageButtonStaticDisabled),h([u[0],u[1]]).addClass(1==n?B.sPageButtonStaticDisabled:
-B.sPageButton),h([u[2],u[3]]).addClass(0===l||n===l||-1===e._iDisplayLength?B.sPageButtonStaticDisabled:B.sPageButton))}}}});h.extend(j.ext.oSort,{"string-pre":function(e){"string"!=typeof e&&(e=null!==e&&e.toString?e.toString():"");return e.toLowerCase()},"string-asc":function(e,h){return e<h?-1:e>h?1:0},"string-desc":function(e,h){return e<h?1:e>h?-1:0},"html-pre":function(e){return e.replace(/<.*?>/g,"").toLowerCase()},"html-asc":function(e,h){return e<h?-1:e>h?1:0},"html-desc":function(e,h){return e<
-h?1:e>h?-1:0},"date-pre":function(e){e=Date.parse(e);if(isNaN(e)||""===e)e=Date.parse("01/01/1970 00:00:00");return e},"date-asc":function(e,h){return e-h},"date-desc":function(e,h){return h-e},"numeric-pre":function(e){return"-"==e||""===e?0:1*e},"numeric-asc":function(e,h){return e-h},"numeric-desc":function(e,h){return h-e}});h.extend(j.ext.aTypes,[function(e){if("number"===typeof e)return"numeric";if("string"!==typeof e)return null;var h,j=!1;h=e.charAt(0);if(-1=="0123456789-".indexOf(h))return null;
-for(var k=1;k<e.length;k++){h=e.charAt(k);if(-1=="0123456789.".indexOf(h))return null;if("."==h){if(j)return null;j=!0}}return"numeric"},function(e){var h=Date.parse(e);return null!==h&&!isNaN(h)||"string"===typeof e&&0===e.length?"date":null},function(e){return"string"===typeof e&&-1!=e.indexOf("<")&&-1!=e.indexOf(">")?"html":null}]);h.fn.DataTable=j;h.fn.dataTable=j;h.fn.dataTableSettings=j.settings;h.fn.dataTableExt=j.ext};"function"===typeof define&&define.amd?define(["jquery"],L):jQuery&&!jQuery.fn.dataTable&&
-L(jQuery)})(window,document);
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+overflow:"scroll"}).append(h('<div class="test"/>').css({width:"100%",height:10}))).appendTo("body"),c=b.find(".test");a.bScrollOversize=100===c[0].offsetWidth;a.bScrollbarLeft=1!==c.offset().left;b.remove()}function gb(a,b,c,d,e,f){var g,j=!1;c!==l&&(g=c,j=!0);for(;d!==e;)a.hasOwnProperty(d)&&(g=j?b(g,a[d],d,a):a[d],j=!0,d+=f);return g}function Aa(a,b){var c=p.defaults.column,d=a.aoColumns.length,c=h.extend({},p.models.oColumn,c,{nTh:b?b:O.createElement("th"),sTitle:c.sTitle?c.sTitle:b?b.innerHTML:
+"",aDataSort:c.aDataSort?c.aDataSort:[d],mData:c.mData?c.mData:d,idx:d});a.aoColumns.push(c);c=a.aoPreSearchCols;c[d]=h.extend({},p.models.oSearch,c[d]);fa(a,d,null)}function fa(a,b,c){var b=a.aoColumns[b],d=a.oClasses,e=h(b.nTh);if(!b.sWidthOrig){b.sWidthOrig=e.attr("width")||null;var f=(e.attr("style")||"").match(/width:\s*(\d+[pxem%]+)/);f&&(b.sWidthOrig=f[1])}c!==l&&null!==c&&(eb(c),G(p.defaults.column,c),c.mDataProp!==l&&!c.mData&&(c.mData=c.mDataProp),c.sType&&(b._sManualType=c.sType),c.className&&
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+a.oScroll;(""!==b.sY||""!==b.sX)&&W(a);u(a,null,"column-sizing",[a])}function ga(a,b){var c=X(a,"bVisible");return"number"===typeof c[b]?c[b]:null}function Y(a,b){var c=X(a,"bVisible"),c=h.inArray(b,c);return-1!==c?c:null}function Z(a){return X(a,"bVisible").length}function X(a,b){var c=[];h.map(a.aoColumns,function(a,e){a[b]&&c.push(e)});return c}function Da(a){var b=a.aoColumns,c=a.aoData,d=p.ext.type.detect,e,f,g,j,i,h,m,o,k;e=0;for(f=b.length;e<f;e++)if(m=b[e],k=[],!m.sType&&m._sManualType)m.sType=
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+c){return ab(this.cells(a,b,c))});r("cell().data()",function(a){var b=this.context,c=this[0];if(a===l)return b.length&&c.length?A(b[0],c[0].row,c[0].column):l;Ea(b[0],c[0].row,c[0].column,a);la(b[0],c[0].row,"data",c[0].column);return this});r("order()",function(a,b){var c=this.context;if(a===l)return 0!==c.length?c[0].aaSorting:l;"number"===typeof a?a=[[a,b]]:h.isArray(a[0])||(a=Array.prototype.slice.call(arguments));return this.iterator("table",function(b){b.aaSorting=a.slice()})});r("order.listener()",
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+c,bCaseInsensitive:null===d?!0:d}),1)})});v("columns().search()","column().search()",function(a,b,c,d){return this.iterator("column",function(e,f){var g=e.aoPreSearchCols;if(a===l)return g[f].sSearch;e.oFeatures.bFilter&&(h.extend(g[f],{sSearch:a+"",bRegex:null===b?!1:b,bSmart:null===c?!0:c,bCaseInsensitive:null===d?!0:d}),ca(e,e.oPreviousSearch,1))})});r("state()",function(){return this.context.length?this.context[0].oSavedState:null});r("state.clear()",function(){return this.iterator("table",function(a){a.fnStateSaveCallback.call(a.oInstance,
+a,{})})});r("state.loaded()",function(){return this.context.length?this.context[0].oLoadedState:null});r("state.save()",function(){return this.iterator("table",function(a){ta(a)})});p.versionCheck=p.fnVersionCheck=function(a){for(var b=p.version.split("."),a=a.split("."),c,d,e=0,f=a.length;e<f;e++)if(c=parseInt(b[e],10)||0,d=parseInt(a[e],10)||0,c!==d)return c>d;return!0};p.isDataTable=p.fnIsDataTable=function(a){var b=h(a).get(0),c=!1;h.each(p.settings,function(a,e){if(e.nTable===b||e.nScrollHead===
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+r("clear()",function(){return this.iterator("table",function(a){ja(a)})});r("settings()",function(){return new q(this.context,this.context)});r("data()",function(){return this.iterator("table",function(a){return C(a.aoData,"_aData")}).flatten()});r("destroy()",function(a){a=a||!1;return this.iterator("table",function(b){var c=b.nTableWrapper.parentNode,d=b.oClasses,e=b.nTable,f=b.nTBody,g=b.nTHead,j=b.nTFoot,i=h(e),f=h(f),l=h(b.nTableWrapper),m=h.map(b.aoData,function(a){return a.nTr}),o;b.bDestroying=
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+[];p.models={};p.models.oSearch={bCaseInsensitive:!0,sSearch:"",bRegex:!1,bSmart:!0};p.models.oRow={nTr:null,anCells:null,_aData:[],_aSortData:null,_aFilterData:null,_sFilterRow:null,_sRowStripe:"",src:null};p.models.oColumn={idx:null,aDataSort:null,asSorting:null,bSearchable:null,bSortable:null,bVisible:null,_sManualType:null,_bAttrSrc:!1,fnCreatedCell:null,fnGetData:null,fnSetData:null,mData:null,mRender:null,nTh:null,nTf:null,sClass:null,sContentPadding:null,sDefaultContent:null,sName:null,sSortDataType:"std",
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+fnCreatedRow:null,fnDrawCallback:null,fnFooterCallback:null,fnFormatNumber:function(a){return a.toString().replace(/\B(?=(\d{3})+(?!\d))/g,this.oLanguage.sThousands)},fnHeaderCallback:null,fnInfoCallback:null,fnInitComplete:null,fnPreDrawCallback:null,fnRowCallback:null,fnServerData:null,fnServerParams:null,fnStateLoadCallback:function(a){try{return JSON.parse((-1===a.iStateDuration?sessionStorage:localStorage).getItem("DataTables_"+a.sInstance+"_"+location.pathname))}catch(b){}},fnStateLoadParams:null,
+fnStateLoaded:null,fnStateSaveCallback:function(a,b){try{(-1===a.iStateDuration?sessionStorage:localStorage).setItem("DataTables_"+a.sInstance+"_"+location.pathname,JSON.stringify(b))}catch(c){}},fnStateSaveParams:null,iStateDuration:7200,iDeferLoading:null,iDisplayLength:10,iDisplayStart:0,iTabIndex:0,oClasses:{},oLanguage:{oAria:{sSortAscending:": activate to sort column ascending",sSortDescending:": activate to sort column descending"},oPaginate:{sFirst:"First",sLast:"Last",sNext:"Next",sPrevious:"Previous"},
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+sScrollX:"",sScrollXInner:"",sScrollY:"",sServerMethod:"GET",renderer:null};T(p.defaults);p.defaults.column={aDataSort:null,iDataSort:-1,asSorting:["asc","desc"],bSearchable:!0,bSortable:!0,bVisible:!0,fnCreatedCell:null,mData:null,mRender:null,sCellType:"td",sClass:"",sContentPadding:"",sDefaultContent:null,sName:"",sSortDataType:"std",sTitle:null,sType:null,sWidth:null};T(p.defaults.column);p.models.oSettings={oFeatures:{bAutoWidth:null,bDeferRender:null,bFilter:null,bInfo:null,bLengthChange:null,
+bPaginate:null,bProcessing:null,bServerSide:null,bSort:null,bSortMulti:null,bSortClasses:null,bStateSave:null},oScroll:{bCollapse:null,iBarWidth:0,sX:null,sXInner:null,sY:null},oLanguage:{fnInfoCallback:null},oBrowser:{bScrollOversize:!1,bScrollbarLeft:!1},ajax:null,aanFeatures:[],aoData:[],aiDisplay:[],aiDisplayMaster:[],aoColumns:[],aoHeader:[],aoFooter:[],oPreviousSearch:{},aoPreSearchCols:[],aaSorting:null,aaSortingFixed:[],asStripeClasses:null,asDestroyStripes:[],sDestroyWidth:0,aoRowCallback:[],
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+fnServerData:null,aoServerParams:[],sServerMethod:null,fnFormatNumber:null,aLengthMenu:null,iDraw:0,bDrawing:!1,iDrawError:-1,_iDisplayLength:10,_iDisplayStart:0,_iRecordsTotal:0,_iRecordsDisplay:0,bJUI:null,oClasses:{},bFiltered:!1,bSorted:!1,bSortCellsTop:null,oInit:null,aoDestroyCallback:[],fnRecordsTotal:function(){return"ssp"==z(this)?1*this._iRecordsTotal:this.aiDisplayMaster.length},fnRecordsDisplay:function(){return"ssp"==z(this)?1*this._iRecordsDisplay:this.aiDisplay.length},fnDisplayEnd:function(){var a=
+this._iDisplayLength,b=this._iDisplayStart,c=b+a,d=this.aiDisplay.length,e=this.oFeatures,f=e.bPaginate;return e.bServerSide?!1===f||-1===a?b+d:Math.min(b+a,this._iRecordsDisplay):!f||c>d||-1===a?d:c},oInstance:null,sInstance:null,iTabIndex:0,nScrollHead:null,nScrollFoot:null,aLastSort:[],oPlugins:{}};p.ext=t={classes:{},errMode:"alert",feature:[],search:[],internal:{},legacy:{ajax:null},pager:{},renderer:{pageButton:{},header:{}},order:{},type:{detect:[],search:{},order:{}},_unique:0,fnVersionCheck:p.fnVersionCheck,
+iApiIndex:0,oJUIClasses:{},sVersion:p.version};h.extend(t,{afnFiltering:t.search,aTypes:t.type.detect,ofnSearch:t.type.search,oSort:t.type.order,afnSortData:t.order,aoFeatures:t.feature,oApi:t.internal,oStdClasses:t.classes,oPagination:t.pager});h.extend(p.ext.classes,{sTable:"dataTable",sNoFooter:"no-footer",sPageButton:"paginate_button",sPageButtonActive:"current",sPageButtonDisabled:"disabled",sStripeOdd:"odd",sStripeEven:"even",sRowEmpty:"dataTables_empty",sWrapper:"dataTables_wrapper",sFilter:"dataTables_filter",
+sInfo:"dataTables_info",sPaging:"dataTables_paginate paging_",sLength:"dataTables_length",sProcessing:"dataTables_processing",sSortAsc:"sorting_asc",sSortDesc:"sorting_desc",sSortable:"sorting",sSortableAsc:"sorting_asc_disabled",sSortableDesc:"sorting_desc_disabled",sSortableNone:"sorting_disabled",sSortColumn:"sorting_",sFilterInput:"",sLengthSelect:"",sScrollWrapper:"dataTables_scroll",sScrollHead:"dataTables_scrollHead",sScrollHeadInner:"dataTables_scrollHeadInner",sScrollBody:"dataTables_scrollBody",
+sScrollFoot:"dataTables_scrollFoot",sScrollFootInner:"dataTables_scrollFootInner",sHeaderTH:"",sFooterTH:"",sSortJUIAsc:"",sSortJUIDesc:"",sSortJUI:"",sSortJUIAscAllowed:"",sSortJUIDescAllowed:"",sSortJUIWrapper:"",sSortIcon:"",sJUIHeader:"",sJUIFooter:""});var ya="",ya="",E=ya+"ui-state-default",ea=ya+"css_right ui-icon ui-icon-",Ub=ya+"fg-toolbar ui-toolbar ui-widget-header ui-helper-clearfix";h.extend(p.ext.oJUIClasses,p.ext.classes,{sPageButton:"fg-button ui-button "+E,sPageButtonActive:"ui-state-disabled",
+sPageButtonDisabled:"ui-state-disabled",sPaging:"dataTables_paginate fg-buttonset ui-buttonset fg-buttonset-multi ui-buttonset-multi paging_",sSortAsc:E+" sorting_asc",sSortDesc:E+" sorting_desc",sSortable:E+" sorting",sSortableAsc:E+" sorting_asc_disabled",sSortableDesc:E+" sorting_desc_disabled",sSortableNone:E+" sorting_disabled",sSortJUIAsc:ea+"triangle-1-n",sSortJUIDesc:ea+"triangle-1-s",sSortJUI:ea+"carat-2-n-s",sSortJUIAscAllowed:ea+"carat-1-n",sSortJUIDescAllowed:ea+"carat-1-s",sSortJUIWrapper:"DataTables_sort_wrapper",
+sSortIcon:"DataTables_sort_icon",sScrollHead:"dataTables_scrollHead "+E,sScrollFoot:"dataTables_scrollFoot "+E,sHeaderTH:E,sFooterTH:E,sJUIHeader:Ub+" ui-corner-tl ui-corner-tr",sJUIFooter:Ub+" ui-corner-bl ui-corner-br"});var Lb=p.ext.pager;h.extend(Lb,{simple:function(){return["previous","next"]},full:function(){return["first","previous","next","last"]},simple_numbers:function(a,b){return["previous",Ua(a,b),"next"]},full_numbers:function(a,b){return["first","previous",Ua(a,b),"next","last"]},_numbers:Ua,
+numbers_length:7});h.extend(!0,p.ext.renderer,{pageButton:{_:function(a,b,c,d,e,f){var g=a.oClasses,j=a.oLanguage.oPaginate,i,l,m=0,o=function(b,d){var k,p,r,q,s=function(b){Ra(a,b.data.action,true)};k=0;for(p=d.length;k<p;k++){q=d[k];if(h.isArray(q)){r=h("<"+(q.DT_el||"div")+"/>").appendTo(b);o(r,q)}else{l=i="";switch(q){case "ellipsis":b.append("<span>&hellip;</span>");break;case "first":i=j.sFirst;l=q+(e>0?"":" "+g.sPageButtonDisabled);break;case "previous":i=j.sPrevious;l=q+(e>0?"":" "+g.sPageButtonDisabled);
+break;case "next":i=j.sNext;l=q+(e<f-1?"":" "+g.sPageButtonDisabled);break;case "last":i=j.sLast;l=q+(e<f-1?"":" "+g.sPageButtonDisabled);break;default:i=q+1;l=e===q?g.sPageButtonActive:""}if(i){r=h("<a>",{"class":g.sPageButton+" "+l,"aria-controls":a.sTableId,"data-dt-idx":m,tabindex:a.iTabIndex,id:c===0&&typeof q==="string"?a.sTableId+"_"+q:null}).html(i).appendTo(b);Ta(r,{action:q},s);m++}}}};try{var k=h(O.activeElement).data("dt-idx");o(h(b).empty(),d);k!==null&&h(b).find("[data-dt-idx="+k+"]").focus()}catch(p){}}}});
+var va=function(a,b,c,d){if(!a||"-"===a)return-Infinity;b&&(a=Pb(a,b));a.replace&&(c&&(a=a.replace(c,"")),d&&(a=a.replace(d,"")));return 1*a};h.extend(t.type.order,{"date-pre":function(a){return Date.parse(a)||0},"html-pre":function(a){return H(a)?"":a.replace?a.replace(/<.*?>/g,"").toLowerCase():a+""},"string-pre":function(a){return H(a)?"":"string"===typeof a?a.toLowerCase():!a.toString?"":a.toString()},"string-asc":function(a,b){return a<b?-1:a>b?1:0},"string-desc":function(a,b){return a<b?1:a>
+b?-1:0}});cb("");h.extend(p.ext.type.detect,[function(a,b){var c=b.oLanguage.sDecimal;return Xa(a,c)?"num"+c:null},function(a){if(a&&(!Yb.test(a)||!Zb.test(a)))return null;var b=Date.parse(a);return null!==b&&!isNaN(b)||H(a)?"date":null},function(a,b){var c=b.oLanguage.sDecimal;return Xa(a,c,!0)?"num-fmt"+c:null},function(a,b){var c=b.oLanguage.sDecimal;return Qb(a,c)?"html-num"+c:null},function(a,b){var c=b.oLanguage.sDecimal;return Qb(a,c,!0)?"html-num-fmt"+c:null},function(a){return H(a)||"string"===
+typeof a&&-1!==a.indexOf("<")?"html":null}]);h.extend(p.ext.type.search,{html:function(a){return H(a)?a:"string"===typeof a?a.replace(Nb," ").replace(wa,""):""},string:function(a){return H(a)?a:"string"===typeof a?a.replace(Nb," "):a}});h.extend(!0,p.ext.renderer,{header:{_:function(a,b,c,d){h(a.nTable).on("order.dt.DT",function(e,f,g,h){if(a===f){e=c.idx;b.removeClass(c.sSortingClass+" "+d.sSortAsc+" "+d.sSortDesc).addClass(h[e]=="asc"?d.sSortAsc:h[e]=="desc"?d.sSortDesc:c.sSortingClass)}})},jqueryui:function(a,
+b,c,d){var e=c.idx;h("<div/>").addClass(d.sSortJUIWrapper).append(b.contents()).append(h("<span/>").addClass(d.sSortIcon+" "+c.sSortingClassJUI)).appendTo(b);h(a.nTable).on("order.dt.DT",function(f,g,h,i){if(a===g){b.removeClass(d.sSortAsc+" "+d.sSortDesc).addClass(i[e]=="asc"?d.sSortAsc:i[e]=="desc"?d.sSortDesc:c.sSortingClass);b.find("span."+d.sSortIcon).removeClass(d.sSortJUIAsc+" "+d.sSortJUIDesc+" "+d.sSortJUI+" "+d.sSortJUIAscAllowed+" "+d.sSortJUIDescAllowed).addClass(i[e]=="asc"?d.sSortJUIAsc:
+i[e]=="desc"?d.sSortJUIDesc:c.sSortingClassJUI)}})}}});p.render={number:function(a,b,c,d){return{display:function(e){var f=0>e?"-":"",e=Math.abs(parseFloat(e)),g=parseInt(e,10),e=c?b+(e-g).toFixed(c).substring(2):"";return f+(d||"")+g.toString().replace(/\B(?=(\d{3})+(?!\d))/g,a)+e}}}};h.extend(p.ext.internal,{_fnExternApiFunc:Mb,_fnBuildAjax:na,_fnAjaxUpdate:jb,_fnAjaxParameters:sb,_fnAjaxUpdateDraw:tb,_fnAjaxDataSrc:oa,_fnAddColumn:Aa,_fnColumnOptions:fa,_fnAdjustColumnSizing:V,_fnVisibleToColumnIndex:ga,
+_fnColumnIndexToVisible:Y,_fnVisbleColumns:Z,_fnGetColumns:X,_fnColumnTypes:Da,_fnApplyColumnDefs:hb,_fnHungarianMap:T,_fnCamelToHungarian:G,_fnLanguageCompat:N,_fnBrowserDetect:fb,_fnAddData:I,_fnAddTr:ha,_fnNodeToDataIndex:function(a,b){return b._DT_RowIndex!==l?b._DT_RowIndex:null},_fnNodeToColumnIndex:function(a,b,c){return h.inArray(c,a.aoData[b].anCells)},_fnGetCellData:A,_fnSetCellData:Ea,_fnSplitObjNotation:Ga,_fnGetObjectDataFn:U,_fnSetObjectDataFn:Ba,_fnGetDataMaster:Ha,_fnClearTable:ja,
+_fnDeleteIndex:ka,_fnInvalidateRow:la,_fnGetRowElements:ia,_fnCreateTr:Fa,_fnBuildHead:ib,_fnDrawHead:ba,_fnDraw:K,_fnReDraw:L,_fnAddOptionsHtml:lb,_fnDetectHeader:aa,_fnGetUniqueThs:ma,_fnFeatureHtmlFilter:nb,_fnFilterComplete:ca,_fnFilterCustom:wb,_fnFilterColumn:vb,_fnFilter:ub,_fnFilterCreateSearch:Na,_fnEscapeRegex:Oa,_fnFilterData:xb,_fnFeatureHtmlInfo:qb,_fnUpdateInfo:Ab,_fnInfoMacros:Bb,_fnInitialise:ra,_fnInitComplete:pa,_fnLengthChange:Pa,_fnFeatureHtmlLength:mb,_fnFeatureHtmlPaginate:rb,
+_fnPageChange:Ra,_fnFeatureHtmlProcessing:ob,_fnProcessingDisplay:B,_fnFeatureHtmlTable:pb,_fnScrollDraw:W,_fnApplyToChildren:F,_fnCalculateColumnWidths:Ca,_fnThrottle:Ma,_fnConvertToWidth:Cb,_fnScrollingWidthAdjust:Eb,_fnGetWidestNode:Db,_fnGetMaxLenString:Fb,_fnStringToCss:s,_fnScrollBarWidth:Gb,_fnSortFlatten:R,_fnSort:kb,_fnSortAria:Ib,_fnSortListener:Sa,_fnSortAttachListener:Ka,_fnSortingClasses:sa,_fnSortData:Hb,_fnSaveState:ta,_fnLoadState:Jb,_fnSettingsFromNode:ua,_fnLog:P,_fnMap:D,_fnBindAction:Ta,
+_fnCallbackReg:x,_fnCallbackFire:u,_fnLengthOverflow:Qa,_fnRenderer:La,_fnDataSource:z,_fnRowAttributes:Ia,_fnCalculateEnd:function(){}});h.fn.dataTable=p;h.fn.dataTableSettings=p.settings;h.fn.dataTableExt=p.ext;h.fn.DataTable=function(a){return h(this).dataTable(a).api()};h.each(p,function(a,b){h.fn.DataTable[a]=b});return h.fn.dataTable};"function"===typeof define&&define.amd?define("datatables",["jquery"],N):"object"===typeof exports?N(require("jquery")):jQuery&&!jQuery.fn.dataTable&&N(jQuery)})(window,
+document);

inst/www/shared/datatables/upgrade1.10.txt

@@ -0,0 +1,95 @@
+aaData	data
+aaSorting	order
+aaSortingFixed	orderFixed
+aDataSort	columns.orderData
+aLengthMenu	lengthMenu
+aoSearchCols	searchCols
+asSorting	columns.orderSequence
+asStripeClasses	stripeClasses
+bAutoWidth	autoWidth
+bDeferRender	deferRender
+bDestroy	destroy
+bFilter	searching
+bInfo	info
+bJQueryUI	jQueryUI
+bLengthChange	lengthChange
+bPaginate	paging
+bProcessing	processing
+bRetrieve	retrieve
+bScrollAutoCss	Removed	
+bScrollCollapse	scrollCollapse
+bScrollInfinite	Removed	
+bSearchable	columns.searchable
+bServerSide	serverSide
+bSort	ordering
+bSortable	columns.orderable
+bSortCellsTop	orderCellsTop
+bSortClasses	orderClasses
+bStateSave	stateSave
+bUseRendered	Removed
+bVisible	columns.visible
+fnCookieCallback	Removed	
+fnCreatedCell	columns.createdCell
+fnCreatedRow	createdRow
+fnDrawCallback	drawCallback
+fnFooterCallback	footerCallback
+fnFormatNumber	formatNumber
+fnHeaderCallback	headerCallback
+fnInfoCallback	infoCallback
+fnInitComplete	initComplete
+fnPreDrawCallback	preDrawCallback
+fnRender	Removed
+fnRowCallback	rowCallback
+fnServerData	ajax
+fnServerParams	ajax
+fnStateLoad	stateLoadCallback
+fnStateLoaded	stateLoaded
+fnStateLoadParams	stateLoadParams
+fnStateSave	stateSaveCallback
+fnStateSaveParams	stateSaveParams
+iCookieDuration	stateDuration
+iDataSort	columns.orderData
+iDeferLoading	deferLoading
+iDisplayLength	pageLength
+iDisplayStart	displayStart
+iScrollLoadGap	Removed	
+iTabIndex	tabIndex
+mData	columns.data
+mRender	columns.render
+oLanguage.oAria.sSortAscending	language.aria.sortAscending
+oLanguage.oAria.sSortDescending	language.aria.sortDescending
+oLanguage.oPaginate.sFirst	language.paginate.first
+oLanguage.oPaginate.sLast	language.paginate.last
+oLanguage.oPaginate.sNext	language.paginate.next
+oLanguage.oPaginate.sPrevious	language.paginate.previous
+oLanguage.sEmptyTable	language.emptyTable
+oLanguage.sInfo	language.info
+oLanguage.sInfoEmpty	language.infoEmpty
+oLanguage.sInfoFiltered	language.infoFiltered
+oLanguage.sInfoPostFix	language.infoPostFix
+oLanguage.sInfoThousands	language.thousands
+oLanguage.sLengthMenu	language.lengthMenu
+oLanguage.sLoadingRecords	language.loadingRecords
+oLanguage.sProcessing	language.processing
+oLanguage.sSearch	language.search
+oLanguage.sUrl	language.url
+oLanguage.sZeroRecords	language.zeroRecords
+oSearch	search
+sAjaxDataProp	ajax.dataSrc
+sAjaxSource	ajax
+sCellType	columns.cellType
+sClass	columns.className
+sContentPadding	contentPadding
+sCookiePrefix	Removed	
+sDefaultContent	columns.defaultContent
+sDom	dom
+sName	columns.name
+sPaginationType	pagingType
+sScrollX	scrollX
+sScrollXInner	scrollXInner
+sScrollY	scrollY
+sServerMethod	ajax
+sSortDataType	columns.orderDataType
+sTitle	columns.title
+sType	columns.type
+sWidth	columns.width

inst/www/shared/json2-min.js

@@ -0,0 +1,22 @@
+("object"!=typeof JSON||JSON.stringify("\uf977").length>3)&&(JSON={}),function(){"use strict"
+function f(t){return 10>t?"0"+t:t}function quote(t){return escapable.lastIndex=0,escapable.test(t)?'"'+t.replace(escapable,function(t){var e=meta[t]
+return"string"==typeof e?e:"\\u"+("0000"+t.charCodeAt(0).toString(16)).slice(-4)})+'"':'"'+t+'"'}function str(t,e){var n,r,o,f,u,p=gap,a=e[t]
+switch(a&&"object"==typeof a&&"function"==typeof a.toJSON&&(a=a.toJSON(t)),"function"==typeof rep&&(a=rep.call(e,t,a)),typeof a){case"string":return quote(a)
+case"number":return isFinite(a)?a+"":"null"
+case"boolean":case"null":return a+""
+case"object":if(!a)return"null"
+if(gap+=indent,u=[],"[object Array]"===Object.prototype.toString.apply(a)){for(f=a.length,n=0;f>n;n+=1)u[n]=str(n,a)||"null"
+return o=0===u.length?"[]":gap?"[\n"+gap+u.join(",\n"+gap)+"\n"+p+"]":"["+u.join(",")+"]",gap=p,o}if(rep&&"object"==typeof rep)for(f=rep.length,n=0;f>n;n+=1)"string"==typeof rep[n]&&(r=rep[n],o=str(r,a),o&&u.push(quote(r)+(gap?": ":":")+o))
+else for(r in a)Object.prototype.hasOwnProperty.call(a,r)&&(o=str(r,a),o&&u.push(quote(r)+(gap?": ":":")+o))
+return o=0===u.length?"{}":gap?"{\n"+gap+u.join(",\n"+gap)+"\n"+p+"}":"{"+u.join(",")+"}",gap=p,o}}"function"!=typeof Date.prototype.toJSON&&(Date.prototype.toJSON=function(){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null},String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(){return this.valueOf()})
+var cx,escapable,gap,indent,meta,rep
+"function"!=typeof JSON.stringify&&(escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,meta={"\b":"\\b","	":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},JSON.stringify=function(t,e,n){var r
+if(gap="",indent="","number"==typeof n)for(r=0;n>r;r+=1)indent+=" "
+else"string"==typeof n&&(indent=n)
+if(rep=e,e&&"function"!=typeof e&&("object"!=typeof e||"number"!=typeof e.length))throw Error("JSON.stringify")
+return str("",{"":t})}),"function"!=typeof JSON.parse&&(cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,JSON.parse=function(text,reviver){function walk(t,e){var n,r,o=t[e]
+if(o&&"object"==typeof o)for(n in o)Object.prototype.hasOwnProperty.call(o,n)&&(r=walk(o,n),void 0!==r?o[n]=r:delete o[n])
+return reviver.call(t,e,o)}var j
+if(text+="",cx.lastIndex=0,cx.test(text)&&(text=text.replace(cx,function(t){return"\\u"+("0000"+t.charCodeAt(0).toString(16)).slice(-4)})),/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,"")))return j=eval("("+text+")"),"function"==typeof reviver?walk({"":j},""):j
+throw new SyntaxError("JSON.parse")})}()
+

inst/www/shared/shiny-showcase.js

@@ -85,6 +85,11 @@
       var code = document.getElementById(srcfile.replace(/\./g, "_") + "_code");
       var start = findTextPoint(code, ref[0], ref[4]);
       var end = findTextPoint(code, ref[2], ref[5]);
+      
+      // If the insertion point can't be found, bail out now
+      if (start.element === null || end.element === null)
+         return;
+
       var range = document.createRange();
       // If the text points are inside different <SPAN>s, we may not be able to
       // surround them without breaking apart the elements to keep the DOM tree

inst/www/shared/shiny.css

@@ -96,6 +96,47 @@ span.jslider {
   transition: none;
 }
 
+.shiny-progress-container {
+  position: fixed;
+  top: 0px;
+  width: 100%;
+}
+
+.shiny-progress .progress {
+  position: absolute;
+  width: 100%;
+  top: 0px;
+  height: 3px;
+  margin: 0px;
+}
+
+.shiny-progress .bar {
+  opacity: 0.6;
+  transition-duration: 250ms;
+}
+
+.shiny-progress .progress-text {
+  position: absolute;
+  right: 10px;
+  height: 18px;
+  width: 240px;
+  background-color: #eef8ff;
+  margin: 0px;
+  padding: 2px 3px;
+  opacity: 0.85;
+}
+
+.shiny-progress .progress-text .progress-message {
+  padding: 0px 3px;
+  font-weight: bold;
+  font-size: 90%;
+}
+
+.shiny-progress .progress-text .progress-detail {
+  padding: 0px 3px;
+  font-size: 80%;
+}
+
 .crosshair {
   cursor: crosshair;
 }

inst/www/shared/shiny.js

@@ -24,6 +24,15 @@
     return val.replace(/([!"#$%&'()*+,.\/:;<=>?@\[\\\]^`{|}~])/g, '\\$1');
   };
 
+  function escapeHTML(str) {
+    return str.replace(/&/g, "&amp;")
+              .replace(/</g, "&lt;")
+              .replace(/>/g, "&gt;")
+              .replace(/"/g, "&quot;")
+              .replace(/'/g, "&#039;")
+              .replace(/\//g,"&#x2F;");
+  }
+
   function randomId() {
     return Math.floor(0x100000000 + (Math.random() * 0xF00000000)).toString(16);
   }
@@ -34,9 +43,14 @@
     var x;
     if (el.currentStyle)
       x = el.currentStyle[styleProp];
-    else if (window.getComputedStyle)
-      x = document.defaultView.getComputedStyle(el, null)
-          .getPropertyValue(styleProp);
+    else if (window.getComputedStyle) {
+      // getComputedStyle can return null when we're inside a hidden iframe on
+      // Firefox; don't attempt to retrieve style props in this case.
+      // https://bugzilla.mozilla.org/show_bug.cgi?id=548397
+      var style = document.defaultView.getComputedStyle(el, null);
+      if (style)
+        x = style.getPropertyValue(styleProp);
+    }
     return x;
   }
 
@@ -67,6 +81,28 @@
     throw "Blob doesn't support slice";
   }
 
+  // Given an element and a function(width, height), returns a function(). When
+  // the output function is called, it calls the input function with the offset
+  // width and height of the input element--but only if the size of the element
+  // is non-zero and the size is different than the last time the output
+  // function was called.
+  //
+  // Basically we are trying to filter out extraneous calls to func, so that
+  // when the window size changes or whatever, we don't run resize logic for
+  // elements that haven't actually changed size or aren't visible anyway.
+  function makeResizeFilter(el, func) {
+    var lastSize = {};
+    return function() {
+      var size = { w: el.offsetWidth, h: el.offsetHeight };
+      if (size.w === 0 && size.h === 0)
+        return;
+      if (size.w === lastSize.w && size.h === lastSize.h)
+        return;
+      lastSize = size;
+      func(size.w, size.h);
+    };
+  }
+
   var _BlobBuilder = window.BlobBuilder || window.WebKitBlobBuilder ||
       window.MozBlobBuilder || window.MSBlobBuilder;
 
@@ -881,13 +917,10 @@
     });
 
     addMessageHandler('progress', function(message) {
-      $(document.documentElement).addClass('shiny-busy');
-      for (var i = 0; i < message.length; i++) {
-        var key = message[i];
-        var binding = this.$bindings[key];
-        if (binding && binding.showProgress) {
-          binding.showProgress(true);
-        }
+      if (message.type && message.message) {
+        var handler = progressHandlers[message.type];
+        if (handler)
+          handler.call(this, message.message);
       }
     });
 
@@ -919,6 +952,96 @@
       this.config = message;
     });
 
+
+    // Progress reporting ====================================================
+
+    var progressHandlers = {
+      // Progress for a particular object
+      binding: function(message) {
+        $(document.documentElement).addClass('shiny-busy');
+        var key = message.id;
+        var binding = this.$bindings[key];
+        if (binding && binding.showProgress) {
+          binding.showProgress(true);
+        }
+      },
+      // Open a page-level progress bar
+      open: function(message) {
+        // Add progress container (for all progress items) if not already present
+        var $container = $('.shiny-progress-container');
+        if ($container.length === 0) {
+          $container = $('<div class="shiny-progress-container"></div>');
+          $('body').append($container);
+        }
+
+        // Add div for just this progress ID
+        var depth = $('.shiny-progress.open').length;
+        var $progress = $(progressHandlers.progressHTML);
+        $progress.attr('id', message.id);
+        $container.append($progress);
+
+        // Stack bars
+        var $progressBar = $progress.find('.progress');
+        $progressBar.css('top', depth * $progressBar.height() + 'px');
+
+        // Stack text objects
+        var $progressText = $progress.find('.progress-text');
+        $progressText.css('top', 3 * $progressBar.height() +
+          depth * $progressText.outerHeight() + 'px');
+
+        $progress.hide();
+      },
+
+      // Update page-level progress bar
+      update: function(message) {
+        var $progress = $('#' + message.id + '.shiny-progress');
+        if (typeof(message.message) !== 'undefined') {
+          $progress.find('.progress-message').text(message.message);
+        }
+        if (typeof(message.detail) !== 'undefined') {
+          $progress.find('.progress-detail').text(message.detail);
+        }
+        if (typeof(message.value) !== 'undefined') {
+          if (message.value !== null) {
+            $progress.find('.progress').show();
+            $progress.find('.bar').width((message.value*100) + '%');
+          }
+          else {
+            $progress.find('.progress').hide();
+          }
+        }
+
+        $progress.fadeIn();
+      },
+
+      // Close page-level progress bar
+      close: function(message) {
+        var $progress = $('#' + message.id + '.shiny-progress');
+        $progress.removeClass('open');
+
+        $progress.fadeOut({
+          complete: function() {
+            $progress.remove();
+
+            // If this was the last shiny-progress, remove container
+            if ($('.shiny-progress').length === 0)
+              $('.shiny-progress-container').remove();
+          }
+        });
+      },
+
+      progressHTML: '<div class="shiny-progress open">' +
+        '<div class="progress progress-striped active"><div class="bar"></div></div>' +
+        '<div class="progress-text">' +
+          '<span class="progress-message">foo</span>' +
+          '<span class="progress-detail"></span>' +
+        '</div>' +
+      '</div>'
+    };
+
+    exports.progressHandlers = progressHandlers;
+
+
   }).call(ShinyApp.prototype);
 
 
@@ -1255,13 +1378,17 @@
   });
   outputBindings.register(htmlOutputBinding, 'shiny.htmlOutput');
 
-  // Render HTML in a DOM element, inserting singletons into head as needed
-  exports.renderHtml = function(html, el, dependencies) {
+  var renderDependencies = exports.renderDependencies = function(dependencies) {
     if (dependencies) {
       $.each(dependencies, function(i, dep) {
         renderDependency(dep);
       });
     }
+  };
+
+  // Render HTML in a DOM element, inserting singletons into head as needed
+  exports.renderHtml = function(html, el, dependencies) {
+    renderDependencies(dependencies);
     return singletons.renderHtml(html, el);
   };
 
@@ -1299,18 +1426,41 @@
     if (dep.stylesheet) {
       var stylesheets = $.map(asArray(dep.stylesheet), function(stylesheet) {
         return $("<link rel='stylesheet' type='text/css'>")
-          .attr("href", href + "/" + stylesheet);
+          .attr("href", href + "/" + encodeURI(stylesheet));
       });
       $head.append(stylesheets);
     }
 
     if (dep.script) {
       var scripts = $.map(asArray(dep.script), function(scriptName) {
-        return $("<script>").attr("src", href + "/" + scriptName);
+        return $("<script>").attr("src", href + "/" + encodeURI(scriptName));
       });
       $head.append(scripts);
     }
 
+    if (dep.attachment) {
+      // dep.attachment might be a single string, an array, or an object.
+      var attachments = dep.attachment;
+      if (typeof(attachments) === "string")
+        attachments = [attachments];
+      if ($.isArray(attachments)) {
+        // The contract for attachments is that arrays of attachments are
+        // addressed using 1-based indexes. Convert this array to an object.
+        var tmp = {};
+        $.each(attachments, function(index, attachment) {
+          tmp[(index + 1) + ""] = attachment;
+        });
+        attachments = tmp;
+      }
+
+      var attach = $.map(attachments, function(attachment, key) {
+        return $("<link rel='attachment'>")
+          .attr("id", dep.name + "-" + key + "-attachment")
+          .attr("href", href + "/" + encodeURI(attachment));
+      });
+      $head.append(attach);
+    }
+
     if (dep.head) {
       var $newHead = $("<head></head>");
       $newHead.html(dep.head);
@@ -1424,9 +1574,12 @@
       }).join('');
       header = '<thead><tr>' + header + '</tr></thead>';
       var footer = '';
-      if (data.options === null || data.options.bFilter !== false) {
+      if (data.options === null || data.options.searching !== false) {
         footer = $.map(colnames, function(x) {
-          return '<th><input type="text" placeholder="' + x + '" /></th>';
+          // placeholder needs to be escaped (and HTML tags are stripped off)
+          return '<th><input type="text" placeholder="' +
+                 escapeHTML(x.replace(/(<([^>]+)>)/ig, '')) +
+                 '" /></th>';
         }).join('');
         footer = '<tfoot>' + footer + '</tfoot>';
       }
@@ -1441,13 +1594,21 @@
           data.options[x] = eval('(' + data.options[x] + ')');
         });
 
-      var oTable = $(el).children("table").dataTable($.extend({
-        "bProcessing": true,
-        "bServerSide": true,
-        "aaSorting": [],
-        "bSortClasses": false,
-        "iDisplayLength": 25,
-        "sAjaxSource": data.action
+      // caseInsensitive searching? default true
+      var searchCI = data.options === null || typeof(data.options.search) === 'undefined' ||
+                     data.options.search.caseInsensitive !== false;
+      var oTable = $(el).children("table").DataTable($.extend({
+        "processing": true,
+        "serverSide": true,
+        "order": [],
+        "orderClasses": false,
+        "pageLength": 25,
+        "ajax": {
+          "url": data.action,
+          "data": function(d) {
+            d.search.caseInsensitive = searchCI;
+          }
+        }
       }, data.options));
       // the table object may need post-processing
       if (typeof data.callback === 'string') {
@@ -1459,16 +1620,18 @@
       // use debouncing for searching boxes
       $el.find('label input').first().unbind('keyup')
            .keyup(debounce(data.searchDelay, function() {
-              oTable.fnFilter(this.value);
+              oTable.search(this.value).draw();
             }));
       var searchInputs = $el.find("tfoot input");
       if (searchInputs.length > 0) {
-        $.each(oTable.fnSettings().aoColumns, function(i, x) {
+        // this is a little weird: aoColumns/bSearchable are still in DT 1.10
+        // https://github.com/DataTables/DataTables/issues/388
+        $.each(oTable.settings()[0].aoColumns, function(i, x) {
           // hide the text box if not searchable
           if (!x.bSearchable) searchInputs.eq(i).hide();
         });
         searchInputs.keyup(debounce(data.searchDelay, function() {
-          oTable.fnFilter(this.value, searchInputs.index(this));
+          oTable.column(searchInputs.index(this)).search(this.value).draw();
         }));
       }
       // FIXME: ugly scrollbars in tab panels b/c Bootstrap uses 'visible: auto'
@@ -2068,7 +2231,7 @@
     },
     setValue: function(el, value) {
       var selectize = this._selectize(el);
-      if (selectize !== undefined) {
+      if (typeof(selectize) !== 'undefined') {
         selectize.setValue(value);
       } else $(el).val(value);
     },
@@ -2091,37 +2254,20 @@
 
       // This will replace all the options
       if (data.hasOwnProperty('options')) {
-        // Clear existing options and add each new one
-        $el.empty();
         selectize = this._selectize(el);
-        if (selectize !== undefined) {
-          selectize.clearOptions();
-          // Selectize.js doesn't maintain insertion order on Chrome on Mac
-          // with >10 items if inserted using addOption (versus being present
-          // in the DOM at selectize() time). Putting $order on each option
-          // makes it work.
-          $.each(data.options, function(i, opt) {
-            opt.$order = i;
-          });
-          selectize.addOption(data.options);
-        }
-        for (var i = 0; i < data.options.length; i++) {
-          var in_opt = data.options[i];
-
-          var $newopt = $('<option/>', {
-            value: in_opt.value,
-            text: in_opt.label
-          });
-
-          $el.append($newopt);
-        }
+        // Must destroy selectize before appending new options, otherwise
+        // selectize will restore the original select
+        if (selectize) selectize.destroy();
+        // Clear existing options and add each new one
+        $el.empty().append(data.options);
+        this._selectize(el);
       }
 
       // re-initialize selectize
-      if (data.hasOwnProperty('newOptions')) {
+      if (data.hasOwnProperty('config')) {
         $el.parent()
            .find('script[data-for="' + $escape(el.id) + '"]')
-           .replaceWith(data.newOptions);
+           .replaceWith(data.config);
         this._selectize(el, true);
       }
 
@@ -2131,13 +2277,14 @@
         selectize.clearOptions();
         selectize.settings.load = function(query, callback) {
           if (!query.length) return callback();
+          var settings = selectize.settings;
           $.ajax({
             url: data.url,
             data: {
               query: query,
-              field: JSON.stringify(selectize.settings.searchField),
-              conju: selectize.settings.searchConjunction,
-              maxop: selectize.settings.maxOptions
+              field: JSON.stringify([settings.searchField]),
+              conju: settings.searchConjunction,
+              maxop: settings.maxOptions
             },
             type: 'GET',
             error: function() {
@@ -2182,7 +2329,7 @@
         searchField: ['label']
       }, JSON.parse(config.html()));
       // selectize created from selectInput()
-      if (config.data('nonempty') !== undefined) {
+      if (typeof(config.data('nonempty')) !== 'undefined') {
         options = $.extend(options, {
           onItemRemove: function(value) {
             if (this.getValue() === "")
@@ -2253,22 +2400,7 @@
       if (data.hasOwnProperty('options')) {
         // Clear existing options and add each new one
         $el.find('label.radio').remove();
-        for (var i = 0; i < data.options.length; i++) {
-          var in_opt = data.options[i];
-
-          var $newopt = $('<label class="radio"/>');
-          var $radio = $('<input/>', {
-            type:  "radio",
-            name:  el.id,
-            id:    el.id + (i+1).toString(),
-            value: in_opt.value
-          });
-
-          $newopt.append($radio);
-          $newopt.append('<span>' + in_opt.label + '</span>');
-
-          $el.append($newopt);
-        }
+        $el.append(data.options);
       }
 
       if (data.hasOwnProperty('value'))
@@ -2378,22 +2510,7 @@
       if (data.hasOwnProperty('options')) {
         // Clear existing options and add each new one
         $el.find('label.checkbox').remove();
-        for (var i = 0; i < data.options.length; i++) {
-          var in_opt = data.options[i];
-
-          var $newopt = $('<label class="checkbox"/>');
-          var $checkbox = $('<input/>', {
-            type:  "checkbox",
-            name:  el.id,
-            id:    el.id + (i+1).toString(),
-            value: in_opt.value
-          });
-
-          $newopt.append($checkbox);
-          $newopt.append('<span>' + in_opt.label + '</span>');
-
-          $el.append($newopt);
-        }
+        $el.append(data.options);
       }
 
       if (data.hasOwnProperty('value'))
@@ -2527,6 +2644,45 @@
   });
   inputBindings.register(bootstrapTabInputBinding, 'shiny.bootstrapTabInput');
 
+  var IE8FileUploader = function(shinyapp, id, fileEl) {
+    this.shinyapp = shinyapp;
+    this.id = id;
+    this.fileEl = fileEl;
+    this.beginUpload();
+  };
+  (function() {
+    this.beginUpload = function() {
+      var self = this;
+      // Create invisible frame
+      var iframeId = 'shinyupload_iframe_' + this.id;
+      this.iframe = document.createElement('iframe');
+      this.iframe.id = iframeId;
+      this.iframe.name = iframeId;
+      this.iframe.setAttribute('style', 'position: fixed; top: 0; left: 0; width: 0; height: 0; border: none');
+      $('body').append(this.iframe);
+      var iframeDestroy = function() {
+        // Forces Shiny to flushReact, flush outputs, etc. Without this we get
+        // invalidated reactives, but observers don't actually execute.
+        self.shinyapp.makeRequest('uploadieFinish', [], function(){}, function(){});
+        $(self.iframe).remove();
+      };
+      if (this.iframe.attachEvent) {
+        this.iframe.attachEvent('onload', iframeDestroy);
+      } else {
+        this.iframe.onload = iframeDestroy;
+      }
+
+      this.form = document.createElement('form');
+      this.form.method = 'POST';
+      this.form.setAttribute('enctype', 'multipart/form-data');
+      this.form.action = "session/" + encodeURI(this.shinyapp.config.sessionId)
+                         + "/uploadie/" + encodeURI(this.id);
+      this.form.id = 'shinyupload_form_' + this.id;
+      this.form.target = iframeId;
+      $(this.form).insertAfter(this.fileEl).append(this.fileEl);
+      this.form.submit();
+    };
+  }).call(IE8FileUploader.prototype);
 
   var FileUploader = function(shinyapp, id, files) {
     this.shinyapp = shinyapp;
@@ -2661,13 +2817,18 @@
       uploader.abort();
 
     var files = evt.target.files;
+    var IE8 = typeof(files) === 'undefined';
     var id = fileInputBinding.getId(evt.target);
 
-    if (files.length === 0)
+    if (!IE8 && files.length === 0)
       return;
 
     // Start the new upload and put the uploader in 'currentUploader'.
-    el.data('currentUploader', new FileUploader(exports.shinyapp, id, files));
+    if (IE8) {
+      new IE8FileUploader(exports.shinyapp, id, evt.target);
+    } else {
+      el.data('currentUploader', new FileUploader(exports.shinyapp, id, files));
+    }
   }
 
   var fileInputBinding = new InputBinding();
@@ -2697,6 +2858,14 @@
   var OutputBindingAdapter = function(el, binding) {
     this.el = el;
     this.binding = binding;
+
+    // If the binding actually has a resize method, override the prototype of
+    // onResize with a version that does a makeResizeFilter on the element.
+    if (binding.resize) {
+      this.onResize = makeResizeFilter(el, function(width, height) {
+        binding.resize(el, width, height);
+      });
+    }
   };
   (function() {
     this.onValueChange = function(data) {
@@ -2708,6 +2877,9 @@
     this.showProgress = function(show) {
       this.binding.showProgress(this.el, show);
     };
+    this.onResize = function() {
+      // Intentionally left blank; see constructor
+    };
   }).call(OutputBindingAdapter.prototype);
 
 
@@ -3038,6 +3210,9 @@
           inputs.setInput('.clientdata_output_' + this.id + '_height', this.offsetHeight);
         }
       });
+      $('.shiny-bound-output').each(function() {
+        $(this).data('shiny-output-binding').onResize();
+      });
     }
 
     // Return true if the object or one of its ancestors in the DOM tree has

man/Progress.Rd

@@ -0,0 +1,94 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\docType{data}
+\name{Progress}
+\alias{Progress}
+\title{Reporting progress (object-oriented API)}
+\arguments{
+\item{session}{The Shiny session object, as provided by
+\code{shinyServer} to the server function.}
+
+\item{min}{The value that represents the starting point of the
+progress bar. Must be less tham \code{max}.}
+
+\item{max}{The value that represents the end of the progress bar.
+Must be greater than \code{min}.}
+
+\item{message}{A single-element character vector; the message to be
+displayed to the user, or \code{NULL} to hide the current message
+(if any).}
+
+\item{detail}{A single-element character vector; the detail message
+to be displayed to the user, or \code{NULL} to hide the current
+detail message (if any). The detail message will be shown with a
+de-emphasized appearance relative to \code{message}.}
+
+\item{value}{A numeric value at which to set
+the progress bar, relative to \code{min} and \code{max}.
+\code{NULL} hides the progress bar, if it is currently visible.}
+
+\item{amount}{Single-element numeric vector; the value at which to set
+the progress bar, relative to \code{min} and \code{max}.
+\code{NULL} hides the progress bar, if it is currently visible.}
+
+\item{amount}{For the \code{inc()} method, a numeric value to increment the
+  progress bar.}
+}
+\description{
+Reports progress to the user during long-running operations.
+}
+\details{
+This package exposes two distinct programming APIs for working with
+progress. \code{\link{withProgress}} and \code{\link{setProgress}}
+together provide a simple function-based interface, while the
+\code{Progress} reference class provides an object-oriented API.
+
+Instantiating a \code{Progress} object causes a progress panel to be
+created, and it will be displayed the first time the \code{set}
+method is called. Calling \code{close} will cause the progress panel
+to be removed.
+
+\strong{Methods}
+  \describe{
+    \item{\code{initialize(session, min = 0, max = 1)}}{
+      Creates a new progress panel (but does not display it).
+    }
+    \item{\code{set(value = NULL, message = NULL, detail = NULL)}}{
+      Updates the progress panel. When called the first time, the
+      progress panel is displayed.
+    }
+    \item{\code{inc(amount = 0.1, message = NULL, detail = NULL)}}{
+      Like \code{set}, this updates the progress panel. The difference is
+      that \code{inc} increases the progress bar by \code{amount}, instead
+      of setting it to a specific value.
+    }
+    \item{\code{close()}}{
+      Removes the progress panel. Future calls to \code{set} and
+      \code{close} will be ignored.
+    }
+  }
+}
+\examples{
+\dontrun{
+# server.R
+shinyServer(function(input, output, session) {
+  output$plot <- renderPlot({
+    progress <- shiny::Progress$new(session, min=1, max=15)
+    on.exit(progress$close())
+
+    progress$set(message = 'Calculation in progress',
+                 detail = 'This may take a while...')
+
+    for (i in 1:15) {
+      progress$set(value = i)
+      Sys.sleep(0.5)
+    }
+    plot(cars)
+  })
+})
+}
+}
+\seealso{
+\code{\link{withProgress}}
+}
+\keyword{datasets}
+

man/absolutePanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{absolutePanel}
 \alias{absolutePanel}
 \alias{fixedPanel}

man/actionButton.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{actionButton}
 \alias{actionButton}
 \alias{actionLink}

man/addResourcePath.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{addResourcePath}
 \alias{addResourcePath}
 \title{Resource Publishing}

man/bootstrapPage.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{bootstrapPage}
 \alias{basicPage}
 \alias{bootstrapPage}

man/checkboxGroupInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{checkboxGroupInput}
 \alias{checkboxGroupInput}
 \title{Checkbox Group Input Control}

man/checkboxInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{checkboxInput}
 \alias{checkboxInput}
 \title{Checkbox Input Control}

man/column.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{column}
 \alias{column}
 \title{Create a column within a UI definition}

man/conditionalPanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{conditionalPanel}
 \alias{conditionalPanel}
 \title{Conditional Panel}
@@ -23,6 +23,13 @@ example, if you have an input with an id of \code{foo}, then you can use
 \code{input.foo} to read its value. (Be sure not to modify the input/output
 objects, as this may cause unpredictable behavior.)
 }
+\note{
+You are not recommended to use special JavaScript characters such as a
+  period \code{.} in the input id's, but if you do use them anyway, for
+  example, \code{inputId = "foo.bar"}, you will have to use
+  \code{input["foo.bar"]} instead of \code{input.foo.bar} to read the input
+  value.
+}
 \examples{
 sidebarPanel(
    selectInput(

man/createWebDependency.Rd

@@ -0,0 +1,23 @@
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{createWebDependency}
+\alias{createWebDependency}
+\title{Create a web dependency}
+\usage{
+createWebDependency(dependency)
+}
+\arguments{
+\item{dependency}{A single HTML dependency object, created using
+  \code{\link{htmlDependency}}. If the \code{src} value is named, then
+  \code{href} and/or \code{file} names must be present.}
+}
+\value{
+A single HTML dependency object that has an \code{href}-named element
+  in its \code{src}.
+}
+\description{
+Ensure that a file-based HTML dependency (from the htmltools package) can be
+served over Shiny's HTTP server. This function works by using
+\code{\link{addResourcePath}} to map the HTML dependency's directory to a
+URL.
+}
+

man/dateInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dateInput}
 \alias{dateInput}
 \title{Create date input}

man/dateRangeInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{dateRangeInput}
 \alias{dateRangeInput}
 \title{Create date range input}
@@ -8,6 +8,10 @@ dateRangeInput(inputId, label, start = NULL, end = NULL, min = NULL,
   language = "en", separator = " to ")
 }
 \arguments{
+\item{inputId}{Input variable to assign the control's value to.}
+
+\item{label}{Display label for the control, or \code{NULL}.}
+
 \item{start}{The initial start date. Either a Date object, or a string in
 \code{yyyy-mm-dd} format. If NULL (the default), will use the current
 date in the client's time zone.}
@@ -16,12 +20,6 @@ date in the client's time zone.}
 \code{yyyy-mm-dd} format. If NULL (the default), will use the current
 date in the client's time zone.}
 
-\item{separator}{String to display between the start and end input boxes.}
-
-\item{inputId}{Input variable to assign the control's value to.}
-
-\item{label}{Display label for the control, or \code{NULL}.}
-
 \item{min}{The minimum allowed date. Either a Date object, or a string in
 \code{yyyy-mm-dd} format.}
 
@@ -42,6 +40,8 @@ from 0 (Sunday) to 6 (Saturday).}
   "fr", "he", "hr", "hu", "id", "is", "it", "ja", "kr", "lt", "lv", "ms",
   "nb", "nl", "pl", "pt", "pt-BR", "ro", "rs", "rs-latin", "ru", "sk", "sl",
   "sv", "sw", "th", "tr", "uk", "zh-CN", and "zh-TW".}
+
+\item{separator}{String to display between the start and end input boxes.}
 }
 \description{
 Creates a pair of text inputs which, when clicked on, bring up calendars that

man/domains.Rd

@@ -1,5 +1,5 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
-\name{getDefaultReactiveDomain}
+% Generated by roxygen2 (4.0.2): do not edit by hand
+\name{domains}
 \alias{domains}
 \alias{getDefaultReactiveDomain}
 \alias{onReactiveDomainEnded}

man/downloadButton.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{downloadButton}
 \alias{downloadButton}
 \alias{downloadLink}

man/downloadHandler.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{downloadHandler}
 \alias{downloadHandler}
 \title{File Downloads}

man/exprToFunction.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{exprToFunction}
 \alias{exprToFunction}
 \title{Convert an expression to a function}

man/fileInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{fileInput}
 \alias{fileInput}
 \title{File Upload Control}
@@ -11,15 +11,14 @@ fileInput(inputId, label, multiple = FALSE, accept = NULL)
 \item{label}{Display label for the control.}
 
 \item{multiple}{Whether the user should be allowed to select and upload
-multiple files at once.}
+multiple files at once. \bold{Does not work on older browsers, including
+Internet Explorer 9 and earlier.}}
 
 \item{accept}{A character vector of MIME types; gives the browser a hint of
   what kind of files the server is expecting.}
 }
 \description{
 Create a file upload control that can be used to upload one or more files.
-\bold{Does not work on older browsers, including Internet Explorer 9 and
-earlier.}
 }
 \details{
 Whenever a file upload completes, the corresponding input variable is set

man/fixedPage.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{fixedPage}
 \alias{fixedPage}
 \alias{fixedRow}

man/flowLayout.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{flowLayout}
 \alias{flowLayout}
 \title{Flow layout}

man/fluidPage.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{fluidPage}
 \alias{fluidPage}
 \alias{fluidRow}

man/headerPanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{headerPanel}
 \alias{headerPanel}
 \title{Create a header panel}

man/helpText.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{helpText}
 \alias{helpText}
 \title{Create a help text element}

man/htmlOutput.Rd

@@ -1,15 +1,18 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{htmlOutput}
 \alias{htmlOutput}
 \alias{uiOutput}
 \title{Create an HTML output element}
 \usage{
-htmlOutput(outputId)
+htmlOutput(outputId, inline = FALSE)
 
-uiOutput(outputId)
+uiOutput(outputId, inline = FALSE)
 }
 \arguments{
 \item{outputId}{output variable to read the value from}
+
+\item{inline}{use an inline (\code{span()}) or block container (\code{div()})
+for the output}
 }
 \value{
 An HTML output element that can be included in a panel

man/icon.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{icon}
 \alias{icon}
 \title{Create an icon}

man/imageOutput.Rd

@@ -1,9 +1,9 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{imageOutput}
 \alias{imageOutput}
 \title{Create a image output element}
 \usage{
-imageOutput(outputId, width = "100\%", height = "400px")
+imageOutput(outputId, width = "100\%", height = "400px", inline = FALSE)
 }
 \arguments{
 \item{outputId}{output variable to read the image from}
@@ -13,6 +13,9 @@ imageOutput(outputId, width = "100\%", height = "400px")
 string and have \code{"px"} appended.}
 
 \item{height}{Image height}
+
+\item{inline}{use an inline (\code{span()}) or block container (\code{div()})
+for the output}
 }
 \value{
 An image output element that can be included in a panel

man/inputPanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{inputPanel}
 \alias{inputPanel}
 \title{Input panel}

man/installExprFunction.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{installExprFunction}
 \alias{installExprFunction}
 \title{Install an expression as a function}

man/invalidateLater.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{invalidateLater}
 \alias{invalidateLater}
 \title{Scheduled Invalidation}

man/is.reactivevalues.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{is.reactivevalues}
 \alias{is.reactivevalues}
 \title{Checks whether an object is a reactivevalues object}

man/isolate.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{isolate}
 \alias{isolate}
 \title{Create a non-reactive scope for an expression}

man/knitr_methods.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{knitr_methods}
 \alias{knit_print.shiny.appobj}
 \alias{knit_print.shiny.render.function}
@@ -7,12 +7,14 @@
 \usage{
 knit_print.shiny.appobj(x, ...)
 
-knit_print.shiny.render.function(x, ...)
+knit_print.shiny.render.function(x, ..., inline = FALSE)
 }
 \arguments{
 \item{x}{Object to knit_print}
 
 \item{...}{Additional knit_print arguments}
+
+\item{inline}{Whether the object is printed inline.}
 }
 \description{
 These S3 methods are necessary to help Shiny applications and UI chunks embed

man/mainPanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{mainPanel}
 \alias{mainPanel}
 \title{Create a main panel}

man/makeReactiveBinding.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{makeReactiveBinding}
 \alias{makeReactiveBinding}
 \title{Make a reactive variable}

man/markRenderFunction.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{markRenderFunction}
 \alias{markRenderFunction}
 \title{Mark a function as a render function}

man/maskReactiveContext.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{maskReactiveContext}
 \alias{maskReactiveContext}
 \title{Evaluate an expression without a reactive context}

man/navbarPage.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{navbarPage}
 \alias{navbarMenu}
 \alias{navbarPage}
@@ -6,7 +6,7 @@
 \usage{
 navbarPage(title, ..., id = NULL, header = NULL, footer = NULL,
   inverse = FALSE, collapsable = FALSE, fluid = TRUE, responsive = TRUE,
-  theme = NULL)
+  theme = NULL, windowTitle = title)
 
 navbarMenu(title, ..., icon = NULL)
 }
@@ -43,6 +43,9 @@ and resize page elements based on the size of the viewing device)}
 www directory). For example, to use the theme located at
 \code{www/bootstrap.css} you would use \code{theme = "bootstrap.css"}.}
 
+\item{windowTitle}{The title that should be displayed by the browser window.
+Useful if \code{title} is not a string.}
+
 \item{icon}{Optional icon to appear on a \code{navbarMenu} tab.}
 }
 \value{

man/navlistPanel.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{navlistPanel}
 \alias{navlistPanel}
 \title{Create a navigation list panel}

man/numericInput.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{numericInput}
 \alias{numericInput}
 \title{Create a numeric input control}

man/observe.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{observe}
 \alias{observe}
 \title{Create a reactive observer}

man/outputOptions.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{outputOptions}
 \alias{outputOptions}
 \title{Set options for an output object.}

man/pageWithSidebar.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{pageWithSidebar}
 \alias{pageWithSidebar}
 \title{Create a page with a sidebar}

man/parseQueryString.Rd

@@ -1,12 +1,19 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{parseQueryString}
 \alias{parseQueryString}
 \title{Parse a GET query string from a URL}
 \usage{
-parseQueryString(str)
+parseQueryString(str, nested = FALSE)
 }
 \arguments{
 \item{str}{The query string. It can have a leading \code{"?"} or not.}
+
+\item{nested}{Whether to parse the query string of as a nested list when it
+contains pairs of square brackets \code{[]}. For example, the query
+\samp{a[i1][j1]=x&b[i1][j1]=y&b[i2][j1]=z} will be parsed as \code{list(a =
+list(i1 = list(j1 = 'x')), b = list(i1 = list(j1 = 'y'), i2 = list(j1 =
+'z')))} when \code{nested = TRUE}, and \code{list(`a[i1][j1]` = 'x',
+`b[i1][j1]` = 'y', `b[i2][j1]` = 'z')} when \code{nested = FALSE}.}
 }
 \description{
 Returns a named character vector of key-value pairs.

man/plotOutput.Rd

@@ -1,33 +1,34 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{plotOutput}
 \alias{plotOutput}
 \title{Create an plot output element}
 \usage{
 plotOutput(outputId, width = "100\%", height = "400px", clickId = NULL,
   hoverId = NULL, hoverDelay = 300, hoverDelayType = c("debounce",
-  "throttle"))
+  "throttle"), inline = FALSE)
 }
 \arguments{
 \item{outputId}{output variable to read the plot from}
 
-\item{width}{Plot width. Must be a valid CSS unit (like \code{"100\%"},
-\code{"400px"}, \code{"auto"}) or a number, which will be coerced to a
-string and have \code{"px"} appended.}
-
-\item{height}{Plot height}
+\item{width,height}{Plot width/height. Must be a valid CSS unit (like
+\code{"100\%"}, \code{"400px"}, \code{"auto"}) or a number, which will be
+coerced to a string and have \code{"px"} appended. These two arguments are
+ignored when \code{inline = TRUE}, in which case the width/height of a plot
+must be specified in \code{renderPlot()}.}
 
 \item{clickId}{If not \code{NULL}, the plot will send coordinates to the
 server whenever it is clicked. This information will be accessible on the
-\code{input} object using \code{input$}\emph{\code{clickId}}. The value will be a
-named list or vector with \code{x} and \code{y} elements indicating the
-mouse position in user units.}
+\code{input} object using \code{input$}\emph{\code{clickId}}. The value
+will be a named list or vector with \code{x} and \code{y} elements
+indicating the mouse position in user units.}
 
 \item{hoverId}{If not \code{NULL}, the plot will send coordinates to the
 server whenever the mouse pauses on the plot for more than the number of
 milliseconds determined by \code{hoverTimeout}. This information will be
-The value will be \code{NULL} if the user is not hovering, and a named
-list or vector with \code{x} and \code{y} elements indicating the mouse
-position in user units.}
+accessible on the \code{input} object using
+\code{input$}\emph{\code{clickId}}. The value will be \code{NULL} if the
+user is not hovering, and a named list or vector with \code{x} and \code{y}
+elements indicating the mouse position in user units.}
 
 \item{hoverDelay}{The delay for hovering, in milliseconds.}
 
@@ -36,6 +37,9 @@ events. Use \code{"throttle"} to limit the number of hover events to one
 every \code{hoverDelay} milliseconds. Use \code{"debounce"} to suspend
 events while the cursor is moving, and wait until the cursor has been at
 rest for \code{hoverDelay} milliseconds before sending an event.}
+
+\item{inline}{use an inline (\code{span()}) or block container (\code{div()})
+for the output}
 }
 \value{
 A plot output element that can be included in a panel
@@ -43,6 +47,12 @@ A plot output element that can be included in a panel
 \description{
 Render a \link{renderPlot} within an application page.
 }
+\note{
+The arguments \code{clickId} and \code{hoverId} only work for R base
+  graphics (see the \pkg{\link{graphics}} package). They do not work for
+  \pkg{\link[grid:grid-package]{grid}}-based graphics, such as \pkg{ggplot2},
+  \pkg{lattice}, and so on.
+}
 \examples{
 # Show a plot of the generated distribution
 mainPanel(

man/plotPNG.Rd

@@ -1,4 +1,4 @@
-% Generated by roxygen2 (4.0.1): do not edit by hand
+% Generated by roxygen2 (4.0.2): do not edit by hand
 \name{plotPNG}
 \alias{plotPNG}
 \title{Run a plotting function and save the output as a PNG}