added NEWS entry

* Fix #1399: Duplicate binding error with insertUI and nested uiOutput

* Update NEWS.md

.Rbuildignore

@@ -6,6 +6,7 @@
 ^shiny\.cmd$
 ^run\.R$
 ^\.gitignore$
+^smoketests$
 ^res$
 ^man-roxygen$
 ^\.travis\.yml$
@@ -14,3 +15,6 @@
 ^srcjs$
 ^CONTRIBUTING.md$
 ^cran-comments.md$
+^.*\.o$
+^appveyor\.yml$
+^revdep$

.gitignore

@@ -8,3 +8,4 @@
 /src-x86_64/
 shinyapps/
 README.html
+.*.Rnb.cached

.travis.yml

@@ -1,10 +1,10 @@
 language: r
-warnings_are_errors: true
-
-r_binary_packages:
-  - Rcpp
-  - cairo
-  - knitr
+r:
+  - oldrel
+  - release
+  - devel
+sudo: false
+cache: packages
 
 notifications:
   email:

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: shiny
 Type: Package
 Title: Web Application Framework for R
-Version: 0.12.2.9005
-Date: 2015-10-28
+Version: 0.14.1.9001
 Authors@R: c(
     person("Winston", "Chang", role = c("aut", "cre"), email = "winston@rstudio.com"),
     person("Joe", "Cheng", role = "aut", email = "joe@rstudio.com"),
@@ -15,7 +14,7 @@ Authors@R: c(
     person(family = "jQuery contributors", role = c("ctb", "cph"),
     comment = "jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt"),
     person(family = "jQuery UI contributors", role = c("ctb", "cph"),
-    comment = "jQuery UI library; authors listed in inst/www/shared/jqueryui/1.10.4/AUTHORS.txt"),
+    comment = "jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt"),
     person("Mark", "Otto", role = "ctb",
     comment = "Bootstrap library"),
     person("Jacob", "Thornton", role = "ctb",
@@ -70,8 +69,9 @@ Imports:
     jsonlite (>= 0.9.16),
     xtable,
     digest,
-    htmltools (>= 0.2.6),
-    R6 (>= 2.0)
+    htmltools (>= 0.3.5),
+    R6 (>= 2.0),
+    sourcetools
 Suggests:
     datasets,
     Cairo (>= 1.5-5),
@@ -82,17 +82,20 @@ Suggests:
     ggplot2
 URL: http://shiny.rstudio.com
 BugReports: https://github.com/rstudio/shiny/issues
-VignetteBuilder: knitr
 Collate:
     'app.R'
+    'bookmark-state-local.R'
+    'stack.R'
+    'bookmark-state.R'
     'bootstrap-layout.R'
+    'conditions.R'
     'map.R'
     'globals.R'
     'utils.R'
     'bootstrap.R'
     'cache.R'
+    'diagnose.R'
     'fileupload.R'
-    'stack.R'
     'graph.R'
     'hooks.R'
     'html-deps.R'
@@ -113,20 +116,27 @@ Collate:
     'input-slider.R'
     'input-submit.R'
     'input-text.R'
+    'input-textarea.R'
     'input-utils.R'
+    'insert-ui.R'
     'jqueryui.R'
     'middleware-shiny.R'
     'middleware.R'
+    'modal.R'
     'modules.R'
+    'notifications.R'
     'priorityqueue.R'
     'progress.R'
     'react.R'
     'reactive-domains.R'
     'reactives.R'
     'render-plot.R'
+    'render-table.R'
     'run-url.R'
+    'serializers.R'
     'server-input-handlers.R'
     'server.R'
+    'shiny-options.R'
     'shiny.R'
     'shinyui.R'
     'shinywrappers.R'
@@ -134,3 +144,4 @@ Collate:
     'tar.R'
     'timer.R'
     'update-input.R'
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 S3method("$",reactivevalues)
 S3method("$",session_proxy)
@@ -11,6 +11,7 @@ S3method("[",shinyoutput)
 S3method("[<-",reactivevalues)
 S3method("[<-",shinyoutput)
 S3method("[[",reactivevalues)
+S3method("[[",session_proxy)
 S3method("[[",shinyoutput)
 S3method("[[<-",reactivevalues)
 S3method("[[<-",shinyoutput)
@@ -25,6 +26,9 @@ S3method(names,reactivevalues)
 S3method(print,reactive)
 S3method(print,shiny.appobj)
 S3method(str,reactivevalues)
+export("conditionStackTrace<-")
+export(..stacktraceoff..)
+export(..stacktraceon..)
 export(HTML)
 export(NS)
 export(Progress)
@@ -34,39 +38,54 @@ export(actionButton)
 export(actionLink)
 export(addResourcePath)
 export(animationOptions)
+export(applyInputHandlers)
 export(as.shiny.appobj)
 export(basicPage)
+export(bookmarkButton)
+export(bootstrapLib)
 export(bootstrapPage)
 export(br)
+export(browserViewer)
 export(brushOpts)
 export(brushedPoints)
 export(callModule)
+export(captureStackTraces)
 export(checkboxGroupInput)
 export(checkboxInput)
 export(clickOpts)
 export(code)
 export(column)
+export(conditionStackTrace)
 export(conditionalPanel)
 export(createWebDependency)
 export(dataTableOutput)
 export(dateInput)
 export(dateRangeInput)
 export(dblclickOpts)
+export(dialogViewer)
 export(div)
 export(downloadButton)
 export(downloadHandler)
 export(downloadLink)
 export(em)
+export(enableBookmarking)
 export(eventReactive)
 export(exprToFunction)
+export(extractStackTrace)
 export(fileInput)
+export(fillCol)
+export(fillPage)
+export(fillRow)
 export(fixedPage)
 export(fixedPanel)
 export(fixedRow)
 export(flowLayout)
 export(fluidPage)
 export(fluidRow)
+export(formatStackTrace)
+export(freezeReactiveValue)
 export(getDefaultReactiveDomain)
+export(getShinyOption)
 export(h1)
 export(h2)
 export(h3)
@@ -78,6 +97,7 @@ export(helpText)
 export(hoverOpts)
 export(hr)
 export(htmlOutput)
+export(htmlTemplate)
 export(icon)
 export(imageOutput)
 export(img)
@@ -88,14 +108,17 @@ export(includeMarkdown)
 export(includeScript)
 export(includeText)
 export(inputPanel)
+export(insertUI)
 export(installExprFunction)
 export(invalidateLater)
 export(is.reactive)
 export(is.reactivevalues)
 export(is.shiny.appobj)
 export(is.singleton)
+export(isTruthy)
 export(isolate)
 export(knit_print.html)
+export(knit_print.reactive)
 export(knit_print.shiny.appobj)
 export(knit_print.shiny.render.function)
 export(knit_print.shiny.tag)
@@ -104,6 +127,8 @@ export(mainPanel)
 export(makeReactiveBinding)
 export(markRenderFunction)
 export(maskReactiveContext)
+export(modalButton)
+export(modalDialog)
 export(navbarMenu)
 export(navbarPage)
 export(navlistPanel)
@@ -113,15 +138,25 @@ export(ns.sep)
 export(numericInput)
 export(observe)
 export(observeEvent)
+export(onBookmark)
+export(onBookmarked)
+export(onFlush)
+export(onFlushed)
 export(onReactiveDomainEnded)
+export(onRestore)
+export(onRestored)
+export(onSessionEnded)
 export(outputOptions)
 export(p)
 export(pageWithSidebar)
+export(paneViewer)
 export(parseQueryString)
 export(passwordInput)
 export(plotOutput)
 export(plotPNG)
 export(pre)
+export(printError)
+export(printStackTrace)
 export(radioButtons)
 export(reactive)
 export(reactiveFileReader)
@@ -136,6 +171,9 @@ export(reactiveValues)
 export(reactiveValuesToList)
 export(registerInputHandler)
 export(removeInputHandler)
+export(removeModal)
+export(removeNotification)
+export(removeUI)
 export(renderDataTable)
 export(renderImage)
 export(renderPlot)
@@ -144,20 +182,29 @@ export(renderTable)
 export(renderText)
 export(renderUI)
 export(repeatable)
+export(req)
+export(restoreInput)
 export(runApp)
 export(runExample)
+export(runGadget)
 export(runGist)
 export(runGitHub)
 export(runUrl)
+export(safeError)
 export(selectInput)
 export(selectizeInput)
 export(serverInfo)
+export(setBookmarkExclude)
 export(setProgress)
 export(shinyApp)
 export(shinyAppDir)
 export(shinyAppFile)
+export(shinyOptions)
 export(shinyServer)
 export(shinyUI)
+export(showBookmarkUrlModal)
+export(showModal)
+export(showNotification)
 export(showReactLog)
 export(sidebarLayout)
 export(sidebarPanel)
@@ -168,6 +215,7 @@ export(splitLayout)
 export(stopApp)
 export(strong)
 export(submitButton)
+export(suppressDependencies)
 export(tabPanel)
 export(tableOutput)
 export(tabsetPanel)
@@ -178,10 +226,12 @@ export(tagAppendChildren)
 export(tagList)
 export(tagSetChildren)
 export(tags)
+export(textAreaInput)
 export(textInput)
 export(textOutput)
 export(titlePanel)
 export(uiOutput)
+export(updateActionButton)
 export(updateCheckboxGroupInput)
 export(updateCheckboxInput)
 export(updateDateInput)
@@ -189,17 +239,21 @@ export(updateDateRangeInput)
 export(updateNavbarPage)
 export(updateNavlistPanel)
 export(updateNumericInput)
+export(updateQueryString)
 export(updateRadioButtons)
 export(updateSelectInput)
 export(updateSelectizeInput)
 export(updateSliderInput)
 export(updateTabsetPanel)
+export(updateTextAreaInput)
 export(updateTextInput)
+export(urlModal)
 export(validate)
 export(validateCssUnit)
 export(verbatimTextOutput)
 export(verticalLayout)
 export(wellPanel)
+export(withLogErrors)
 export(withMathJax)
 export(withProgress)
 export(withReactiveDomain)

NEWS

@@ -1,905 +0,0 @@
-shiny 0.12.2.9000
---------------------------------------------------------------------------------
-
-* Fixed #962: plot interactions did not work with the development version of
-  ggplot2 (after ggplot2 1.0.1).
-
-* Fixed #902: the `drag_drop` plugin of the selectize input did not work.
-
-* Fixed #933: `updateSliderInput()` does not work when only the label is
-  updated.
-
-* Multiple imageOutput/plotOutput calls can now share the same brush id. Shiny
-  will ensure that performing a brush operation will clear any other brush with
-  the same id.
-
-* Added `placeholder` option to `textInput`.
-
-* Improved support for Unicode characters on Windows (#968).
-
-* Fixed bug in `selectInput` and `selectizeInput` where values with double
-  quotes were not properly escaped.
-
-* `runApp()` can now take a path to any .R file that yields a `shinyApp` object;
-  previously, the path had to be a directory that contained an app.R file (or
-  server.R if using separately defined server and UI). Similarly, introduced
-  `shinyAppFile()` function which creates a `shinyApp` object for an .R file
-  path, just as `shinyAppDir()` does for a directory path.
-
-* Introduced Shiny Modules, which are designed to 1) simplify the reuse of
-  Shiny UI/server logic and 2) make authoring and maintaining complex Shiny
-  apps much easier. See the article linked from `?callModule`.
-
-* `invalidateLater` and `reactiveTimer` no longer require an explicit `session`
-  argument; the default value uses the current session.
-
-shiny 0.12.2
---------------------------------------------------------------------------------
-
-* GitHub changed URLs for gists from .tar.gz to .zip, so `runGist` was updated
-  to work with the new URLs.
-
-* Callbacks from the session object are now guaranteed to execute in the order
-  in which registration occurred.
-
-* Minor bugs in sliderInput's animation behavior have been fixed. (#852)
-
-* Updated to ion.rangeSlider to 2.0.12.
-
-* Added `shiny.minified` option, which controls whether the minified version
-  of shiny.js is used. Setting it to FALSe can be useful for debugging. (#826,
-  #850)
-
-* Fixed an issue for outputting plots from ggplot objects which also have an
-  additional class whose print method takes precedence over `print.ggplot`.
-  (#840, 841)
-
-* Added `width` option to Shiny's input functions. (#589, #834)
-
-* Added two alias functions of `updateTabsetPanel()` to update the selected tab:
-  `updateNavbarPage()` and `updateNavlistPanel()`. (#881)
-
-* All non-base functions are now explicitly namespaced, to pass checks in
-  R-devel.
-
-* Shiny now correctly handles HTTP HEAD requests. (#876)
-
-shiny 0.12.1
---------------------------------------------------------------------------------
-
-* Fixed an issue where unbindAll() causes subsequent bindAll() to be ignored for
-  previously bound outputs. (#856)
-
-* Undeprecate `dataTableOutput` and `renderDataTable`, which had been deprecated
-  in favor of the new DT package. The DT package is a bit too new and has a
-  slightly different API, we were too hasty in deprecating the existing Shiny
-  functions.
-
-shiny 0.12.0
---------------------------------------------------------------------------------
-
-* Switched from RJSONIO to jsonlite. This improves consistency and speed when
-  converting between R data structures and JSON. One notable change is that
-  POSIXt objects are now serialized to JSON in UTC8601 format (like
-  "2015-03-20T20:00:00Z"), instead of as seconds from the epoch).
-
-* In addition to the existing support for clicking and hovering on plots
-  created by base graphics, added support for double-clicking and brushing.
-  (#769)
-
-* Added support for clicking, hovering, double-clicking, and brushing for
-  plots created by ggplot2, including support for facets. (#802)
-
-* Added `nearPoints` and `brushedPoints` functions for easily selecting rows of
-  data that are clicked/hovered, or brushed. (#802)
-
-* Added `shiny.port` option. If this is option is set, `runApp()` will listen on
-  this port by default. (#756)
-
-* `runUrl`, `runGist`, and `runGitHub` now can save downloaded applications,
-  with the `destdir` argument. (#688)
-
-* Restored ability to set labels for `selectInput`. (#741)
-
-* Travis continuous integration now uses Travis's native R support.
-
-* Fixed encoding issue when the server receives data from the client browser.
-  (#742)
-
-* The `session` object now has class `ShinySession`, making it easier to test
-  whether an object is indeed a session object. (#720, #746)
-
-* Fix JavaScript error when an output appears in nested uiOutputs. (Thanks,
-  Gregory Zhang. #749)
-
-* Eliminate delay on receiving new value when `updateSliderInput(value=...)` is
-  called.
-
-* Updated to DataTables (Javascript library) 1.10.5.
-
-* Fixed downloading of files that have no filename extension. (#575, #753)
-
-* Fixed bug where nested UI outputs broke outputs. (#749, #750)
-
-* Removed unneeded HTML ID attributes for `checkboxGroupInputs` and
-  `radioButtons`. (#684)
-
-* Fixed bug where checkboxes were still active even after `Shiny.unbindAll()`
-  was called. (#206)
-
-* The server side selectize input will load the first 1000 options by default
-  before users start to type and search in the box. (#823)
-
-* renderDataTable() and dataTableOutput() have been deprecated in shiny and will
-  be removed in future versions of shiny. Please use the DT package instead:
-  http://rstudio.github.io/DT/ (#807)
-
-shiny 0.11.1
---------------------------------------------------------------------------------
-
-* Major client-side performance improvements for pages that have many
-  conditionalPanels, tabPanels, and plotOutputs. (#693, #717, #723)
-
-* `tabPanel`s now use the `title` for `value` by default. This fixes a bug
-  in which an icon in the title caused problems with a conditionalPanel's test
-  condition. (#725, #728)
-
-* `selectInput` now has a `size` argument to control the height of the input
-  box. (#729)
-
-* `navbarPage` no longer includes a first row of extra whitespace when
-  `header=NULL`. (#722)
-
-* `selectInput`s now use Bootstrap styling when `selectize=FALSE`. (#724)
-
-* Better vertical spacing of label for checkbox groups and radio buttons.
-
-* `selectInput` correctly uses width for both selectize and non-selectize
-  inputs. (#702)
-
-* The wrapper tag generated by `htmlOutput` and `uiOutput` can now be any type
-  of HTML tag, instead of just span and div. Also, custom classes are now
-  allowed on the tag. (#704)
-
-* Slider problems in IE 11 and Chrome on touchscreen-equipped Windows computers
-  have been fixed. (#700)
-
-* Sliders now work correctly with draggable panels. (#711)
-
-* Fixed arguments in `fixedPanel`. (#709)
-
-* downloadHandler content callback functions are now invoked with a temp file
-  name that has the same extension as the final filename that will be used by
-  the download. This is to deal with the fact that some file writing functions
-  in R will auto-append the extension for their file type (pdf, zip).
-
-shiny 0.11
---------------------------------------------------------------------------------
-
-* Changed sliders from jquery-slider to ion.rangeSlider. These sliders have
-  an improved appearance, support updating more properties from the server,
-  and can be controlled with keyboard input.
-
-* Switched from Bootstrap 2 to Bootstrap 3. For most users, this will work
-  seamlessly, but some users may need to use the shinybootstrap2 package for
-  backward compatibility.
-
-* The UI of a Shiny app can now have a body tag. This is useful for CSS
-  templates that use classes on the body tag.
-
-* `actionButton` and `actionLink` now pass their `...` arguments to the
-  underlying tag function. (#607)
-
-* Added `observeEvent` and `eventReactive` functions for clearer, more concise
-  handling of `actionButton`, plot clicks, and other naturally-imperative
-  inputs.
-
-* Errors that happen in reactives no longer prevent any remaining pending
-  observers from executing. It is also now possible for users to control how
-  errors are handled, with the 'shiny.observer.error' global option. (#603,
-  #604)
-
-* Added an `escape` argument to `renderDataTable()` to escape the HTML entities
-  in the data table for security reasons. This might break tables from previous
-  versions of shiny that use raw HTML in the table content, and the old behavior
-  can be brought back by `escape = FALSE` if you are aware of the security
-  implications. (#627)
-
-* Changed the URI encoding/decoding functions internally to use `encodeURI()`,
-  `encodeURIComponent()`, and `decodeURIComponent()` from the httpuv package
-  instead of `utils::URLencode()` and `utils::URLdecode()`. (#630)
-
-* Shiny's web assets are now minified.
-
-* The default reactive domain is now available in event handler functions. (#669)
-
-* Password input fields can now be used, with `passwordInput()`. (#672)
-
-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)
-
-* Updated selectize.js to version 0.11.2. (#596)
-* Added `position` parameter to `navbarPage`.
-
-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
---------------------------------------------------------------------------------
-
-* BREAKING CHANGE: By default, observers now terminate themselves if they were
-  created during a session and that session ends. See ?domains for more details.
-
-* Shiny can now be used in R Markdown v2 documents, to create "Shiny Docs":
-  reports and presentations that combine narrative, statically computed output,
-  and fully dynamic inputs and outputs. For more info, including examples, see
-  http://rmarkdown.rstudio.com/authoring_shiny.html.
-
-* The `session` object that can be passed into a server function (e.g.
-  shinyServer(function(input, output, session) {...})) is now documented: see
-  `?session`.
-
-* Most inputs can now accept `NULL` label values to omit the label altogether.
-
-* New `actionLink` input control; like `actionButton`, but with the appearance
-  of a normal link.
-
-* `renderPlot` now calls `print` on its result if it's visible (i.e. no more
-  explicit `print()` required for ggplot2).
-
-* Introduced Shiny app objects (see `?shinyApp`). These essentially replace the
-  little-advertised ability for `runApp` to take a `list(ui=..., server=...)`
-  as the first argument instead of a directory (though that ability remains for
-  backward compatibility). Unlike those lists, Shiny app objects are tagged with
-  class `shiny.appobj` so they can be run simply by printing them.
-
-* Added `maskReactiveContext` function. It blocks the current reactive context,
-  to evaluate expressions that shouldn't use reactive sources directly. (This
-  should not be commonly needed.)
-
-* Added `flowLayout`, `splitLayout`, and `inputPanel` functions for putting UI
-  elements side by side. `flowLayout` lays out its children in a left-to-right,
-  top-to-bottom arrangement. `splitLayout` evenly divides its horizontal space
-  among its children (or unevenly divides if `cellWidths` argument is provided).
-  `inputPanel` is like `flowPanel`, but with a light grey background, and is
-  intended to be used to encapsulate small input controls wherever vertical
-  space is at a premium.
-
-* Added `serverInfo` to obtain info about the Shiny Server if the app is served
-  through it.
-
-* Added an `inline` argument (TRUE/FALSE) in `checkboxGroupInput()` and
-  `radioButtons()` to allow the horizontal layout (inline = TRUE) of checkboxes
-  or radio buttons. (Thanks, @saurfang, #481)
-
-* `sliderInput` and `selectizeInput`/`selectInput` now use a standard horizontal
-  size instead of filling up all available horizontal space. Pass `width="100%"`
-  explicitly for the old behavior.
-
-* Added the `updateSelectizeInput()` function to make it possible to process
-  searching on the server side (i.e. using R), which can be much faster than the
-  client side processing (i.e. using HTML and JavaScript). See the article at
-  http://shiny.rstudio.com/articles/selectize.html for a detailed introduction.
-
-* Fixed a bug of renderDataTable() when the data object only has 1 row and 1
-  column. (Thanks, ZJ Dai, #429)
-
-* `renderPrint` gained a new argument 'width' to control the width of the text
-  output, e.g. renderPrint({mtcars}, width = 40).
-
-* 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
---------------------------------------------------------------------------------
-
-* Fixed warning 'Error in Context$new : could not find function "loadMethod"'
-  that was happening to dependent packages on "R CMD check".
-
-shiny 0.9.0
---------------------------------------------------------------------------------
-
-* BREAKING CHANGE: Added a `host` parameter to runApp() and runExample(),
-  which defaults to the shiny.host option if it is non-NULL, or "127.0.0.1"
-  otherwise. This means that by default, Shiny applications can only be
-  accessed on the same machine from which they are served. To allow other
-  clients to connect, as in previous versions of Shiny, use "0.0.0.0"
-  (or the IP address of one of your network interfaces, if you care to be
-  explicit about it).
-
-* Added a new function `selectizeInput()` to use the JavaScript library
-  selectize.js (https://github.com/brianreavis/selectize.js), which extends
-  the basic select input in many aspects.
-
-* The `selectInput()` function also gained a new argument `selectize = TRUE`
-  to makes use of selectize.js by default. If you want to revert back to the
-  original select input, you have to call selectInput(..., selectize = FALSE).
-
-* Added Showcase mode, which displays the R code for an app right in the app
-  itself. You can invoke Showcase mode by passing `display.mode="showcase"`
-  to the `runApp()` function. Or, if an app is designed to run in Showcase
-  mode by default, add a DESCRIPTION file in the app dir with Title, Author,
-  and License fields; with "Type: Shiny"; and with "DisplayMode: Showcase".
-
-* Upgraded to Bootstrap 2.3.2 and jQuery 1.11.0.
-
-* Make `tags$head()` and `singleton()` behave correctly when used with
-  `renderUI()` and `uiOutput()`. Previously, "hoisting content to the head"
-  and "only rendering items a single time" were features that worked only
-  when the page was initially loading, not in dynamic rendering.
-
-* Files are now sourced with the `keep.source` option, to help with debugging
-  and profiling.
-
-* Support user-defined input parsers for data coming in from JavaScript using
-  the parseShinyInput method.
-
-* Fixed the bug #299: renderDataTable() can deal with 0-row data frames now.
-  (reported by Harlan Harris)
-
-* Added `navbarPage()` and `navbarMenu()` functions to create applications
-  with multiple top level panels.
-
-* Added `navlistPanel()` function to create layouts with a a bootstrap
-  navlist on the left and tabPanels on the right
-
-* Added `type` parameter to `tabsetPanel()` to enable the use of pill
-  style tabs in addition to the standard ones.
-
-* Added `position` paramter to `tabsetPanel()` to enable positioning of tabs
-  above, below, left, or right of tab content.
-
-* Added `fluidPage()` and `fixedPage()` functions as well as related row and
-  column layout functions for creating arbitrary bootstrap grid layouts.
-
-* Added `hr()` builder function for creating horizontal rules.
-
-* Automatically concatenate duplicate attributes in tag definitions
-
-* Added `responsive` parameter to page building functions for opting-out of
-  bootstrap responsive css.
-
-* Added `theme` parameter to page building functions for specifying alternate
-  bootstrap css styles.
-
-* Added `icon()` function for embedding icons from the
-  [font awesome](http://fontawesome.io/) icon library
-
-* Added `makeReactiveBinding` function to turn a "regular" variable into a
-  reactive one (i.e. reading the variable makes the current reactive context
-  dependent on it, and setting the variable is a source of reactivity).
-
-* Added a function `withMathJax()` to include the MathJax library in an app.
-
-* The argument `selected` in checkboxGroupInput(), selectInput(), and
-  radioButtons() refers to the value(s) instead of the name(s) of the
-  argument `choices` now. For example, the value of the `selected` argument
-  in selectInput(..., choices = c('Label 1' = 'x1', 'Label 2' = 'x2'),
-  selected = 'Label 2') must be updated to 'x2', although names/labels will
-  be automatically converted to values internally for backward
-  compatibility. The same change applies to updateCheckboxGroupInput(),
-  updateSelectInput(), and updateRadioButtons() as well. (#340)
-
-* Now it is possible to only update the value of a checkbox group, select input,
-  or radio buttons using the `selected` argument without providing the
-  `choices` argument in updateCheckboxGroupInput(), updateSelectInput(), and
-  updateRadioButtons(), respectively. (#340)
-
-* Added `absolutePanel` and `fixedPanel` functions for creating absolute-
-  and fixed-position panels. They can be easily made user-draggable by
-  specifying `draggable = TRUE`.
-
-* For the `options` argument of the function `renderDataTable()`, we can
-  pass literal JavaScript code to the DataTables library via `I()`. This
-  makes it possible to use any JavaScript object in the options, e.g. a
-  JavaScript function (which is not supported in JSON). See
-  `?renderDataTable` for details and examples.
-
-* DataTables also works under IE8 now.
-
-* Fixed a bug in DataTables pagination when searching is turned on, which
-  caused failures for matrices as well as empty rows when displaying data
-  frames using renderDataTable().
-
-* The `options` argument in `renderDataTable()` can also take a function
-  that returns a list. This makes it possible to use reactive values in the
-  options. (#392)
-
-* `renderDataTable()` respects more DataTables options now: (1) either
-  bPaginate = FALSE or iDisplayLength = -1 will disable pagination (i.e. all
-  rows are returned from the data); besides, this means we can also use -1
-  in the length menu, e.g. aLengthMenu = list(c(10, 30, -1), list(10, 30,
-  'All')); (2) we can disable searching for individual columns through the
-  bSearchable option, e.g. aoColumns = list(list(bSearchable = FALSE),
-  list(bSearchable = TRUE),...) (the search box for the first column is
-  hidden); (3) we can turn off searching entirely (for both global searching
-  and individual columns) using the option bFilter = FALSE.
-
-* Added an argument `callback` in `renderDataTable()` so that a custom
-  JavaScript function can be applied to the DataTable object. This makes it
-  much easier to use DataTables plug-ins.
-
-* For numeric columns in a DataTable, the search boxes support lower and
-  upper bounds now: a search query of the form "lower,upper" (without
-  quotes) indicates the limits [lower, upper]. For a column X, this means
-  the rows corresponding to X >= lower & X <= upper are returned. If we omit
-  either the lower limit or the upper limit, only the other limit will be
-  used, e.g. ",upper" means X <= upper.
-
-* `updateNumericInput(value)` tries to preserve numeric precision by avoiding
-  scientific notation when possible, e.g. 102145 is no longer rounded to
-  1.0214e+05 = 102140. (Thanks, Martin Loos. #401)
-
-* `sliderInput()` no longer treats a label wrapped in HTML() as plain text,
-  e.g. the label in sliderInput(..., label = HTML('<em>A Label</em>')) will
-  not be escaped any more. (#119)
-
-* Fixed #306: the trailing slash in a path could fail `addResourcePath()`
-  under Windows. (Thanks, ZJ Dai)
-
-* Dots are now legal characters for inputId/outputId. (Thanks, Kevin
-  Lindquist. #358)
-
-shiny 0.8.0
---------------------------------------------------------------------------------
-
-* Debug hooks are registered on all user-provided functions and (reactive)
-  expressions (e.g., in renderPlot()), which makes it possible to set
-  breakpoints in these functions using the latest version of the RStudio
-  IDE, and the RStudio visual debugging tools can be used to debug Shiny
-  apps. Internally, the registration is done via installExprFunction(),
-  which is a new function introduced in this version to replace
-  exprToFunction() so that the registration can be automatically done.
-
-* Added a new function renderDataTable() to display tables using the
-  JavaScript library DataTables. It includes basic features like pagination,
-  searching (global search or search by individual columns), sorting (by
-  single or multiple columns). All these features are implemented on the R
-  side; for example, we can use R regular expressions for searching.
-  Besides, it also uses the Bootstrap CSS style. See the full
-  documentation and examples in the tutorial:
-  http://rstudio.github.io/shiny/tutorial/#datatables
-
-* Added a new option `shiny.error` which can take a function as an error
-  handler. It is called when an error occurs in an app (in user-provided
-  code), e.g., after we set options(shiny.error = recover), we can enter a
-  specified environment in the call stack to debug our code after an error
-  occurs.
-
-* The argument `launch.browser` in runApp() can also be a function,
-  which takes the URL of the shiny app as its input value.
-
-* runApp() uses a random port between 3000 and 8000 instead of 8100 now. It
-  will try up to 20 ports in case certain ports are not available.
-
-* Fixed a bug for conditional panels: the value `input.id` in the condition
-  was not correctly retrieved when the input widget had a type, such as
-  numericInput(). (reported by Jason Bryer)
-
-* Fixed two bugs in plotOutput(); clickId and hoverId did not give correct
-  coordinates in Firefox, or when the axis limits of the plot were changed.
-  (reported by Chris Warth and Greg D)
-
-* The minimal required version for the httpuv package was increased to 1.2
-  (on CRAN now).
-
-
-shiny 0.7.0
---------------------------------------------------------------------------------
-
-* Stopped sending websocket subprotocol. This fixes a compatibility issue with
-  Google Chrome 30.
-
-* The `input` and `output` objects are now also accessible via `session$input`
-  and `session$output`.
-
-* Added click and hover events for static plots; see `?plotOutput` for details.
-
-* Added optional logging of the execution states of a reactive program, and
-  tools for visualizing the log data. To use, start a new R session and call
-  `options(shiny.reactlog=TRUE)`. Then launch a Shiny app and interact with it.
-  Press Ctrl+F3 (or for Mac, Cmd+F3) in the browser to launch an interactive
-  visualization of the reactivity that has occurred. See `?showReactLog` for
-  more information.
-
-* Added `includeScript()` and `includeCSS()` functions.
-
-* Reactive expressions now have class="reactive" attribute. Also added
-  `is.reactive()` and `is.reactivevalues()` functions.
-
-* New `stopApp()` function, which stops an app and returns a value to the caller
-  of `runApp()`.
-
-* Added the `shiny.usecairo` option, which can be used to tell Shiny not to use
-  Cairo for PNG output even when it is installed. (Defaults to `TRUE`.)
-
-* Speed increases for `selectInput()` and `radioButtons()`, and their
-  corresponding updater functions, for when they have many options.
-
-* Added `tagSetChildren()` and `tagAppendChildren()` functions.
-
-* The HTTP request object that created the websocket is now accessible from the
-  `session` object, as `session$request`. This is a Rook-like request
-  environment that can be used to access HTTP headers, among other things.
-  (Note: When running in a Shiny Server environment, the request will reflect
-  the proxy HTTP request that was made from the Shiny Server process to the R
-  process, not the request that was made from the web browser to Shiny Server.)
-
-* Fix `getComputedStyle` issue, for IE8 browser compatibility (#196). Note:
-  Shiny Server is still required for IE8/9 compatibility.
-
-* Add shiny.sharedSecret option, to require the HTTP header Shiny-Shared-Secret
-  to be set to the given value.
-
-shiny 0.6.0
---------------------------------------------------------------------------------
-
-* `tabsetPanel()` can be directed to start with a specific tab selected.
-
-* Fix bug where multiple file uploads with 3 or more files result in incorrect
-  data.
-
-* Add `withTags()` function.
-
-* Add dateInput and dateRangeInput.
-
-* `shinyServer()` now takes an optional `session` argument, which is used for
-  communication with the session object.
-
-* Add functions to update values of existing inputs on a page, instead of
-  replacing them entirely.
-
-* Allow listening on domain sockets.
-
-* Added `actionButton()` to Shiny.
-
-* The server can now send custom JSON messages to the client. On the client
-  side, functions can be registered to handle these messages.
-
-* Callbacks can be registered to be called at the end of a client session.
-
-* Add ability to set priority of observers and outputs. Each priority level
-  gets its own queue.
-
-* Fix bug where the presence of a submit button would prevent sending of
-  metadata until the button was clicked.
-
-* `reactiveTimer()` and `invalidateLater()` by default no longer invalidate
-  reactive objects after the client session has closed.
-
-* Shiny apps can be run without a server.r and ui.r file.
-
-shiny 0.5.0
---------------------------------------------------------------------------------
-
-* Switch from websockets package for handling websocket connections to httpuv.
-
-* New method for detecting hidden output objects. Instead of checking that
-  height and width are 0, it checks that the object or any ancestor in the DOM
-  has style display:none.
-
-* Add `clientData` reactive values object, which carries information about the
-  client. This includes the hidden status of output objects, height/width plot
-  output objects, and the URL of the browser.
-
-* Add `parseQueryString()` function.
-
-* Add `renderImage()` function for sending arbitrary image files to the client,
-  and its counterpart, `imageOutput()`.
-
-* Add support for high-resolution (Retina) displays.
-
-* Fix bug #55, where `renderTable()` would throw error with an empty data frame.
-
-shiny 0.4.1
---------------------------------------------------------------------------------
-
-* Fix bug where width and height weren't passed along properly from
-  `reactivePlot` to `renderPlot`.
-
-* Fix bug where infinite recursion would happen when `reactivePlot` was passed
-  a function for width or height.
-
-shiny 0.4.0
---------------------------------------------------------------------------------
-
-* Added suspend/resume capability to observers.
-
-* Output objects are automatically suspended when they are hidden on the user's
-  web browser.
-
-* `runGist()` accepts GitHub's new URL format, which includes the username.
-
-* `reactive()` and `observe()` now take expressions instead of functions.
-
-* `reactiveText()`, `reactivePlot()`, and so on, have been renamed to
-  `renderText()`, `renderPlot()`, etc.  They also now take expressions instead
-  of functions.
-
-* Fixed a bug where empty values in a numericInput were sent to the R process
-  as 0. They are now sent as NA.
-
-shiny 0.3.1
---------------------------------------------------------------------------------
-
-* Fix issue #91: bug where downloading files did not work.
-
-* Add [[<- operator for shinyoutput object, making it possible to assign values
-  with `output[['plot1']] <- ...`.
-
-* Reactive functions now preserve the visible/invisible state of their returned
-  values.
-
-shiny 0.3.0
---------------------------------------------------------------------------------
-
-* Reactive functions are now evaluated lazily.
-
-* Add `reactiveValues()`.
-
-* Using `as.list()` to convert a reactivevalues object (like `input`) to a list
-  is deprecated. The new function `reactiveValuesToList()` should be used
-  instead.
-
-* Add `isolate()`. This function is used for accessing reactive functions,
-  without them invalidating their parent contexts.
-
-* Fix issue #58: bug where reactive functions are not re-run when all items in
-  a checkboxGroup are unchecked.
-
-* Fix issue #71, where `reactiveTable()` would return blank if the first
-  element of a data frame was NA.
-
-* In `plotOutput`, better validation for CSS units when specifying width and
-  height.
-
-* `reactivePrint()` no longer displays invisible output.
-
-* `reactiveText()` no longer displays printed output, only the return value
-  from a function.
-
-* The `runGitHub()` and `runUrl()` functions have been added, for running
-  Shiny apps from GitHub repositories and zip/tar files at remote URLs.
-
-* Fix issue #64, where pressing Enter in a textbox would cause a form to
-  submit.
-
-shiny 0.2.4
---------------------------------------------------------------------------------
-
-* `runGist` has been updated to use the new download URLs from
-  https://gist.github.com.
-
-* Shiny now uses `CairoPNG()` for output, when the Cairo package is available.
-  This provides better-looking output on Linux and Windows.
-
-shiny 0.2.3
---------------------------------------------------------------------------------
-
-* Ignore request variables for routing purposes
-
-shiny 0.2.2
---------------------------------------------------------------------------------
-
-* Fix CRAN warning (assigning to global environment)
-
-
-shiny 0.2.1
---------------------------------------------------------------------------------
-
-* [BREAKING] Modify API of `downloadHandler`: The `content` function now takes
-  a file path, not writable connection, as an argument. This makes it much
-  easier to work with APIs that only write to file paths, not connections.
-
-
-shiny 0.2.0
---------------------------------------------------------------------------------
-
-* Fix subtle name resolution bug--the usual symptom being S4 methods not being
-  invoked correctly when called from inside of ui.R or server.R
-
-
-shiny 0.1.14
---------------------------------------------------------------------------------
-
-* Fix slider animator, which broke in 0.1.10
-
-
-shiny 0.1.13
---------------------------------------------------------------------------------
-
-* Fix temp file leak in reactivePlot
-
-
-shiny 0.1.12
---------------------------------------------------------------------------------
-
-* Fix problems with runGist on Windows
-* Add feature for on-the-fly file downloads (e.g. CSV data, PDFs)
-* Add CSS hooks for app-wide busy indicators
-
-
-shiny 0.1.11
---------------------------------------------------------------------------------
-
-* Fix input binding with IE8 on Shiny Server
-* Fix issue #41: reactiveTable should allow print options too
-* Allow dynamic sizing of reactivePlot (i.e. using a function instead of a fixed
-  value)
-
-
-shiny 0.1.10
---------------------------------------------------------------------------------
-
-* Support more MIME types when serving out of www
-* Fix issue #35: Allow modification of untar args
-* headerPanel can take an explicit window title parameter
-* checkboxInput uses correct attribute `checked` instead of `selected`
-* Fix plot rendering with IE8 on Shiny Server
-
-
-shiny 0.1.9
---------------------------------------------------------------------------------
-
-* Much less flicker when updating plots
-* More customizable error display
-* Add `includeText`, `includeHTML`, and `includeMarkdown` functions for putting
-  text, HTML, and Markdown content from external files in the application's UI.
-
-
-shiny 0.1.8
---------------------------------------------------------------------------------
-
-* Add `runGist` function for conveniently running a Shiny app that is published
-  on gist.github.com.
-* Fix issue #27: Warnings cause reactive functions to stop executing.
-* The server.R and ui.R filenames are now case insensitive.
-* Add `wellPanel` function for creating inset areas on the page.
-* Add `bootstrapPage` function for creating new Bootstrap based
-  layouts from scratch.
-
-
-shiny 0.1.7
---------------------------------------------------------------------------------
-
-* Fix issue #26: Shiny.OutputBindings not correctly exported.
-* Add `repeatable` function for making easily repeatable versions of random
-  number generating functions.
-* Transcode JSON into UTF-8 (prevents non-ASCII reactivePrint values from
-  causing errors on Windows).
-
-
-shiny 0.1.6
---------------------------------------------------------------------------------
-
-* Import package dependencies, instead of attaching them (with the exception of
-  websockets, which doesn't currently work unless attached).
-* conditionalPanel was animated, now it is not.
-* bindAll was not correctly sending initial values to the server; fixed.
-
-
-shiny 0.1.5
---------------------------------------------------------------------------------
-
-* BREAKING CHANGE: JS APIs Shiny.bindInput and Shiny.bindOutput removed and
-  replaced with Shiny.bindAll; Shiny.unbindInput and Shiny.unbindOutput removed
-  and replaced with Shiny.unbindAll.
-* Add file upload support (currently only works with Chrome and Firefox). Use
-  a normal HTML file input, or call the `fileInput` UI function.
-* Shiny.unbindOutputs did not work, now it does.
-* Generally improved robustness of dynamic input/output bindings.
-* Add conditionalPanel UI function to allow showing/hiding UI based on a JS
-  expression; for example, whether an input is a particular value. Also works in
-  raw HTML (add the `data-display-if` attribute to the element that should be
-  shown/hidden).
-* htmlOutput (CSS class `shiny-html-output`) can contain inputs and outputs.
-
-
-shiny 0.1.4
---------------------------------------------------------------------------------
-
-* Allow Bootstrap tabsets to act as reactive inputs; their value indicates which
-  tab is active
-* Upgrade to Bootstrap 2.1
-* Add `checkboxGroupInput` control, which presents a list of checkboxes and
-  returns a vector of the selected values
-* Add `addResourcePath`, intended for reusable component authors to access CSS,
-  JavaScript, image files, etc. from their package directories
-* Add Shiny.bindInputs(scope), .unbindInputs(scope), .bindOutputs(scope), and
-  .unbindOutputs(scope) JS API calls to allow dynamic binding/unbinding of HTML
-  elements
-
-
-shiny 0.1.3
---------------------------------------------------------------------------------
-
-* Introduce Shiny.inputBindings.register JS API and InputBinding class, for
-  creating custom input controls
-* Add `step` parameter to numericInput
-* Read names of input using `names(input)`
-* Access snapshot of input as a list using `as.list(input)`
-* Fix issue #10: Plots in tabsets not rendered
-
-
-shiny 0.1.2
---------------------------------------------------------------------------------
-
-Initial private beta release!

R/app.R

@@ -27,6 +27,12 @@
 #'   request to determine whether the \code{ui} should be used to handle the
 #'   request. Note that the entire request path must match the regular
 #'   expression in order for the match to be considered successful.
+#' @param enableBookmarking Can be one of \code{"url"}, \code{"server"}, or
+#'   \code{"disable"}. This is equivalent to calling the
+#'   \code{\link{enableBookmarking}()} function just before calling
+#'   \code{shinyApp()}. With the default value (\code{NULL}), the app will
+#'   respect the setting from any previous calls to \code{enableBookmarking()}.
+#'   See \code{\link{enableBookmarking}} for more information.
 #' @return An object that represents the app. Printing the object or passing it
 #'   to \code{\link{runApp}} will run the app.
 #'
@@ -59,10 +65,9 @@
 #'
 #'   runApp(app)
 #' }
-#'
 #' @export
 shinyApp <- function(ui=NULL, server=NULL, onStart=NULL, options=list(),
-                     uiPattern="/") {
+                     uiPattern="/", enableBookmarking = NULL) {
   if (is.null(server)) {
     stop("`server` missing from shinyApp")
   }
@@ -76,12 +81,24 @@ shinyApp <- function(ui=NULL, server=NULL, onStart=NULL, options=list(),
     server
   }
 
+  if (!is.null(enableBookmarking)) {
+    bookmarkStore <- match.arg(enableBookmarking, c("url", "server", "disable"))
+    enableBookmarking(bookmarkStore)
+  }
+
+  # Store the appDir and bookmarking-related options, so that we can read them
+  # from within the app.
+  shinyOptions(appDir = getwd())
+  appOptions <- consumeAppOptions()
+
   structure(
     list(
       httpHandler = httpHandler,
       serverFuncSource = serverFuncSource,
       onStart = onStart,
-      options = options),
+      options = options,
+      appOptions = appOptions
+    ),
     class = "shiny.appobj"
   )
 }
@@ -113,7 +130,9 @@ shinyAppDir <- function(appDir, options=list()) {
 #' @export
 shinyAppFile <- function(appFile, options=list()) {
   appFile <- normalizePath(appFile, mustWork = TRUE)
-  shinyAppDir_appR(basename(appFile), dirname(appFile), options = options)
+  appDir <- dirname(appFile)
+
+  shinyAppDir_appR(basename(appFile), appDir, options = options)
 }
 
 # This reads in an app dir in the case that there's a server.R (and ui.R/www)
@@ -178,15 +197,21 @@ shinyAppDir_serverR <- function(appDir, options=list()) {
     }
   }
 
+  shinyOptions(appDir = appDir)
+
   oldwd <- NULL
+  monitorHandle <- NULL
   onStart <- function() {
     oldwd <<- getwd()
     setwd(appDir)
+    monitorHandle <<- initAutoReloadMonitor(appDir)
     if (file.exists(file.path.ci(appDir, "global.R")))
       sourceUTF8(file.path.ci(appDir, "global.R"))
   }
   onEnd <- function() {
     setwd(oldwd)
+    monitorHandle()
+    monitorHandle <<- NULL
   }
 
   structure(
@@ -195,14 +220,62 @@ shinyAppDir_serverR <- function(appDir, options=list()) {
       serverFuncSource = serverFuncSource,
       onStart = onStart,
       onEnd = onEnd,
-      options = options),
+      options = options
+    ),
     class = "shiny.appobj"
   )
 }
 
+# Start a reactive observer that continually monitors dir for changes to files
+# that have the extensions: r, htm, html, js, css, png, jpg, jpeg, gif. Case is
+# ignored when checking extensions. If any changes are detected, all connected
+# Shiny sessions are reloaded.
+#
+# Use options(shiny.autoreload = TRUE) to enable this behavior. Since monitoring
+# for changes is expensive (we are polling for mtimes here, nothing fancy) this
+# feature is intended only for development.
+#
+# You can customize the file patterns Shiny will monitor by setting the
+# shiny.autoreload.pattern option. For example, to monitor only ui.R:
+# options(shiny.autoreload.pattern = glob2rx("ui.R"))
+#
+# The return value is a function that halts monitoring when called.
+initAutoReloadMonitor <- function(dir) {
+  if (!getOption("shiny.autoreload", FALSE)) {
+    return(function(){})
+  }
+
+  filePattern <- getOption("shiny.autoreload.pattern",
+    ".*\\.(r|html?|js|css|png|jpe?g|gif)$")
+
+  lastValue <- NULL
+  obs <- observe({
+    files <- sort(list.files(dir, pattern = filePattern, recursive = TRUE,
+      ignore.case = TRUE))
+    times <- file.info(files)$mtime
+    names(times) <- files
+
+    if (is.null(lastValue)) {
+      # First run
+      lastValue <<- times
+    } else if (!identical(lastValue, times)) {
+      # We've changed!
+      lastValue <<- times
+      for (session in appsByToken$values()) {
+        session$reload()
+      }
+    }
+
+    invalidateLater(getOption("shiny.autoreload.interval", 500))
+  })
+
+  obs$destroy
+}
+
 # This reads in an app dir for a single-file application (e.g. app.R), and
 # returns a shiny.appobj.
-shinyAppDir_appR <- function(fileName, appDir, options=list()) {
+shinyAppDir_appR <- function(fileName, appDir, options=list())
+{
   fullpath <- file.path.ci(appDir, fileName)
 
   # This sources app.R and caches the content. When appObj() is called but
@@ -215,6 +288,8 @@ shinyAppDir_appR <- function(fileName, appDir, options=list()) {
       if (!is.shiny.appobj(result))
         stop("app.R did not return a shiny.appobj object.")
 
+      unconsumeAppOptions(result$appOptions)
+
       return(result)
     }
   )
@@ -233,12 +308,16 @@ shinyAppDir_appR <- function(fileName, appDir, options=list()) {
   fallbackWWWDir <- system.file("www-dir", package = "shiny")
 
   oldwd <- NULL
+  monitorHandle <- NULL
   onStart <- function() {
     oldwd <<- getwd()
     setwd(appDir)
+    monitorHandle <<- initAutoReloadMonitor(appDir)
   }
   onEnd <- function() {
     setwd(oldwd)
+    monitorHandle()
+    monitorHandle <<- NULL
   }
 
   structure(
@@ -313,7 +392,20 @@ as.tags.shiny.appobj <- function(x, ...) {
   height <- if (is.null(opts$height)) "400" else opts$height
 
   path <- addSubApp(x)
-  tags$iframe(src=path, width=width, height=height, class="shiny-frame")
+  deferredIFrame(path, width, height)
+}
+
+# Generate subapp iframes in such a way that they will not actually load right
+# away. Loading subapps immediately upon app load can result in a storm of
+# connections, all of which are contending for the few concurrent connections
+# that a browser will make to a specific origin. Instead, we load dummy iframes
+# and let the client load them when convenient. (See the initIframes function in
+# init_shiny.js.)
+deferredIFrame <- function(path, width, height) {
+  tags$iframe("data-deferred-src" = path,
+    width = width, height = height,
+    class = "shiny-frame shiny-frame-deferred"
+  )
 }
 
 #' Knitr S3 methods
@@ -364,8 +456,7 @@ knit_print.shiny.appobj <- function(x, ...) {
   }
   else {
     path <- addSubApp(x)
-    output <- tags$iframe(src=path, width=width, height=height,
-                          class="shiny-frame")
+    output <- deferredIFrame(path, width, height)
   }
 
   # If embedded Shiny apps ever have JS/CSS dependencies (like pym.js) we'll
@@ -389,3 +480,14 @@ knit_print.shiny.render.function <- function(x, ..., inline = FALSE) {
                                       shiny_rmd_warning())
   output
 }
+
+# Lets us drop reactive expressions directly into a knitr chunk and have the
+# value printed out! Nice for teaching if nothing else.
+#' @rdname knitr_methods
+#' @export
+knit_print.reactive <- function(x, ..., inline = FALSE) {
+  renderFunc <- if (inline) renderText else renderPrint
+  knitr::knit_print(renderFunc({
+    x()
+  }), inline = inline)
+}

R/bookmark-state-local.R

@@ -0,0 +1,28 @@
+# Function wrappers for saving and restoring state to/from disk when running
+# Shiny locally.
+#
+# These functions provide a directory to the callback function.
+#
+# @param id A session ID to save.
+# @param callback A callback function that saves state to or restores state from
+#   a directory. It must take one argument, \code{stateDir}, which is a
+#   directory to which it writes/reads.
+
+saveInterfaceLocal <- function(id, callback) {
+  # Try to save in app directory
+  appDir <- getShinyOption("appDir", default = getwd())
+
+  stateDir <- file.path(appDir, "shiny_bookmarks", id)
+  if (!dirExists(stateDir))
+    dir.create(stateDir, recursive = TRUE)
+
+  callback(stateDir)
+}
+
+loadInterfaceLocal <- function(id, callback) {
+  # Try to load from app directory
+  appDir <- getShinyOption("appDir", default = getwd())
+
+  stateDir <- file.path(appDir, "shiny_bookmarks", id)
+  callback(stateDir)
+}

R/bootstrap-layout.R

@@ -31,7 +31,11 @@
 #' @seealso \code{\link{column}}, \code{\link{sidebarLayout}}
 #'
 #' @examples
-#' shinyUI(fluidPage(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' # Example of UI with fluidPage
+#' ui <- fluidPage(
 #'
 #'   # Application title
 #'   titlePanel("Hello Shiny!"),
@@ -52,9 +56,21 @@
 #'       plotOutput("distPlot")
 #'     )
 #'   )
-#' ))
+#' )
 #'
-#' shinyUI(fluidPage(
+#' # Server logic
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     hist(rnorm(input$obs))
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#'
+#'
+#' # UI demonstrating column layouts
+#' ui <- fluidPage(
 #'   title = "Hello Shiny!",
 #'   fluidRow(
 #'     column(width = 4,
@@ -64,8 +80,10 @@
 #'       "3 offset 2"
 #'     )
 #'   )
-#' ))
+#' )
 #'
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @rdname fluidPage
 #' @export
 fluidPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
@@ -115,7 +133,10 @@ fluidRow <- function(...) {
 #' @seealso \code{\link{column}}
 #'
 #' @examples
-#' shinyUI(fixedPage(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fixedPage(
 #'   title = "Hello, Shiny!",
 #'   fixedRow(
 #'     column(width = 4,
@@ -125,7 +146,10 @@ fluidRow <- function(...) {
 #'       "3 offset 2"
 #'     )
 #'   )
-#' ))
+#' )
+#'
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #'
 #' @rdname fixedPage
 #' @export
@@ -160,24 +184,43 @@ fixedRow <- function(...) {
 #' @seealso \code{\link{fluidRow}}, \code{\link{fixedRow}}.
 #'
 #' @examples
-#' fluidRow(
-#'   column(4,
-#'     sliderInput("obs", "Number of observations:",
-#'                 min = 1, max = 1000, value = 500)
-#'   ),
-#'   column(8,
-#'     plotOutput("distPlot")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   fluidRow(
+#'     column(4,
+#'       sliderInput("obs", "Number of observations:",
+#'                   min = 1, max = 1000, value = 500)
+#'     ),
+#'     column(8,
+#'       plotOutput("distPlot")
+#'     )
 #'   )
 #' )
 #'
-#' fluidRow(
-#'   column(width = 4,
-#'     "4"
-#'   ),
-#'   column(width = 3, offset = 2,
-#'     "3 offset 2"
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     hist(rnorm(input$obs))
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#'
+#'
+#'
+#' ui <- fluidPage(
+#'   fluidRow(
+#'     column(width = 4,
+#'       "4"
+#'     ),
+#'     column(width = 3, offset = 2,
+#'       "3 offset 2"
+#'     )
 #'   )
 #' )
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 column <- function(width, ..., offset = 0) {
 
@@ -202,8 +245,14 @@ column <- function(width, ..., offset = 0) {
 #'
 #'
 #' @examples
-#' titlePanel("Hello Shiny!")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   titlePanel("Hello Shiny!")
+#' )
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 titlePanel <- function(title, windowTitle=title) {
   tagList(
@@ -226,8 +275,11 @@ titlePanel <- function(title, windowTitle=title) {
 #'   layout.
 #'
 #' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
 #' # Define UI
-#' shinyUI(fluidPage(
+#' ui <- fluidPage(
 #'
 #'   # Application title
 #'   titlePanel("Hello Shiny!"),
@@ -248,8 +300,18 @@ titlePanel <- function(title, windowTitle=title) {
 #'       plotOutput("distPlot")
 #'     )
 #'   )
-#' ))
+#' )
 #'
+#' # Server logic
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     hist(rnorm(input$obs))
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#' }
 #' @export
 sidebarLayout <- function(sidebarPanel,
                           mainPanel,
@@ -286,13 +348,18 @@ sidebarLayout <- function(sidebarPanel,
 #' @seealso \code{\link{fluidPage}}, \code{\link{flowLayout}}
 #'
 #' @examples
-#' shinyUI(fluidPage(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
 #'   verticalLayout(
 #'     a(href="http://example.com/link1", "Link One"),
 #'     a(href="http://example.com/link2", "Link Two"),
 #'     a(href="http://example.com/link3", "Link Three")
 #'   )
-#' ))
+#' )
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 verticalLayout <- function(..., fluid = TRUE) {
   lapply(list(...), function(row) {
@@ -319,11 +386,16 @@ verticalLayout <- function(..., fluid = TRUE) {
 #' @seealso \code{\link{verticalLayout}}
 #'
 #' @examples
-#' flowLayout(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- flowLayout(
 #'   numericInput("rows", "How many rows?", 5),
 #'   selectInput("letter", "Which letter?", LETTERS),
 #'   sliderInput("value", "What value?", 0, 100, 50)
 #' )
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 flowLayout <- function(..., cellArgs = list()) {
 
@@ -346,7 +418,6 @@ flowLayout <- function(..., cellArgs = list()) {
 #' suitable for wrapping inputs.
 #'
 #' @param ... Input controls or other HTML elements.
-#'
 #' @export
 inputPanel <- function(...) {
   div(class = "shiny-input-panel",
@@ -369,21 +440,33 @@ inputPanel <- function(...) {
 #'   of the layout.
 #'
 #' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' # Server code used for all examples
+#' server <- function(input, output) {
+#'   output$plot1 <- renderPlot(plot(cars))
+#'   output$plot2 <- renderPlot(plot(pressure))
+#'   output$plot3 <- renderPlot(plot(AirPassengers))
+#' }
+#'
 #' # Equal sizing
-#' splitLayout(
+#' ui <- splitLayout(
 #'   plotOutput("plot1"),
 #'   plotOutput("plot2")
 #' )
+#' shinyApp(ui, server)
 #'
 #' # Custom widths
-#' splitLayout(cellWidths = c("25%", "75%"),
+#' ui <- splitLayout(cellWidths = c("25%", "75%"),
 #'   plotOutput("plot1"),
 #'   plotOutput("plot2")
 #' )
+#' shinyApp(ui, server)
 #'
 #' # All cells at 300 pixels wide, with cell padding
 #' # and a border around everything
-#' splitLayout(
+#' ui <- splitLayout(
 #'   style = "border: 1px solid silver;",
 #'   cellWidths = 300,
 #'   cellArgs = list(style = "padding: 6px"),
@@ -391,6 +474,8 @@ inputPanel <- function(...) {
 #'   plotOutput("plot2"),
 #'   plotOutput("plot3")
 #' )
+#' shinyApp(ui, server)
+#' }
 #' @export
 splitLayout <- function(..., cellWidths = NULL, cellArgs = list()) {
 
@@ -417,3 +502,193 @@ splitLayout <- function(..., cellWidths = NULL, cellArgs = list()) {
     }, SIMPLIFY = FALSE)
   ))
 }
+
+#' Flex Box-based row/column layouts
+#'
+#' Creates row and column layouts with proportionally-sized cells, using the
+#' Flex Box layout model of CSS3. These can be nested to create arbitrary
+#' proportional-grid layouts. \strong{Warning:} Flex Box is not well supported
+#' by Internet Explorer, so these functions should only be used where modern
+#' browsers can be assumed.
+#'
+#' @details If you try to use \code{fillRow} and \code{fillCol} inside of other
+#'   Shiny containers, such as \code{\link{sidebarLayout}},
+#'   \code{\link{navbarPage}}, or even \code{tags$div}, you will probably find
+#'   that they will not appear. This is due to \code{fillRow} and \code{fillCol}
+#'   defaulting to \code{height="100\%"}, which will only work inside of
+#'   containers that have determined their own size (rather than shrinking to
+#'   the size of their contents, as is usually the case in HTML).
+#'
+#'   To avoid this problem, you have two options:
+#'   \itemize{
+#'     \item only use \code{fillRow}/\code{fillCol} inside of \code{fillPage},
+#'       \code{fillRow}, or \code{fillCol}
+#'     \item provide an explicit \code{height} argument to
+#'       \code{fillRow}/\code{fillCol}
+#'   }
+#'
+#' @param ... UI objects to put in each row/column cell; each argument will
+#'   occupy a single cell. (To put multiple items in a single cell, you can use
+#'   \code{\link{tagList}} or \code{\link{div}} to combine them.) Named
+#'   arguments will be used as attributes on the \code{div} element that
+#'   encapsulates the row/column.
+#' @param flex Determines how space should be distributed to the cells. Can be a
+#'   single value like \code{1} or \code{2} to evenly distribute the available
+#'   space; or use a vector of numbers to specify the proportions. For example,
+#'   \code{flex = c(2, 3)} would cause the space to be split 40\%/60\% between
+#'   two cells. NA values will cause the corresponding cell to be sized
+#'   according to its contents (without growing or shrinking).
+#' @param width,height The total amount of width and height to use for the
+#'   entire row/column. For the default height of \code{"100\%"} to be
+#'   effective, the parent must be \code{fillPage}, another
+#'   \code{fillRow}/\code{fillCol}, or some other HTML element whose height is
+#'   not determined by the height of its contents.
+#'
+#' @examples
+#' # Only run this example in interactive R sessions.
+#' if (interactive()) {
+#'
+#' ui <- fillPage(fillRow(
+#'   plotOutput("plotLeft", height = "100%"),
+#'   fillCol(
+#'     plotOutput("plotTopRight", height = "100%"),
+#'     plotOutput("plotBottomRight", height = "100%")
+#'   )
+#' ))
+#'
+#' server <- function(input, output, session) {
+#'   output$plotLeft <- renderPlot(plot(cars))
+#'   output$plotTopRight <- renderPlot(plot(pressure))
+#'   output$plotBottomRight <- renderPlot(plot(AirPassengers))
+#' }
+#'
+#' shinyApp(ui, server)
+#'
+#' }
+#' @export
+fillRow <- function(..., flex = 1, width = "100%", height = "100%") {
+  flexfill(..., direction = "row", flex = flex, width = width, height = height)
+}
+
+#' @rdname fillRow
+#' @export
+fillCol <- function(..., flex = 1, width = "100%", height = "100%") {
+  flexfill(..., direction = "column", flex = flex, width = width, height = height)
+}
+
+flexfill <- function(..., direction, flex, width = width, height = height) {
+  children <- list(...)
+  attrs <- list()
+
+  if (!is.null(names(children))) {
+    attrs <- children[names(children) != ""]
+    children <- children[names(children) == ""]
+  }
+
+  if (length(flex) > length(children)) {
+    flex <- flex[1:length(children)]
+  }
+
+  # The dimension along the main axis
+  main <- switch(direction,
+    row = "width",
+    "row-reverse" = "width",
+    column = "height",
+    "column-reverse" = "height",
+    stop("Unexpected direction")
+  )
+  # The dimension along the cross axis
+  cross <- if (main == "width") "height" else "width"
+
+  divArgs <- list(
+    class = sprintf("flexfill-container flexfill-container-%s", direction),
+    style = css(
+      display = "-webkit-flex",
+      display = "-ms-flexbox",
+      display = "flex",
+      .webkit.flex.direction = direction,
+      .ms.flex.direction = direction,
+      flex.direction = direction,
+      width = validateCssUnit(width),
+      height = validateCssUnit(height)
+    ),
+    mapply(children, flex, FUN = function(el, flexValue) {
+      if (is.na(flexValue)) {
+        # If the flex value is NA, then put the element in a simple flex item
+        # that sizes itself (along the main axis) to its contents
+        tags$div(
+          class = "flexfill-item",
+          style = css(
+            position = "relative",
+            "-webkit-flex" = "none",
+            "-ms-flex" = "none",
+            flex = "none"
+          ),
+          style = paste0(main, ":auto;", cross, ":100%;"),
+          el
+        )
+      } else if (is.numeric(flexValue)) {
+        # If the flex value is numeric, we need *two* wrapper divs. The outer is
+        # the flex item, and the inner is an absolute-fill div that is needed to
+        # make percentage-based sizing for el work correctly. I don't understand
+        # why this is needed but the truth is probably in this SO page:
+        # http://stackoverflow.com/questions/15381172/css-flexbox-child-height-100
+        tags$div(
+          class = "flexfill-item",
+          style = css(
+            position = "relative",
+            "-webkit-flex" = flexValue,
+            "-ms-flex" = flexValue,
+            flex = flexValue,
+            width = "100%", height = "100%"
+          ),
+          tags$div(
+            class = "flexfill-item-inner",
+            style = css(
+              position = "absolute",
+              top = 0, left = 0, right = 0, bottom = 0
+            ),
+            el
+          )
+        )
+      } else {
+        stop("Unexpected flex argument: ", flexValue)
+      }
+    }, SIMPLIFY = FALSE, USE.NAMES = FALSE)
+  )
+  do.call(tags$div, c(attrs, divArgs))
+}
+
+css <- function(..., collapse_ = "") {
+  props <- list(...)
+  if (length(props) == 0) {
+    return("")
+  }
+
+  if (is.null(names(props)) || any(names(props) == "")) {
+    stop("cssList expects all arguments to be named")
+  }
+
+  # Necessary to make factors show up as level names, not numbers
+  props[] <- lapply(props, paste, collapse = " ")
+
+  # Drop null args
+  props <- props[!sapply(props, empty)]
+  if (length(props) == 0) {
+    return("")
+  }
+
+  # Replace all '.' and '_' in property names to '-'
+  names(props) <- gsub("[._]", "-", tolower(gsub("([A-Z])", "-\\1", names(props))))
+
+  # Create "!important" suffix for each property whose name ends with !, then
+  # remove the ! from the property name
+  important <- ifelse(grepl("!$", names(props), perl = TRUE), " !important", "")
+  names(props) <- sub("!$", "", names(props), perl = TRUE)
+
+  paste0(names(props), ":", props, important, ";", collapse = collapse_)
+}
+
+empty <- function(x) {
+  length(x) == 0 || (is.character(x) && !any(nzchar(x)))
+}

R/bootstrap.R

@@ -25,7 +25,6 @@ NULL
 #'   \code{\link{fluidPage}} function instead.
 #'
 #' @seealso \code{\link{fluidPage}}, \code{\link{fixedPage}}
-#'
 #' @export
 bootstrapPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
 
@@ -33,26 +32,6 @@ bootstrapPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
     shinyDeprecated("The 'responsive' argument is no longer used with Bootstrap 3.")
   }
 
-  # required head tags for boostrap
-  importBootstrap <- function() {
-    list(
-      htmlDependency("bootstrap", "3.3.1",
-        c(
-          href = "shared/bootstrap",
-          file = system.file("www/shared/bootstrap", package = "shiny")
-        ),
-        script = c(
-          "js/bootstrap.min.js",
-          # These shims are necessary for IE 8 compatibility
-          "shim/html5shiv.min.js",
-          "shim/respond.min.js"
-        ),
-        stylesheet = if (is.null(theme)) "css/bootstrap.min.css",
-        meta = list(viewport = "width=device-width, initial-scale=1")
-      )
-    )
-  }
-
   attachDependencies(
     tagList(
       if (!is.null(title)) tags$head(tags$title(title)),
@@ -63,7 +42,37 @@ bootstrapPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
       # remainder of tags passed to the function
       list(...)
     ),
-    importBootstrap()
+    bootstrapLib()
+  )
+}
+
+#' Bootstrap libraries
+#'
+#' This function returns a set of web dependencies necessary for using Bootstrap
+#' components in a web page.
+#'
+#' It isn't necessary to call this function if you use
+#' \code{\link{bootstrapPage}} or others which use \code{bootstrapPage}, such
+#' \code{\link{basicPage}}, \code{\link{fluidPage}}, \code{\link{fillPage}},
+#' \code{\link{pageWithSidebar}}, and \code{\link{navbarPage}}, because they
+#' already include the Bootstrap web dependencies.
+#'
+#' @inheritParams bootstrapPage
+#' @export
+bootstrapLib <- function(theme = NULL) {
+  htmlDependency("bootstrap", "3.3.7",
+    c(
+      href = "shared/bootstrap",
+      file = system.file("www/shared/bootstrap", package = "shiny")
+    ),
+    script = c(
+      "js/bootstrap.min.js",
+      # These shims are necessary for IE 8 compatibility
+      "shim/html5shiv.min.js",
+      "shim/respond.min.js"
+    ),
+    stylesheet = if (is.null(theme)) "css/bootstrap.min.css",
+    meta = list(viewport = "width=device-width, initial-scale=1")
   )
 }
 
@@ -73,6 +82,102 @@ basicPage <- function(...) {
   bootstrapPage(div(class="container-fluid", list(...)))
 }
 
+
+#' Create a page that fills the window
+#'
+#' \code{fillPage} creates a page whose height and width always fill the
+#' available area of the browser window.
+#'
+#' The \code{\link{fluidPage}} and \code{\link{fixedPage}} functions are used
+#' for creating web pages that are laid out from the top down, leaving
+#' whitespace at the bottom if the page content's height is smaller than the
+#' browser window, and scrolling if the content is larger than the window.
+#'
+#' \code{fillPage} is designed to latch the document body's size to the size of
+#' the window. This makes it possible to fill it with content that also scales
+#' to the size of the window.
+#'
+#' For example, \code{fluidPage(plotOutput("plot", height = "100\%"))} will not
+#' work as expected; the plot element's effective height will be \code{0},
+#' because the plot's containing elements (\code{<div>} and \code{<body>}) have
+#' \emph{automatic} height; that is, they determine their own height based on
+#' the height of their contained elements. However,
+#' \code{fillPage(plotOutput("plot", height = "100\%"))} will work because
+#' \code{fillPage} fixes the \code{<body>} height at 100\% of the window height.
+#'
+#' Note that \code{fillPage(plotOutput("plot"))} will not cause the plot to fill
+#' the page. Like most Shiny output widgets, \code{plotOutput}'s default height
+#' is a fixed number of pixels. You must explicitly set \code{height = "100\%"}
+#' if you want a plot (or htmlwidget, say) to fill its container.
+#'
+#' One must be careful what layouts/panels/elements come between the
+#' \code{fillPage} and the plots/widgets. Any container that has an automatic
+#' height will cause children with \code{height = "100\%"} to misbehave. Stick
+#' to functions that are designed for fill layouts, such as the ones in this
+#' package.
+#'
+#' @param ... Elements to include within the page.
+#' @param padding Padding to use for the body. This can be a numeric vector
+#'   (which will be interpreted as pixels) or a character vector with valid CSS
+#'   lengths. The length can be between one and four. If one, then that value
+#'   will be used for all four sides. If two, then the first value will be used
+#'   for the top and bottom, while the second value will be used for left and
+#'   right. If three, then the first will be used for top, the second will be
+#'   left and right, and the third will be bottom. If four, then the values will
+#'   be interpreted as top, right, bottom, and left respectively.
+#' @param title The title to use for the browser window/tab (it will not be
+#'   shown in the document).
+#' @param bootstrap If \code{TRUE}, load the Bootstrap CSS library.
+#' @param theme URL to alternative Bootstrap stylesheet.
+#'
+#' @examples
+#' fillPage(
+#'   tags$style(type = "text/css",
+#'     ".half-fill { width: 50%; height: 100%; }",
+#'     "#one { float: left; background-color: #ddddff; }",
+#'     "#two { float: right; background-color: #ccffcc; }"
+#'   ),
+#'   div(id = "one", class = "half-fill",
+#'     "Left half"
+#'   ),
+#'   div(id = "two", class = "half-fill",
+#'     "Right half"
+#'   ),
+#'   padding = 10
+#' )
+#'
+#' fillPage(
+#'   fillRow(
+#'     div(style = "background-color: red; width: 100%; height: 100%;"),
+#'     div(style = "background-color: blue; width: 100%; height: 100%;")
+#'   )
+#' )
+#' @export
+fillPage <- function(..., padding = 0, title = NULL, bootstrap = TRUE,
+  theme = NULL) {
+
+  fillCSS <- tags$head(tags$style(type = "text/css",
+    "html, body { width: 100%; height: 100%; overflow: hidden; }",
+    sprintf("body { padding: %s; margin: 0; }", collapseSizes(padding))
+  ))
+
+  if (isTRUE(bootstrap)) {
+    bootstrapPage(title = title, theme = theme, fillCSS, ...)
+  } else {
+    tagList(
+      fillCSS,
+      if (!is.null(title)) tags$head(tags$title(title)),
+      ...
+    )
+  }
+}
+
+collapseSizes <- function(padding) {
+  paste(
+    sapply(padding, shiny::validateCssUnit, USE.NAMES = FALSE),
+    collapse = " ")
+}
+
 #' Create a page with a sidebar
 #'
 #' Create a Shiny UI that contains a header with the application title, a
@@ -89,7 +194,7 @@ basicPage <- function(...) {
 #'
 #' @examples
 #' # Define UI
-#' shinyUI(pageWithSidebar(
+#' pageWithSidebar(
 #'
 #'   # Application title
 #'   headerPanel("Hello Shiny!"),
@@ -107,8 +212,7 @@ basicPage <- function(...) {
 #'   mainPanel(
 #'     plotOutput("distPlot")
 #'   )
-#' ))
-#'
+#' )
 #' @export
 pageWithSidebar <- function(headerPanel,
                             sidebarPanel,
@@ -135,18 +239,24 @@ pageWithSidebar <- function(headerPanel,
 #' toggle a set of \code{\link{tabPanel}} elements.
 #'
 #' @param title The title to display in the navbar
-#' @param ... \code{\link{tabPanel}} elements to include in the page
+#' @param ... \code{\link{tabPanel}} elements to include in the page. The
+#'   \code{navbarMenu} function also accepts strings, which will be used as menu
+#'   section headers. If the string is a set of dashes like \code{"----"} a
+#'   horizontal separator will be displayed in the menu.
 #' @param id If provided, you can use \code{input$}\emph{\code{id}} in your
 #'   server logic to determine which of the current tabs is active. The value
 #'   will correspond to the \code{value} argument that is passed to
 #'   \code{\link{tabPanel}}.
+#' @param selected The \code{value} (or, if none was supplied, the \code{title})
+#'   of the tab that should be selected by default. If \code{NULL}, the first
+#'   tab will be selected.
 #' @param position Determines whether the navbar should be displayed at the top
-#'   of the page with normal scrolling behavior (\code{"static-top"}), pinned
-#'   at the top (\code{"fixed-top"}), or pinned at the bottom
+#'   of the page with normal scrolling behavior (\code{"static-top"}), pinned at
+#'   the top (\code{"fixed-top"}), or pinned at the bottom
 #'   (\code{"fixed-bottom"}). Note that using \code{"fixed-top"} or
 #'   \code{"fixed-bottom"} will cause the navbar to overlay your body content,
-#'   unless you add padding, e.g.:
-#'   \code{tags$style(type="text/css", "body {padding-top: 70px;}")}
+#'   unless you add padding, e.g.: \code{tags$style(type="text/css", "body
+#'   {padding-top: 70px;}")}
 #' @param header Tag or list of tags to display as a common header above all
 #'   tabPanels.
 #' @param footer Tag or list of tags to display as a common footer below all
@@ -178,23 +288,26 @@ pageWithSidebar <- function(headerPanel,
 #'   \code{\link{updateNavbarPage}}
 #'
 #' @examples
-#' shinyUI(navbarPage("App Title",
+#' navbarPage("App Title",
 #'   tabPanel("Plot"),
 #'   tabPanel("Summary"),
 #'   tabPanel("Table")
-#' ))
+#' )
 #'
-#' shinyUI(navbarPage("App Title",
+#' navbarPage("App Title",
 #'   tabPanel("Plot"),
 #'   navbarMenu("More",
 #'     tabPanel("Summary"),
+#'     "----",
+#'     "Section header",
 #'     tabPanel("Table")
 #'   )
-#' ))
+#' )
 #' @export
 navbarPage <- function(title,
                        ...,
                        id = NULL,
+                       selected = NULL,
                        position = c("static-top", "fixed-top", "fixed-bottom"),
                        header = NULL,
                        footer = NULL,
@@ -222,9 +335,12 @@ navbarPage <- function(title,
   if (inverse)
     navbarClass <- paste(navbarClass, "navbar-inverse")
 
+  if (!is.null(id))
+    selected <- restoreInput(id = id, default = selected)
+
   # build the tabset
   tabs <- list(...)
-  tabset <- buildTabset(tabs, "nav navbar-nav", NULL, id)
+  tabset <- buildTabset(tabs, "nav navbar-nav", NULL, id, selected)
 
   # built the container div dynamically to support optional collapsibility
   if (collapsible) {
@@ -314,7 +430,6 @@ headerPanel <- function(title, windowTitle=title) {
 #'
 #' @param ... UI elements to include inside the panel.
 #' @return The newly created panel.
-#'
 #' @export
 wellPanel <- function(...) {
   div(class="well", ...)
@@ -418,7 +533,6 @@ mainPanel <- function(..., width = 8) {
 #'       )
 #'    )
 #' )
-#'
 #' @export
 conditionalPanel <- function(condition, ...) {
   div('data-display-if'=condition, ...)
@@ -491,10 +605,8 @@ tabPanel <- function(title, ..., value = title, icon = NULL) {
 #'   tab will be selected.
 #' @param type Use "tabs" for the standard look; Use "pills" for a more plain
 #'   look where tabs are selected using a background fill color.
-#' @param position The position of the tabs relative to the content. Valid
-#'   values are "above", "below", "left", and "right" (defaults to "above").
-#'   Note that the \code{position} argument is not valid when \code{type} is
-#'   "pill".
+#' @param position This argument is deprecated; it has been discontinued in
+#'   Bootstrap 3.
 #' @return A tabset that can be passed to \code{\link{mainPanel}}
 #'
 #' @seealso \code{\link{tabPanel}}, \code{\link{updateTabsetPanel}}
@@ -514,25 +626,28 @@ tabsetPanel <- function(...,
                         id = NULL,
                         selected = NULL,
                         type = c("tabs", "pills"),
-                        position = c("above", "below", "left", "right")) {
+                        position = NULL) {
+  if (!is.null(position)) {
+    shinyDeprecated(msg = paste("tabsetPanel: argument 'position' is deprecated;",
+                                "it has been discontinued in Bootstrap 3."),
+                    version = "0.10.2.2")
+  }
+
+  if (!is.null(id))
+    selected <- restoreInput(id = id, default = selected)
 
   # build the tabset
   tabs <- list(...)
   type <- match.arg(type)
+
   tabset <- buildTabset(tabs, paste0("nav nav-", type), NULL, id, selected)
 
-  # position the nav list and content appropriately
-  position <- match.arg(position)
-  if (position %in% c("above", "left", "right")) {
-    first <- tabset$navList
-    second <- tabset$content
-  } else if (position %in% c("below")) {
-    first <- tabset$content
-    second <- tabset$navList
-  }
+  # create the content
+  first <- tabset$navList
+  second <- tabset$content
 
   # create the tab div
-  tags$div(class = paste("tabbable tabs-", position, sep=""), first, second)
+  tags$div(class = "tabbable", first, second)
 }
 
 #' Create a navigation list panel
@@ -563,7 +678,7 @@ tabsetPanel <- function(...,
 #'
 #' @seealso \code{\link{tabPanel}}, \code{\link{updateNavlistPanel}}
 #' @examples
-#' shinyUI(fluidPage(
+#' fluidPage(
 #'
 #'   titlePanel("Application Title"),
 #'
@@ -573,7 +688,7 @@ tabsetPanel <- function(...,
 #'     tabPanel("Second"),
 #'     tabPanel("Third")
 #'   )
-#' ))
+#' )
 #' @export
 navlistPanel <- function(...,
                          id = NULL,
@@ -587,6 +702,9 @@ navlistPanel <- function(...,
       tags$li(class="navbar-brand", text)
   }
 
+  if (!is.null(id))
+    selected <- restoreInput(id = id, default = selected)
+
   # build the tabset
   tabs <- list(...)
   tabset <- buildTabset(tabs,
@@ -609,117 +727,188 @@ navlistPanel <- function(...,
 }
 
 
-buildTabset <- function(tabs,
-                        ulClass,
-                        textFilter = NULL,
-                        id = NULL,
-                        selected = NULL) {
+buildTabset <- function(tabs, ulClass, textFilter = NULL,
+                        id = NULL, selected = NULL) {
 
-  # build tab nav list and tab content div
+  # This function proceeds in two phases. First, it scans over all the items
+  # to find and mark which tab should start selected. Then it actually builds
+  # the tab nav and tab content lists.
 
-  # add tab input sentinel class if we have an id
-  if (!is.null(id))
-    ulClass <- paste(ulClass, "shiny-tab-input")
-
-  tabNavList <- tags$ul(class = ulClass, id = id)
-  tabContent <- tags$div(class = "tab-content")
-  firstTab <- TRUE
-  tabsetId <- p_randomInt(1000, 10000)
-  tabId <- 1
-  for (divTag in tabs) {
-
-    # check for text; pass it to the textFilter or skip it if there is none
-    if (is.character(divTag)) {
-      if (!is.null(textFilter))
-        tabNavList <- tagAppendChild(tabNavList, textFilter(divTag))
-      next
-    }
-
-    # compute id and assign it to the div
-    thisId <- paste("tab", tabsetId, tabId, sep="-")
-    divTag$attribs$id <- thisId
-    tabId <- tabId + 1
-
-    tabValue <- divTag$attribs$`data-value`
-
-    # function to append an optional icon to an aTag
-    appendIcon <- function(aTag, iconClass) {
-      if (!is.null(iconClass)) {
-        # for font-awesome we specify fixed-width
-        if (grepl("fa-", iconClass, fixed = TRUE))
-          iconClass <- paste(iconClass, "fa-fw")
-        aTag <- tagAppendChild(aTag, icon(name = NULL, class = iconClass))
-      }
-      aTag
-    }
-
-    # check for a navbarMenu and handle appropriately
-    if (inherits(divTag, "shiny.navbarmenu")) {
-
-      # create the a tag
-      aTag <- tags$a(href="#",
-                     class="dropdown-toggle",
-                     `data-toggle`="dropdown")
-
-      # add optional icon
-      aTag <- appendIcon(aTag, divTag$iconClass)
-
-      # add the title and caret
-      aTag <- tagAppendChild(aTag, divTag$title)
-      aTag <- tagAppendChild(aTag, tags$b(class="caret"))
-
-      # build the dropdown list element
-      liTag <- tags$li(class = "dropdown", aTag)
-
-      # build the child tabset
-      tabset <- buildTabset(divTag$tabs, "dropdown-menu")
-      liTag <- tagAppendChild(liTag, tabset$navList)
-
-      # don't add a standard tab content div, rather add the list of tab
-      # content divs that are contained within the tabset
-      divTag <- NULL
-      tabContent <- tagAppendChildren(tabContent,
-                                      list = tabset$content$children)
-    }
-    # else it's a standard navbar item
-    else {
-      # create the a tag
-      aTag <- tags$a(href=paste("#", thisId, sep=""),
-                     `data-toggle` = "tab",
-                     `data-value` = tabValue)
-
-      # append optional icon
-      aTag <- appendIcon(aTag, divTag$attribs$`data-icon-class`)
-
-      # add the title
-      aTag <- tagAppendChild(aTag, divTag$attribs$title)
-
-      # create the li tag
-      liTag <- tags$li(aTag)
-    }
-
-    if (is.null(tabValue)) {
-      tabValue <- divTag$attribs$title
-    }
-
-    # If appropriate, make this the selected tab (don't ever do initial
-    # selection of tabs that are within a navbarMenu)
-    if ((ulClass != "dropdown-menu") &&
-       ((firstTab && is.null(selected)) ||
-        (!is.null(selected) && identical(selected, tabValue)))) {
-      liTag$attribs$class <- "active"
-      divTag$attribs$class <- "tab-pane active"
-      firstTab = FALSE
-    }
-
-    divTag$attribs$title <- NULL
-
-    # append the elements to our lists
-    tabNavList <- tagAppendChild(tabNavList, liTag)
-    tabContent <- tagAppendChild(tabContent, divTag)
+  # Mark an item as selected
+  markSelected <- function(x) {
+    attr(x, "selected") <- TRUE
+    x
   }
 
-  list(navList = tabNavList, content = tabContent)
+  # Returns TRUE if an item is selected
+  isSelected <- function(x) {
+    isTRUE(attr(x, "selected", exact = TRUE))
+  }
+
+  # Returns TRUE if a list of tab items contains a selected tab, FALSE
+  # otherwise.
+  containsSelected <- function(tabs) {
+    any(vapply(tabs, isSelected, logical(1)))
+  }
+
+  # Take a pass over all tabs, and mark the selected tab.
+  foundSelectedItem <- FALSE
+  findAndMarkSelected <- function(tabs, selected) {
+    lapply(tabs, function(divTag) {
+      if (foundSelectedItem) {
+        # If we already found the selected tab, no need to keep looking
+
+      } else if (is.character(divTag)) {
+        # Strings don't represent selectable items
+
+      } else if (inherits(divTag, "shiny.navbarmenu")) {
+        # Navbar menu
+        divTag$tabs <- findAndMarkSelected(divTag$tabs, selected)
+
+      } else {
+        # Regular tab item
+        if (is.null(selected)) {
+          # If selected tab isn't specified, mark first available item
+          # as selected.
+          foundSelectedItem <<- TRUE
+          divTag <- markSelected(divTag)
+
+        } else {
+          # If selected tab is specified, check for a match
+          tabValue <- divTag$attribs$`data-value` %OR% divTag$attribs$title
+          if (identical(selected, tabValue)) {
+            foundSelectedItem <<- TRUE
+            divTag <- markSelected(divTag)
+          }
+        }
+      }
+
+      return(divTag)
+    })
+  }
+
+
+  # Append an optional icon to an aTag
+  appendIcon <- function(aTag, iconClass) {
+    if (!is.null(iconClass)) {
+      # for font-awesome we specify fixed-width
+      if (grepl("fa-", iconClass, fixed = TRUE))
+        iconClass <- paste(iconClass, "fa-fw")
+      aTag <- tagAppendChild(aTag, icon(name = NULL, class = iconClass))
+    }
+    aTag
+  }
+
+  # Build the tabset
+  build <- function(tabs, ulClass, textFilter = NULL, id = NULL) {
+    # add tab input sentinel class if we have an id
+    if (!is.null(id))
+      ulClass <- paste(ulClass, "shiny-tab-input")
+
+    if (anyNamed(tabs)) {
+      nms <- names(tabs)
+      nms <- nms[nzchar(nms)]
+      stop("Tabs should all be unnamed arguments, but some are named: ",
+           paste(nms, collapse = ", "))
+    }
+
+    tabNavList <- tags$ul(class = ulClass, id = id)
+    tabContent <- tags$div(class = "tab-content")
+    tabsetId <- p_randomInt(1000, 10000)
+    tabId <- 1
+
+    buildItem <- function(divTag) {
+      # check for text; pass it to the textFilter or skip it if there is none
+      if (is.character(divTag)) {
+        if (!is.null(textFilter)) {
+          tabNavList <<- tagAppendChild(tabNavList, textFilter(divTag))
+        }
+
+      } else if (inherits(divTag, "shiny.navbarmenu")) {
+
+        # create the a tag
+        aTag <- tags$a(href="#",
+                       class="dropdown-toggle",
+                       `data-toggle`="dropdown")
+
+        # add optional icon
+        aTag <- appendIcon(aTag, divTag$iconClass)
+
+        # add the title and caret
+        aTag <- tagAppendChild(aTag, divTag$title)
+        aTag <- tagAppendChild(aTag, tags$b(class="caret"))
+
+        # build the dropdown list element
+        liTag <- tags$li(class = "dropdown", aTag)
+
+        # text filter for separators
+        textFilter <- function(text) {
+          if (grepl("^\\-+$", text))
+            tags$li(class="divider")
+          else
+            tags$li(class="dropdown-header", text)
+        }
+
+        # build the child tabset
+        tabset <- build(divTag$tabs, "dropdown-menu", textFilter)
+        liTag <- tagAppendChild(liTag, tabset$navList)
+
+        # If this navbar menu contains a selected item, mark it as active
+        if (containsSelected(divTag$tabs)) {
+          liTag$attribs$class <- paste(liTag$attribs$class, "active")
+        }
+
+        tabNavList <<- tagAppendChild(tabNavList, liTag)
+        # don't add a standard tab content div, rather add the list of tab
+        # content divs that are contained within the tabset
+        tabContent <<- tagAppendChildren(tabContent,
+                                        list = tabset$content$children)
+
+      } else {
+        # Standard navbar item
+        # compute id and assign it to the div
+        thisId <- paste("tab", tabsetId, tabId, sep="-")
+        divTag$attribs$id <- thisId
+        tabId <<- tabId + 1
+
+        tabValue <- divTag$attribs$`data-value`
+
+        # create the a tag
+        aTag <- tags$a(href=paste("#", thisId, sep=""),
+                       `data-toggle` = "tab",
+                       `data-value` = tabValue)
+
+        # append optional icon
+        aTag <- appendIcon(aTag, divTag$attribs$`data-icon-class`)
+
+        # add the title
+        aTag <- tagAppendChild(aTag, divTag$attribs$title)
+
+        # create the li tag
+        liTag <- tags$li(aTag)
+
+        # If selected, set appropriate classes on li tag and div tag.
+        if (isSelected(divTag)) {
+          liTag$attribs$class <- "active"
+          divTag$attribs$class <- "tab-pane active"
+        }
+
+        divTag$attribs$title <- NULL
+
+        # append the elements to our lists
+        tabNavList <<- tagAppendChild(tabNavList, liTag)
+        tabContent <<- tagAppendChild(tabContent, divTag)
+      }
+    }
+
+    lapply(tabs, buildItem)
+    list(navList = tabNavList, content = tabContent)
+  }
+
+
+  # Finally, actually invoke the functions to do the processing.
+  tabs <- findAndMarkSelected(tabs, selected)
+  build(tabs, ulClass, textFilter, id)
 }
 
 
@@ -764,6 +953,7 @@ verbatimTextOutput <- function(outputId) {
 }
 
 
+#' @name plotOutput
 #' @rdname plotOutput
 #' @export
 imageOutput <- function(outputId, width = "100%", height="400px",
@@ -1305,12 +1495,11 @@ downloadLink <- function(outputId, label="Download", class=NULL) {
 #' # add an icon to a submit button
 #' submitButton("Update View", icon = icon("refresh"))
 #'
-#' shinyUI(navbarPage("App Title",
+#' navbarPage("App Title",
 #'   tabPanel("Plot", icon = icon("bar-chart-o")),
 #'   tabPanel("Summary", icon = icon("list-alt")),
 #'   tabPanel("Table", icon = icon("table"))
-#' ))
-#'
+#' )
 #' @export
 icon <- function(name, class = NULL, lib = "font-awesome") {
   prefixes <- list(
@@ -1338,7 +1527,7 @@ icon <- function(name, class = NULL, lib = "font-awesome") {
   # font-awesome needs an additional dependency (glyphicon is in bootstrap)
   if (lib == "font-awesome") {
     htmlDependencies(iconTag) <- htmlDependency(
-      "font-awesome", "4.4.0", c(href="shared/font-awesome"),
+      "font-awesome", "4.6.3", c(href="shared/font-awesome"),
       stylesheet = "css/font-awesome.min.css"
     )
   }

R/conditions.R

@@ -0,0 +1,334 @@
+#' Stack trace manipulation functions
+#'
+#' Advanced (borderline internal) functions for capturing, printing, and
+#' manipulating stack traces.
+#'
+#' @return \code{printError} and \code{printStackTrace} return
+#'   \code{invisible()}. The other functions pass through the results of
+#'   \code{expr}.
+#'
+#' @examples
+#' # Keeps tryCatch and withVisible related calls off the
+#' # pretty-printed stack trace
+#'
+#' visibleFunction1 <- function() {
+#'   stop("Kaboom!")
+#' }
+#'
+#' visibleFunction2 <- function() {
+#'   visibleFunction1()
+#' }
+#'
+#' hiddenFunction <- function(expr) {
+#'   expr
+#' }
+#'
+#' # An example without ..stacktraceon/off.. manipulation.
+#' # The outer "try" is just to prevent example() from stopping.
+#' try({
+#'   # The withLogErrors call ensures that stack traces are captured
+#'   # and that errors that bubble up are logged using warning().
+#'   withLogErrors({
+#'     # tryCatch and withVisible are just here to add some noise to
+#'     # the stack trace.
+#'     tryCatch(
+#'       withVisible({
+#'         hiddenFunction(visibleFunction2())
+#'       })
+#'     )
+#'   })
+#' })
+#'
+#' # Now the same example, but with ..stacktraceon/off.. to hide some
+#' # of the less-interesting bits (tryCatch and withVisible).
+#' ..stacktraceoff..({
+#'   try({
+#'     withLogErrors({
+#'       tryCatch(
+#'         withVisible(
+#'           hiddenFunction(
+#'             ..stacktraceon..(visibleFunction2())
+#'           )
+#'         )
+#'       )
+#'     })
+#'   })
+#' })
+#'
+#'
+#' @name stacktrace
+#' @rdname stacktrace
+#' @keywords internal
+NULL
+
+getCallNames <- function(calls) {
+  sapply(calls, function(call) {
+    if (is.function(call[[1]])) {
+      "<Anonymous>"
+    } else if (inherits(call[[1]], "call")) {
+      paste0(format(call[[1]]), collapse = " ")
+    } else if (typeof(call[[1]]) == "promise") {
+      "<Promise>"
+    } else {
+      paste0(as.character(call[[1]]), collapse = " ")
+    }
+  })
+}
+
+getLocs <- function(calls) {
+  vapply(calls, function(call) {
+    srcref <- attr(call, "srcref", exact = TRUE)
+    if (!is.null(srcref)) {
+      srcfile <- attr(srcref, "srcfile", exact = TRUE)
+      if (!is.null(srcfile) && !is.null(srcfile$filename)) {
+        loc <- paste0(srcfile$filename, "#", srcref[[1]])
+        return(paste0(" [", loc, "]"))
+      }
+    }
+    return("")
+  }, character(1))
+}
+
+#' @details \code{captureStackTraces} runs the given \code{expr} and if any
+#'   \emph{uncaught} errors occur, annotates them with stack trace info for use
+#'   by \code{printError} and \code{printStackTrace}. It is not necessary to use
+#'   \code{captureStackTraces} around the same expression as
+#'   \code{withLogErrors}, as the latter includes a call to the former. Note
+#'   that if \code{expr} contains calls (either directly or indirectly) to
+#'   \code{try}, or \code{tryCatch} with an error handler, stack traces therein
+#'   cannot be captured unless another \code{captureStackTraces} call is
+#'   inserted in the interior of the \code{try} or \code{tryCatch}. This is
+#'   because these calls catch the error and prevent it from traveling up to the
+#'   condition handler installed by \code{captureStackTraces}.
+#'
+#' @param expr The expression to wrap.
+#' @rdname stacktrace
+#' @export
+captureStackTraces <- function(expr) {
+  withCallingHandlers(expr,
+    error = function(e) {
+      if (is.null(attr(e, "stack.trace", exact = TRUE))) {
+        calls <- sys.calls()
+        attr(e, "stack.trace") <- calls
+        stop(e)
+      }
+    }
+  )
+}
+
+#' @details \code{withLogErrors} captures stack traces and logs errors that
+#'   occur in \code{expr}, but does allow errors to propagate beyond this point
+#'   (i.e. it doesn't catch the error). The same caveats that apply to
+#'   \code{captureStackTraces} with regard to \code{try}/\code{tryCatch} apply
+#'   to \code{withLogErrors}.
+#' @rdname stacktrace
+#' @export
+withLogErrors <- function(expr,
+  full = getOption("shiny.fullstacktrace", FALSE),
+  offset = getOption("shiny.stacktraceoffset", TRUE)) {
+
+  withCallingHandlers(
+    captureStackTraces(expr),
+    error = function(cond) {
+      # Don't print shiny.silent.error (i.e. validation errors)
+      if (inherits(cond, "shiny.silent.error")) return()
+      if (isTRUE(getOption("show.error.messages"))) {
+        printError(cond, full = full, offset = offset)
+      }
+    }
+  )
+}
+
+#' @details \code{printError} prints the error and stack trace (if any) using
+#'   \code{warning(immediate.=TRUE)}. \code{printStackTrace} prints the stack
+#'   trace only.
+#'
+#' @param cond An condition object (generally, an error).
+#' @param full If \code{TRUE}, then every element of \code{sys.calls()} will be
+#'   included in the stack trace. By default (\code{FALSE}), calls that Shiny
+#'   deems uninteresting will be hidden.
+#' @param offset If \code{TRUE} (the default), srcrefs will be reassigned from
+#'   the calls they originated from, to the destinations of those calls. If
+#'   you're used to stack traces from other languages, this feels more
+#'   intuitive, as the definition of the function indicated in the call and the
+#'   location specified by the srcref match up. If \code{FALSE}, srcrefs will be
+#'   left alone (traditional R treatment where the srcref is of the callsite).
+#' @rdname stacktrace
+#' @export
+printError <- function(cond,
+  full = getOption("shiny.fullstacktrace", FALSE),
+  offset = getOption("shiny.stacktraceoffset", TRUE)) {
+
+  warning(call. = FALSE, immediate. = TRUE, sprintf("Error in %s: %s",
+    getCallNames(list(conditionCall(cond))), conditionMessage(cond)))
+  printStackTrace(cond, full = full, offset = offset)
+  invisible()
+}
+
+#' @rdname stacktrace
+#' @export
+printStackTrace <- function(cond,
+  full = getOption("shiny.fullstacktrace", FALSE),
+  offset = getOption("shiny.stacktraceoffset", TRUE)) {
+
+  stackTrace <- attr(cond, "stack.trace", exact = TRUE)
+  tryCatch(
+    if (!is.null(stackTrace)) {
+      message(paste0(
+        "Stack trace (innermost first):\n",
+        paste0(collapse = "\n",
+          formatStackTrace(stackTrace, full = full, offset = offset,
+            indent = "    ")
+        )
+      ))
+    } else {
+      message("No stack trace available")
+    },
+
+    error = function(cond) {
+      warning("Failed to write stack trace: ", cond)
+    }
+  )
+  invisible()
+}
+
+#' @details \code{extractStackTrace} takes a list of calls (e.g. as returned
+#'   from \code{conditionStackTrace(cond)}) and returns a data frame with one
+#'   row for each stack frame and the columns \code{num} (stack frame number),
+#'   \code{call} (a function name or similar), and \code{loc} (source file path
+#'   and line number, if available).
+#' @rdname stacktrace
+#' @export
+extractStackTrace <- function(calls,
+  full = getOption("shiny.fullstacktrace", FALSE),
+  offset = getOption("shiny.stacktraceoffset", TRUE)) {
+
+  srcrefs <- getSrcRefs(calls)
+  if (offset) {
+    # Offset calls vs. srcrefs by 1 to make them more intuitive.
+    # E.g. for "foo [bar.R:10]", line 10 of bar.R will be part of
+    # the definition of foo().
+    srcrefs <- c(utils::tail(srcrefs, -1), list(NULL))
+  }
+  calls <- setSrcRefs(calls, srcrefs)
+
+  callnames <- getCallNames(calls)
+
+  # Hide and show parts of the callstack based on ..stacktrace(on|off)..
+  if (full) {
+    toShow <- rep.int(TRUE, length(calls))
+  } else {
+    # Remove stop(), .handleSimpleError(), and h() calls from the end of
+    # the calls--they don't add any helpful information. But only remove
+    # the last *contiguous* block of them, and then, only if they are the
+    # last thing in the calls list.
+    hideable <- callnames %in% c("stop", ".handleSimpleError", "h")
+    # What's the last that *didn't* match stop/.handleSimpleError/h?
+    lastGoodCall <- max(which(!hideable))
+    toRemove <- length(calls) - lastGoodCall
+    # But don't remove more than 5 levels--that's an indication we might
+    # have gotten it wrong, I guess
+    if (toRemove > 0 && toRemove < 5) {
+      calls <- utils::head(calls, -toRemove)
+      callnames <- utils::head(callnames, -toRemove)
+    }
+
+    # This uses a ref-counting scheme. It might make sense to switch this
+    # to a toggling scheme, so the most recent ..stacktrace(on|off)..
+    # directive wins, regardless of what came before it.
+    # Also explicitly remove ..stacktraceon.. because it can appear with
+    # score > 0 but still should never be shown.
+    score <- rep.int(0, length(callnames))
+    score[callnames == "..stacktraceoff.."] <- -1
+    score[callnames == "..stacktraceon.."] <- 1
+    toShow <- (1 + cumsum(score)) > 0 & !(callnames %in% c("..stacktraceon..", "..stacktraceoff.."))
+  }
+  calls <- calls[toShow]
+
+  calls <- rev(calls) # Show in traceback() order
+  index <- rev(which(toShow))
+  width <- floor(log10(max(index))) + 1
+
+  data.frame(
+    num = index,
+    call = getCallNames(calls),
+    loc = getLocs(calls),
+    stringsAsFactors = FALSE
+  )
+}
+
+#' @details \code{formatStackTrace} is similar to \code{extractStackTrace}, but
+#'   it returns a preformatted character vector instead of a data frame.
+#' @param indent A string to prefix every line of the stack trace.
+#' @rdname stacktrace
+#' @export
+formatStackTrace <- function(calls, indent = "    ",
+  full = getOption("shiny.fullstacktrace", FALSE),
+  offset = getOption("shiny.stacktraceoffset", TRUE)) {
+
+  st <- extractStackTrace(calls, full = full, offset = offset)
+  if (nrow(st) == 0) {
+    return(character(0))
+  }
+
+  width <- floor(log10(max(st$num))) + 1
+  paste0(
+    indent,
+    formatC(st$num, width = width),
+    ": ",
+    st$call,
+    st$loc
+  )
+}
+
+getSrcRefs <- function(calls) {
+  lapply(calls, function(call) {
+    attr(call, "srcref", exact = TRUE)
+  })
+}
+
+setSrcRefs <- function(calls, srcrefs) {
+  mapply(function(call, srcref) {
+    structure(call, srcref = srcref)
+  }, calls, srcrefs)
+}
+
+stripStackTrace <- function(cond) {
+  conditionStackTrace(cond) <- NULL
+}
+
+#' @details \code{conditionStackTrace} and \code{conditionStackTrace<-} are
+#'   accessor functions for getting/setting stack traces on conditions.
+#'
+#' @param cond A condition that may have previously been annotated by
+#'   \code{captureStackTraces} (or \code{withLogErrors}).
+#' @rdname stacktrace
+#' @export
+conditionStackTrace <- function(cond) {
+  attr(cond, "stack.trace", exact = TRUE)
+}
+
+#' @param value The stack trace value to assign to the condition.
+#' @rdname stacktrace
+#' @export
+`conditionStackTrace<-` <- function(cond, value) {
+  attr(cond, "stack.trace") <- value
+  invisible(cond)
+}
+
+#' @details The two functions \code{..stacktraceon..} and
+#'   \code{..stacktraceoff..} have no runtime behavior during normal execution;
+#'   they exist only to create artifacts on the stack trace (sys.call()) that
+#'   instruct the stack trace pretty printer what parts of the stack trace are
+#'   interesting or not. The initial state is 1 and we walk from the outermost
+#'   call inwards. Each ..stacktraceoff.. decrements the state by one, and each
+#'   ..stacktraceon.. increments the state by one. Any stack trace frame whose
+#'   value is less than 1 is hidden, and finally, the ..stacktraceon.. and
+#'   ..stacktraceoff.. calls themselves are hidden too.
+#'
+#' @rdname stacktrace
+#' @export
+..stacktraceon.. <- function(expr) expr
+#' @rdname stacktrace
+#' @export
+..stacktraceoff.. <- function(expr) expr

R/diagnose.R

@@ -0,0 +1,157 @@
+# Analyze an R file for possible extra or missing commas. Returns FALSE if any
+# problems detected, TRUE otherwise.
+diagnoseCode <- function(path = NULL, text = NULL) {
+  if (!xor(is.null(path), is.null(text))) {
+    stop("Must specify `path` or `text`, but not both.")
+  }
+
+  if (!is.null(path)) {
+    tokens <- sourcetools::tokenize_file(path)
+  } else {
+    tokens <- sourcetools::tokenize_string(text)
+  }
+
+  find_scopes <- function(tokens) {
+    # Strip whitespace and comments
+    tokens <- tokens[!(tokens$type %in% c("whitespace", "comment")),]
+
+    # Replace various types of things with "value"
+    tokens$type[tokens$type %in% c("string", "number", "symbol", "keyword")] <- "value"
+
+    # Record types for close and open brace/bracket/parens, and commas
+    brace_idx <- tokens$value %in% c("(", ")", "{", "}", "[", "]", ",")
+    tokens$type[brace_idx] <- tokens$value[brace_idx]
+
+    # Stack-related function for recording scope. Starting scope is "{"
+    stack <- "{"
+    push <- function(x) {
+      stack <<- c(stack, x)
+    }
+    pop <- function() {
+      if (length(stack) == 1) {
+        # Stack underflow, but we need to keep going
+        return(NA_character_)
+      }
+      res <- stack[length(stack)]
+      stack <<- stack[-length(stack)]
+      res
+    }
+    peek <- function() {
+      stack[length(stack)]
+    }
+
+    # First, establish a scope for each token. For opening and closing
+    # braces/brackets/parens, the scope at that location is the *surrounding*
+    # scope, not the new scope created by the brace/bracket/paren.
+    for (i in seq_len(nrow(tokens))) {
+      value <- tokens$value[i]
+
+      tokens$scope[i] <- peek()
+      if (value %in% c("{", "(", "[")) {
+        push(value)
+
+      } else if (value == "}") {
+        if (!identical(pop(), "{"))
+          tokens$err[i] <- "unmatched_brace"
+        # For closing brace/paren/bracket, get the scope after popping
+        tokens$scope[i] <- peek()
+
+      } else if (value == ")") {
+        if (!identical(pop(), "("))
+          tokens$err[i] <- "unmatched_paren"
+        tokens$scope[i] <- peek()
+
+      } else if (value == "]") {
+        if (!identical(pop(), "["))
+          tokens$err[i] <- "unmatched_bracket"
+        tokens$scope[i] <- peek()
+      }
+    }
+
+    tokens
+  }
+
+  check_commas <- function(tokens) {
+    # Find extra and missing commas
+    tokens$err <- mapply(
+      tokens$type,
+      c("", tokens$type[-length(tokens$type)]),
+      c(tokens$type[-1],  ""),
+      tokens$scope,
+      tokens$err,
+      SIMPLIFY = FALSE,
+      FUN = function(type, prevType, nextType, scope, err) {
+        # If an error was already found, just return it. This could have
+        # happened in the brace/paren/bracket matching phase.
+        if (!is.na(err)) {
+          return(err)
+        }
+        if (scope == "(") {
+          if (type == "," &&
+              (prevType == "(" || prevType == "," || nextType == ")"))
+          {
+            return("extra_comma")
+          }
+
+          if ((prevType == ")" && type == "value") ||
+              (prevType == "value" && type == "value")) {
+            return("missing_comma")
+          }
+        }
+
+        NA_character_
+      }
+    )
+
+    tokens
+  }
+
+
+  tokens$err <- NA_character_
+  tokens <- find_scopes(tokens)
+  tokens <- check_commas(tokens)
+
+  # No errors found
+  if (all(is.na(tokens$err))) {
+    return(TRUE)
+  }
+
+  # If we got here, errors were found; print messages.
+  if (!is.null(path)) {
+    lines <- readLines(path)
+  } else {
+    lines <- strsplit(text, "\n")[[1]]
+  }
+
+  # Print out the line of code with the error, and point to the column with
+  # the error.
+  show_code_error <- function(msg, lines, row, col) {
+    message(paste0(
+      msg, "\n",
+      row, ":", lines[row], "\n",
+      paste0(rep.int(" ", nchar(as.character(row)) + 1), collapse = ""),
+      gsub(perl = TRUE, "[^\\s]", " ", substr(lines[row], 1, col-1)), "^"
+    ))
+  }
+
+  err_idx <- which(!is.na(tokens$err))
+  msg <- ""
+  for (i in err_idx) {
+    row <- tokens$row[i]
+    col <- tokens$column[i]
+    err <- tokens$err[i]
+
+    if (err == "missing_comma") {
+      show_code_error("Possible missing comma at:", lines, row, col)
+    } else if (err == "extra_comma") {
+      show_code_error("Possible extra comma at:", lines, row, col)
+    } else if (err == "unmatched_brace") {
+      show_code_error("Possible unmatched '}' at:", lines, row, col)
+    } else if (err == "unmatched_paren") {
+      show_code_error("Possible unmatched ')' at:", lines, row, col)
+    } else if (err == "unmatched_bracket") {
+      show_code_error("Possible unmatched ']' at:", lines, row, col)
+    }
+  }
+  return(FALSE)
+}

R/fileupload.R

@@ -94,7 +94,7 @@ FileUploadContext <- R6Class(
     },
     createUploadOperation = function(fileInfos) {
       while (TRUE) {
-        id <- paste(as.raw(p_runif(12, min=0, max=0xFF)), collapse='')
+        id <- createUniqueId(12)
         private$ids <- c(private$ids, id)
         dir <- file.path(private$basedir, id)
         if (!dir.create(dir))

R/graph.R

@@ -41,12 +41,14 @@ writeReactLog <- function(file=stdout(), sessionToken = NULL) {
 #' enabled, it's possible for any user of your app to see at least some
 #' of the source code of your reactive expressions and observers.
 #'
+#' @param time A boolean that specifies whether or not to display the
+#' time that each reactive.
 #' @export
-showReactLog <- function() {
-  utils::browseURL(renderReactLog())
+showReactLog <- function(time = TRUE) {
+  utils::browseURL(renderReactLog(time = as.logical(time)))
 }
 
-renderReactLog <- function(sessionToken = NULL) {
+renderReactLog <- function(sessionToken = NULL, time = TRUE) {
   templateFile <- system.file('www/reactive-graph.html', package='shiny')
   html <- paste(readLines(templateFile, warn=FALSE), collapse='\r\n')
   tc <- textConnection(NULL, 'w')
@@ -55,6 +57,7 @@ renderReactLog <- function(sessionToken = NULL) {
   cat('\n', file=tc)
   flush(tc)
   html <- sub('__DATA__', paste(textConnectionValue(tc), collapse='\r\n'), html, fixed=TRUE)
+  html <- sub('__TIME__', paste0('"', time, '"'), html, fixed=TRUE)
   file <- tempfile(fileext = '.html')
   writeLines(html, file)
   return(file)

R/html-deps.R

@@ -6,7 +6,7 @@
 #' URL.
 #'
 #' @param dependency A single HTML dependency object, created using
-#'   \code{\link{htmlDependency}}. If the \code{src} value is named, then
+#'   \code{\link[htmltools]{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
@@ -27,3 +27,21 @@ createWebDependency <- function(dependency) {
 
   return(dependency)
 }
+
+
+# Given a Shiny tag object, process singletons and dependencies. Returns a list
+# with rendered HTML and dependency objects.
+processDeps <- function(tags, session) {
+  ui <- takeSingletons(tags, session$singletons, desingleton=FALSE)$ui
+  ui <- surroundSingletons(ui)
+  dependencies <- lapply(
+    resolveDependencies(findDependencies(ui)),
+    createWebDependency
+  )
+  names(dependencies) <- NULL
+
+  list(
+    html = doRenderTags(ui),
+    deps = dependencies
+  )
+}

R/htmltools.R

@@ -4,4 +4,5 @@
 #' @export tag tagAppendAttributes tagAppendChild tagAppendChildren tagList tags tagSetChildren withTags
 #' @export validateCssUnit
 #' @export knit_print.html knit_print.shiny.tag knit_print.shiny.tag.list
+#' @export htmlTemplate suppressDependencies
 NULL

R/imageutils.R

@@ -25,7 +25,6 @@
 #'   R; it won't change the actual ppi of the browser.
 #' @param ... Arguments to be passed through to \code{\link[grDevices]{png}}.
 #'   These can be used to set the width, height, background color, etc.
-#'
 #' @export
 plotPNG <- function(func, filename=tempfile(fileext='.png'),
                     width=400, height=400, res=72, ...) {
@@ -50,9 +49,14 @@ plotPNG <- function(func, filename=tempfile(fileext='.png'),
   # guarantee user's code in func() will not trigger the error -- they may have
   # to set par(mar = smaller_value) before they draw base graphics.
   op <- graphics::par(mar = rep(0, 4))
-  tryCatch(graphics::plot.new(), finally = graphics::par(op))
+  tryCatch(
+    graphics::plot.new(),
+    finally = graphics::par(op)
+  )
+
   dv <- grDevices::dev.cur()
-  tryCatch(shinyCallingHandlers(func()), finally = grDevices::dev.off(dv))
+  on.exit(grDevices::dev.off(dv), add = TRUE)
+  func()
 
   filename
 }

R/input-action.R

@@ -11,30 +11,43 @@
 #'
 #' @family input elements
 #' @examples
-#' \dontrun{
-#' # In server.R
-#' output$distPlot <- renderPlot({
-#'   # Take a dependency on input$goButton
-#'   input$goButton
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#'   # Use isolate() to avoid dependency on input$obs
-#'   dist <- isolate(rnorm(input$obs))
-#'   hist(dist)
-#' })
+#' ui <- fluidPage(
+#'   sliderInput("obs", "Number of observations", 0, 1000, 500),
+#'   actionButton("goButton", "Go!"),
+#'   plotOutput("distPlot")
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     # Take a dependency on input$goButton. This will run once initially,
+#'     # because the value changes from NULL to 0.
+#'     input$goButton
+#'
+#'     # Use isolate() to avoid dependency on input$obs
+#'     dist <- isolate(rnorm(input$obs))
+#'     hist(dist)
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
 #'
-#' # In ui.R
-#' actionButton("goButton", "Go!")
 #' }
 #'
 #' @seealso \code{\link{observeEvent}} and \code{\link{eventReactive}}
-#'
 #' @export
 actionButton <- function(inputId, label, icon = NULL, width = NULL, ...) {
+
+  value <- restoreInput(id = inputId, default = NULL)
+
   tags$button(id=inputId,
     style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
     type="button",
     class="btn btn-default action-button",
-    list(icon, label),
+    `data-val` = value,
+    list(validateIcon(icon), label),
     ...
   )
 }
@@ -42,10 +55,32 @@ actionButton <- function(inputId, label, icon = NULL, width = NULL, ...) {
 #' @rdname actionButton
 #' @export
 actionLink <- function(inputId, label, icon = NULL, ...) {
+  value <- restoreInput(id = inputId, default = NULL)
+
   tags$a(id=inputId,
     href="#",
     class="action-button",
-    list(icon, label),
+    `data-val` = value,
+    list(validateIcon(icon), label),
     ...
   )
 }
+
+
+# Check that the icon parameter is valid:
+# 1) Check  if the user wants to actually add an icon:
+#    -- if icon=NULL, it means leave the icon unchanged
+#    -- if icon=character(0), it means don't add an icon or, more usefully,
+#       remove the previous icon
+# 2) If so, check that the icon has the right format (this does not check whether
+# it is a *real* icon - currently that would require a massive cross reference
+# with the "font-awesome" and the "glyphicon" libraries)
+validateIcon <- function(icon) {
+  if (is.null(icon) || identical(icon, character(0))) {
+    return(icon)
+  } else if (inherits(icon, "shiny.tag") && icon$name == "i") {
+    return(icon)
+  } else {
+    stop("Invalid icon. Use Shiny's 'icon()' function to generate a valid icon")
+  }
+}

R/input-checkbox.R

@@ -10,9 +10,23 @@
 #' @seealso \code{\link{checkboxGroupInput}}, \code{\link{updateCheckboxInput}}
 #'
 #' @examples
-#' checkboxInput("outliers", "Show outliers", FALSE)
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   checkboxInput("somevalue", "Some value", FALSE),
+#'   verbatimTextOutput("value")
+#' )
+#' server <- function(input, output) {
+#'   output$value <- renderText({ input$somevalue })
+#' }
+#' shinyApp(ui, server)
+#' }
 #' @export
 checkboxInput <- function(inputId, label, value = FALSE, width = NULL) {
+
+  value <- restoreInput(id = inputId, default = value)
+
   inputTag <- tags$input(id = inputId, type="checkbox")
   if (!is.null(value) && value)
     inputTag$attribs$checked <- "checked"

R/input-checkboxgroup.R

@@ -15,15 +15,31 @@
 #' @seealso \code{\link{checkboxInput}}, \code{\link{updateCheckboxGroupInput}}
 #'
 #' @examples
-#' checkboxGroupInput("variable", "Variable:",
-#'                    c("Cylinders" = "cyl",
-#'                      "Transmission" = "am",
-#'                      "Gears" = "gear"))
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   checkboxGroupInput("variable", "Variables to show:",
+#'                      c("Cylinders" = "cyl",
+#'                        "Transmission" = "am",
+#'                        "Gears" = "gear")),
+#'   tableOutput("data")
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$data <- renderTable({
+#'     mtcars[, c("mpg", input$variable), drop = FALSE]
+#'   }, rownames = TRUE)
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
 #' @export
 checkboxGroupInput <- function(inputId, label, choices, selected = NULL,
   inline = FALSE, width = NULL) {
 
+  selected <- restoreInput(id = inputId, default = selected)
+
   # resolve names
   choices <- choicesWithNames(choices)
   if (!is.null(selected))

R/input-date.R

@@ -21,48 +21,58 @@
 #'
 #' @inheritParams textInput
 #' @param value The starting 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.
+#'   \code{yyyy-mm-dd} format. If NULL (the default), will use the current date
+#'   in the client's time zone.
 #' @param min The minimum allowed date. Either a Date object, or a string in
 #'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
 #'   \code{yyyy-mm-dd} format.
 #' @param format The format of the date to display in the browser. Defaults to
 #'   \code{"yyyy-mm-dd"}.
-#' @param startview The date range shown when the input object is first
-#'   clicked. Can be "month" (the default), "year", or "decade".
+#' @param startview The date range shown when the input object is first clicked.
+#'   Can be "month" (the default), "year", or "decade".
 #' @param weekstart Which day is the start of the week. Should be an integer
 #'   from 0 (Sunday) to 6 (Saturday).
 #' @param language The language used for month and day names. Default is "en".
-#'   Other valid values include "bg", "ca", "cs", "da", "de", "el", "es", "fi",
-#'   "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".
+#'   Other valid values include "ar", "az", "bg", "bs", "ca", "cs", "cy", "da",
+#'   "de", "el", "en-AU", "en-GB", "eo", "es", "et", "eu", "fa", "fi", "fo",
+#'   "fr-CH", "fr", "gl", "he", "hr", "hu", "hy", "id", "is", "it-CH", "it",
+#'   "ja", "ka", "kh", "kk", "ko", "kr", "lt", "lv", "me", "mk", "mn", "ms",
+#'   "nb", "nl-BE", "nl", "no", "pl", "pt-BR", "pt", "ro", "rs-latin", "rs",
+#'   "ru", "sk", "sl", "sq", "sr-latin", "sr", "sv", "sw", "th", "tr", "uk",
+#'   "vi", "zh-CN", and "zh-TW".
 #'
 #' @family input elements
 #' @seealso \code{\link{dateRangeInput}}, \code{\link{updateDateInput}}
 #'
 #' @examples
-#' dateInput("date", "Date:", value = "2012-02-29")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#' # Default value is the date in client's time zone
-#' dateInput("date", "Date:")
+#' ui <- fluidPage(
+#'   dateInput("date1", "Date:", value = "2012-02-29"),
 #'
-#' # value is always yyyy-mm-dd, even if the display format is different
-#' dateInput("date", "Date:", value = "2012-02-29", format = "mm/dd/yy")
+#'   # Default value is the date in client's time zone
+#'   dateInput("date2", "Date:"),
 #'
-#' # Pass in a Date object
-#' dateInput("date", "Date:", value = Sys.Date()-10)
+#'   # value is always yyyy-mm-dd, even if the display format is different
+#'   dateInput("date3", "Date:", value = "2012-02-29", format = "mm/dd/yy"),
 #'
-#' # Use different language and different first day of week
-#' dateInput("date", "Date:",
-#'           language = "de",
-#'           weekstart = 1)
+#'   # Pass in a Date object
+#'   dateInput("date4", "Date:", value = Sys.Date()-10),
 #'
-#' # Start with decade view instead of default month view
-#' dateInput("date", "Date:",
-#'           startview = "decade")
+#'   # Use different language and different first day of week
+#'   dateInput("date5", "Date:",
+#'           language = "ru",
+#'           weekstart = 1),
 #'
+#'   # Start with decade view instead of default month view
+#'   dateInput("date6", "Date:",
+#'             startview = "decade")
+#' )
+#'
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 dateInput <- function(inputId, label, value = NULL, min = NULL, max = NULL,
   format = "yyyy-mm-dd", startview = "month", weekstart = 0, language = "en",
@@ -74,29 +84,36 @@ dateInput <- function(inputId, label, value = NULL, min = NULL, max = NULL,
   if (inherits(min,   "Date"))  min   <- format(min,   "%Y-%m-%d")
   if (inherits(max,   "Date"))  max   <- format(max,   "%Y-%m-%d")
 
-  attachDependencies(
-    tags$div(id = inputId,
-      class = "shiny-date-input form-group shiny-input-container",
-      style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
+  value <- restoreInput(id = inputId, default = value)
 
-      controlLabel(inputId, label),
-      tags$input(type = "text",
-                 # datepicker class necessary for dropdown to display correctly
-                 class = "form-control datepicker",
-                 `data-date-language` = language,
-                 `data-date-weekstart` = weekstart,
-                 `data-date-format` = format,
-                 `data-date-start-view` = startview,
-                 `data-min-date` = min,
-                 `data-max-date` = max,
-                 `data-initial-date` = value
-      )
+  tags$div(id = inputId,
+    class = "shiny-date-input form-group shiny-input-container",
+    style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
+
+    controlLabel(inputId, label),
+    tags$input(type = "text",
+               class = "form-control",
+               `data-date-language` = language,
+               `data-date-week-start` = weekstart,
+               `data-date-format` = format,
+               `data-date-start-view` = startview,
+               `data-min-date` = min,
+               `data-max-date` = max,
+               `data-initial-date` = value
     ),
     datePickerDependency
   )
 }
 
 datePickerDependency <- htmlDependency(
-  "bootstrap-datepicker", "1.0.2", c(href = "shared/datepicker"),
+  "bootstrap-datepicker", "1.6.4", c(href = "shared/datepicker"),
   script = "js/bootstrap-datepicker.min.js",
-  stylesheet = "css/datepicker.css")
+  stylesheet = "css/bootstrap-datepicker3.min.css",
+  # Need to enable noConflict mode. See #1346.
+  head = "<script>
+(function() {
+  var datepicker = $.fn.datepicker.noConflict();
+  $.fn.bsDatepicker = datepicker;
+})();
+</script>"
+)

R/input-daterange.R

@@ -32,37 +32,44 @@
 #' @seealso \code{\link{dateInput}}, \code{\link{updateDateRangeInput}}
 #'
 #' @examples
-#' dateRangeInput("daterange", "Date range:",
-#'                start = "2001-01-01",
-#'                end   = "2010-12-31")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#' # Default start and end is the current date in the client's time zone
-#' dateRangeInput("daterange", "Date range:")
+#' ui <- fluidPage(
+#'   dateRangeInput("daterange1", "Date range:",
+#'                  start = "2001-01-01",
+#'                  end   = "2010-12-31"),
 #'
-#' # start and end are always specified in yyyy-mm-dd, even if the display
-#' # format is different
-#' dateRangeInput("daterange", "Date range:",
-#'                start  = "2001-01-01",
-#'                end    = "2010-12-31",
-#'                min    = "2001-01-01",
-#'                max    = "2012-12-21",
-#'                format = "mm/dd/yy",
-#'                separator = " - ")
+#'   # Default start and end is the current date in the client's time zone
+#'   dateRangeInput("daterange2", "Date range:"),
 #'
-#' # Pass in Date objects
-#' dateRangeInput("daterange", "Date range:",
-#'                start = Sys.Date()-10,
-#'                end = Sys.Date()+10)
+#'   # start and end are always specified in yyyy-mm-dd, even if the display
+#'   # format is different
+#'   dateRangeInput("daterange3", "Date range:",
+#'                  start  = "2001-01-01",
+#'                  end    = "2010-12-31",
+#'                  min    = "2001-01-01",
+#'                  max    = "2012-12-21",
+#'                  format = "mm/dd/yy",
+#'                  separator = " - "),
 #'
-#' # Use different language and different first day of week
-#' dateRangeInput("daterange", "Date range:",
-#'                language = "de",
-#'                weekstart = 1)
+#'   # Pass in Date objects
+#'   dateRangeInput("daterange4", "Date range:",
+#'                  start = Sys.Date()-10,
+#'                  end = Sys.Date()+10),
 #'
-#' # Start with decade view instead of default month view
-#' dateRangeInput("daterange", "Date range:",
-#'                startview = "decade")
+#'   # Use different language and different first day of week
+#'   dateRangeInput("daterange5", "Date range:",
+#'                  language = "de",
+#'                  weekstart = 1),
 #'
+#'   # Start with decade view instead of default month view
+#'   dateRangeInput("daterange6", "Date range:",
+#'                  startview = "decade")
+#' )
+#'
+#' shinyApp(ui, server = function(input, output) { })
+#' }
 #' @export
 dateRangeInput <- function(inputId, label, start = NULL, end = NULL,
     min = NULL, max = NULL, format = "yyyy-mm-dd", startview = "month",
@@ -75,6 +82,10 @@ dateRangeInput <- function(inputId, label, start = NULL, end = NULL,
   if (inherits(min,   "Date"))  min   <- format(min,   "%Y-%m-%d")
   if (inherits(max,   "Date"))  max   <- format(max,   "%Y-%m-%d")
 
+  restored <- restoreInput(id = inputId, default = list(start, end))
+  start <- restored[[1]]
+  end <- restored[[2]]
+
   attachDependencies(
     div(id = inputId,
       class = "shiny-date-range-input form-group shiny-input-container",

R/input-file.R

@@ -28,20 +28,92 @@
 #' @param accept A character vector of MIME types; gives the browser a hint of
 #'   what kind of files the server is expecting.
 #'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   sidebarLayout(
+#'     sidebarPanel(
+#'       fileInput("file1", "Choose CSV File",
+#'         accept = c(
+#'           "text/csv",
+#'           "text/comma-separated-values,text/plain",
+#'           ".csv")
+#'         ),
+#'       tags$hr(),
+#'       checkboxInput("header", "Header", TRUE)
+#'     ),
+#'     mainPanel(
+#'       tableOutput("contents")
+#'     )
+#'   )
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$contents <- renderTable({
+#'     # input$file1 will be NULL initially. After the user selects
+#'     # and uploads a file, it will be a data frame with 'name',
+#'     # 'size', 'type', and 'datapath' columns. The 'datapath'
+#'     # column will contain the local filenames where the data can
+#'     # be found.
+#'     inFile <- input$file1
+#'
+#'     if (is.null(inFile))
+#'       return(NULL)
+#'
+#'     read.csv(inFile$datapath, header = input$header)
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
 #' @export
 fileInput <- function(inputId, label, multiple = FALSE, accept = NULL,
   width = NULL) {
 
-  inputTag <- tags$input(id = inputId, name = inputId, type = "file")
+  restoredValue <- restoreInput(id = inputId, default = NULL)
+
+  # Catch potential edge case - ensure that it's either NULL or a data frame.
+  if (!is.null(restoredValue) && !is.data.frame(restoredValue)) {
+    warning("Restored value for ", inputId, " has incorrect format.")
+    restoredValue <- NULL
+  }
+
+  if (!is.null(restoredValue)) {
+    restoredValue <- toJSON(restoredValue, strict_atomic = FALSE)
+  }
+
+  inputTag <- tags$input(
+    id = inputId,
+    name = inputId,
+    type = "file",
+    style = "display: none;",
+    `data-restore` = restoredValue
+  )
+
   if (multiple)
     inputTag$attribs$multiple <- "multiple"
   if (length(accept) > 0)
     inputTag$attribs$accept <- paste(accept, collapse=',')
 
+
   div(class = "form-group shiny-input-container",
     style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
     label %AND% tags$label(label),
-    inputTag,
+
+    div(class = "input-group",
+      tags$label(class = "input-group-btn",
+        span(class = "btn btn-default btn-file",
+          "Browse...",
+          inputTag
+        )
+      ),
+      tags$input(type = "text", class = "form-control",
+        placeholder = "No file selected", readonly = "readonly"
+      )
+    ),
+
     tags$div(
       id=paste(inputId, "_progress", sep=""),
       class="progress progress-striped active shiny-file-input-progress",

R/input-numeric.R

@@ -1,4 +1,3 @@
-
 #' Create a numeric input control
 #'
 #' Create an input control for entry of numeric values
@@ -13,12 +12,24 @@
 #' @seealso \code{\link{updateNumericInput}}
 #'
 #' @examples
-#' numericInput("obs", "Observations:", 10,
-#'              min = 1, max = 100)
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   numericInput("obs", "Observations:", 10, min = 1, max = 100),
+#'   verbatimTextOutput("value")
+#' )
+#' server <- function(input, output) {
+#'   output$value <- renderText({ input$obs })
+#' }
+#' shinyApp(ui, server)
+#' }
 #' @export
 numericInput <- function(inputId, label, value, min = NA, max = NA, step = NA,
   width = NULL) {
 
+  value <- restoreInput(id = inputId, default = value)
+
   # build input tag
   inputTag <- tags$input(id = inputId, type = "number", class="form-control",
                          value = formatNoSci(value))

R/input-password.R

@@ -9,12 +9,29 @@
 #' @seealso \code{\link{updateTextInput}}
 #'
 #' @examples
-#' passwordInput("password", "Password:")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   passwordInput("password", "Password:"),
+#'   actionButton("go", "Go"),
+#'   verbatimTextOutput("value")
+#' )
+#' server <- function(input, output) {
+#'   output$value <- renderText({
+#'     req(input$go)
+#'     isolate(input$password)
+#'   })
+#' }
+#' shinyApp(ui, server)
+#' }
 #' @export
-passwordInput <- function(inputId, label, value = "", width = NULL) {
+passwordInput <- function(inputId, label, value = "", width = NULL,
+                          placeholder = NULL) {
   div(class = "form-group shiny-input-container",
     style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
     label %AND% tags$label(label, `for` = inputId),
-    tags$input(id = inputId, type="password", class="form-control", value=value)
+    tags$input(id = inputId, type="password", class="form-control", value=value,
+               placeholder = placeholder)
   )
 }

R/input-radiobuttons.R

@@ -21,11 +21,33 @@
 #' @seealso \code{\link{updateRadioButtons}}
 #'
 #' @examples
-#' radioButtons("dist", "Distribution type:",
-#'              c("Normal" = "norm",
-#'                "Uniform" = "unif",
-#'                "Log-normal" = "lnorm",
-#'                "Exponential" = "exp"))
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   radioButtons("dist", "Distribution type:",
+#'                c("Normal" = "norm",
+#'                  "Uniform" = "unif",
+#'                  "Log-normal" = "lnorm",
+#'                  "Exponential" = "exp")),
+#'   plotOutput("distPlot")
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     dist <- switch(input$dist,
+#'                    norm = rnorm,
+#'                    unif = runif,
+#'                    lnorm = rlnorm,
+#'                    exp = rexp,
+#'                    rnorm)
+#'
+#'     hist(dist(500))
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
 #' @export
 radioButtons <- function(inputId, label, choices, selected = NULL,
   inline = FALSE, width = NULL) {
@@ -33,6 +55,8 @@ radioButtons <- function(inputId, label, choices, selected = NULL,
   # resolve names
   choices <- choicesWithNames(choices)
 
+  selected <- restoreInput(id = inputId, default = selected)
+
   # default value if it's not specified
   selected <- if (is.null(selected)) choices[[1]] else {
     validateSelected(selected, choices, inputId)

R/input-select.R

@@ -31,14 +31,32 @@
 #' @seealso \code{\link{updateSelectInput}}
 #'
 #' @examples
-#' selectInput("variable", "Variable:",
-#'             c("Cylinders" = "cyl",
-#'               "Transmission" = "am",
-#'               "Gears" = "gear"))
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   selectInput("variable", "Variable:",
+#'               c("Cylinders" = "cyl",
+#'                 "Transmission" = "am",
+#'                 "Gears" = "gear")),
+#'   tableOutput("data")
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$data <- renderTable({
+#'     mtcars[, c("mpg", input$variable), drop = FALSE]
+#'   }, rownames = TRUE)
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
 #' @export
 selectInput <- function(inputId, label, choices, selected = NULL,
                         multiple = FALSE, selectize = TRUE, width = NULL,
                         size = NULL) {
+
+  selected <- restoreInput(id = inputId, default = selected)
+
   # resolve names
   choices <- choicesWithNames(choices)
 
@@ -154,7 +172,7 @@ selectizeIt <- function(inputId, select, options, nonempty = FALSE) {
 
   if ('drag_drop' %in% options$plugins) {
     selectizeDep <- list(selectizeDep, htmlDependency(
-      'jqueryui', '1.11.4', c(href = 'shared/jqueryui'),
+      'jqueryui', '1.12.1', c(href = 'shared/jqueryui'),
       script = 'jquery-ui.min.js'
     ))
   }

R/input-slider.R

@@ -48,6 +48,27 @@
 #' @family input elements
 #' @seealso \code{\link{updateSliderInput}}
 #'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   sliderInput("obs", "Number of observations:",
+#'     min = 0, max = 1000, value = 500
+#'   ),
+#'   plotOutput("distPlot")
+#' )
+#'
+#' # Server logic
+#' server <- function(input, output) {
+#'   output$distPlot <- renderPlot({
+#'     hist(rnorm(input$obs))
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#' }
 #' @export
 sliderInput <- function(inputId, label, min, max, value, step = NULL,
                         round = FALSE, format = NULL, locale = NULL,
@@ -64,6 +85,8 @@ sliderInput <- function(inputId, label, min, max, value, step = NULL,
                     version = "0.10.2.2")
   }
 
+  value <- restoreInput(id = inputId, default = value)
+
   # If step is NULL, use heuristic to set the step size.
   findStepSize <- function(min, max, step) {
     if (!is.null(step)) return(step)
@@ -140,7 +163,6 @@ sliderInput <- function(inputId, label, min, max, value, step = NULL,
     `data-grid` = ticks,
     `data-grid-num` = n_ticks,
     `data-grid-snap` = FALSE,
-    `data-prettify-separator` = sep,
     `data-prefix` = pre,
     `data-postfix` = post,
     `data-keyboard` = TRUE,
@@ -152,6 +174,12 @@ sliderInput <- function(inputId, label, min, max, value, step = NULL,
     `data-timezone` = timezone
   ))
 
+  if (sep == "") {
+    sliderProps$`data-prettify-enabled` <- "0"
+  } else {
+    sliderProps$`data-prettify-separator` <- sep
+  }
+
   # Replace any TRUE and FALSE with "true" and "false"
   sliderProps <- lapply(sliderProps, function(x) {
     if (identical(x, TRUE)) "true"
@@ -191,7 +219,7 @@ sliderInput <- function(inputId, label, min, max, value, step = NULL,
   }
 
   dep <- list(
-    htmlDependency("ionrangeslider", "2.0.12", c(href="shared/ionrangeslider"),
+    htmlDependency("ionrangeslider", "2.1.2", c(href="shared/ionrangeslider"),
       script = "js/ion.rangeSlider.min.js",
       # ion.rangeSlider also needs normalize.css, which is already included in
       # Bootstrap.
@@ -221,7 +249,6 @@ hasDecimals <- function(value) {
 #'   or list of tags (using \code{\link{tag}} and friends), or raw HTML (using
 #'   \code{\link{HTML}}).
 #' @param pauseButton Similar to \code{playButton}, but for the pause button.
-#'
 #' @export
 animationOptions <- function(interval=1000,
                              loop=FALSE,

R/input-text.R

@@ -16,11 +16,24 @@
 #' @seealso \code{\link{updateTextInput}}
 #'
 #' @examples
-#' textInput("caption", "Caption:", "Data Summary")
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   textInput("caption", "Caption", "Data Summary"),
+#'   verbatimTextOutput("value")
+#' )
+#' server <- function(input, output) {
+#'   output$value <- renderText({ input$caption })
+#' }
+#' shinyApp(ui, server)
+#' }
 #' @export
 textInput <- function(inputId, label, value = "", width = NULL,
   placeholder = NULL) {
 
+  value <- restoreInput(id = inputId, default = value)
+
   div(class = "form-group shiny-input-container",
     style = if (!is.null(width)) paste0("width: ", validateCssUnit(width), ";"),
     label %AND% tags$label(label, `for` = inputId),

R/input-textarea.R

@@ -0,0 +1,69 @@
+#' Create a textarea input control
+#'
+#' Create a textarea input control for entry of unstructured text values.
+#'
+#' @inheritParams textInput
+#' @param height The height of the input, e.g. \code{'400px'}, or
+#'   \code{'100\%'}; see \code{\link{validateCssUnit}}.
+#' @param cols Value of the visible character columns of the input, e.g.
+#'   \code{80}. If used with \code{width}, \code{width} will take precedence in
+#'   the browser's rendering.
+#' @param rows The value of the visible character rows of the input, e.g.
+#'   \code{6}. If used with \code{height}, \code{height} will take precedence in
+#'   the browser's rendering.
+#' @param resize Which directions the textarea box can be resized. Can be one of
+#'   \code{"both"}, \code{"none"}, \code{"vertical"}, and \code{"horizontal"}.
+#'   The default, \code{NULL}, will use the client browser's default setting for
+#'   resizing textareas.
+#' @return A textarea input control that can be added to a UI definition.
+#'
+#' @family input elements
+#' @seealso \code{\link{updateTextAreaInput}}
+#'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   textAreaInput("caption", "Caption", "Data Summary", width = "1000px"),
+#'   verbatimTextOutput("value")
+#' )
+#' server <- function(input, output) {
+#'   output$value <- renderText({ input$caption })
+#' }
+#' shinyApp(ui, server)
+#'
+#' }
+#' @export
+textAreaInput <- function(inputId, label, value = "", width = NULL, height = NULL,
+  cols = NULL, rows = NULL, placeholder = NULL, resize = NULL) {
+
+  value <- restoreInput(id = inputId, default = value)
+
+  if (!is.null(resize)) {
+    resize <- match.arg(resize, c("both", "none", "vertical", "horizontal"))
+  }
+
+  style <- paste(
+    if (!is.null(width))  paste0("width: ",  validateCssUnit(width),  ";"),
+    if (!is.null(height)) paste0("height: ", validateCssUnit(height), ";"),
+    if (!is.null(resize)) paste0("resize: ", resize, ";")
+  )
+
+  # Workaround for tag attribute=character(0) bug:
+  #   https://github.com/rstudio/htmltools/issues/65
+  if (length(style) == 0) style <- NULL
+
+  div(class = "form-group shiny-input-container",
+    label %AND% tags$label(label, `for` = inputId),
+    tags$textarea(
+      id = inputId,
+      class = "form-control",
+      placeholder = placeholder,
+      style = style,
+      rows = rows,
+      cols = cols,
+      value
+    )
+  )
+}

R/input-utils.R

@@ -4,10 +4,13 @@ controlLabel <- function(controlName, label) {
 
 
 # Before shiny 0.9, `selected` refers to names/labels of `choices`; now it
-# refers to values. Below is a function for backward compatibility.
+# refers to values. Below is a function for backward compatibility. It also
+# coerces the value to `character`.
 validateSelected <- function(selected, choices, inputId) {
-  # drop names, otherwise toJSON() keeps them too
-  selected <- unname(selected)
+  # this line accomplishes two tings:
+  #   - coerces selected to character
+  #   - drops name, otherwise toJSON() keeps it too
+  selected <- as.character(selected)
   # 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)
@@ -48,10 +51,10 @@ generateOptions <- function(inputId, choices, selected, inline, type = 'checkbox
       # If inline, there's no wrapper div, and the label needs a class like
       # checkbox-inline.
       if (inline) {
-        tags$label(class = paste0(type, "-inline"), inputTag, tags$span(name))
+        tags$label(class = paste0(type, "-inline"), inputTag, tags$span(HTML(name)))
       } else {
         tags$div(class = type,
-          tags$label(inputTag, tags$span(name))
+          tags$label(inputTag, tags$span(HTML(name)))
         )
       }
     },
@@ -63,7 +66,7 @@ generateOptions <- function(inputId, choices, selected, inline, type = 'checkbox
 
 
 # Takes a vector or list, and adds names (same as the value) to any entries
-# without names.
+# without names. Coerces all leaf nodes to `character`.
 choicesWithNames <- function(choices) {
   # 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,
@@ -79,7 +82,7 @@ choicesWithNames <- function(choices) {
       if (is.list(val))
         listify(val)
       else if (length(val) == 1 && is.null(names(val)))
-        val
+        as.character(val)
       else
         makeNamed(as.list(val))
     })

R/insert-ui.R

@@ -0,0 +1,174 @@
+#' Insert UI objects
+#'
+#' Insert a UI object into the app.
+#'
+#' This function allows you to dynamically add an arbitrarily large UI
+#' object into your app, whenever you want, as many times as you want.
+#' Unlike \code{\link{renderUI}}, the UI generated with \code{insertUI}
+#' is not updatable as a whole: once it's created, it stays there. Each
+#' new call to \code{insertUI} creates more UI objects, in addition to
+#' the ones already there (all independent from one another). To
+#' update a part of the UI (ex: an input object), you must use the
+#' appropriate \code{render} function or a customized \code{reactive}
+#' function. To remove any part of your UI, use \code{\link{removeUI}}.
+#'
+#' @param selector A string that is accepted by jQuery's selector (i.e. the
+#' string \code{s} to be placed in a \code{$(s)} jQuery call). This selector
+#' will determine the element(s) relative to which you want to insert your
+#' UI object.
+#'
+#' @param where Where your UI object should go relative to the selector:
+#' \describe{
+#'   \item{\code{beforeBegin}}{Before the selector element itself}
+#'   \item{\code{afterBegin}}{Just inside the selector element, before its
+#'   first child}
+#'   \item{\code{beforeEnd}}{Just inside the selector element, after its
+#'   last child (default)}
+#'   \item{\code{afterEnd}}{After the selector element itself}
+#' }
+#' Adapted from
+#' \href{https://developer.mozilla.org/en-US/docs/Web/API/Element/insertAdjacentHTML}{here}.
+#'
+#' @param ui The UI object you want to insert. This can be anything that
+#' you usually put inside your apps's \code{ui} function. If you're inserting
+#' multiple elements in one call, make sure to wrap them in either a
+#' \code{tagList()} or a \code{tags$div()} (the latter option has the
+#' advantage that you can give it an \code{id} to make it easier to
+#' reference or remove it later on). If you want to insert raw html, use
+#' \code{ui = HTML()}.
+#'
+#' @param multiple In case your selector matches more than one element,
+#' \code{multiple} determines whether Shiny should insert the UI object
+#' relative to all matched elements or just relative to the first
+#' matched element (default).
+#'
+#' @param immediate Whether the UI object should be immediately inserted into
+#' the app when you call \code{insertUI}, or whether Shiny should wait until
+#' all outputs have been updated and all observers have been run (default).
+#'
+#' @param session The shiny session within which to call \code{insertUI}.
+#'
+#' @seealso \code{\link{removeUI}}
+#'
+#' @examples
+#' ## Only run this example in interactive R sessions
+#' if (interactive()) {
+#' # Define UI
+#' ui <- fluidPage(
+#'   actionButton("add", "Add UI")
+#' )
+#'
+#' # Server logic
+#' server <- function(input, output, session) {
+#'   observeEvent(input$add, {
+#'     insertUI(
+#'       selector = "#add",
+#'       where = "afterEnd",
+#'       ui = textInput(paste0("txt", input$add),
+#'                      "Insert some text")
+#'     )
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#' }
+#' @export
+insertUI <- function(selector,
+  where = c("beforeBegin", "afterBegin", "beforeEnd", "afterEnd"),
+  ui,
+  multiple = FALSE,
+  immediate = FALSE,
+  session = getDefaultReactiveDomain()) {
+
+  force(selector)
+  force(ui)
+  force(session)
+  force(multiple)
+  if (missing(where)) where <- "beforeEnd"
+  where <- match.arg(where)
+
+  callback <- function() {
+    session$sendInsertUI(selector = selector,
+                         multiple = multiple,
+                         where = where,
+                         content = processDeps(ui, session))
+  }
+
+  if (!immediate) session$onFlushed(callback, once = TRUE)
+  else callback()
+}
+
+
+#' Remove UI objects
+#'
+#' Remove a UI object from the app.
+#'
+#' This function allows you to remove any part of your UI. Once \code{removeUI}
+#' is executed on some element, it is gone forever.
+#'
+#' While it may be a particularly useful pattern to pair this with
+#' \code{\link{insertUI}} (to remove some UI you had previously inserted),
+#' there is no restriction on what you can use \code{removeUI} on. Any
+#' element that can be selected through a jQuery selector can be removed
+#' through this function.
+#'
+#' @param selector A string that is accepted by jQuery's selector (i.e. the
+#' string \code{s} to be placed in a \code{$(s)} jQuery call). This selector
+#' will determine the element(s) to be removed. If you want to remove a
+#' Shiny input or output, note that many of these are wrapped in \code{div}s,
+#' so you may need to use a somewhat complex selector -- see the Examples below.
+#' (Alternatively, you could also wrap the inputs/outputs that you want to be
+#' able to remove easily in a \code{div} with an id.)
+#'
+#' @param multiple In case your selector matches more than one element,
+#' \code{multiple} determines whether Shiny should remove all the matched
+#' elements or just the first matched element (default).
+#'
+#' @param immediate Whether the element(s) should be immediately removed from
+#' the app when you call \code{removeUI}, or whether Shiny should wait until
+#' all outputs have been updated and all observers have been run (default).
+#'
+#' @param session The shiny session within which to call \code{removeUI}.
+#'
+#' @seealso \code{\link{insertUI}}
+#'
+#' @examples
+#' ## Only run this example in interactive R sessions
+#' if (interactive()) {
+#' # Define UI
+#' ui <- fluidPage(
+#'   actionButton("rmv", "Remove UI"),
+#'   textInput("txt", "This is no longer useful")
+#' )
+#'
+#' # Server logic
+#' server <- function(input, output, session) {
+#'   observeEvent(input$rmv, {
+#'     removeUI(
+#'       selector = "div:has(> #txt)"
+#'     )
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#' }
+#' @export
+removeUI <- function(selector,
+  multiple = FALSE,
+  immediate = FALSE,
+  session = getDefaultReactiveDomain()) {
+
+  force(selector)
+  force(multiple)
+  force(session)
+
+  callback <- function() {
+    session$sendRemoveUI(selector = selector,
+                         multiple = multiple)
+  }
+
+  if (!immediate) session$onFlushed(callback, once = TRUE)
+  else callback()
+}

R/jqueryui.R

@@ -53,7 +53,6 @@
 #'   over text). The default is \code{"auto"}, which is equivalent to
 #'   \code{ifelse(draggable, "move", "inherit")}.
 #' @return An HTML element or list of elements.
-#'
 #' @export
 absolutePanel <- function(...,
                           top = NULL, left = NULL, right = NULL, bottom = NULL,
@@ -80,8 +79,6 @@ absolutePanel <- function(...,
   if (isTRUE(draggable)) {
     divTag <- tagAppendAttributes(divTag, class='draggable')
     return(tagList(
-      # IMPORTANT NOTE: If you update jqueryui, make sure you DON'T include the datepicker,
-      # as it collides with our bootstrap datepicker!
       singleton(tags$head(tags$script(src='shared/jqueryui/jquery-ui.min.js'))),
       divTag,
       tags$script('$(".draggable").draggable();')

R/middleware-shiny.R

@@ -41,35 +41,3 @@ sessionHandler <- function(req) {
     shinysession$handleRequest(subreq)
   })
 }
-
-dynamicHandler <- function(filePath, dependencyFiles=filePath) {
-  lastKnownTimestamps <- NA
-  metaHandler <- function(req) NULL
-
-  if (!file.exists(filePath))
-    return(metaHandler)
-
-  cacheContext <- CacheContext$new()
-
-  return (function(req) {
-    # Check if we need to rebuild
-    if (cacheContext$isDirty()) {
-      cacheContext$reset()
-      for (dep in dependencyFiles)
-        cacheContext$addDependencyFile(dep)
-
-      clearClients()
-      if (file.exists(filePath)) {
-        local({
-          cacheContext$with(function() {
-            sys.source(filePath, envir=new.env(parent=globalenv()), keep.source=TRUE)
-          })
-        })
-      }
-      metaHandler <<- joinHandlers(.globals$clients)
-      clearClients()
-    }
-
-    return(metaHandler(req))
-  })
-}

R/middleware.R

@@ -299,9 +299,7 @@ HandlerManager <- R6Class("HandlerManager",
 
           if (reqSize > maxSize) {
             return(list(status = 413L,
-              headers = list(
-                'Content-Type' = 'text/plain'
-              ),
+              headers = list('Content-Type' = 'text/plain'),
               body = 'Maximum upload size exceeded'))
           }
           else {
@@ -310,7 +308,18 @@ HandlerManager <- R6Class("HandlerManager",
         },
         call = .httpServer(
           function (req) {
-            return(handlers$invoke(req))
+            withCallingHandlers(withLogErrors(handlers$invoke(req)),
+              error = function(cond) {
+                sanitizeErrors <- getOption('shiny.sanitize.errors', FALSE)
+                if (inherits(cond, 'shiny.custom.error') || !sanitizeErrors) {
+                  stop(cond$message, call. = FALSE)
+                } else {
+                  stop(paste("An error has occurred. Check your logs or",
+                             "contact the app author for clarification."),
+                       call. = FALSE)
+                }
+              }
+            )
           },
           getOption('shiny.sharedSecret')
         ),
@@ -333,7 +342,7 @@ HandlerManager <- R6Class("HandlerManager",
         }
 
         # Catch HEAD requests. For the purposes of handler functions, they
-        # should be treated like GET. The difference is that  they shouldn't
+        # should be treated like GET. The difference is that they shouldn't
         # return a body in the http response.
         head_request <- FALSE
         if (identical(req$REQUEST_METHOD, "HEAD")) {

R/modal.R

@@ -0,0 +1,183 @@
+#' Show or remove a modal dialog
+#'
+#' This causes a modal dialog to be displayed in the client browser, and is
+#' typically used with \code{\link{modalDialog}}.
+#'
+#' @param ui UI content to show in the modal.
+#' @param session The \code{session} object passed to function given to
+#'   \code{shinyServer}.
+#'
+#' @seealso \code{\link{modalDialog}} for examples.
+#' @export
+showModal <- function(ui, session = getDefaultReactiveDomain()) {
+  res <- processDeps(ui, session)
+
+  session$sendModal("show",
+    list(
+      html = res$html,
+      deps = res$deps
+    )
+  )
+}
+
+#' @rdname showModal
+#' @export
+removeModal <- function(session = getDefaultReactiveDomain()) {
+  session$sendModal("remove", NULL)
+}
+
+
+#' Create a modal dialog UI
+#'
+#' This creates the UI for a modal dialog, using Bootstrap's modal class. Modals
+#' are typically used for showing important messages, or for presenting UI that
+#' requires input from the user, such as a username and password input.
+#'
+#' @param ... UI elements for the body of the modal dialog box.
+#' @param title An optional title for the dialog.
+#' @param footer UI for footer. Use \code{NULL} for no footer.
+#' @param size One of \code{"s"} for small, \code{"m"} (the default) for medium,
+#'   or \code{"l"} for large.
+#' @param easyClose If \code{TRUE}, the modal dialog can be dismissed by
+#'   clicking outside the dialog box, or be pressing the Escape key. If
+#'   \code{FALSE} (the default), the modal dialog can't be dismissed in those
+#'   ways; instead it must be dismissed by clicking on the dismiss button, or
+#'   from a call to \code{\link{removeModal}} on the server.
+#' @param fade If \code{FALSE}, the modal dialog will have no fade-in animation
+#'   (it will simply appear rather than fade in to view).
+#'
+#' @examples
+#' if (interactive()) {
+#' # Display an important message that can be dismissed only by clicking the
+#' # dismiss button.
+#' shinyApp(
+#'   ui = basicPage(
+#'     actionButton("show", "Show modal dialog")
+#'   ),
+#'   server = function(input, output) {
+#'     observeEvent(input$show, {
+#'       showModal(modalDialog(
+#'         title = "Important message",
+#'         "This is an important message!"
+#'       ))
+#'     })
+#'   }
+#' )
+#'
+#'
+#' # Display a message that can be dismissed by clicking outside the modal dialog,
+#' # or by pressing Esc.
+#' shinyApp(
+#'   ui = basicPage(
+#'     actionButton("show", "Show modal dialog")
+#'   ),
+#'   server = function(input, output) {
+#'     observeEvent(input$show, {
+#'       showModal(modalDialog(
+#'         title = "Somewhat important message",
+#'         "This is a somewhat important message.",
+#'         easyClose = TRUE,
+#'         footer = NULL
+#'       ))
+#'     })
+#'   }
+#' )
+#'
+#'
+#' # Display a modal that requires valid input before continuing.
+#' shinyApp(
+#'   ui = basicPage(
+#'     actionButton("show", "Show modal dialog"),
+#'     verbatimTextOutput("dataInfo")
+#'   ),
+#'
+#'   server = function(input, output) {
+#'     # reactiveValues object for storing current data set.
+#'     vals <- reactiveValues(data = NULL)
+#'
+#'     # Return the UI for a modal dialog with data selection input. If 'failed' is
+#'     # TRUE, then display a message that the previous value was invalid.
+#'     dataModal <- function(failed = FALSE) {
+#'       modalDialog(
+#'         textInput("dataset", "Choose data set",
+#'           placeholder = 'Try "mtcars" or "abc"'
+#'         ),
+#'         span('(Try the name of a valid data object like "mtcars", ',
+#'              'then a name of a non-existent object like "abc")'),
+#'         if (failed)
+#'           div(tags$b("Invalid name of data object", style = "color: red;")),
+#'
+#'         footer = tagList(
+#'           modalButton("Cancel"),
+#'           actionButton("ok", "OK")
+#'         )
+#'       )
+#'     }
+#'
+#'     # Show modal when button is clicked.
+#'     observeEvent(input$show, {
+#'       showModal(dataModal())
+#'     })
+#'
+#'     # When OK button is pressed, attempt to load the data set. If successful,
+#'     # remove the modal. If not show another modal, but this time with a failure
+#'     # message.
+#'     observeEvent(input$ok, {
+#'       # Check that data object exists and is data frame.
+#'       if (!is.null(input$dataset) && nzchar(input$dataset) &&
+#'           exists(input$dataset) && is.data.frame(get(input$dataset))) {
+#'         vals$data <- get(input$dataset)
+#'         removeModal()
+#'       } else {
+#'         showModal(dataModal(failed = TRUE))
+#'       }
+#'     })
+#'
+#'     # Display information about selected data
+#'     output$dataInfo <- renderPrint({
+#'       if (is.null(vals$data))
+#'         "No data selected"
+#'       else
+#'         summary(vals$data)
+#'     })
+#'   }
+#' )
+#' }
+#' @export
+modalDialog <- function(..., title = NULL, footer = modalButton("Dismiss"),
+  size = c("m", "s", "l"), easyClose = FALSE, fade = TRUE) {
+
+  size <- match.arg(size)
+
+  cls <- if (fade) "modal fade" else "modal"
+  div(id = "shiny-modal", class = cls, tabindex = "-1",
+    `data-backdrop` = if (!easyClose) "static",
+    `data-keyboard` = if (!easyClose) "false",
+
+    div(
+      class = "modal-dialog",
+      class = switch(size, s = "modal-sm", m = NULL, l = "modal-lg"),
+      div(class = "modal-content",
+        if (!is.null(title)) div(class = "modal-header",
+          tags$h4(class = "modal-title", title)
+        ),
+        div(class = "modal-body", ...),
+        if (!is.null(footer)) div(class = "modal-footer", footer)
+      )
+    ),
+    tags$script("$('#shiny-modal').modal().focus();")
+  )
+}
+
+#' Create a button for a modal dialog
+#'
+#' When clicked, a \code{modalButton} will dismiss the modal dialog.
+#'
+#' @inheritParams actionButton
+#' @seealso \code{\link{modalDialog}} for examples.
+#' @export
+modalButton <- function(label, icon = NULL) {
+  tags$button(type = "button", class = "btn btn-default",
+    `data-dismiss` = "modal", validateIcon(icon), label
+  )
+}

R/modules.R

@@ -1,4 +1,4 @@
-# Creates an object whose $ and $<- pass through to the parent
+# Creates an object whose $ and [[ pass through to the parent
 # session, unless the name is matched in ..., in which case
 # that value is returned instead. (See Decorator pattern.)
 createSessionProxy <- function(parentSession, ...) {
@@ -14,18 +14,24 @@ createSessionProxy <- function(parentSession, ...) {
 
 #' @export
 `$.session_proxy` <- function(x, name) {
-  if (name %in% names(x[["overrides"]]))
-    x[["overrides"]][[name]]
+  if (name %in% names(.subset2(x, "overrides")))
+    .subset2(x, "overrides")[[name]]
   else
-    x[["parent"]][[name]]
+    .subset2(x, "parent")[[name]]
 }
 
+#' @export
+`[[.session_proxy` <- `$.session_proxy`
+
+
 #' @export
 `$<-.session_proxy` <- function(x, name, value) {
-  x[["parent"]][[name]] <- value
-  x
+  stop("Attempted to assign value on session proxy.")
 }
 
+`[[<-.session_proxy` <- `$<-.session_proxy`
+
+
 #' Invoke a Shiny module
 #'
 #' Shiny's module feature lets you break complicated UI and server logic into
@@ -42,7 +48,6 @@ createSessionProxy <- function(parentSession, ...) {
 #'
 #' @return The return value, if any, from executing the module server function
 #' @seealso \url{http://shiny.rstudio.com/articles/modules.html}
-#'
 #' @export
 callModule <- function(module, id, ..., session = getDefaultReactiveDomain()) {
   childScope <- session$makeScope(id)

R/notifications.R

@@ -0,0 +1,106 @@
+#' Show or remove a notification
+#'
+#' These functions show and remove notifications in a Shiny application.
+#'
+#' @param ui Content of message.
+#' @param action Message content that represents an action. For example, this
+#'   could be a link that the user can click on. This is separate from \code{ui}
+#'   so customized layouts can handle the main notification content separately
+#'   from action content.
+#' @param duration Number of seconds to display the message before it
+#'   disappears. Use \code{NULL} to make the message not automatically
+#'   disappear.
+#' @param closeButton If \code{TRUE}, display a button which will make the
+#'   notification disappear when clicked. If \code{FALSE} do not display.
+#' @param id An ID string. This can be used to change the contents of an
+#'   existing message with \code{showNotification}, or to remove it with
+#'   \code{removeNotification}. If not provided, one will be generated
+#'   automatically. If an ID is provided and there does not currently exist a
+#'   notification with that ID, a new notification will be created with that ID.
+#' @param type A string which controls the color of the notification. One of
+#'   "default" (gray), "message" (blue), "warning" (yellow), or "error" (red).
+#' @param session Session object to send notification to.
+#'
+#' @return An ID for the notification.
+#'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#' # Show a message when button is clicked
+#' shinyApp(
+#'   ui = fluidPage(
+#'     actionButton("show", "Show")
+#'   ),
+#'   server = function(input, output) {
+#'     observeEvent(input$show, {
+#'       showNotification("Message text",
+#'         action = a(href = "javascript:location.reload();", "Reload page")
+#'       )
+#'     })
+#'   }
+#' )
+#'
+#' # App with show and remove buttons
+#' shinyApp(
+#'   ui = fluidPage(
+#'     actionButton("show", "Show"),
+#'     actionButton("remove", "Remove")
+#'   ),
+#'   server = function(input, output) {
+#'     # A queue of notification IDs
+#'     ids <- character(0)
+#'     # A counter
+#'     n <- 0
+#'
+#'     observeEvent(input$show, {
+#'       # Save the ID for removal later
+#'       id <- showNotification(paste("Message", n), duration = NULL)
+#'       ids <<- c(ids, id)
+#'       n <<- n + 1
+#'     })
+#'
+#'     observeEvent(input$remove, {
+#'       if (length(ids) > 0)
+#'         removeNotification(ids[1])
+#'       ids <<- ids[-1]
+#'     })
+#'   }
+#' )
+#' }
+#' @export
+showNotification <- function(ui, action = NULL, duration = 5,
+  closeButton = TRUE, id = NULL,
+  type = c("default", "message", "warning", "error"),
+  session = getDefaultReactiveDomain())
+{
+
+  if (is.null(id))
+    id <- createUniqueId(8)
+
+  res <- processDeps(ui, session)
+  actionRes <- processDeps(action, session)
+
+  session$sendNotification("show",
+    list(
+      html = res$html,
+      action = actionRes$html,
+      deps = c(res$deps, actionRes$deps),
+      duration = if (!is.null(duration)) duration * 1000,
+      closeButton = closeButton,
+      id = id,
+      type = match.arg(type)
+    )
+  )
+
+  id
+}
+
+#' @rdname showNotification
+#' @export
+removeNotification <- function(id = NULL, session = getDefaultReactiveDomain()) {
+  if (is.null(id)) {
+    stop("id is required.")
+  }
+  session$sendNotification("remove", id)
+  id
+}

R/progress.R

@@ -12,6 +12,14 @@
 #' method is called. Calling \code{close} will cause the progress panel
 #' to be removed.
 #'
+#' As of version 0.14, the progress indicators use Shiny's new notification API.
+#' If you want to use the old styling (for example, you may have used customized
+#' CSS), you can use \code{style="old"} each time you call
+#' \code{Progress$new()}. If you don't want to set the style each time
+#' \code{Progress$new} is called, you can instead call
+#' \code{\link{shinyOptions}(progress.style="old")} just once, inside the server
+#' function.
+#'
 #' \strong{Methods}
 #'   \describe{
 #'     \item{\code{initialize(session, min = 0, max = 1)}}{
@@ -48,6 +56,10 @@
 #' @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 style Progress display style. If \code{"notification"} (the default),
+#'   the progress indicator will show using Shiny's notification API. If
+#'   \code{"old"}, use the same HTML and CSS used in Shiny 0.13.2 and below
+#'   (this is for backward-compatibility).
 #' @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.
@@ -55,11 +67,16 @@
 #'   progress bar.
 #'
 #' @examples
-#' \dontrun{
-#' # server.R
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   plotOutput("plot")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   output$plot <- renderPlot({
-#'     progress <- shiny::Progress$new(session, min=1, max=15)
+#'     progress <- Progress$new(session, min=1, max=15)
 #'     on.exit(progress$close())
 #'
 #'     progress$set(message = 'Calculation in progress',
@@ -71,7 +88,9 @@
 #'     }
 #'     plot(cars)
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @seealso \code{\link{withProgress}}
 #' @format NULL
@@ -82,18 +101,22 @@ Progress <- R6Class(
   portable = TRUE,
   public = list(
 
-    initialize = function(session = getDefaultReactiveDomain(), min = 0, max = 1) {
-      if (!inherits(session, "ShinySession"))
+    initialize = function(session = getDefaultReactiveDomain(),
+      min = 0, max = 1,
+      style = getShinyOption("progress.style", default = "notification"))
+    {
+      if (is.null(session$progressStack))
         stop("'session' is not a ShinySession object.")
 
       private$session <- session
-      private$id <- paste(as.character(as.raw(stats::runif(8, min=0, max=255))), collapse='')
+      private$id <- createUniqueId(8)
       private$min <- min
       private$max <- max
+      private$style <- match.arg(style, choices = c("notification", "old"))
       private$value <- NULL
       private$closed <- FALSE
 
-      session$sendProgress('open', list(id = private$id))
+      session$sendProgress('open', list(id = private$id, style = private$style))
     },
 
     set = function(value = NULL, message = NULL, detail = NULL) {
@@ -115,7 +138,8 @@ Progress <- R6Class(
         id = private$id,
         message = message,
         detail = detail,
-        value = value
+        value = value,
+        style = private$style
       ))
 
        private$session$sendProgress('update', data)
@@ -141,7 +165,9 @@ Progress <- R6Class(
         return()
       }
 
-      private$session$sendProgress('close', list(id = private$id))
+      private$session$sendProgress('close',
+        list(id = private$id, style = private$style)
+      )
       private$closed <- TRUE
     }
   ),
@@ -151,6 +177,7 @@ Progress <- R6Class(
     id = character(0),
     min = numeric(0),
     max = numeric(0),
+    style = character(0),
     value = NULL,
     closed = logical(0)
   )
@@ -179,6 +206,14 @@ Progress <- R6Class(
 #' is not common) or otherwise cannot be encapsulated by a single scope. In that
 #' case, you can use the \code{Progress} reference class.
 #'
+#' As of version 0.14, the progress indicators use Shiny's new notification API.
+#' If you want to use the old styling (for example, you may have used customized
+#' CSS), you can use \code{style="old"} each time you call
+#' \code{withProgress()}. If you don't want to set the style each time
+#' \code{withProgress} is called, you can instead call
+#' \code{\link{shinyOptions}(progress.style="old")} just once, inside the server
+#' function.
+#'
 #' @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.
@@ -199,14 +234,23 @@ Progress <- R6Class(
 #'   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 style Progress display style. If \code{"notification"} (the default),
+#'   the progress indicator will show using Shiny's notification API. If
+#'   \code{"old"}, use the same HTML and CSS used in Shiny 0.13.2 and below
+#'   (this is for backward-compatibility).
 #' @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) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   plotOutput("plot")
+#' )
+#'
+#' server <- function(input, output) {
 #'   output$plot <- renderPlot({
 #'     withProgress(message = 'Calculation in progress',
 #'                  detail = 'This may take a while...', value = 0, {
@@ -217,24 +261,30 @@ Progress <- R6Class(
 #'     })
 #'     plot(cars)
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @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) {
+  value = min + (max - min) * 0.1,
+  message = NULL, detail = NULL,
+  style = getShinyOption("progress.style", default = "notification"),
+  session = getDefaultReactiveDomain(),
+  env = parent.frame(), quoted = FALSE)
+{
 
   if (!quoted)
     expr <- substitute(expr)
 
-  if (!inherits(session, "ShinySession"))
+  if (is.null(session$progressStack))
     stop("'session' is not a ShinySession object.")
 
-  p <- Progress$new(session, min = min, max = max)
+  style <- match.arg(style, c("notification", "old"))
+
+  p <- Progress$new(session, min = min, max = max, style = style)
 
   session$progressStack$push(p)
   on.exit({
@@ -252,7 +302,7 @@ withProgress <- function(expr, min = 0, max = 1,
 setProgress <- function(value = NULL, message = NULL, detail = NULL,
                         session = getDefaultReactiveDomain()) {
 
-  if (!inherits(session, "ShinySession"))
+  if (is.null(session$progressStack))
     stop("'session' is not a ShinySession object.")
 
   if (session$progressStack$size() == 0) {
@@ -269,7 +319,7 @@ setProgress <- function(value = NULL, message = NULL, detail = NULL,
 incProgress <- function(amount = 0.1, message = NULL, detail = NULL,
                         session = getDefaultReactiveDomain()) {
 
-  if (!inherits(session, "ShinySession"))
+  if (is.null(session$progressStack))
     stop("'session' is not a ShinySession object.")
 
   if (session$progressStack$size() == 0) {

R/react.R

@@ -21,10 +21,8 @@ Context <- R6Class(
       withReactiveDomain(.domain, {
         env <- .getReactiveEnvironment()
         .graphEnterContext(id)
-        tryCatch(
-          env$runWith(self, func),
-          finally = .graphExitContext(id)
-        )
+        on.exit(.graphExitContext(id), add = TRUE)
+        env$runWith(self, func)
       })
     },
     invalidate = function() {
@@ -112,18 +110,21 @@ ReactiveEnvironment <- R6Class(
       old.ctx <- .currentContext
       .currentContext <<- ctx
       on.exit(.currentContext <<- old.ctx)
-      shinyCallingHandlers(contextFunc())
+      contextFunc()
     },
     addPendingFlush = function(ctx, priority) {
       .pendingFlush$enqueue(ctx, priority)
     },
+    hasPendingFlush = function() {
+      return(!.pendingFlush$isEmpty())
+    },
     flush = function() {
       # If already in a flush, don't start another one
       if (.inFlush) return()
       .inFlush <<- TRUE
       on.exit(.inFlush <<- FALSE)
 
-      while (!.pendingFlush$isEmpty()) {
+      while (hasPendingFlush()) {
         ctx <- .pendingFlush$dequeue()
         ctx$executeFlushCallbacks()
       }

R/reactive-domains.R

@@ -42,11 +42,11 @@ NULL
 #
 ## ------------------------------------------------------------------------
 createMockDomain <- function() {
-  callbacks <- list()
+  callbacks <- Callbacks$new()
   ended <- FALSE
   domain <- new.env(parent = emptyenv())
   domain$onEnded <- function(callback) {
-    callbacks <<- c(callbacks, callback)
+    return(callbacks$register(callback))
   }
   domain$isEnded <- function() {
     ended
@@ -55,7 +55,7 @@ createMockDomain <- function() {
   domain$end <- function() {
     if (!ended) {
       ended <<- TRUE
-      lapply(callbacks, do.call, list())
+      callbacks$invoke()
     }
     invisible()
   }

R/reactives.R

@@ -47,6 +47,7 @@ ReactiveValues <- R6Class(
     # For debug purposes
     .label = character(0),
     .values = 'environment',
+    .metadata = 'environment',
     .dependents = 'environment',
     # Dependents for the list of all names, including hidden
     .namesDeps = 'Dependents',
@@ -60,32 +61,40 @@ ReactiveValues <- R6Class(
                        p_randomInt(1000, 10000),
                        sep="")
       .values <<- new.env(parent=emptyenv())
+      .metadata <<- new.env(parent=emptyenv())
       .dependents <<- new.env(parent=emptyenv())
       .namesDeps <<- Dependents$new()
       .allValuesDeps <<- Dependents$new()
       .valuesDeps <<- Dependents$new()
     },
+
     get = function(key) {
+      # Register the "downstream" reactive which is accessing this value, so
+      # that we know to invalidate them when this value changes.
       ctx <- .getReactiveEnvironment()$currentContext()
       dep.key <- paste(key, ':', ctx$id, sep='')
-      if (!exists(dep.key, where=.dependents, inherits=FALSE)) {
+      if (!exists(dep.key, envir=.dependents, inherits=FALSE)) {
         .graphDependsOn(ctx$id, sprintf('%s$%s', .label, key))
-        assign(dep.key, ctx, pos=.dependents, inherits=FALSE)
+        .dependents[[dep.key]] <- ctx
         ctx$onInvalidate(function() {
-          rm(list=dep.key, pos=.dependents, inherits=FALSE)
+          rm(list=dep.key, envir=.dependents, inherits=FALSE)
         })
       }
 
-      if (!exists(key, where=.values, inherits=FALSE))
+      if (isFrozen(key))
+        reactiveStop()
+
+      if (!exists(key, envir=.values, inherits=FALSE))
         NULL
       else
-        base::get(key, pos=.values, inherits=FALSE)
+        .values[[key]]
     },
+
     set = function(key, value) {
       hidden <- substr(key, 1, 1) == "."
 
-      if (exists(key, where=.values, inherits=FALSE)) {
-        if (identical(base::get(key, pos=.values, inherits=FALSE), value)) {
+      if (exists(key, envir=.values, inherits=FALSE)) {
+        if (identical(.values[[key]], value)) {
           return(invisible())
         }
       }
@@ -98,14 +107,14 @@ ReactiveValues <- R6Class(
       else
         .valuesDeps$invalidate()
 
-      assign(key, value, pos=.values, inherits=FALSE)
+      .values[[key]] <- value
 
       .graphValueChange(sprintf('names(%s)', .label), ls(.values, all.names=TRUE))
       .graphValueChange(sprintf('%s (all)', .label), as.list(.values))
       .graphValueChange(sprintf('%s$%s', .label, key), value)
 
       dep.keys <- objects(
-        pos=.dependents,
+        envir=.dependents,
         pattern=paste('^\\Q', key, ':', '\\E', '\\d+$', sep=''),
         all.names=TRUE
       )
@@ -118,18 +127,54 @@ ReactiveValues <- R6Class(
       )
       invisible()
     },
+
     mset = function(lst) {
       lapply(base::names(lst),
              function(name) {
                self$set(name, lst[[name]])
              })
     },
+
     names = function() {
       .graphDependsOn(.getReactiveEnvironment()$currentContext()$id,
                       sprintf('names(%s)', .label))
       .namesDeps$register()
       return(ls(.values, all.names=TRUE))
     },
+
+    # Get a metadata value. Does not trigger reactivity.
+    getMeta = function(key, metaKey) {
+      # Make sure to use named (not numeric) indexing into list.
+      metaKey <- as.character(metaKey)
+      .metadata[[key]][[metaKey]]
+    },
+
+    # Set a metadata value. Does not trigger reactivity.
+    setMeta = function(key, metaKey, value) {
+      # Make sure to use named (not numeric) indexing into list.
+      metaKey <- as.character(metaKey)
+
+      if (!exists(key, envir = .metadata, inherits = FALSE)) {
+        .metadata[[key]] <<- list()
+      }
+
+      .metadata[[key]][[metaKey]] <<- value
+    },
+
+    # Mark a value as frozen If accessed while frozen, a shiny.silent.error will
+    # be thrown.
+    freeze = function(key) {
+      setMeta(key, "frozen", TRUE)
+    },
+
+    thaw = function(key) {
+      setMeta(key, "frozen", NULL)
+    },
+
+    isFrozen = function(key) {
+      isTRUE(getMeta(key, "frozen"))
+    },
+
     toList = function(all.names=FALSE) {
       .graphDependsOn(.getReactiveEnvironment()$currentContext()$id,
                       sprintf('%s (all)', .label))
@@ -140,6 +185,7 @@ ReactiveValues <- R6Class(
 
       return(as.list(.values, all.names=all.names))
     },
+
     .setLabel = function(label) {
       .label <<- label
     }
@@ -186,7 +232,6 @@ ReactiveValues <- R6Class(
 #'   these objects must be named.
 #'
 #' @seealso \code{\link{isolate}} and \code{\link{is.reactivevalues}}.
-#'
 #' @export
 reactiveValues <- function(...) {
   args <- list(...)
@@ -317,10 +362,25 @@ as.list.reactivevalues <- function(x, all.names=FALSE, ...) {
 #' # isolate() can also be used when calling from outside a reactive context (e.g.
 #' # at the console)
 #' isolate(reactiveValuesToList(values))
-#'
 #' @export
 reactiveValuesToList <- function(x, all.names=FALSE) {
-  .subset2(x, 'impl')$toList(all.names)
+  # Default case
+  res <- .subset2(x, 'impl')$toList(all.names)
+
+  prefix <- .subset2(x, 'ns')("")
+  # Special handling for namespaces
+  if (nzchar(prefix)) {
+    fullNames <- names(res)
+
+    # Filter out items that match namespace
+    fullNames <- fullNames[substring(fullNames, 1, nchar(prefix)) == prefix]
+    res <- res[fullNames]
+
+    # Remove namespace prefix
+    names(res) <- substring(fullNames, nchar(prefix) + 1)
+  }
+
+  res
 }
 
 # This function is needed because str() on a reactivevalues object will call
@@ -334,6 +394,67 @@ str.reactivevalues <- function(object, indent.str = " ", ...) {
   utils::str(class(object))
 }
 
+
+#' Freeze a reactive value
+#'
+#' This freezes a reactive value. If the value is accessed while frozen, a
+#' "silent" exception is raised and the operation is stopped. This is the same
+#' thing that happens if \code{req(FALSE)} is called. The value is thawed
+#' (un-frozen; accessing it will no longer raise an exception) when the current
+#' reactive domain is flushed. In a Shiny application, this occurs after all of
+#' the observers are executed.
+#'
+#' @param x A \code{\link{reactiveValues}} object (like \code{input}).
+#' @param name The name of a value in the \code{\link{reactiveValues}} object.
+#'
+#' @seealso \code{\link{req}}
+#' @examples
+#' ## Only run this examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   selectInput("data", "Data Set", c("mtcars", "pressure")),
+#'   checkboxGroupInput("cols", "Columns (select 2)", character(0)),
+#'   plotOutput("plot")
+#' )
+#'
+#' server <- function(input, output, session) {
+#'   observe({
+#'     data <- get(input$data)
+#'     # Sets a flag on input$cols to essentially do req(FALSE) if input$cols
+#'     # is accessed. Without this, an error will momentarily show whenever a
+#'     # new data set is selected.
+#'     freezeReactiveValue(input, "cols")
+#'     updateCheckboxGroupInput(session, "cols", choices = names(data))
+#'   })
+#'
+#'   output$plot <- renderPlot({
+#'     # When a new data set is selected, input$cols will have been invalidated
+#'     # above, and this will essentially do the same as req(FALSE), causing
+#'     # this observer to stop and raise a silent exception.
+#'     cols <- input$cols
+#'     data <- get(input$data)
+#'
+#'     if (length(cols) == 2) {
+#'       plot(data[[ cols[1] ]], data[[ cols[2] ]])
+#'     }
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
+#' @export
+freezeReactiveValue <- function(x, name) {
+  domain <- getDefaultReactiveDomain()
+  if (is.null(getDefaultReactiveDomain)) {
+    stop("freezeReactiveValue() must be called when a default reactive domain is active.")
+  }
+
+  domain$freezeValue(x, name)
+  invisible()
+}
+
+
 # Observable ----------------------------------------------------------------
 
 Observable <- R6Class(
@@ -347,17 +468,30 @@ Observable <- R6Class(
     .invalidated = logical(0),
     .running = logical(0),
     .value = NULL,
+    .error = FALSE,
     .visible = logical(0),
     .execCount = integer(0),
     .mostRecentCtxId = character(0),
 
     initialize = function(func, label = deparse(substitute(func)),
-                          domain = getDefaultReactiveDomain()) {
+                          domain = getDefaultReactiveDomain(),
+                          ..stacktraceon = TRUE) {
       if (length(formals(func)) > 0)
         stop("Can't make a reactive expression from a function that takes one ",
              "or more parameters; only functions without parameters can be ",
              "reactive.")
-      .func <<- func
+
+      # This is to make sure that the function labels that show in the profiler
+      # and in stack traces doesn't contain whitespace. See
+      # https://github.com/rstudio/profvis/issues/58
+      if (grepl("\\s", label, perl = TRUE)) {
+        funcLabel <- "<reactive>"
+      } else {
+        funcLabel <- paste0("<reactive:", label, ">")
+      }
+
+      .func <<- wrapFunctionLabel(func, funcLabel,
+        ..stacktraceon = ..stacktraceon)
       .label <<- label
       .domain <<- domain
       .dependents <<- Dependents$new()
@@ -370,13 +504,16 @@ Observable <- R6Class(
       .dependents$register()
 
       if (.invalidated || .running) {
-        self$.updateValue()
+        ..stacktraceoff..(
+          self$.updateValue()
+        )
       }
 
       .graphDependsOnId(getCurrentContext()$id, .mostRecentCtxId)
 
-      if (identical(class(.value), 'try-error'))
-        stop(attr(.value, 'condition'))
+      if (.error) {
+        stop(.value)
+      }
 
       if (.visible)
         .value
@@ -400,9 +537,36 @@ Observable <- R6Class(
       on.exit(.running <<- wasRunning)
 
       ctx$run(function() {
-        result <- withVisible(try(shinyCallingHandlers(.func()), silent=TRUE))
-        .visible <<- result$visible
+        result <- withCallingHandlers(
+
+          {
+            .error <<- FALSE
+            withVisible(.func())
+          },
+
+          error = function(cond) {
+            # If an error occurs, we want to propagate the error, but we also
+            # want to save a copy of it, so future callers of this reactive will
+            # get the same error (i.e. the error is cached).
+
+            # We stripStackTrace in the next line, just in case someone
+            # downstream of us (i.e. deeper into the call stack) used
+            # captureStackTraces; otherwise the entire stack would always be the
+            # same (i.e. you'd always see the whole stack trace of the *first*
+            # time the code was run and the condition raised; there'd be no way
+            # to see the stack trace of the call site that caused the cached
+            # exception to be re-raised, and you need that information to figure
+            # out what's triggering the re-raise).
+            #
+            # We use try(stop()) as an easy way to generate a try-error object
+            # out of this condition.
+            .value <<- cond
+            .error <<- TRUE
+            .visible <<- FALSE
+          }
+        )
         .value <<- result$value
+        .visible <<- result$visible
       })
     }
   )
@@ -434,6 +598,8 @@ Observable <- R6Class(
 #'   variable; to do so, it must be quoted with \code{quote()}.
 #' @param label A label for the reactive expression, useful for debugging.
 #' @param domain See \link{domains}.
+#' @param ..stacktraceon Advanced use only. For stack manipulation purposes; see
+#'   \code{\link{stacktrace}}.
 #' @return a function, wrapped in a S3 class "reactive"
 #'
 #' @examples
@@ -454,10 +620,10 @@ Observable <- R6Class(
 #' isolate(reactiveB())
 #' isolate(reactiveC())
 #' isolate(reactiveD())
-#'
 #' @export
 reactive <- function(x, env = parent.frame(), quoted = FALSE, label = NULL,
-                     domain = getDefaultReactiveDomain()) {
+                     domain = getDefaultReactiveDomain(),
+                     ..stacktraceon = TRUE) {
   fun <- exprToFunction(x, env, quoted)
   # Attach a label and a reference to the original user source for debugging
   srcref <- attr(substitute(x), "srcref", exact = TRUE)
@@ -467,8 +633,7 @@ reactive <- function(x, env = parent.frame(), quoted = FALSE, label = NULL,
   }
   if (length(srcref) >= 2) attr(label, "srcref") <- srcref[[2]]
   attr(label, "srcfile") <- srcFileOfRef(srcref[[1]])
-  o <- Observable$new(fun, label, domain)
-  registerDebugHook(".func", o, "Reactive")
+  o <- Observable$new(fun, label, domain, ..stacktraceon = ..stacktraceon)
   structure(o$getValue, observable = o, class = "reactive")
 }
 
@@ -488,7 +653,18 @@ srcrefToLabel <- function(srcref, defaultLabel) {
   if (is.null(srcfile$lines))
     return(defaultLabel)
 
-  firstLine <- substring(srcfile$lines[srcref[1]], 1, srcref[2] - 1)
+  lines <- srcfile$lines
+  # When pasting at the Console, srcfile$lines is not split
+  if (length(lines) == 1) {
+    lines <- strsplit(lines, "\n")[[1]]
+  }
+
+  if (length(lines) < srcref[1]) {
+    return(defaultLabel)
+  }
+
+  firstLine <- substring(lines[srcref[1]], 1, srcref[2] - 1)
+
   m <- regexec("(.*)(<-|=)\\s*reactive\\s*\\($", firstLine)
   if (m[[1]][1] == -1) {
     return(defaultLabel)
@@ -506,7 +682,7 @@ srcrefToLabel <- function(srcref, defaultLabel) {
 
 #' @export
 print.reactive <- function(x, ...) {
-  label <- attr(x, "observable")$.label
+  label <- attr(x, "observable", exact = TRUE)$.label
   cat(label, "\n")
 }
 
@@ -517,7 +693,7 @@ 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.reactive(x))
-    return(attr(x, "observable")$.execCount)
+    return(attr(x, "observable", exact = TRUE)$.execCount)
   else if (inherits(x, 'Observer'))
     return(x$.execCount)
   else
@@ -535,32 +711,40 @@ Observer <- R6Class(
     .domain = 'ANY',
     .priority = numeric(0),
     .autoDestroy = logical(0),
+    # A function that, when invoked, unsubscribes the autoDestroy
+    # listener (or NULL if autodestroy is disabled for this observer).
+    # We must unsubscribe when this observer is destroyed, or else
+    # the observer cannot be garbage collected until the session ends.
+    .autoDestroyHandle = 'ANY',
     .invalidateCallbacks = list(),
     .execCount = integer(0),
     .onResume = 'function',
     .suspended = logical(0),
     .destroyed = logical(0),
     .prevId = character(0),
+    .ctx = NULL,
 
     initialize = function(observerFunc, label, suspended = FALSE, priority = 0,
                           domain = getDefaultReactiveDomain(),
-                          autoDestroy = TRUE) {
+                          autoDestroy = TRUE, ..stacktraceon = TRUE) {
       if (length(formals(observerFunc)) > 0)
         stop("Can't make an observer from a function that takes parameters; ",
              "only functions without parameters can be reactive.")
-
+registerDebugHook("observerFunc", environment(), label)
       .func <<- function() {
         tryCatch(
-          observerFunc(),
-          validation = function(e) {
-            # It's OK for a validation error to cause an observer to stop
-            # running
-          }
+          if (..stacktraceon)
+            ..stacktraceon..(observerFunc())
+          else
+            observerFunc(),
+          # It's OK for shiny.silent.error errors to cause an observer to stop running
+          shiny.silent.error = function(e) NULL
+          # validation = function(e) NULL,
+          # shiny.output.cancel = function(e) NULL
         )
       }
       .label <<- label
       .domain <<- domain
-      .autoDestroy <<- autoDestroy
       .priority <<- normalizePriority(priority)
       .execCount <<- 0L
       .suspended <<- suspended
@@ -568,7 +752,9 @@ Observer <- R6Class(
       .destroyed <<- FALSE
       .prevId <<- ''
 
-      onReactiveDomainEnded(.domain, self$.onDomainEnded)
+      .autoDestroy <<- FALSE
+      .autoDestroyHandle <<- NULL
+      setAutoDestroy(autoDestroy)
 
       # Defer the first running of this until flushReact is called
       .createContext()$invalidate()
@@ -577,7 +763,23 @@ Observer <- R6Class(
       ctx <- Context$new(.domain, .label, type='observer', prevId=.prevId)
       .prevId <<- ctx$id
 
+      if (!is.null(.ctx)) {
+        # If this happens, something went wrong.
+        warning("Created a new context without invalidating previous context.")
+      }
+      # Store the context explicitly in the Observer object. This is necessary
+      # to make sure that when the observer is destroyed, it also gets
+      # invalidated. Otherwise the upstream reactive (on which the observer
+      # depends) will hold a (indirect) reference to this context until the
+      # reactive is invalidated, which may not happen immediately or at all.
+      # This can lead to a memory leak (#1253).
+      .ctx <<- ctx
+
       ctx$onInvalidate(function() {
+        # Context is invalidated, so we don't need to store a reference to it
+        # anymore.
+        .ctx <<- NULL
+
         lapply(.invalidateCallbacks, function(invalidateCallback) {
           invalidateCallback()
           NULL
@@ -596,24 +798,13 @@ Observer <- R6Class(
       ctx$onFlush(function() {
         tryCatch({
           if (!.destroyed)
-            run()
+            shinyCallingHandlers(run())
 
         }, error = function(e) {
-          # A function to handle errors that occur during a flush
-          flushErrorHandler <- getOption('shiny.observer.error')
-
-          # Default handler function, if not available from global option
-          if (is.null(flushErrorHandler)) {
-            flushErrorHandler <- function(e, label, domain) {
-              warning("Unhandled error in observer: ",
-                e$message, "\n", label, immediate. = TRUE, call. = FALSE)
-              if (!is.null(domain)) {
-                domain$unhandledError(e)
-              }
-            }
+          printError(e)
+          if (!is.null(.domain)) {
+            .domain$unhandledError(e)
           }
-
-          flushErrorHandler(e, .label, .domain)
         })
       })
 
@@ -641,11 +832,28 @@ Observer <- R6Class(
       "Sets whether this observer should be automatically destroyed when its
       domain (if any) ends. If autoDestroy is TRUE and the domain already
       ended, then destroy() is called immediately."
+
+      if (.autoDestroy == autoDestroy) {
+        return(.autoDestroy)
+      }
+
       oldValue <- .autoDestroy
       .autoDestroy <<- autoDestroy
-      if (!is.null(.domain) && .domain$isEnded()) {
-        destroy()
+
+      if (autoDestroy) {
+        if (!.destroyed && !is.null(.domain)) { # Make sure to not try to destroy twice.
+          if (.domain$isEnded()) {
+            destroy()
+          } else {
+            .autoDestroyHandle <<- onReactiveDomainEnded(.domain, .onDomainEnded)
+          }
+        }
+      } else {
+        if (!is.null(.autoDestroyHandle))
+          .autoDestroyHandle()
+        .autoDestroyHandle <<- NULL
       }
+
       invisible(oldValue)
     },
     suspend = function() {
@@ -671,8 +879,21 @@ Observer <- R6Class(
       "Prevents this observer from ever executing again (even if a flush has
       already been scheduled)."
 
+      # Make sure to not try to destory twice.
+      if (.destroyed)
+        return()
+
       suspend()
       .destroyed <<- TRUE
+
+      if (!is.null(.autoDestroyHandle)) {
+        .autoDestroyHandle()
+      }
+      .autoDestroyHandle <<- NULL
+
+      if (!is.null(.ctx)) {
+        .ctx$invalidate()
+      }
     },
     .onDomainEnded = function() {
       if (isTRUE(.autoDestroy)) {
@@ -701,8 +922,8 @@ Observer <- R6Class(
 #' soon as their dependencies change, they schedule themselves to re-execute.
 #'
 #' Starting with Shiny 0.10.0, observers are automatically destroyed by default
-#' when the \link[=domains]{domain} that owns them ends (e.g. when a Shiny session
-#' ends).
+#' when the \link[=domains]{domain} that owns them ends (e.g. when a Shiny
+#' session ends).
 #'
 #' @param x An expression (quoted or unquoted). Any return value will be
 #'   ignored.
@@ -713,15 +934,18 @@ Observer <- R6Class(
 #'   This is useful when you want to use an expression that is stored in a
 #'   variable; to do so, it must be quoted with \code{quote()}.
 #' @param label A label for the observer, useful for debugging.
-#' @param suspended If \code{TRUE}, start the observer in a suspended state.
-#'   If \code{FALSE} (the default), start in a non-suspended state.
+#' @param suspended If \code{TRUE}, start the observer in a suspended state. If
+#'   \code{FALSE} (the default), start in a non-suspended state.
 #' @param priority An integer or numeric that controls the priority with which
-#'   this observer should be executed. An observer with a given priority level
-#'   will always execute sooner than all observers with a lower priority level.
-#'   Positive, negative, and zero values are allowed.
+#'   this observer should be executed. A higher value means higher priority: an
+#'   observer with a higher priority value will execute before all observers
+#'   with lower priority values. Positive, negative, and zero values are
+#'   allowed.
 #' @param domain See \link{domains}.
 #' @param autoDestroy If \code{TRUE} (the default), the observer will be
 #'   automatically destroyed when its domain (if any) ends.
+#' @param ..stacktraceon Advanced use only. For stack manipulation purposes; see
+#'   \code{\link{stacktrace}}.
 #' @return An observer reference class object. This object has the following
 #'   methods:
 #'   \describe{
@@ -775,19 +999,19 @@ Observer <- R6Class(
 #' # In a normal Shiny app, the web client will trigger flush events. If you
 #' # are at the console, you can force a flush with flushReact()
 #' shiny:::flushReact()
-#'
 #' @export
 observe <- function(x, env=parent.frame(), quoted=FALSE, label=NULL,
                     suspended=FALSE, priority=0,
-                    domain=getDefaultReactiveDomain(), autoDestroy = TRUE) {
+                    domain=getDefaultReactiveDomain(), autoDestroy = TRUE,
+                    ..stacktraceon = TRUE) {
 
   fun <- exprToFunction(x, env, quoted)
   if (is.null(label))
     label <- sprintf('observe(%s)', paste(deparse(body(fun)), collapse='\n'))
 
   o <- Observer$new(fun, label=label, suspended=suspended, priority=priority,
-                    domain=domain, autoDestroy=autoDestroy)
-  registerDebugHook(".func", o, "Observer")
+                    domain=domain, autoDestroy=autoDestroy,
+                    ..stacktraceon=..stacktraceon)
   invisible(o)
 }
 
@@ -814,9 +1038,9 @@ observe <- function(x, env=parent.frame(), quoted=FALSE, label=NULL,
 #' }
 #' @export
 makeReactiveBinding <- function(symbol, env = parent.frame()) {
-  if (exists(symbol, where = env, inherits = FALSE)) {
-    initialValue <- get(symbol, pos = env, inherits = FALSE)
-    rm(list = symbol, pos = env, inherits = FALSE)
+  if (exists(symbol, envir = env, inherits = FALSE)) {
+    initialValue <- env[[symbol]]
+    rm(list = symbol, envir = env, inherits = FALSE)
   }
   else
     initialValue <- NULL
@@ -889,8 +1113,15 @@ setAutoflush <- local({
 #' @seealso \code{\link{invalidateLater}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   sliderInput("n", "Number of observations", 2, 1000, 500),
+#'   plotOutput("plot")
+#' )
+#'
+#' server <- function(input, output) {
 #'
 #'   # Anything that calls autoInvalidate will automatically invalidate
 #'   # every 2 seconds.
@@ -911,11 +1142,12 @@ setAutoflush <- local({
 #'   # input$n changes.
 #'   output$plot <- renderPlot({
 #'     autoInvalidate()
-#'     hist(isolate(input$n))
+#'     hist(rnorm(isolate(input$n)))
 #'   })
-#' })
 #' }
 #'
+#' shinyApp(ui, server)
+#' }
 #' @export
 reactiveTimer <- function(intervalMs=1000, session = getDefaultReactiveDomain()) {
   dependents <- Map$new()
@@ -967,8 +1199,15 @@ reactiveTimer <- function(intervalMs=1000, session = getDefaultReactiveDomain())
 #' @seealso \code{\link{reactiveTimer}} is a slightly less safe alternative.
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   sliderInput("n", "Number of observations", 2, 1000, 500),
+#'   plotOutput("plot")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'
 #'   observe({
 #'     # Re-execute this reactive expression after 1000 milliseconds
@@ -985,11 +1224,12 @@ reactiveTimer <- function(intervalMs=1000, session = getDefaultReactiveDomain())
 #'   output$plot <- renderPlot({
 #'     # Re-execute this reactive expression after 2000 milliseconds
 #'     invalidateLater(2000)
-#'     hist(isolate(input$n))
+#'     hist(rnorm(isolate(input$n)))
 #'   })
-#' })
 #' }
 #'
+#' shinyApp(ui, server)
+#' }
 #' @export
 invalidateLater <- function(millis, session = getDefaultReactiveDomain()) {
   ctx <- .getReactiveEnvironment()$currentContext()
@@ -1059,16 +1299,13 @@ coerceToFunc <- function(x) {
 #' @seealso \code{\link{reactiveFileReader}}
 #'
 #' @examples
-#' \dontrun{
 #' # Assume the existence of readTimestamp and readValue functions
-#' shinyServer(function(input, output, session) {
+#' function(input, output, session) {
 #'   data <- reactivePoll(1000, session, readTimestamp, readValue)
 #'   output$dataTable <- renderTable({
 #'     data()
 #'   })
-#' })
 #' }
-#'
 #' @export
 reactivePoll <- function(intervalMillis, session, checkFunc, valueFunc) {
   intervalMillis <- coerceToFunc(intervalMillis)
@@ -1128,7 +1365,7 @@ reactivePoll <- function(intervalMillis, session, checkFunc, valueFunc) {
 #' @examples
 #' \dontrun{
 #' # Per-session reactive file reader
-#' shinyServer(function(input, output, session)) {
+#' function(input, output, session) {
 #'   fileData <- reactiveFileReader(1000, session, 'data.csv', read.csv)
 #'
 #'   output$data <- renderTable({
@@ -1140,13 +1377,12 @@ reactivePoll <- function(intervalMillis, session, checkFunc, valueFunc) {
 #' # the same reader, so read.csv only gets executed once no matter how many
 #' # user sessions are connected.
 #' fileData <- reactiveFileReader(1000, session, 'data.csv', read.csv)
-#' shinyServer(function(input, output, session)) {
+#' function(input, output, session) {
 #'   output$data <- renderTable({
 #'     fileData()
 #'   })
 #' }
 #' }
-#'
 #' @export
 reactiveFileReader <- function(intervalMillis, session, filePath, readFunc, ...) {
   filePath <- coerceToFunc(filePath)
@@ -1234,14 +1470,14 @@ reactiveFileReader <- function(intervalMillis, session, filePath, readFunc, ...)
 #'
 #' # isolate also works if the reactive expression accesses values from the
 #' # input object, like input$x
-#'
 #' @export
 isolate <- function(expr) {
   ctx <- Context$new(getDefaultReactiveDomain(), '[isolate]', type='isolate')
   on.exit(ctx$invalidate())
-  ctx$run(function() {
-    expr
-  })
+  # Matching ..stacktraceon../..stacktraceoff.. pair
+  ..stacktraceoff..(ctx$run(function() {
+    ..stacktraceon..(expr)
+  }))
 }
 
 #' Evaluate an expression without a reactive context
@@ -1255,7 +1491,6 @@ isolate <- function(expr) {
 #' @return The value of \code{expr}.
 #'
 #' @seealso \code{\link{isolate}}
-#'
 #' @export
 maskReactiveContext <- function(expr) {
   .getReactiveEnvironment()$runWith(NULL, function() {
@@ -1382,7 +1617,6 @@ maskReactiveContext <- function(expr) {
 #'   }
 #'   shinyApp(ui=ui, server=server)
 #' }
-#'
 #' @export
 observeEvent <- function(eventExpr, handlerExpr,
   event.env = parent.frame(), event.quoted = FALSE,
@@ -1393,8 +1627,10 @@ observeEvent <- function(eventExpr, handlerExpr,
   eventFunc <- exprToFunction(eventExpr, event.env, event.quoted)
   if (is.null(label))
     label <- sprintf('observeEvent(%s)', paste(deparse(body(eventFunc)), collapse='\n'))
+  eventFunc <- wrapFunctionLabel(eventFunc, "observeEventExpr", ..stacktraceon = TRUE)
 
   handlerFunc <- exprToFunction(handlerExpr, handler.env, handler.quoted)
+  handlerFunc <- wrapFunctionLabel(handlerFunc, "observeEventHandler", ..stacktraceon = TRUE)
 
   invisible(observe({
     e <- eventFunc()
@@ -1405,7 +1641,7 @@ observeEvent <- function(eventExpr, handlerExpr,
 
     isolate(handlerFunc())
   }, label = label, suspended = suspended, priority = priority, domain = domain,
-    autoDestroy = TRUE))
+    autoDestroy = TRUE, ..stacktraceon = FALSE))
 }
 
 #' @rdname observeEvent
@@ -1419,8 +1655,10 @@ eventReactive <- function(eventExpr, valueExpr,
   eventFunc <- exprToFunction(eventExpr, event.env, event.quoted)
   if (is.null(label))
     label <- sprintf('eventReactive(%s)', paste(deparse(body(eventFunc)), collapse='\n'))
+  eventFunc <- wrapFunctionLabel(eventFunc, "eventReactiveExpr", ..stacktraceon = TRUE)
 
   handlerFunc <- exprToFunction(valueExpr, value.env, value.quoted)
+  handlerFunc <- wrapFunctionLabel(handlerFunc, "eventReactiveHandler", ..stacktraceon = TRUE)
 
   invisible(reactive({
     e <- eventFunc()
@@ -1431,7 +1669,7 @@ eventReactive <- function(eventExpr, valueExpr,
     ))
 
     isolate(handlerFunc())
-  }, label = label, domain = domain))
+  }, label = label, domain = domain, ..stacktraceon = FALSE))
 }
 
 isNullEvent <- function(value) {

R/render-plot.R

@@ -6,6 +6,15 @@
 #' The corresponding HTML output tag should be \code{div} or \code{img} and have
 #' the CSS class name \code{shiny-plot-output}.
 #'
+#' @section Interactive plots:
+#'
+#'   With ggplot2 graphics, the code in \code{renderPlot} should return a ggplot
+#'   object; if instead the code prints the ggplot2 object with something like
+#'   \code{print(p)}, then the coordinates for interactive graphics will not be
+#'   properly scaled to the data space.
+#'
+#'   See \code{\link{plotOutput}} for more information about interactive plots.
+#'
 #' @seealso For the corresponding client-side output function, and example
 #'   usage, see \code{\link{plotOutput}}. For more details on how the plots are
 #'   generated, and how to control the output, see \code{\link{plotPNG}}.
@@ -26,29 +35,226 @@
 #' @param env The environment in which to evaluate \code{expr}.
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
 #'   is useful if you want to save an expression in a variable.
-#' @param func A function that generates a plot (deprecated; use \code{expr}
-#'   instead).
-#'
+#' @param execOnResize If \code{FALSE} (the default), then when a plot is
+#'   resized, Shiny will \emph{replay} the plot drawing commands with
+#'   \code{\link[grDevices]{replayPlot}()} instead of re-executing \code{expr}.
+#'   This can result in faster plot redrawing, but there may be rare cases where
+#'   it is undesirable. If you encounter problems when resizing a plot, you can
+#'   have Shiny re-execute the code on resize by setting this to \code{TRUE}.
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{plotOutput}} when \code{renderPlot} is used in an
+#'   interactive R Markdown document.
 #' @export
 renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
-                       env=parent.frame(), quoted=FALSE, func=NULL) {
-  if (!is.null(func)) {
-    shinyDeprecated(msg="renderPlot: argument 'func' is deprecated. Please use 'expr' instead.")
-  } else {
-    installExprFunction(expr, "func", env, quoted)
-  }
+                       env=parent.frame(), quoted=FALSE,
+                       execOnResize=FALSE, outputArgs=list()
+) {
+  # This ..stacktraceon is matched by a ..stacktraceoff.. when plotFunc
+  # is called
+  installExprFunction(expr, "func", env, quoted, ..stacktraceon = TRUE)
 
   args <- list(...)
 
   if (is.function(width))
     widthWrapper <- reactive({ width() })
   else
-    widthWrapper <- NULL
+    widthWrapper <- function() { width }
 
   if (is.function(height))
     heightWrapper <- reactive({ height() })
   else
-    heightWrapper <- NULL
+    heightWrapper <- function() { height }
+
+  # A modified version of print.ggplot which returns the built ggplot object
+  # as well as the gtable grob. This overrides the ggplot::print.ggplot
+  # method, but only within the context of renderPlot. The reason this needs
+  # to be a (pseudo) S3 method is so that, if an object has a class in
+  # addition to ggplot, and there's a print method for that class, that we
+  # won't override that method. https://github.com/rstudio/shiny/issues/841
+  print.ggplot <- function(x) {
+    grid::grid.newpage()
+
+    build <- ggplot2::ggplot_build(x)
+
+    gtable <- ggplot2::ggplot_gtable(build)
+    grid::grid.draw(gtable)
+
+    structure(list(
+      build = build,
+      gtable = gtable
+    ), class = "ggplot_build_gtable")
+  }
+
+
+  getDims <- function() {
+    width <- widthWrapper()
+    height <- heightWrapper()
+
+    # Note that these are reactive calls. A change to the width and height
+    # will inherently cause a reactive plot to redraw (unless width and
+    # height were explicitly specified).
+    if (width == 'auto')
+      width <- session$clientData[[paste0('output_', outputName, '_width')]]
+    if (height == 'auto')
+      height <- session$clientData[[paste0('output_', outputName, '_height')]]
+
+    list(width = width, height = height)
+  }
+
+  # Vars to store session and output, so that they can be accessed from
+  # the plotObj() reactive.
+  session <- NULL
+  outputName <- NULL
+
+  # This function is the one that's returned from renderPlot(), and gets
+  # wrapped in an observer when the output value is assigned. The expression
+  # passed to renderPlot() is actually run in plotObj(); this function can only
+  # replay a plot if the width/height changes.
+  renderFunc <- function(shinysession, name, ...) {
+    session <<- shinysession
+    outputName <<- name
+
+    dims <- getDims()
+
+    if (is.null(dims$width) || is.null(dims$height) ||
+        dims$width <= 0 || dims$height <= 0) {
+      return(NULL)
+    }
+
+    # The reactive that runs the expr in renderPlot()
+    plotData <- plotObj()
+
+    img <- plotData$img
+
+    # If only the width/height have changed, simply replay the plot and make a
+    # new img.
+    if (dims$width != img$width || dims$height != img$height) {
+      pixelratio <- session$clientData$pixelratio %OR% 1
+
+      coordmap <- NULL
+      plotFunc <- function() {
+        ..stacktraceon..(grDevices::replayPlot(plotData$recordedPlot))
+
+        # Coordmap must be recalculated after replaying plot, because pixel
+        # dimensions will have changed.
+        if (inherits(plotData$plotResult, "ggplot_build_gtable")) {
+          coordmap <<- getGgplotCoordmap(plotData$plotResult, pixelratio, res)
+        } else {
+          coordmap <<- getPrevPlotCoordmap(dims$width, dims$height)
+        }
+      }
+      outfile <- ..stacktraceoff..(
+        plotPNG(plotFunc, width = dims$width*pixelratio, height = dims$height*pixelratio,
+                res = res*pixelratio)
+      )
+      on.exit(unlink(outfile))
+
+      img <- dropNulls(list(
+        src = session$fileUrl(name, outfile, contentType='image/png'),
+        width = dims$width,
+        height = dims$height,
+        coordmap = coordmap,
+        # Get coordmap error message if present
+        error = attr(coordmap, "error", exact = TRUE)
+      ))
+    }
+
+    img
+  }
+
+
+  plotObj <- reactive(label = "plotObj", {
+    if (execOnResize) {
+      dims <- getDims()
+    } else {
+      isolate({ dims <- getDims() })
+    }
+
+    if (is.null(dims$width) || is.null(dims$height) ||
+        dims$width <= 0 || dims$height <= 0) {
+      return(NULL)
+    }
+
+    # Resolution multiplier
+    pixelratio <- session$clientData$pixelratio %OR% 1
+
+    plotResult <- NULL
+    recordedPlot <- NULL
+    coordmap <- NULL
+    plotFunc <- function() {
+      success <-FALSE
+      tryCatch(
+        {
+          # This is necessary to enable displaylist recording
+          grDevices::dev.control(displaylist = "enable")
+
+          # Actually perform the plotting
+          result <- withVisible(func())
+          success <- TRUE
+        },
+        finally = {
+          if (!success) {
+            # If there was an error in making the plot, there's a good chance
+            # it's "Error in plot.new: figure margins too large". We need to
+            # take a reactive dependency on the width and height, so that the
+            # user's plotting code will re-execute when the plot is resized,
+            # instead of just replaying the previous plot (which errored).
+            getDims()
+          }
+        }
+      )
+
+      if (result$visible) {
+        # Use capture.output to squelch printing to the actual console; we
+        # are only interested in plot output
+        utils::capture.output({
+          # This ..stacktraceon.. negates the ..stacktraceoff.. that wraps
+          # the call to plotFunc. The value needs to be printed just in case
+          # it's an object that requires printing to generate plot output,
+          # similar to ggplot2. But for base graphics, it would already have
+          # been rendered when func was called above, and the print should
+          # have no effect.
+          plotResult <<- ..stacktraceon..(print(result$value))
+        })
+      }
+
+      recordedPlot <<- grDevices::recordPlot()
+
+      if (inherits(plotResult, "ggplot_build_gtable")) {
+        coordmap <<- getGgplotCoordmap(plotResult, pixelratio, res)
+      } else {
+        coordmap <<- getPrevPlotCoordmap(dims$width, dims$height)
+      }
+    }
+
+    # This ..stacktraceoff.. is matched by the `func` function's
+    # wrapFunctionLabel(..stacktraceon=TRUE) call near the beginning of
+    # renderPlot, and by the ..stacktraceon.. in plotFunc where ggplot objects
+    # are printed
+    outfile <- ..stacktraceoff..(
+      do.call(plotPNG, c(plotFunc, width=dims$width*pixelratio,
+        height=dims$height*pixelratio, res=res*pixelratio, args))
+    )
+    on.exit(unlink(outfile))
+
+    list(
+      # img is the content that gets sent to the client.
+      img = dropNulls(list(
+        src = session$fileUrl(outputName, outfile, contentType='image/png'),
+        width = dims$width,
+        height = dims$height,
+        coordmap = coordmap,
+        # Get coordmap error message if present.
+        error = attr(coordmap, "error", exact = TRUE)
+      )),
+      # Returned value from expression in renderPlot() -- may be a printable
+      # object like ggplot2. Needed just in case we replayPlot and need to get
+      # a coordmap again.
+      plotResult = plotResult,
+      recordedPlot = recordedPlot
+    )
+  })
+
 
   # If renderPlot isn't going to adapt to the height of the div, then the
   # div needs to adapt to the height of renderPlot. By default, plotOutput
@@ -57,71 +263,7 @@ renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
   outputFunc <- plotOutput
   if (!identical(height, 'auto')) formals(outputFunc)['height'] <- list(NULL)
 
-  return(markRenderFunction(outputFunc, function(shinysession, name, ...) {
-    if (!is.null(widthWrapper))
-      width <- widthWrapper()
-    if (!is.null(heightWrapper))
-      height <- heightWrapper()
-
-    # Note that these are reactive calls. A change to the width and height
-    # will inherently cause a reactive plot to redraw (unless width and
-    # height were explicitly specified).
-    prefix <- 'output_'
-    if (width == 'auto')
-      width <- shinysession$clientData[[paste(prefix, name, '_width', sep='')]];
-    if (height == 'auto')
-      height <- shinysession$clientData[[paste(prefix, name, '_height', sep='')]];
-
-    if (is.null(width) || is.null(height) || width <= 0 || height <= 0)
-      return(NULL)
-
-    # Resolution multiplier
-    pixelratio <- shinysession$clientData$pixelratio
-    if (is.null(pixelratio))
-      pixelratio <- 1
-
-    coordmap <- NULL
-    plotFunc <- function() {
-      # Actually perform the plotting
-      result <- withVisible(func())
-
-      coordmap <<- NULL
-
-      if (result$visible) {
-        # Use capture.output to squelch printing to the actual console; we
-        # are only interested in plot output
-
-        # Special case for ggplot objects - need to capture coordmap
-        if (inherits(result$value, "ggplot")) {
-          utils::capture.output(coordmap <<- getGgplotCoordmap(result$value, pixelratio))
-        } else {
-          utils::capture.output(print(result$value))
-        }
-      }
-
-      if (is.null(coordmap)) {
-        coordmap <<- getPrevPlotCoordmap(width, height)
-      }
-    }
-
-    outfile <- do.call(plotPNG, c(plotFunc, width=width*pixelratio,
-                                  height=height*pixelratio, res=res*pixelratio, args))
-    on.exit(unlink(outfile))
-
-    # A list of attributes for the img
-    res <- list(
-      src=shinysession$fileUrl(name, outfile, contentType='image/png'),
-      width=width, height=height, coordmap=coordmap
-    )
-
-    # Get error message if present (from attribute on the coordmap)
-    error <- attr(coordmap, "error", exact = TRUE)
-    if (!is.null(error)) {
-      res$error <- error
-    }
-
-    res
-  }))
+  markRenderFunction(outputFunc, renderFunc, outputArgs = outputArgs)
 }
 
 # The coordmap extraction functions below return something like the examples
@@ -273,61 +415,42 @@ getPrevPlotCoordmap <- function(width, height) {
   ))
 }
 
-# Print a ggplot object and return a coordmap for it.
-getGgplotCoordmap <- function(p, pixelratio) {
-  if (!inherits(p, "ggplot"))
+
+# Given a ggplot_build_gtable object, return a coordmap for it.
+getGgplotCoordmap <- function(p, pixelratio, res) {
+  # Structure of ggplot objects changed after 2.1.0
+  new_ggplot <- (utils::packageVersion("ggplot2") > "2.1.0")
+
+  if (!inherits(p, "ggplot_build_gtable"))
     return(NULL)
 
-  # A modified version of print.ggplot which returns the built ggplot object as
-  # well as the gtable grob. This overrides the ggplot::print.ggplot method, but
-  # only within the context of getGgplotCoordmap. The reason this needs to be an
-  # (pseudo) S3 method is so that, if an object has a class in addition to
-  # ggplot, and there's a print method for that class, that we won't override
-  # that method.
-  # https://github.com/rstudio/shiny/issues/841
-  print.ggplot <- function(x) {
-    grid::grid.newpage()
-
-    build <- ggplot2::ggplot_build(x)
-
-    gtable <- ggplot2::ggplot_gtable(build)
-    grid::grid.draw(gtable)
-
-    list(
-      build = build,
-      gtable = gtable
-    )
-  }
-
-  # Given the name of a generic function and an object, return the class name
-  # for the method that would be used on the object.
-  which_method <- function(generic, x) {
-    classes <- class(x)
-    method_names <- paste(generic, classes, sep = ".")
-    idx <- which(method_names %in% utils::methods(generic))
-
-    if (length(idx) == 0)
-      return(NULL)
-
-    # Return name of first class with matching method
-    classes[idx[1]]
-  }
-
-
   # Given a built ggplot object, return x and y domains (data space coords) for
   # each panel.
   find_panel_info <- function(b) {
-    layout <- b$panel$layout
+    if (new_ggplot) {
+      layout <- b$layout$panel_layout
+    } else {
+      layout <- b$panel$layout
+    }
     # Convert factor to numbers
     layout$PANEL <- as.integer(as.character(layout$PANEL))
 
     # Names of facets
-    facet <- b$plot$facet
     facet_vars <- NULL
-    if (inherits(facet, "grid")) {
-      facet_vars <- vapply(c(facet$cols, facet$rows), as.character, character(1))
-    } else if (inherits(facet, "wrap")) {
-      facet_vars <- vapply(facet$facets, as.character, character(1))
+    if (new_ggplot) {
+      facet <- b$layout$facet
+      if (inherits(facet, "FacetGrid")) {
+        facet_vars <- vapply(c(facet$params$cols, facet$params$rows), as.character, character(1))
+      } else if (inherits(facet, "FacetWrap")) {
+        facet_vars <- vapply(facet$params$facets, as.character, character(1))
+      }
+    } else {
+      facet <- b$plot$facet
+      if (inherits(facet, "grid")) {
+        facet_vars <- vapply(c(facet$cols, facet$rows), as.character, character(1))
+      } else if (inherits(facet, "wrap")) {
+        facet_vars <- vapply(facet$facets, as.character, character(1))
+      }
     }
 
     # Iterate over each row in the layout data frame
@@ -369,8 +492,12 @@ getGgplotCoordmap <- function(p, pixelratio) {
   # Given a single range object (representing the data domain) from a built
   # ggplot object, return the domain.
   find_panel_domain <- function(b, panel_num, scalex_num = 1, scaley_num = 1) {
-    range <- b$panel$ranges[[panel_num]]
-    res <- list(
+    if (new_ggplot) {
+      range <- b$layout$panel_ranges[[panel_num]]
+    } else {
+      range <- b$panel$ranges[[panel_num]]
+    }
+    domain <- list(
       left   = range$x.range[1],
       right  = range$x.range[2],
       bottom = range$y.range[1],
@@ -378,19 +505,23 @@ getGgplotCoordmap <- function(p, pixelratio) {
     )
 
     # Check for reversed scales
-    xscale <- b$panel$x_scales[[scalex_num]]
-    yscale <- b$panel$y_scales[[scaley_num]]
-
+    if (new_ggplot) {
+      xscale <- b$layout$panel_scales$x[[scalex_num]]
+      yscale <- b$layout$panel_scales$y[[scaley_num]]
+    } else {
+      xscale <- b$panel$x_scales[[scalex_num]]
+      yscale <- b$panel$y_scales[[scaley_num]]
+    }
     if (!is.null(xscale$trans) && xscale$trans$name == "reverse") {
-      res$left  <- -res$left
-      res$right <- -res$right
+      domain$left  <- -domain$left
+      domain$right <- -domain$right
     }
     if (!is.null(yscale$trans) && yscale$trans$name == "reverse") {
-      res$top    <- -res$top
-      res$bottom <- -res$bottom
+      domain$top    <- -domain$top
+      domain$bottom <- -domain$bottom
     }
 
-    res
+    domain
   }
 
   # Given built ggplot object, return object with the log base for x and y if
@@ -415,10 +546,18 @@ getGgplotCoordmap <- function(p, pixelratio) {
     y_names <- character(0)
 
     # Continuous scales have a trans; discrete ones don't
-    if (!is.null(b$panel$x_scales[[scalex_num]]$trans))
-      x_names <- b$panel$x_scales[[scalex_num]]$trans$name
-    if (!is.null(b$panel$y_scales[[scaley_num]]$trans))
-      y_names <- b$panel$y_scales[[scaley_num]]$trans$name
+    if (new_ggplot) {
+      if (!is.null(b$layout$panel_scales$x[[scalex_num]]$trans))
+        x_names <- b$layout$panel_scales$x[[scalex_num]]$trans$name
+      if (!is.null(b$layout$panel_scales$y[[scaley_num]]$trans))
+        y_names <- b$layout$panel_scales$y[[scaley_num]]$trans$name
+
+    } else {
+      if (!is.null(b$panel$x_scales[[scalex_num]]$trans))
+        x_names <- b$panel$x_scales[[scalex_num]]$trans$name
+      if (!is.null(b$panel$y_scales[[scaley_num]]$trans))
+        y_names <- b$panel$y_scales[[scaley_num]]$trans$name
+    }
 
     coords <- b$plot$coordinates
     if (!is.null(coords$trans)) {
@@ -472,6 +611,11 @@ getGgplotCoordmap <- function(p, pixelratio) {
       )
     }
 
+    # Look for CoordFlip
+    if (inherits(b$plot$coordinates, "CoordFlip")) {
+      mappings[c("x", "y")] <- mappings[c("y", "x")]
+    }
+
     mappings_cache <<- mappings
     mappings
   }
@@ -498,9 +642,22 @@ getGgplotCoordmap <- function(p, pixelratio) {
       }
     }
 
+    # Workaround for a bug in the quartz device. If you have a 400x400 image and
+    # run `convertWidth(unit(1, "npc"), "native")`, the result will depend on
+    # res setting of the device. If res=72, then it returns 400 (as expected),
+    # but if, e.g., res=96, it will return 300, which is incorrect.
+    devScaleFactor <- 1
+    if (grepl("quartz", names(grDevices::dev.cur()), fixed = TRUE)) {
+      devScaleFactor <- res / 72
+    }
+
     # Convert a unit (or vector of units) to a numeric vector of pixel sizes
-    h_px <- function(x) as.numeric(grid::convertHeight(x, "native"))
-    w_px <- function(x) as.numeric(grid::convertWidth(x, "native"))
+    h_px <- function(x) {
+      devScaleFactor * grid::convertHeight(x, "native", valueOnly = TRUE)
+    }
+    w_px <- function(x) {
+      devScaleFactor * grid::convertWidth(x, "native", valueOnly = TRUE)
+    }
 
     # Given a vector of relative sizes (in grid units), and a function for
     # converting grid units to numeric pixels, return a numeric vector of
@@ -567,36 +724,25 @@ getGgplotCoordmap <- function(p, pixelratio) {
     })
   }
 
-  # If print(p) gets dispatched to print.ggplot(p), attempt to extract coordmap.
-  # If dispatched to another method, just print the object and don't attempt to
-  # extract the coordmap. This can happen if there's another print method that
-  # takes precedence.
-  if (identical(which_method("print", p), "ggplot")) {
-    res <- print(p)
 
-    tryCatch({
-      # Get info from built ggplot object
-      info <- find_panel_info(res$build)
+  tryCatch({
+    # Get info from built ggplot object
+    info <- find_panel_info(p$build)
 
-      # Get ranges from gtable - it's possible for this to return more elements than
-      # info, because it calculates positions even for panels that aren't present.
-      # This can happen with facet_wrap.
-      ranges <- find_panel_ranges(res$gtable, pixelratio)
+    # Get ranges from gtable - it's possible for this to return more elements than
+    # info, because it calculates positions even for panels that aren't present.
+    # This can happen with facet_wrap.
+    ranges <- find_panel_ranges(p$gtable, pixelratio)
 
-      for (i in seq_along(info)) {
-        info[[i]]$range <- ranges[[i]]
-      }
+    for (i in seq_along(info)) {
+      info[[i]]$range <- ranges[[i]]
+    }
 
-      return(info)
+    return(info)
 
-    }, error = function(e) {
-      # If there was an error extracting info from the ggplot object, just return
-      # a list with the error message.
-      return(structure(list(), error = e$message))
-    })
-
-  } else {
-    print(p)
-    return(list())
-  }
+  }, error = function(e) {
+    # If there was an error extracting info from the ggplot object, just return
+    # a list with the error message.
+    return(structure(list(), error = e$message))
+  })
 }

R/render-table.R

@@ -0,0 +1,223 @@
+#' Table Output
+#'
+#' Creates a reactive table that is suitable for assigning to an \code{output}
+#' slot.
+#'
+#' The corresponding HTML output tag should be \code{div} and have the CSS
+#' class name \code{shiny-html-output}.
+#'
+#' @param expr An expression that returns an R object that can be used with
+#'   \code{\link[xtable]{xtable}}.
+#' @param striped,hover,bordered Logicals: if \code{TRUE}, apply the
+#'   corresponding Bootstrap table format to the output table.
+#' @param spacing The spacing between the rows of the table (\code{xs}
+#'   stands for "extra small", \code{s} for "small", \code{m} for "medium"
+#'   and \code{l} for "large").
+#' @param width Table width. Must be a valid CSS unit (like "100%", "400px",
+#'   "auto") or a number, which will be coerced to a string and
+#'   have "px" appended.
+#' @param align A string that specifies the column alignment. If equal to
+#'   \code{'l'}, \code{'c'} or \code{'r'}, then all columns will be,
+#'   respectively, left-, center- or right-aligned. Otherwise, \code{align}
+#'   must have the same number of characters as the resulting table (if
+#'   \code{rownames = TRUE}, this will be equal to \code{ncol()+1}), with
+#'   the \emph{i}-th character specifying the alignment for the
+#'   \emph{i}-th column (besides \code{'l'}, \code{'c'} and
+#'   \code{'r'}, \code{'?'} is also permitted - \code{'?'} is a placeholder
+#'   for that particular column, indicating that it should keep its default
+#'   alignment). If \code{NULL}, then all numeric/integer columns (including
+#'   the row names, if they are numbers) will be right-aligned and
+#'   everything else will be left-aligned (\code{align = '?'} produces the
+#'   same result).
+#' @param rownames,colnames Logicals: include rownames? include colnames
+#'   (column headers)?
+#' @param digits An integer specifying the number of decimal places for
+#'   the numeric columns (this will not apply to columns with an integer
+#'   class). If \code{digits} is set to a negative value, then the numeric
+#'   columns will be displayed in scientific format with a precision of
+#'   \code{abs(digits)} digits.
+#' @param na The string to use in the table cells whose values are missing
+#'   (i.e. they either evaluate to \code{NA} or \code{NaN}).
+#' @param ... Arguments to be passed through to \code{\link[xtable]{xtable}}
+#'   and \code{\link[xtable]{print.xtable}}.
+#' @param env The environment in which to evaluate \code{expr}.
+#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})?
+#'   This is useful if you want to save an expression in a variable.
+#' @param outputArgs A list of arguments to be passed through to the
+#'   implicit call to \code{\link{tableOutput}} when \code{renderTable} is
+#'   used in an interactive R Markdown document.
+#' @export
+renderTable <- function(expr, striped = FALSE, hover = FALSE,
+                        bordered = FALSE, spacing = c("s", "xs", "m", "l"),
+                        width = "auto", align = NULL,
+                        rownames = FALSE, colnames = TRUE,
+                        digits = NULL, na = "NA", ...,
+                        env = parent.frame(), quoted = FALSE,
+                        outputArgs=list()) {
+  installExprFunction(expr, "func", env, quoted)
+
+  if (!is.function(spacing)) spacing <- match.arg(spacing)
+
+  # A small helper function to create a wrapper for an argument that was
+  # passed to renderTable()
+  createWrapper <- function(arg) {
+    if (is.function(arg)) wrapper <- arg
+    else wrapper <- function() arg
+    return(wrapper)
+  }
+
+  # Create wrappers for most arguments so that functions can also be passed
+  # in, rather than only literals (useful for shiny apps)
+  stripedWrapper <- createWrapper(striped)
+  hoverWrapper <- createWrapper(hover)
+  borderedWrapper <- createWrapper(bordered)
+  spacingWrapper <- createWrapper(spacing)
+  widthWrapper <- createWrapper(width)
+  alignWrapper <- createWrapper(align)
+  rownamesWrapper <- createWrapper(rownames)
+  colnamesWrapper <- createWrapper(colnames)
+  digitsWrapper <- createWrapper(digits)
+  naWrapper <- createWrapper(na)
+
+  dots <- list(...)  ## used later (but defined here because of scoping)
+
+  renderFunc <- function(shinysession, name, ...) {
+    striped <- stripedWrapper()
+    hover <- hoverWrapper()
+    bordered <- borderedWrapper()
+    format <- c(striped = striped, hover = hover, bordered = bordered)
+    spacing <- spacingWrapper()
+    width <- widthWrapper()
+    align <- alignWrapper()
+    rownames <- rownamesWrapper()
+    colnames <- colnamesWrapper()
+    digits <- digitsWrapper()
+    na <- naWrapper()
+
+    spacing_choices <- c("s", "xs", "m", "l")
+    if (!(spacing %in% spacing_choices)) {
+      stop(paste("`spacing` must be one of",
+                 paste0("'", spacing_choices, "'", collapse=", ")))
+    }
+
+    # For css styling
+    classNames <- paste0("table shiny-table",
+                         paste0(" table-", names(format)[format], collapse = "" ),
+                         paste0(" spacing-", spacing))
+
+    data <- func()
+    data <- as.data.frame(data)
+
+    # Return NULL if no data is provided
+    if (is.null(data) ||
+        (is.data.frame(data) && nrow(data) == 0 && ncol(data) == 0))
+      return(NULL)
+
+    # Separate the ... args to pass to xtable() vs print.xtable()
+    xtable_argnames <- setdiff(names(formals(xtable)), c("x", "..."))
+    xtable_args <- dots[intersect(names(dots), xtable_argnames)]
+    non_xtable_args <- dots[setdiff(names(dots), xtable_argnames)]
+
+    # By default, numbers are right-aligned and everything else is left-aligned.
+    defaultAlignment <- function(col) {
+      if (is.numeric(col)) "r" else "l"
+    }
+
+    # Figure out column alignment
+    ## Case 1: default alignment
+    if (is.null(align) || align == "?") {
+      names <- defaultAlignment(attr(data, "row.names"))
+      cols <- paste(vapply(data, defaultAlignment, character(1)), collapse = "")
+      cols <- paste0(names, cols)
+    } else {
+      ## Case 2: user-specified alignment
+      num_cols <- if (rownames) nchar(align) else nchar(align)+1
+      valid <- !grepl("[^lcr\\?]", align)
+      if (num_cols == ncol(data)+1 && valid) {
+        cols <- if (rownames) align else paste0("r", align)
+        defaults <- grep("\\?", strsplit(cols,"")[[1]])
+        if (length(defaults) != 0) {
+          vals <- vapply(data[,defaults-1], defaultAlignment, character(1))
+          for (i in seq_len(length(defaults))) {
+            substr(cols, defaults[i], defaults[i]) <- vals[i]
+          }
+        }
+      } else if (nchar(align) == 1 && valid) {
+        cols <- paste0(rep(align, ncol(data)+1), collapse="")
+      } else {
+        stop("`align` must contain only the characters `l`, `c`, `r` and/or `?` and",
+             "have length either equal to 1 or to the total number of columns")
+      }
+    }
+
+    # Call xtable with its (updated) args
+    xtable_args <- c(xtable_args, align = cols, digits = digits)
+    xtable_res <- do.call(xtable, c(list(data), xtable_args))
+
+    # Set up print args
+    print_args <- list(
+      x = xtable_res,
+      type = 'html',
+      include.rownames = {
+        if ("include.rownames" %in% names(dots)) dots$include.rownames
+        else rownames
+      },
+      include.colnames = {
+        if ("include.colnames" %in% names(dots)) dots$include.colnames
+        else colnames
+      },
+      NA.string = {
+        if ("NA.string" %in% names(dots)) dots$NA.string
+        else na
+      },
+      html.table.attributes =
+        paste0({
+          if ("html.table.attributes" %in% names(dots)) dots$html.table.attributes
+          else ""
+        }, " ",
+        "class = '", htmlEscape(classNames, TRUE), "' ",
+        "style = 'width:", validateCssUnit(width), ";'"))
+
+    print_args <- c(print_args, non_xtable_args)
+    print_args <- print_args[unique(names(print_args))]
+
+    # Capture the raw html table returned by print.xtable(), and store it in
+    # a variable for further processing
+    tab <- paste(utils::capture.output(do.call(print, print_args)),collapse = "\n")
+
+    # Add extra class to cells with NA value, to be able to style them separately
+    tab <- gsub(paste(">", na, "<"), paste(" class='NA'>", na, "<"), tab)
+
+    # All further processing concerns the table headers, so we don't need to run
+    # any of this if colnames=FALSE
+    if (colnames) {
+      # Make sure that the final html table has a proper header (not included
+      # in the print.xtable() default)
+      tab <- sub("<tr>", "<thead> <tr>", tab)
+      tab <- sub("</tr>", "</tr> </thead> <tbody>", tab)
+      tab <- sub("</table>$", "</tbody> </table>", tab)
+
+      # Update the `cols` string (which stores the alignment of each column) so
+      # that it only includes the alignment for the table variables (and not
+      # for the row.names)
+      cols <- if (rownames) cols else substr(cols, 2, nchar(cols))
+
+      # Create a vector whose i-th entry corresponds to the i-th table variable
+      # alignment (substituting "l" by "left", "c" by "center" and "r" by "right")
+      cols <- strsplit(cols, "")[[1]]
+      cols[cols == "l"] <- "left"
+      cols[cols == "r"] <- "right"
+      cols[cols == "c"] <- "center"
+
+      # Align each header accordingly (this guarantees that each header and its
+      # corresponding column have the same alignment)
+      for (i in seq_len(length(cols))) {
+        tab <- sub("<th>", paste0("<th style='text-align: ", cols[i], ";'>"), tab)
+      }
+    }
+    return(tab)
+  }
+
+  # Main render function
+  markRenderFunction(tableOutput, renderFunc, outputArgs = outputArgs)
+}

R/run-url.R

@@ -22,7 +22,7 @@
 #' @export
 #' @examples
 #' ## Only run this example in interactive R sessions
-#'   if (interactive()) {
+#' if (interactive()) {
 #'   runUrl('https://github.com/rstudio/shiny_example/archive/master.tar.gz')
 #'
 #'   # Can run an app from a subdirectory in the archive

R/serializers.R

@@ -0,0 +1,72 @@
+# For most types of values, simply return the value unchanged.
+serializerDefault <- function(value, stateDir) {
+  value
+}
+
+
+serializerFileInput <- function(value, stateDir = NULL) {
+  # File inputs can be serialized only if there's a stateDir
+  if (is.null(stateDir)) {
+    return(serializerUnserializable())
+  }
+
+  # value is a data frame. When persisting files, we need to copy the file to
+  # the persistent dir and then strip the original path before saving.
+  newpaths <- file.path(stateDir, basename(value$datapath))
+  file.copy(value$datapath, newpaths, overwrite = TRUE)
+  value$datapath <- basename(newpaths)
+
+  value
+}
+
+
+# Return a sentinel value that represents "unserializable". This is applied to
+# for example, passwords and actionButtons.
+serializerUnserializable <- function(value, stateDir) {
+  structure(
+    list(),
+    serializable = FALSE
+  )
+}
+
+# Is this an "unserializable" sentinel value?
+isUnserializable <- function(x) {
+  identical(
+    attr(x, "serializable", exact = TRUE),
+    FALSE
+  )
+}
+
+
+# Given a reactiveValues object and optional directory for saving state, apply
+# serializer function to each of the values, and return a list of the returned
+# values. This function passes stateDir to the serializer functions, so if
+# stateDir is non-NULL, it can have a side effect of writing values to disk (in
+# stateDir).
+serializeReactiveValues <- function(values, exclude, stateDir = NULL) {
+  impl <- .subset2(values, "impl")
+
+  # Get named list where keys and values are the names of inputs; we'll retrieve
+  # actual values later.
+  vals <- isolate(impl$names())
+  vals <- setdiff(vals, exclude)
+  names(vals) <- vals
+
+  # Get values and apply serializer functions
+  vals <- lapply(vals, function(name) {
+    val <- impl$get(name)
+
+    # Get the serializer function for this input value. If none specified, use
+    # the default.
+    serializer <- impl$getMeta(name, "shiny.serializer")
+    if (is.null(serializer))
+      serializer <- serializerDefault
+
+    # Apply serializer function.
+    serializer(val, stateDir)
+  })
+
+  # Filter out any values that were marked as unserializable.
+  vals <- Filter(Negate(isUnserializable), vals)
+  vals
+}

R/server-input-handlers.R

@@ -71,6 +71,72 @@ removeInputHandler <- function(type){
   inputHandlers$remove(type)
 }
 
+
+# Apply input handler to a single input value
+applyInputHandler <- function(name, val) {
+  splitName <- strsplit(name, ':')[[1]]
+  if (length(splitName) > 1) {
+    if (!inputHandlers$containsKey(splitName[[2]])) {
+      # No input handler registered for this type
+      stop("No handler registered for type ", name)
+    }
+
+    inputName <- splitName[[1]]
+
+    # Get the function for processing this type of input
+    inputHandler <- inputHandlers$get(splitName[[2]])
+
+    return(inputHandler(val, shinysession, inputName))
+
+  } else if (is.list(val) && is.null(names(val))) {
+    return(unlist(val, recursive = TRUE))
+  } else {
+    return(val)
+  }
+}
+
+#' Apply input handlers to raw input values
+#'
+#' The purpose of this function is to make it possible for external packages to
+#' test Shiny inputs. It takes a named list of raw input values, applies input
+#' handlers to those values, and then returns a named list of the processed
+#' values.
+#'
+#' The raw input values should be in a named list. Some values may have names
+#' like \code{"x:shiny.date"}. This function would apply the \code{"shiny.date"}
+#' input handler to the value, and then rename the result to \code{"x"}, in the
+#' output.
+#'
+#' @param inputs A named list of input values.
+#'
+#' @seealso registerInputHandler
+#'
+#' @examples
+#' applyInputHandlers(list(
+#'   "m1" = list(list(1, 2), list(3, 4)),
+#'   "m2:shiny.matrix" = list(list(1, 2), list(3, 4)),
+#'
+#'   "d1" = "2016-01-01",
+#'   "d2:shiny.date" = "2016-01-01",  # Date object
+#'
+#'   "n1" = NULL,
+#'   "n2:shiny.number" = NULL  # Converts to NA
+#' ))
+#' @export
+applyInputHandlers <- function(inputs) {
+  inputs <- mapply(applyInputHandler, names(inputs), inputs, SIMPLIFY = FALSE)
+
+  # Convert names like "button1:shiny.action" to "button1"
+  names(inputs) <- vapply(
+    names(inputs),
+    function(name) { strsplit(name, ":")[[1]][1] },
+    FUN.VALUE = character(1)
+  )
+
+  inputs
+}
+
+
 # Takes a list-of-lists and returns a matrix. The lists
 # must all be the same length. NULL is replaced by NA.
 registerInputHandler("shiny.matrix", function(data, ...) {
@@ -89,10 +155,29 @@ registerInputHandler("shiny.number", function(val, ...){
   ifelse(is.null(val), NA, val)
 })
 
+registerInputHandler("shiny.password", function(val, shinysession, name) {
+  # Mark passwords as not serializable
+  .subset2(shinysession$input, "impl")$setMeta(name, "shiny.serializer", serializerUnserializable)
+  val
+})
+
 registerInputHandler("shiny.date", function(val, ...){
   # First replace NULLs with NA, then convert to Date vector
   datelist <- ifelse(lapply(val, is.null), NA, val)
-  as.Date(unlist(datelist))
+
+  res <- NULL
+  tryCatch({
+      res <- as.Date(unlist(datelist))
+    },
+    error = function(e) {
+      # It's possible for client to send a string like "99999-01-01", which
+      # as.Date can't handle.
+      warning(e$message)
+      res <<- as.Date(rep(NA, length(datelist)))
+    }
+  )
+
+  res
 })
 
 registerInputHandler("shiny.datetime", function(val, ...){
@@ -104,8 +189,41 @@ registerInputHandler("shiny.datetime", function(val, ...){
   as.POSIXct(unlist(times), origin = "1970-01-01", tz = "UTC")
 })
 
-registerInputHandler("shiny.action", function(val, ...) {
+registerInputHandler("shiny.action", function(val, shinysession, name) {
   # mark up the action button value with a special class so we can recognize it later
   class(val) <- c(class(val), "shinyActionButtonValue")
   val
 })
+
+registerInputHandler("shiny.file", function(val, shinysession, name) {
+  # This function is only used when restoring a Shiny fileInput. When a file is
+  # uploaded the usual way, it takes a different code path and won't hit this
+  # function.
+  if (is.null(val))
+    return(NULL)
+
+  # The data will be a named list of lists; convert to a data frame.
+  val <- as.data.frame(lapply(val, unlist), stringsAsFactors = FALSE)
+
+  # `val$datapath` should be a filename without a path, for security reasons.
+  if (basename(val$datapath) != val$datapath) {
+    stop("Invalid '/' found in file input path.")
+  }
+
+  # Prepend the persistent dir
+  oldfile <- file.path(getCurrentRestoreContext()$dir, val$datapath)
+
+  # Copy the original file to a new temp dir, so that a restored session can't
+  # modify the original.
+  newdir <- file.path(tempdir(), createUniqueId(12))
+  dir.create(newdir)
+  val$datapath <- file.path(newdir, val$datapath)
+  file.copy(oldfile, val$datapath)
+
+  # Need to mark this input value with the correct serializer. When a file is
+  # uploaded the usual way (instead of being restored), this occurs in
+  # session$`@uploadEnd`.
+  .subset2(shinysession$input, "impl")$setMeta(name, "shiny.serializer", serializerFileInput)
+
+  val
+})

R/server.R

@@ -49,7 +49,6 @@ registerClient <- function(client) {
 #'
 #' @examples
 #' addResourcePath('datasets', system.file('data', package='datasets'))
-#'
 #' @export
 addResourcePath <- function(prefix, directoryPath) {
   prefix <- prefix[1]
@@ -141,7 +140,6 @@ resourcePathHandler <- function(req) {
 #'   })
 #' }
 #' }
-#'
 #' @export
 shinyServer <- function(func) {
   .globals$server <- list(func)
@@ -202,11 +200,19 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
         return(TRUE)
       }
 
+      if (!is.null(getOption("shiny.observer.error", NULL))) {
+        warning(
+          call. = FALSE,
+          "options(shiny.observer.error) is no longer supported; please unset it!"
+        )
+        stopApp()
+      }
+
       shinysession <- ShinySession$new(ws)
       appsByToken$set(shinysession$token, shinysession)
       shinysession$setShowcase(.globals$showcaseDefault)
 
-      ws$onMessage(function(binary, msg) {
+      messageHandler <- function(binary, msg) {
         withReactiveDomain(shinysession, {
           # To ease transition from websockets-based code. Should remove once we're stable.
           if (is.character(msg))
@@ -224,126 +230,111 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
 
           msg <- decodeMessage(msg)
 
-          # Do our own list simplifying here. sapply/simplify2array give names to
-          # character vectors, which is rarely what we want.
-          if (!is.null(msg$data)) {
-            for (name in names(msg$data)) {
-              val <- msg$data[[name]]
-
-              splitName <- strsplit(name, ':')[[1]]
-              if (length(splitName) > 1) {
-                msg$data[[name]] <- NULL
-
-                if (!inputHandlers$containsKey(splitName[[2]])){
-                  # No input handler registered for this type
-                  stop("No handler registered for for type ", name)
-                }
-
-                msg$data[[ splitName[[1]] ]] <-
-                  inputHandlers$get(splitName[[2]])(
-                    val,
-                    shinysession,
-                    splitName[[1]] )
-              }
-              else if (is.list(val) && is.null(names(val))) {
-                val_flat <- unlist(val, recursive = TRUE)
-
-                if (is.null(val_flat)) {
-                  # This is to assign NULL instead of deleting the item
-                  msg$data[name] <- list(NULL)
-                } else {
-                  msg$data[[name]] <- val_flat
-                }
-              }
+          # Set up a restore context from .clientdata_url_search before
+          # handling all the input values, because the restore context may be
+          # used by an input handler (like the one for "shiny.file"). This
+          # should only happen once, when the app starts.
+          if (is.null(shinysession$restoreContext)) {
+            bookmarkStore <- getShinyOption("bookmarkStore", default = "disable")
+            if (bookmarkStore == "disable") {
+              # If bookmarking is disabled, use empty context
+              shinysession$restoreContext <- RestoreContext$new()
+            } else {
+              # If there's bookmarked state, save it on the session object
+              shinysession$restoreContext <- RestoreContext$new(msg$data$.clientdata_url_search)
             }
           }
 
-          switch(
-            msg$method,
-            init = {
+          withRestoreContext(shinysession$restoreContext, {
 
-              serverFunc <- withReactiveDomain(NULL, serverFuncSource())
-              if (!identicalFunctionBodies(serverFunc, appvars$server)) {
-                appvars$server <- serverFunc
-                if (!is.null(appvars$server))
-                {
-                  # Tag this function as the Shiny server function. A debugger may use this
-                  # tag to give this function special treatment.
-                  # It's very important that it's appvars$server itself and NOT a copy that
-                  # is invoked, otherwise new breakpoints won't be picked up.
-                  attr(appvars$server, "shinyServerFunction") <- TRUE
-                  registerDebugHook("server", appvars, "Server Function")
+            msg$data <- applyInputHandlers(msg$data)
+
+            switch(
+              msg$method,
+              init = {
+
+                serverFunc <- withReactiveDomain(NULL, serverFuncSource())
+                if (!identicalFunctionBodies(serverFunc, appvars$server)) {
+                  appvars$server <- serverFunc
+                  if (!is.null(appvars$server))
+                  {
+                    # Tag this function as the Shiny server function. A debugger may use this
+                    # tag to give this function special treatment.
+                    # It's very important that it's appvars$server itself and NOT a copy that
+                    # is invoked, otherwise new breakpoints won't be picked up.
+                    attr(appvars$server, "shinyServerFunction") <- TRUE
+                    registerDebugHook("server", appvars, "Server Function")
+                  }
                 }
-              }
 
-              # Check for switching into/out of showcase mode
-              if (.globals$showcaseOverride &&
-                  exists(".clientdata_url_search", where = msg$data)) {
-                mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search)
-                if (!is.null(mode))
-                  shinysession$setShowcase(mode)
-              }
+                # Check for switching into/out of showcase mode
+                if (.globals$showcaseOverride &&
+                    exists(".clientdata_url_search", where = msg$data)) {
+                  mode <- showcaseModeOfQuerystring(msg$data$.clientdata_url_search)
+                  if (!is.null(mode))
+                    shinysession$setShowcase(mode)
+                }
 
-              shinysession$manageInputs(msg$data)
+                shinysession$manageInputs(msg$data)
 
-              # The client tells us what singletons were rendered into
-              # the initial page
-              if (!is.null(msg$data$.clientdata_singletons)) {
-                shinysession$singletons <- strsplit(
-                  msg$data$.clientdata_singletons, ',')[[1]]
-              }
+                # The client tells us what singletons were rendered into
+                # the initial page
+                if (!is.null(msg$data$.clientdata_singletons)) {
+                  shinysession$singletons <- strsplit(
+                    msg$data$.clientdata_singletons, ',')[[1]]
+                }
 
-              local({
-                args <- list(
-                  input=shinysession$input,
-                  output=.createOutputWriter(shinysession))
+                local({
+                  args <- argsForServerFunc(serverFunc, shinysession)
 
-                # The clientData and session arguments are optional; check if
-                # each exists
-                if ('clientData' %in% names(formals(serverFunc)))
-                  args$clientData <- shinysession$clientData
-
-                if ('session' %in% names(formals(serverFunc)))
-                  args$session <- shinysession
-
-                withReactiveDomain(shinysession, {
-                  do.call(appvars$server, args)
+                  withReactiveDomain(shinysession, {
+                    do.call(
+                      # No corresponding ..stacktraceoff; the server func is pure
+                      # user code
+                      wrapFunctionLabel(appvars$server, "server",
+                        ..stacktraceon = TRUE
+                      ),
+                      args
+                    )
+                  })
                 })
-              })
-            },
-            update = {
-              shinysession$manageInputs(msg$data)
-            },
-            shinysession$dispatch(msg)
-          )
-          shinysession$manageHiddenOutputs()
+              },
+              update = {
+                shinysession$manageInputs(msg$data)
+              },
+              shinysession$dispatch(msg)
+            )
+            shinysession$manageHiddenOutputs()
 
-          if (exists(".shiny__stdout", globalenv()) &&
-              exists("HTTP_GUID", ws$request)) {
-            # safe to assume we're in shiny-server
-            shiny_stdout <- get(".shiny__stdout", globalenv())
+            if (exists(".shiny__stdout", globalenv()) &&
+                exists("HTTP_GUID", ws$request)) {
+              # safe to assume we're in shiny-server
+              shiny_stdout <- get(".shiny__stdout", globalenv())
 
-            # eNter a flushReact
-            writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request),
-              " @ ", sprintf("%.3f", as.numeric(Sys.time())),
-              sep=""), con=shiny_stdout)
-            flush(shiny_stdout)
+              # eNter a flushReact
+              writeLines(paste("_n_flushReact ", get("HTTP_GUID", ws$request),
+                " @ ", sprintf("%.3f", as.numeric(Sys.time())),
+                sep=""), con=shiny_stdout)
+              flush(shiny_stdout)
 
-            flushReact()
+              flushReact()
 
-            # eXit a flushReact
-            writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request),
-              " @ ", sprintf("%.3f", as.numeric(Sys.time())),
-              sep=""), con=shiny_stdout)
-            flush(shiny_stdout)
-          } else {
-            flushReact()
-          }
-          lapply(appsByToken$values(), function(shinysession) {
-            shinysession$flushOutput()
-            NULL
+              # eXit a flushReact
+              writeLines(paste("_x_flushReact ", get("HTTP_GUID", ws$request),
+                " @ ", sprintf("%.3f", as.numeric(Sys.time())),
+                sep=""), con=shiny_stdout)
+              flush(shiny_stdout)
+            } else {
+              flushReact()
+            }
+
+            flushAllSessions()
           })
         })
+      }
+      ws$onMessage(function(binary, msg) {
+        # If unhandled errors occur, make sure they get properly logged
+        withLogErrors(messageHandler(binary, msg))
       })
 
       ws$onClose(function() {
@@ -357,6 +348,26 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
   return(appHandlers)
 }
 
+# Determine what arguments should be passed to this serverFunc. All server funcs
+# must take input and output, but clientData (obsolete) and session are
+# optional.
+argsForServerFunc <- function(serverFunc, session) {
+  args <- list(input = session$input, output = .createOutputWriter(session))
+
+  paramNames <- names(formals(serverFunc))
+
+  # The clientData and session arguments are optional; check if
+  # each exists
+
+  if ("clientData" %in% paramNames)
+    args$clientData <- session$clientData
+
+  if ("session" %in% paramNames)
+    args$session <- session
+
+  args
+}
+
 getEffectiveBody <- function(func) {
   # Note: NULL values are OK. isS4(NULL) returns FALSE, body(NULL)
   # returns NULL.
@@ -418,6 +429,12 @@ startApp <- function(appObj, port, host, quiet) {
       message('\n', 'Listening on domain socket ', port)
     }
     mask <- attr(port, 'mask')
+    if (is.null(mask)) {
+      stop("`port` is not a valid domain socket (missing `mask` attribute). ",
+           "Note that if you're using the default `host` + `port` ",
+           "configuration (and not domain sockets), then `port` must ",
+           "be numeric, not a string.")
+    }
     return(startPipeServer(port, mask, handlerManager$createHttpuvApp()))
   }
 }
@@ -431,10 +448,7 @@ serviceApp <- function() {
     }
 
     flushReact()
-
-    for (shinysession in appsByToken$values()) {
-      shinysession$flushOutput()
-    }
+    flushAllSessions()
   }
 
   # If this R session is interactive, then call service() with a short timeout
@@ -536,17 +550,23 @@ runApp <- function(appDir=getwd(),
     handlerManager$clear()
   }, add = TRUE)
 
+  # Enable per-app Shiny options
+  oldOptionSet <- .globals$options
+  on.exit({
+    .globals$options <- oldOptionSet
+  },add = TRUE)
 
   if (is.null(host) || is.na(host))
     host <- '0.0.0.0'
 
   # Make warnings print immediately
-  ops <- options(warn = 1)
+  # Set pool.scheduler to support pool package
+  ops <- options(warn = 1, pool.scheduler = scheduleTask)
   on.exit(options(ops), add = TRUE)
 
   workerId(workerId)
 
-  if (nzchar(Sys.getenv('SHINY_PORT'))) {
+  if (inShinyServer()) {
     # If SHINY_PORT is set, we're running under Shiny Server. Check the version
     # to make sure it is compatible. Older versions of Shiny Server don't set
     # SHINY_SERVER_VERSION, those will return "" which is considered less than
@@ -578,21 +598,38 @@ runApp <- function(appDir=getwd(),
       on.exit(close(con), add = TRUE)
       settings <- read.dcf(con)
       if ("DisplayMode" %in% colnames(settings)) {
-        mode <- settings[1,"DisplayMode"]
+        mode <- settings[1, "DisplayMode"]
         if (mode == "Showcase") {
           setShowcaseDefault(1)
+          if ("IncludeWWW" %in% colnames(settings)) {
+            .globals$IncludeWWW <- as.logical(settings[1, "IncludeWWW"])
+            if (is.na(.globals$IncludeWWW)) {
+              stop("In your Description file, `IncludeWWW` ",
+                   "must be set to `True` (default) or `False`")
+            }
+          } else {
+            .globals$IncludeWWW <- TRUE
+          }
         }
       }
     }
   }
 
+  ## default is to show the .js, .css and .html files in the www directory
+  ## (if not in showcase mode, this variable will simply be ignored)
+  if (is.null(.globals$IncludeWWW) || is.na(.globals$IncludeWWW)) {
+    .globals$IncludeWWW <- TRUE
+  }
+
   # If display mode is specified as an argument, apply it (overriding the
   # value specified in DESCRIPTION, if any).
   display.mode <- match.arg(display.mode)
-  if (display.mode == "normal")
+  if (display.mode == "normal") {
     setShowcaseDefault(0)
-  else if (display.mode == "showcase")
+  }
+  else if (display.mode == "showcase") {
     setShowcaseDefault(1)
+  }
 
   require(shiny)
 
@@ -613,7 +650,14 @@ runApp <- function(appDir=getwd(),
       }
       else {
         # Try up to 20 random ports
-        port <- p_randomInt(3000, 8000)
+        while (TRUE) {
+          port <- p_randomInt(3000, 8000)
+          # Reject ports in this range that are considered unsafe by Chrome
+          # http://superuser.com/questions/188058/which-ports-are-considered-unsafe-on-chrome
+          if (!port %in% c(3659, 4045, 6000, 6665:6669)) {
+            break
+          }
+        }
       }
 
       # Test port to see if we can use it
@@ -627,6 +671,12 @@ runApp <- function(appDir=getwd(),
   }
 
   appParts <- as.shiny.appobj(appDir)
+
+  # Extract appOptions (which is a list) and store them as shinyOptions, for
+  # this app. (This is the only place we have to store settings that are
+  # accessible both the UI and server portion of the app.)
+  unconsumeAppOptions(appParts$appOptions)
+
   # Set up the onEnd before we call onStart, so that it gets called even if an
   # error happens in onStart.
   if (!is.null(appParts$onEnd))
@@ -659,19 +709,27 @@ runApp <- function(appDir=getwd(),
     callAppHook("onAppStop", appUrl)
   }, add = TRUE)
 
+  .globals$reterror <- NULL
   .globals$retval <- NULL
   .globals$stopped <- FALSE
-  shinyCallingHandlers(
-    while (!.globals$stopped) {
-      serviceApp()
-      Sys.sleep(0.001)
-    }
+  # Top-level ..stacktraceoff..; matches with ..stacktraceon in observe(),
+  # reactive(), Callbacks$invoke(), and others
+  ..stacktraceoff..(
+    captureStackTraces(
+      while (!.globals$stopped) {
+        serviceApp()
+        Sys.sleep(0.001)
+      }
+    )
   )
 
-  if (inherits(.globals$retval, "try-error"))
-    stop(attr(.globals$retval, "condition", exact = TRUE))
+  if (isTRUE(.globals$reterror)) {
+    stop(.globals$retval)
+  }
+  else if (.globals$retval$visible)
+    .globals$retval$value
   else
-    return(.globals$retval)
+    invisible(.globals$retval$value)
 }
 
 #' Stop the currently running Shiny app
@@ -681,10 +739,26 @@ runApp <- function(appDir=getwd(),
 #'
 #' @param returnValue The value that should be returned from
 #'   \code{\link{runApp}}.
-#'
 #' @export
-stopApp <- function(returnValue = NULL) {
-  .globals$retval <- try(force(returnValue), silent = TRUE)
+stopApp <- function(returnValue = invisible()) {
+  # reterror will indicate whether retval is an error (i.e. it should be passed
+  # to stop() when the serviceApp loop stops) or a regular value (in which case
+  # it should simply be returned with the appropriate visibility).
+  .globals$reterror <- FALSE
+  ..stacktraceoff..(
+    tryCatch(
+      {
+        captureStackTraces(
+          .globals$retval <- withVisible(..stacktraceon..(force(returnValue)))
+        )
+      },
+      error = function(e) {
+        .globals$retval <- e
+        .globals$reterror <- TRUE
+      }
+    )
+  )
+
   .globals$stopped <- TRUE
   httpuv::interrupt()
 }
@@ -747,3 +821,140 @@ runExample <- function(example=NA,
            display.mode = display.mode)
   }
 }
+
+#' Run a gadget
+#'
+#' Similar to \code{runApp}, but handles \code{input$cancel} automatically, and
+#' if running in RStudio, defaults to viewing the app in the Viewer pane.
+#'
+#' @param app Either a Shiny app object as created by
+#'   \code{\link[=shiny]{shinyApp}} et al, or, a UI object.
+#' @param server Ignored if \code{app} is a Shiny app object; otherwise, passed
+#'   along to \code{shinyApp} (i.e. \code{shinyApp(ui = app, server = server)}).
+#' @param port See \code{\link[=shiny]{runApp}}.
+#' @param viewer Specify where the gadget should be displayed--viewer pane,
+#'   dialog window, or external browser--by passing in a call to one of the
+#'   \code{\link{viewer}} functions.
+#' @param stopOnCancel If \code{TRUE} (the default), then an \code{observeEvent}
+#'   is automatically created that handles \code{input$cancel} by calling
+#'   \code{stopApp()} with an error. Pass \code{FALSE} if you want to handle
+#'   \code{input$cancel} yourself.
+#' @return The value returned by the gadget.
+#'
+#' @examples
+#' \dontrun{
+#' library(shiny)
+#'
+#' ui <- fillPage(...)
+#'
+#' server <- function(input, output, session) {
+#'   ...
+#' }
+#'
+#' # Either pass ui/server as separate arguments...
+#' runGadget(ui, server)
+#'
+#' # ...or as a single app object
+#' runGadget(shinyApp(ui, server))
+#' }
+#' @export
+runGadget <- function(app, server = NULL, port = getOption("shiny.port"),
+  viewer = paneViewer(), stopOnCancel = TRUE) {
+
+  if (!is.shiny.appobj(app)) {
+    app <- shinyApp(app, server)
+  }
+
+  if (isTRUE(stopOnCancel)) {
+    app <- decorateServerFunc(app, function(input, output, session) {
+      observeEvent(input$cancel, {
+        stopApp(stop("User cancel", call. = FALSE))
+      })
+    })
+  }
+
+  if (is.null(viewer)) {
+    viewer <- utils::browseURL
+  }
+
+  shiny::runApp(app, port = port, launch.browser = viewer)
+}
+
+# Add custom functionality to a Shiny app object's server func
+decorateServerFunc <- function(appobj, serverFunc) {
+  origServerFuncSource <- appobj$serverFuncSource
+  appobj$serverFuncSource <- function() {
+    origServerFunc <- origServerFuncSource()
+    function(input, output, session) {
+      serverFunc(input, output, session)
+
+      # The clientData and session arguments are optional; check if
+      # each exists
+      args <- argsForServerFunc(origServerFunc, session)
+      do.call(origServerFunc, args)
+    }
+  }
+  appobj
+}
+
+#' Viewer options
+#'
+#' Use these functions to control where the gadget is displayed in RStudio (or
+#' other R environments that emulate RStudio's viewer pane/dialog APIs). If
+#' viewer APIs are not available in the current R environment, then the gadget
+#' will be displayed in the system's default web browser (see
+#' \code{\link[utils]{browseURL}}).
+#'
+#' @return A function that takes a single \code{url} parameter, suitable for
+#'   passing as the \code{viewer} argument of \code{\link{runGadget}}.
+#'
+#' @rdname viewer
+#' @name viewer
+NULL
+
+#' @param minHeight The minimum height (in pixels) desired to show the gadget in
+#'   the viewer pane. If a positive number, resize the pane if necessary to show
+#'   at least that many pixels. If \code{NULL}, use the existing viewer pane
+#'   size. If \code{"maximize"}, use the maximum available vertical space.
+#' @rdname viewer
+#' @export
+paneViewer <- function(minHeight = NULL) {
+  viewer <- getOption("viewer")
+  if (is.null(viewer)) {
+    utils::browseURL
+  } else {
+    function(url) {
+      viewer(url, minHeight)
+    }
+  }
+}
+
+#' @param dialogName The window title to display for the dialog.
+#' @param width,height The desired dialog width/height, in pixels.
+#' @rdname viewer
+#' @export
+dialogViewer <- function(dialogName, width = 600, height = 600) {
+  viewer <- getOption("shinygadgets.showdialog")
+  if (is.null(viewer)) {
+    utils::browseURL
+  } else {
+    function(url) {
+      viewer(dialogName, url, width = width, height = height)
+    }
+  }
+}
+
+#' @param browser See \code{\link[utils]{browseURL}}.
+#' @rdname viewer
+#' @export
+browserViewer <- function(browser = getOption("browser")) {
+  function(url) {
+    utils::browseURL(url, browser = browser)
+  }
+}
+
+# Returns TRUE if we're running in Shiny Server or other hosting environment,
+# otherwise returns FALSE.
+inShinyServer <- function() {
+  nzchar(Sys.getenv('SHINY_PORT'))
+}

R/shiny-options.R

@@ -0,0 +1,83 @@
+.globals$options <- list()
+
+#' @param name Name of an option to get.
+#' @param default Value to be returned if the option is not currently set.
+#' @rdname shinyOptions
+#' @export
+getShinyOption <- function(name, default = NULL) {
+  # Make sure to use named (not numeric) indexing
+  name <- as.character(name)
+
+  if (name %in% names(.globals$options))
+    .globals$options[[name]]
+  else
+    default
+}
+
+#' Get or set Shiny options
+#'
+#' \code{getShinyOption} retrieves the value of a Shiny option.
+#' \code{shinyOptions} sets the value of Shiny options; it can also be used to
+#' return a list of all currently-set Shiny options.
+#'
+#' There is a global option set, which is available by default. When a Shiny
+#' application is run with \code{\link{runApp}}, that option set is duplicated
+#' and the new option set is available for getting or setting values. If options
+#' are set from global.R, app.R, ui.R, or server.R, or if they are set from
+#' inside the server function, then the options will be scoped to the
+#' application. When the application exits, the new option set is discarded and
+#' the global option set is restored.
+#'
+#' @param ... Options to set, with the form \code{name = value}.
+#'
+#' @examples
+#' \dontrun{
+#' shinyOptions(myOption = 10)
+#' getShinyOption("myOption")
+#' }
+#' @export
+shinyOptions <- function(...) {
+  newOpts <- list(...)
+
+  if (length(newOpts) > 0) {
+    .globals$options <- dropNulls(mergeVectors(.globals$options, newOpts))
+    invisible(.globals$options)
+  } else {
+    .globals$options
+  }
+}
+
+
+# Eval an expression with a new option set
+withLocalOptions <- function(expr) {
+  oldOptionSet <- .globals$options
+  on.exit(.globals$options <- oldOptionSet)
+
+  expr
+}
+
+
+# Get specific shiny options and put them in a list, reset those shiny options,
+# and then return the options list. This should be during the creation of a
+# shiny app object, which happens before another option frame is added to the
+# options stack (the new option frame is added when the app is run). This
+# function "consumes" the options when the shinyApp object is created, so the
+# options won't affect another app that is created later.
+consumeAppOptions <- function() {
+  options <- list(
+    appDir = getwd(),
+    bookmarkStore = getShinyOption("bookmarkStore")
+  )
+
+  shinyOptions(appDir = NULL, bookmarkStore = NULL)
+
+  options
+}
+
+# Do the inverse of consumeAppOptions. This should be called once the app is
+# started.
+unconsumeAppOptions <- function(options) {
+  if (!is.null(options)) {
+    do.call(shinyOptions, options)
+  }
+}

R/shinyui.R

@@ -20,62 +20,38 @@ withMathJax <- function(...) {
       singleton(tags$script(src = path, type = 'text/javascript'))
     ),
     ...,
-    tags$script(HTML('MathJax.Hub.Queue(["Typeset", MathJax.Hub]);'))
+    tags$script(HTML('if (window.MathJax) MathJax.Hub.Queue(["Typeset", MathJax.Hub]);'))
   )
 }
 
 renderPage <- function(ui, connection, showcase=0) {
+  # If the ui is a NOT complete document (created by htmlTemplate()), then do some
+  # preprocessing and make sure it's a complete document.
+  if (!inherits(ui, "html_document")) {
+    if (showcase > 0)
+      ui <- showcaseUI(ui)
 
-  if (showcase > 0)
-    ui <- showcaseUI(ui)
+    # Wrap ui in body tag if it doesn't already have a single top-level body tag.
+    if (!(inherits(ui, "shiny.tag") && ui$name == "body"))
+      ui <- tags$body(ui)
 
-  # Wrap ui in body tag if it doesn't already have a single top-level body tag.
-  if (!(inherits(ui, "shiny.tag") && ui$name == "body"))
-    ui <- tags$body(ui)
+    # Put the body into the default template
+    ui <- htmlTemplate(
+      system.file("template", "default.html", package = "shiny"),
+      body = ui
+    )
+  }
 
-  result <- renderTags(ui)
-
-  deps <- c(
-    list(
-      htmlDependency("json2", "2014.02.04", c(href="shared"), script = "json2-min.js"),
-      htmlDependency("jquery", "1.11.3", c(href="shared"), script = "jquery.min.js"),
-      htmlDependency("shiny", utils::packageVersion("shiny"), c(href="shared"),
-        script = if (getOption("shiny.minified", TRUE)) "shiny.min.js" else "shiny.js",
-        stylesheet = "shiny.css")
-    ),
-    result$dependencies
+  shiny_deps <- list(
+    htmlDependency("json2", "2014.02.04", c(href="shared"), script = "json2-min.js"),
+    htmlDependency("jquery", "1.12.4", c(href="shared"), script = "jquery.min.js"),
+    htmlDependency("babel-polyfill", "6.7.2", c(href="shared"), script = "babel-polyfill.min.js"),
+    htmlDependency("shiny", utils::packageVersion("shiny"), c(href="shared"),
+      script = if (getOption("shiny.minified", TRUE)) "shiny.min.js" else "shiny.js",
+      stylesheet = "shiny.css")
   )
-  deps <- resolveDependencies(deps)
-  deps <- lapply(deps, createWebDependency)
-  depStr <- paste(sapply(deps, function(dep) {
-    sprintf("%s[%s]", dep$name, dep$version)
-  }), collapse = ";")
-  depHtml <- renderDependencies(deps, "href")
-
-  # write preamble
-  writeUTF8(c('<!DOCTYPE html>',
-               '<html>',
-               '<head>',
-               '  <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>',
-               sprintf('  <script type="application/shiny-singletons">%s</script>',
-                       paste(result$singletons, collapse = ',')
-               ),
-               sprintf('  <script type="application/html-dependencies">%s</script>',
-                       depStr
-               ),
-               depHtml
-              ),
-              con = connection)
-  writeUTF8(c(result$head,
-               '</head>',
-               recursive=TRUE),
-             con = connection)
-
-  writeUTF8(result$html, con = connection)
-
-  # write end document
-  writeUTF8('</html>',
-             con = connection)
+  html <- renderDocument(ui, shiny_deps, processDep = createWebDependency)
+  writeUTF8(html, con = connection)
 }
 
 #' Create a Shiny UI handler
@@ -88,7 +64,6 @@ renderPage <- function(ui, connection, showcase=0) {
 #'
 #' @param ui A user interace definition
 #' @return The user interface definition, without modifications or side effects.
-#'
 #' @export
 shinyUI <- function(ui) {
   .globals$ui <- list(ui)
@@ -115,14 +90,34 @@ uiHttpHandler <- function(ui, uiPattern = "^/$") {
       if (!is.null(mode))
         showcaseMode <- mode
     }
-    uiValue <- if (is.function(ui)) {
-      if (length(formals(ui)) > 0)
-        ui(req)
-      else
-        ui()
+
+    # Create a restore context using query string
+    bookmarkStore <- getShinyOption("bookmarkStore", default = "disable")
+    if (bookmarkStore == "disable") {
+      # If bookmarking is disabled, use empty context
+      restoreContext <- RestoreContext$new()
     } else {
-      ui
+      restoreContext <- RestoreContext$new(req$QUERY_STRING)
     }
+
+    withRestoreContext(restoreContext, {
+      uiValue <- NULL
+
+      if (is.function(ui)) {
+        if (length(formals(ui)) > 0) {
+          # No corresponding ..stacktraceoff.., this is pure user code
+          uiValue <- ..stacktraceon..(ui(req))
+        } else {
+          # No corresponding ..stacktraceoff.., this is pure user code
+          uiValue <- ..stacktraceon..(ui())
+        }
+      } else {
+        if (getCurrentRestoreContext()$active) {
+          warning("Trying to restore saved app state, but UI code must be a function for this to work! See ?enableBookmarking")
+        }
+        uiValue <- ui
+      }
+    })
     if (is.null(uiValue))
       return(NULL)
 

R/shinywrappers.R

@@ -12,24 +12,74 @@ globalVariables('func')
 #'   an output ID.
 #' @param renderFunc A function that is suitable for assigning to a Shiny output
 #'   slot.
+#' @param outputArgs A list of arguments to pass to the \code{uiFunc}. Render
+#'   functions should include \code{outputArgs = list()} in their own parameter
+#'   list, and pass through the value to \code{markRenderFunction}, to allow
+#'   app authors to customize outputs. (Currently, this is only supported for
+#'   dynamically generated UIs, such as those created by Shiny code snippets
+#'   embedded in R Markdown documents).
 #' @return The \code{renderFunc} function, with annotations.
-#'
 #' @export
-markRenderFunction <- function(uiFunc, renderFunc) {
+markRenderFunction <- function(uiFunc, renderFunc, outputArgs = list()) {
+  # a mutable object that keeps track of whether `useRenderFunction` has been
+  # executed (this usually only happens when rendering Shiny code snippets in
+  # an interactive R Markdown document); its initial value is FALSE
+  hasExecuted <- Mutable$new()
+  hasExecuted$set(FALSE)
+
+  origRenderFunc <- renderFunc
+  renderFunc <- function(...) {
+    # if the user provided something through `outputArgs` BUT the
+    # `useRenderFunction` was not executed, then outputArgs will be ignored,
+    # so throw a warning to let user know the correct usage
+    if (length(outputArgs) != 0 && !hasExecuted$get()) {
+      warning("Unused argument: outputArgs. The argument outputArgs is only ",
+              "meant to be used when embedding snippets of Shiny code in an ",
+              "R Markdown code chunk (using runtime: shiny). When running a ",
+              "full Shiny app, please set the output arguments directly in ",
+              "the corresponding output function of your UI code.")
+      # stop warning from happening again for the same object
+      hasExecuted$set(TRUE)
+    }
+    if (is.null(formals(origRenderFunc))) origRenderFunc()
+    else origRenderFunc(...)
+  }
+
   structure(renderFunc,
-            class      = c("shiny.render.function", "function"),
-            outputFunc = uiFunc)
+            class       = c("shiny.render.function", "function"),
+            outputFunc  = uiFunc,
+            outputArgs  = outputArgs,
+            hasExecuted = hasExecuted)
 }
 
 useRenderFunction <- function(renderFunc, inline = FALSE) {
   outputFunction <- attr(renderFunc, "outputFunc")
+  outputArgs <- attr(renderFunc, "outputArgs")
+  hasExecuted <- attr(renderFunc, "hasExecuted")
+  hasExecuted$set(TRUE)
+
+  for (arg in names(outputArgs)) {
+    if (!arg %in% names(formals(outputFunction))) {
+      stop(paste0("Unused argument: in 'outputArgs', '",
+                  arg, "' is not an valid argument for ",
+                  "the output function"))
+      outputArgs[[arg]] <- NULL
+    }
+  }
+
   id <- createUniqueId(8, "out")
+  # Make the id the first positional argument
+  outputArgs <- c(list(id), outputArgs)
+
   o <- getDefaultReactiveDomain()$output
   if (!is.null(o))
     o[[id]] <- renderFunc
-  if (is.logical(formals(outputFunction)[["inline"]])) {
-    outputFunction(id, inline = inline)
-  } else outputFunction(id)
+
+  if (is.logical(formals(outputFunction)[["inline"]]) && !("inline" %in% names(outputArgs))) {
+    outputArgs[["inline"]] <- inline
+  }
+
+  do.call(outputFunction, outputArgs)
 }
 
 #' @export
@@ -69,13 +119,23 @@ as.tags.shiny.render.function <- function(x, ..., inline = FALSE) {
 #'   it is sent to the client browser? Generally speaking, if the image is a
 #'   temp file generated within \code{func}, then this should be \code{TRUE};
 #'   if the image is not a temp file, this should be \code{FALSE}.
-#'
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{imageOutput}} when \code{renderImage} is used in an
+#'   interactive R Markdown document.
 #' @export
 #'
 #' @examples
-#' \dontrun{
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#' shinyServer(function(input, output, clientData) {
+#' ui <- fluidPage(
+#'   sliderInput("n", "Number of observations", 2, 1000, 500),
+#'   plotOutput("plot1"),
+#'   plotOutput("plot2"),
+#'   plotOutput("plot3")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'
 #'   # A plot of fixed size
 #'   output$plot1 <- renderImage({
@@ -97,14 +157,14 @@ as.tags.shiny.render.function <- function(x, ..., inline = FALSE) {
 #'   output$plot2 <- renderImage({
 #'     # Read plot2's width and height. These are reactive values, so this
 #'     # expression will re-run whenever these values change.
-#'     width  <- clientData$output_plot2_width
-#'     height <- clientData$output_plot2_height
+#'     width  <- session$clientData$output_plot2_width
+#'     height <- session$clientData$output_plot2_height
 #'
 #'     # A temp file to save the output.
 #'     outfile <- tempfile(fileext='.png')
 #'
 #'     png(outfile, width=width, height=height)
-#'     hist(rnorm(input$obs))
+#'     hist(rnorm(input$n))
 #'     dev.off()
 #'
 #'     # Return a list containing the filename
@@ -115,6 +175,8 @@ as.tags.shiny.render.function <- function(x, ..., inline = FALSE) {
 #'   }, deleteFile = TRUE)
 #'
 #'   # Send a pre-rendered image, and don't delete the image after sending it
+#'   # NOTE: For this example to work, it would require files in a subdirectory
+#'   # named images/
 #'   output$plot3 <- renderImage({
 #'     # When input$n is 1, filename is ./images/image1.jpeg
 #'     filename <- normalizePath(file.path('./images',
@@ -123,14 +185,15 @@ as.tags.shiny.render.function <- function(x, ..., inline = FALSE) {
 #'     # Return a list containing the filename
 #'     list(src = filename)
 #'   }, deleteFile = FALSE)
-#' })
+#' }
 #'
+#' shinyApp(ui, server)
 #' }
 renderImage <- function(expr, env=parent.frame(), quoted=FALSE,
-                        deleteFile=TRUE) {
+                        deleteFile=TRUE, outputArgs=list()) {
   installExprFunction(expr, "func", env, quoted)
 
-  return(markRenderFunction(imageOutput, function(shinysession, name, ...) {
+  renderFunc <- function(shinysession, name, ...) {
     imageinfo <- func()
     # Should the file be deleted after being sent? If .deleteFile not set or if
     # TRUE, then delete; otherwise don't delete.
@@ -147,55 +210,12 @@ renderImage <- function(expr, env=parent.frame(), quoted=FALSE,
     # Return a list with src, and other img attributes
     c(src = shinysession$fileUrl(name, file=imageinfo$src, contentType=contentType),
       extra_attr)
-  }))
-}
-
-
-#' Table Output
-#'
-#' Creates a reactive table that is suitable for assigning to an \code{output}
-#' slot.
-#'
-#' The corresponding HTML output tag should be \code{div} and have the CSS class
-#' name \code{shiny-html-output}.
-#'
-#' @param expr An expression that returns an R object that can be used with
-#'   \code{\link[xtable]{xtable}}.
-#' @param ... Arguments to be passed through to \code{\link[xtable]{xtable}} and
-#'   \code{\link[xtable]{print.xtable}}.
-#' @param env The environment in which to evaluate \code{expr}.
-#' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
-#'   is useful if you want to save an expression in a variable.
-#' @param func A function that returns an R object that can be used with
-#'   \code{\link[xtable]{xtable}} (deprecated; use \code{expr} instead).
-#'
-#' @export
-renderTable <- function(expr, ..., env=parent.frame(), quoted=FALSE, func=NULL) {
-  if (!is.null(func)) {
-    shinyDeprecated(msg="renderTable: argument 'func' is deprecated. Please use 'expr' instead.")
-  } else {
-    installExprFunction(expr, "func", env, quoted)
   }
 
-  markRenderFunction(tableOutput, function() {
-    classNames <- getOption('shiny.table.class') %OR% 'data table table-bordered table-condensed'
-    data <- func()
-
-    if (is.null(data) || identical(data, data.frame()))
-      return("")
-
-    return(paste(
-      utils::capture.output(
-        print(xtable(data, ...),
-              type='html',
-              html.table.attributes=paste('class="',
-                                          htmlEscape(classNames, TRUE),
-                                          '"',
-                                          sep=''), ...)),
-      collapse="\n"))
-  })
+  markRenderFunction(imageOutput, renderFunc, outputArgs = outputArgs)
 }
 
+
 #' Printable Output
 #'
 #' Makes a reactive version of the given function that captures any printed
@@ -218,28 +238,27 @@ renderTable <- function(expr, ..., env=parent.frame(), quoted=FALSE, func=NULL)
 #'   object.
 #' @param env The environment in which to evaluate \code{expr}.
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
-#' @param func A function that may print output and/or return a printable R
-#'   object (deprecated; use \code{expr} instead).
+#'   is useful if you want to save an expression in a variable.
 #' @param width The value for \code{\link{options}('width')}.
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{verbatimTextOutput}} when \code{renderPrint} is used
+#'   in an interactive R Markdown document.
 #' @seealso \code{\link{renderText}} for displaying the value returned from a
 #'   function, instead of the printed output.
 #'
 #' @example res/text-example.R
-#'
 #' @export
-renderPrint <- function(expr, env = parent.frame(), quoted = FALSE, func = NULL,
-                        width = getOption('width')) {
-  if (!is.null(func)) {
-    shinyDeprecated(msg="renderPrint: argument 'func' is deprecated. Please use 'expr' instead.")
-  } else {
-    installExprFunction(expr, "func", env, quoted)
-  }
+renderPrint <- function(expr, env = parent.frame(), quoted = FALSE,
+                        width = getOption('width'), outputArgs=list()) {
+  installExprFunction(expr, "func", env, quoted)
 
-  markRenderFunction(verbatimTextOutput, function() {
+  renderFunc <- function(shinysession, name, ...) {
     op <- options(width = width)
     on.exit(options(op), add = TRUE)
     paste(utils::capture.output(func()), collapse = "\n")
-  })
+  }
+
+  markRenderFunction(verbatimTextOutput, renderFunc, outputArgs = outputArgs)
 }
 
 #' Text Output
@@ -260,26 +279,25 @@ renderPrint <- function(expr, env = parent.frame(), quoted = FALSE, func = NULL,
 #' @param env The environment in which to evaluate \code{expr}.
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
 #'   is useful if you want to save an expression in a variable.
-#' @param func A function that returns an R object that can be used as an
-#'   argument to \code{cat}.(deprecated; use \code{expr} instead).
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{textOutput}} when \code{renderText} is used in an
+#'   interactive R Markdown document.
 #'
 #' @seealso \code{\link{renderPrint}} for capturing the print output of a
 #'   function, rather than the returned text value.
 #'
 #' @example res/text-example.R
-#'
 #' @export
-renderText <- function(expr, env=parent.frame(), quoted=FALSE, func=NULL) {
-  if (!is.null(func)) {
-    shinyDeprecated(msg="renderText: argument 'func' is deprecated. Please use 'expr' instead.")
-  } else {
-    installExprFunction(expr, "func", env, quoted)
-  }
+renderText <- function(expr, env=parent.frame(), quoted=FALSE,
+                       outputArgs=list()) {
+  installExprFunction(expr, "func", env, quoted)
 
-  markRenderFunction(textOutput, function() {
+  renderFunc <- function(shinysession, name, ...) {
     value <- func()
     return(paste(utils::capture.output(cat(value)), collapse="\n"))
-  })
+  }
+
+  markRenderFunction(textOutput, renderFunc, outputArgs = outputArgs)
 }
 
 #' UI Output
@@ -295,46 +313,44 @@ renderText <- function(expr, env=parent.frame(), quoted=FALSE, func=NULL) {
 #' @param env The environment in which to evaluate \code{expr}.
 #' @param quoted Is \code{expr} a quoted expression (with \code{quote()})? This
 #'   is useful if you want to save an expression in a variable.
-#' @param func A function that returns a Shiny tag object, \code{\link{HTML}},
-#'   or a list of such objects (deprecated; use \code{expr} instead).
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{uiOutput}} when \code{renderUI} is used in an
+#'   interactive R Markdown document.
 #'
 #' @seealso conditionalPanel
-#'
 #' @export
 #' @examples
-#' \dontrun{
-#'   output$moreControls <- renderUI({
-#'     list(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   uiOutput("moreControls")
+#' )
+#'
+#' server <- function(input, output) {
+#'   output$moreControls <- renderUI({
+#'     tagList(
+#'       sliderInput("n", "N", 1, 1000, 500),
+#'       textInput("label", "Label")
 #'     )
 #'   })
 #' }
-renderUI <- function(expr, env=parent.frame(), quoted=FALSE, func=NULL) {
-  if (!is.null(func)) {
-    shinyDeprecated(msg="renderUI: argument 'func' is deprecated. Please use 'expr' instead.")
-  } else {
-    installExprFunction(expr, "func", env, quoted)
-  }
+#' shinyApp(ui, server)
+#' }
+#'
+renderUI <- function(expr, env=parent.frame(), quoted=FALSE,
+                     outputArgs=list()) {
+  installExprFunction(expr, "func", env, quoted)
 
-  markRenderFunction(uiOutput, function(shinysession, name, ...) {
+  renderFunc <- function(shinysession, name, ...) {
     result <- func()
     if (is.null(result) || length(result) == 0)
       return(NULL)
 
-    result <- takeSingletons(result, shinysession$singletons, desingleton=FALSE)$ui
-    result <- surroundSingletons(result)
-    dependencies <- lapply(resolveDependencies(findDependencies(result)),
-      createWebDependency)
-    names(dependencies) <- NULL
+    processDeps(result, shinysession)
+  }
 
-    # renderTags returns a list with head, singletons, and html
-    output <- list(
-      html = doRenderTags(result),
-      deps = dependencies
-    )
-
-    return(output)
-  })
+  markRenderFunction(uiOutput, renderFunc, outputArgs = outputArgs)
 }
 
 #' File Downloads
@@ -360,28 +376,40 @@ renderUI <- function(expr, env=parent.frame(), quoted=FALSE, func=NULL) {
 #'   example \code{"text/csv"} or \code{"image/png"}. If \code{NULL} or
 #'   \code{NA}, the content type will be guessed based on the filename
 #'   extension, or \code{application/octet-stream} if the extension is unknown.
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{downloadButton}} when \code{downloadHandler} is used
+#'   in an interactive R Markdown document.
 #'
 #' @examples
-#' \dontrun{
-#' # In server.R:
-#' output$downloadData <- downloadHandler(
-#'   filename = function() {
-#'     paste('data-', Sys.Date(), '.csv', sep='')
-#'   },
-#'   content = function(file) {
-#'     write.csv(data, file)
-#'   }
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   downloadLink("downloadData", "Download")
 #' )
 #'
-#' # In ui.R:
-#' downloadLink('downloadData', 'Download')
+#' server <- function(input, output) {
+#'   # Our dataset
+#'   data <- mtcars
+#'
+#'   output$downloadData <- downloadHandler(
+#'     filename = function() {
+#'       paste("data-", Sys.Date(), ".csv", sep="")
+#'     },
+#'     content = function(file) {
+#'       write.csv(data, file)
+#'     }
+#'   )
 #' }
 #'
+#' shinyApp(ui, server)
+#' }
 #' @export
-downloadHandler <- function(filename, content, contentType=NA) {
-  return(markRenderFunction(downloadButton, function(shinysession, name, ...) {
+downloadHandler <- function(filename, content, contentType=NA, outputArgs=list()) {
+  renderFunc <- function(shinysession, name, ...) {
     shinysession$registerDownload(name, filename, contentType, content)
-  }))
+  }
+  markRenderFunction(downloadButton, renderFunc, outputArgs = outputArgs)
 }
 
 #' Table output with the JavaScript library DataTables
@@ -412,6 +440,10 @@ downloadHandler <- function(filename, content, contentType=NA) {
 #'   indicate which columns to escape, e.g. \code{1:5} (the first 5 columns),
 #'   \code{c(1, 3, 4)}, or \code{c(-1, -3)} (all columns except the first and
 #'   third), or \code{c('Species', 'Sepal.Length')}.
+#' @param outputArgs A list of arguments to be passed through to the implicit
+#'   call to \code{\link{dataTableOutput}} when \code{renderDataTable} is used
+#'   in an interactive R Markdown document.
+#'
 #' @references \url{http://datatables.net}
 #' @note This function only provides the server-side version of DataTables
 #'   (using R to process the data object on the server side). There is a
@@ -446,10 +478,11 @@ downloadHandler <- function(filename, content, contentType=NA) {
 #' }
 renderDataTable <- function(expr, options = NULL, searchDelay = 500,
                             callback = 'function(oTable) {}', escape = TRUE,
-                            env = parent.frame(), quoted = FALSE) {
+                            env = parent.frame(), quoted = FALSE,
+                            outputArgs=list()) {
   installExprFunction(expr, "func", env, quoted)
 
-  markRenderFunction(dataTableOutput, function(shinysession, name, ...) {
+  renderFunc <- function(shinysession, name, ...) {
     if (is.function(options)) options <- options()
     options <- checkDT9(options)
     res <- checkAsIs(options)
@@ -475,7 +508,9 @@ renderDataTable <- function(expr, options = NULL, searchDelay = 500,
       evalOptions = if (length(res$eval)) I(res$eval), searchDelay = searchDelay,
       callback = paste(callback, collapse = '\n'), escape = escape
     )
-  })
+  }
+
+  markRenderFunction(dataTableOutput, renderFunc, outputArgs = outputArgs)
 }
 
 # a data frame containing the DataTables 1.9 and 1.10 names

R/showcase.R

@@ -31,7 +31,7 @@ licenseLink <- function(licenseName) {
 showcaseHead <- function() {
 
   deps  <- list(
-    htmlDependency("jqueryui", "1.11.4", c(href="shared/jqueryui"),
+    htmlDependency("jqueryui", "1.12.1", c(href="shared/jqueryui"),
       script = "jquery-ui.min.js"),
     htmlDependency("showdown", "0.3.1", c(href="shared/showdown/compressed"),
       script = "showdown.js"),
@@ -77,10 +77,60 @@ appMetadata <- function(desc) {
   else ""
 }
 
+navTabsHelper <- function(files, prefix = "") {
+  lapply(files, function(file) {
+    with(tags,
+      li(class=if (tolower(file) %in% c("app.r", "server.r")) "active" else "",
+         a(href=paste("#", gsub(".", "_", file, fixed=TRUE), "_code", sep=""),
+           "data-toggle"="tab", paste0(prefix, file)))
+    )
+  })
+}
+
+navTabsDropdown <- function(files) {
+  if (length(files) > 0) {
+    with(tags,
+      li(role="presentation", class="dropdown",
+        a(class="dropdown-toggle", `data-toggle`="dropdown", href="#",
+          role="button", `aria-haspopup`="true", `aria-expanded`="false",
+          "www", span(class="caret")
+        ),
+        ul(class="dropdown-menu", navTabsHelper(files))
+      )
+    )
+  }
+}
+
+tabContentHelper <- function(files, path, language) {
+  lapply(files, function(file) {
+    with(tags,
+      div(class=paste("tab-pane",
+                      if (tolower(file) %in% c("app.r", "server.r")) " active"
+                      else "",
+                      sep=""),
+          id=paste(gsub(".", "_", file, fixed=TRUE),
+                   "_code", sep=""),
+          pre(class="shiny-code",
+              # we need to prevent the indentation of <code> ... </code>
+              HTML(format(tags$code(
+                class=paste0("language-", language),
+                paste(readUTF8(file.path.ci(path, file)), collapse="\n")
+              ), indent = FALSE))))
+    )
+  })
+}
+
 # Returns tags containing the application's code in Bootstrap-style tabs in
 # showcase mode.
 showcaseCodeTabs <- function(codeLicense) {
   rFiles <- list.files(pattern = "\\.[rR]$")
+  wwwFiles <- list()
+  if (isTRUE(.globals$IncludeWWW)) {
+    path <- file.path(getwd(), "www")
+    wwwFiles$jsFiles <- list.files(path, pattern = "\\.js$")
+    wwwFiles$cssFiles <- list.files(path, pattern = "\\.css$")
+    wwwFiles$htmlFiles <- list.files(path, pattern = "\\.html$")
+  }
   with(tags, div(id="showcase-code-tabs",
     a(id="showcase-code-position-toggle",
       class="btn btn-default btn-sm",
@@ -88,27 +138,21 @@ showcaseCodeTabs <- function(codeLicense) {
       icon("level-up"),
       "show with app"),
     ul(class="nav nav-tabs",
-       lapply(rFiles, function(rFile) {
-         li(class=if (tolower(rFile) %in% c("app.r", "server.r")) "active" else "",
-            a(href=paste("#", gsub(".", "_", rFile, fixed=TRUE),
-                         "_code", sep=""),
-              "data-toggle"="tab", rFile))
-       })),
+       navTabsHelper(rFiles),
+       navTabsDropdown(unlist(wwwFiles))
+    ),
     div(class="tab-content", id="showcase-code-content",
-        lapply(rFiles, function(rFile) {
-          div(class=paste("tab-pane",
-                          if (tolower(rFile) %in% c("app.r", "server.r")) " active"
-                          else "",
-                          sep=""),
-              id=paste(gsub(".", "_", rFile, fixed=TRUE),
-                       "_code", sep=""),
-              pre(class="shiny-code",
-                  # we need to prevent the indentation of <code> ... </code>
-                  HTML(format(tags$code(
-                    class="language-r",
-                    paste(readUTF8(file.path.ci(getwd(), rFile)), collapse="\n")
-                  ), indent = FALSE))))
-        })),
+        tabContentHelper(rFiles, path = getwd(), language = "r"),
+        tabContentHelper(wwwFiles$jsFiles,
+                         path = paste0(getwd(), "/www"),
+                         language = "javascript"),
+        tabContentHelper(wwwFiles$cssFiles,
+                         path = paste0(getwd(), "/www"),
+                         language = "css"),
+        tabContentHelper(wwwFiles$htmlFiles,
+                         path = paste0(getwd(), "/www"),
+                         language = "xml")
+    ),
     codeLicense))
 }
 
@@ -177,3 +221,4 @@ showcaseUI <- function(ui) {
     showcaseBody(ui)
   )
 }
+

R/timer.R

@@ -22,6 +22,11 @@ TimerCallbacks <- R6Class(
       .times <<- data.frame()
     },
     schedule = function(millis, func) {
+      # If args could fail to evaluate, let's make them do that before
+      # we change any state
+      force(millis)
+      force(func)
+
       id <- .nextId
       .nextId <<- .nextId + 1L
 
@@ -56,7 +61,7 @@ TimerCallbacks <- R6Class(
     },
     executeElapsed = function() {
       elapsed <- takeElapsed()
-      if (length(elapsed) == 0)
+      if (nrow(elapsed) == 0)
         return(FALSE)
 
       for (id in elapsed$id) {
@@ -71,3 +76,16 @@ TimerCallbacks <- R6Class(
 )
 
 timerCallbacks <- TimerCallbacks$new()
+
+scheduleTask <- function(millis, callback) {
+  cancelled <- FALSE
+  timerCallbacks$schedule(millis, function() {
+    if (!cancelled)
+      callback()
+  })
+
+  function() {
+    cancelled <<- TRUE
+    callback <<- NULL # to allow for callback to be gc'ed
+  }
+}

R/update-input.R

@@ -6,9 +6,16 @@
 #' @seealso \code{\link{textInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   sliderInput("controller", "Controller", 0, 20, 10),
+#'   textInput("inText", "Input text"),
+#'   textInput("inText2", "Input text 2")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
 #'     # We'll use the input$controller variable multiple times, so save it as x
 #'     # for convenience.
@@ -22,7 +29,9 @@
 #'       label = paste("New label", x),
 #'       value = paste("New text", x))
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateTextInput <- function(session, inputId, label = NULL, value = NULL) {
@@ -30,6 +39,44 @@ updateTextInput <- function(session, inputId, label = NULL, value = NULL) {
   session$sendInputMessage(inputId, message)
 }
 
+#' Change the value of a textarea input on the client
+#'
+#' @template update-input
+#' @param value The value to set for the input object.
+#'
+#' @seealso \code{\link{textAreaInput}}
+#'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   sliderInput("controller", "Controller", 0, 20, 10),
+#'   textAreaInput("inText", "Input textarea"),
+#'   textAreaInput("inText2", "Input textarea 2")
+#' )
+#'
+#' server <- function(input, output, session) {
+#'   observe({
+#'     # We'll use the input$controller variable multiple times, so save it as x
+#'     # for convenience.
+#'     x <- input$controller
+#'
+#'     # This will change the value of input$inText, based on x
+#'     updateTextAreaInput(session, "inText", value = paste("New text", x))
+#'
+#'     # Can also set the label, this time for input$inText2
+#'     updateTextAreaInput(session, "inText2",
+#'       label = paste("New label", x),
+#'       value = paste("New text", x))
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
+#' @export
+updateTextAreaInput <- updateTextInput
+
 
 #' Change the value of a checkbox input on the client
 #'
@@ -39,26 +86,87 @@ updateTextInput <- function(session, inputId, label = NULL, value = NULL) {
 #' @seealso \code{\link{checkboxInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   sliderInput("controller", "Controller", 0, 1, 0, step = 1),
+#'   checkboxInput("inCheckbox", "Input checkbox")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # TRUE if input$controller is even, FALSE otherwise.
-#'     x_even <- input$controller %% 2 == 0
+#'     # TRUE if input$controller is odd, FALSE if even.
+#'     x_even <- input$controller %% 2 == 1
 #'
 #'     updateCheckboxInput(session, "inCheckbox", value = x_even)
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateCheckboxInput <- updateTextInput
 
 
+#' Change the label or icon of an action button on the client
+#'
+#' @template update-input
+#' @param icon The icon to set for the input object. To remove the
+#' current icon, use \code{icon=character(0)}.
+#'
+#' @seealso \code{\link{actionButton}}
+#'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
+#'   actionButton("update", "Update other buttons"),
+#'   br(),
+#'   actionButton("goButton", "Go"),
+#'   br(),
+#'   actionButton("goButton2", "Go 2", icon = icon("area-chart")),
+#'   br(),
+#'   actionButton("goButton3", "Go 3")
+#' )
+#'
+#' server <- function(input, output, session) {
+#'   observe({
+#'     req(input$update)
+#'
+#'     # Updates goButton's label and icon
+#'     updateActionButton(session, "goButton",
+#'       label = "New label",
+#'       icon = icon("calendar"))
+#'
+#'     # Leaves goButton2's label unchaged and
+#'     # removes its icon
+#'     updateActionButton(session, "goButton2",
+#'       icon = character(0))
+#'
+#'     # Leaves goButton3's icon, if it exists,
+#'     # unchaged and changes its label
+#'     updateActionButton(session, "goButton3",
+#'       label = "New label 3")
+#'   })
+#' }
+#'
+#' shinyApp(ui, server)
+#' }
+#' @export
+updateActionButton <- function(session, inputId, label = NULL, icon = NULL) {
+  if (!is.null(icon)) icon <- as.character(validateIcon(icon))
+  message <- dropNulls(list(label=label, icon=icon))
+  session$sendInputMessage(inputId, message)
+}
+
+
 #' Change the value of a date input on the client
 #'
 #' @template update-input
 #' @param value The desired date value. Either a Date object, or a string in
-#'   \code{yyyy-mm-dd} format.
+#'   \code{yyyy-mm-dd} format. Supply \code{NA} to clear the date.
 #' @param min The minimum allowed date. Either a Date object, or a string in
 #'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
@@ -67,32 +175,44 @@ updateCheckboxInput <- updateTextInput
 #' @seealso \code{\link{dateInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   sliderInput("n", "Day of month", 1, 30, 10),
+#'   dateInput("inDate", "Input date")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # We'll use the input$controller variable multiple times, so save it as x
-#'     # for convenience.
-#'     x <- input$controller
-#'
+#'     date <- as.Date(paste0("2013-04-", input$n))
 #'     updateDateInput(session, "inDate",
-#'       label = paste("Date label", x),
-#'       value = paste("2013-04-", x, sep=""),
-#'       min   = paste("2013-04-", x-1, sep=""),
-#'       max   = paste("2013-04-", x+1, sep="")
+#'       label = paste("Date label", input$n),
+#'       value = date,
+#'       min   = date - 3,
+#'       max   = date + 3
 #'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateDateInput <- function(session, inputId, label = NULL, value = 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
-  if (inherits(value, "Date"))  value <- format(value, "%Y-%m-%d")
-  if (inherits(min, "Date"))    min   <- format(min,   "%Y-%m-%d")
-  if (inherits(max, "Date"))    max   <- format(max,   "%Y-%m-%d")
+  # Make sure values are NULL or Date objects. This is so we can ensure that
+  # they will be formatted correctly. For example, the string "2016-08-9" is not
+  # correctly formatted, but the conversion to Date and back to string will fix
+  # it.
+  formatDate <- function(x) {
+    if (is.null(x))
+      return(NULL)
+    format(as.Date(x), "%Y-%m-%d")
+  }
+  value <- formatDate(value)
+  min   <- formatDate(min)
+  max   <- formatDate(max)
 
   message <- dropNulls(list(label=label, value=value, min=min, max=max))
   session$sendInputMessage(inputId, message)
@@ -103,9 +223,9 @@ updateDateInput <- function(session, inputId, label = NULL, value = NULL,
 #'
 #' @template update-input
 #' @param start The start date. Either a Date object, or a string in
-#'   \code{yyyy-mm-dd} format.
+#'   \code{yyyy-mm-dd} format. Supplying \code{NA} clears the start date.
 #' @param end The end date. Either a Date object, or a string in
-#'   \code{yyyy-mm-dd} format.
+#'   \code{yyyy-mm-dd} format. Supplying \code{NA} clears the end date.
 #' @param min The minimum allowed date. Either a Date object, or a string in
 #'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
@@ -114,20 +234,29 @@ updateDateInput <- function(session, inputId, label = NULL, value = NULL,
 #' @seealso \code{\link{dateRangeInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   sliderInput("n", "Day of month", 1, 30, 10),
+#'   dateRangeInput("inDateRange", "Input date range")
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # We'll use the input$controller variable multiple times, so save it as x
-#'     # for convenience.
-#'     x <- input$controller
+#'     date <- as.Date(paste0("2013-04-", input$n))
 #'
 #'     updateDateRangeInput(session, "inDateRange",
-#'       label = paste("Date range label", x),
-#'       start = paste("2013-01-", x, sep=""))
-#'       end = paste("2013-12-", x, sep=""))
+#'       label = paste("Date range label", input$n),
+#'       start = date - 1,
+#'       end = date + 1,
+#'       min = date - 5,
+#'       max = date + 5
+#'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateDateRangeInput <- function(session, inputId, label = NULL,
@@ -142,7 +271,7 @@ updateDateRangeInput <- function(session, inputId, label = NULL,
 
   message <- dropNulls(list(
     label = label,
-    value = c(start, end),
+    value = dropNulls(list(start = start, end = end)),
     min = min,
     max = max
   ))
@@ -162,22 +291,31 @@ updateDateRangeInput <- function(session, inputId, label = NULL,
 #' \code{\link{navbarPage}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#'   observe({
-#'     # TRUE if input$controller is even, FALSE otherwise.
-#'     x_even <- input$controller %% 2 == 0
+#' ui <- fluidPage(sidebarLayout(
+#'   sidebarPanel(
+#'     sliderInput("controller", "Controller", 1, 3, 1)
+#'   ),
+#'   mainPanel(
+#'     tabsetPanel(id = "inTabset",
+#'       tabPanel(title = "Panel 1", value = "panel1", "Panel 1 content"),
+#'       tabPanel(title = "Panel 2", value = "panel2", "Panel 2 content"),
+#'       tabPanel(title = "Panel 3", value = "panel3", "Panel 3 content")
+#'     )
+#'   )
+#' ))
 #'
-#'     # Change the selected tab.
-#'     # Note that the tabset container must have been created with an 'id' argument
-#'     if (x_even) {
-#'       updateTabsetPanel(session, "inTabset", selected = "panel2")
-#'     } else {
-#'       updateTabsetPanel(session, "inTabset", selected = "panel1")
-#'     }
+#' server <- function(input, output, session) {
+#'   observeEvent(input$controller, {
+#'     updateTabsetPanel(session, "inTabset",
+#'       selected = paste0("panel", input$controller)
+#'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateTabsetPanel <- function(session, inputId, selected = NULL) {
@@ -204,10 +342,18 @@ updateNavlistPanel <- updateTabsetPanel
 #' @seealso \code{\link{numericInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
-#'   observe({
+#' ui <- fluidPage(
+#'   sliderInput("controller", "Controller", 0, 20, 10),
+#'   numericInput("inNumber", "Input number", 0),
+#'   numericInput("inNumber2", "Input number 2", 0)
+#' )
+#'
+#' server <- function(input, output, session) {
+#'
+#'   observeEvent(input$controller, {
 #'     # We'll use the input$controller variable multiple times, so save it as x
 #'     # for convenience.
 #'     x <- input$controller
@@ -218,7 +364,9 @@ updateNavlistPanel <- updateTabsetPanel
 #'       label = paste("Number label ", x),
 #'       value = x, min = x-10, max = x+10, step = 5)
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateNumericInput <- function(session, inputId, label = NULL, value = NULL,
@@ -309,11 +457,11 @@ updateInputOptions <- function(session, inputId, label = NULL, choices = NULL,
   if (!is.null(choices))
     choices <- choicesWithNames(choices)
   if (!is.null(selected))
-    selected <- validateSelected(selected, choices, inputId)
+    selected <- validateSelected(selected, choices, session$ns(inputId))
 
   options <- if (!is.null(choices)) {
     format(tagList(
-      generateOptions(inputId, choices, selected, inline, type = type)
+      generateOptions(session$ns(inputId), choices, selected, inline, type = type)
     ))
   }
 
@@ -330,31 +478,35 @@ updateInputOptions <- function(session, inputId, label = NULL, choices = NULL,
 #' @seealso \code{\link{checkboxGroupInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   p("The first checkbox group controls the second"),
+#'   checkboxGroupInput("inCheckboxGroup", "Input checkbox",
+#'     c("Item A", "Item B", "Item C")),
+#'   checkboxGroupInput("inCheckboxGroup2", "Input checkbox 2",
+#'     c("Item A", "Item B", "Item C"))
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # We'll use the input$controller variable multiple times, so save it as x
-#'     # for convenience.
-#'     x <- input$controller
+#'     x <- input$inCheckboxGroup
 #'
-#'     # Create a list of new options, where the name of the items is something
-#'     # like 'option label x 1', and the values are 'option-x-1'.
-#'     cb_options <- list()
-#'     cb_options[[sprintf("option label %d 1", x)]] <- sprintf("option-%d-1", x)
-#'     cb_options[[sprintf("option label %d 2", x)]] <- sprintf("option-%d-2", x)
-#'
-#'     # Change values for input$inCheckboxGroup
-#'     updateCheckboxGroupInput(session, "inCheckboxGroup", choices = cb_options)
+#'     # Can use character(0) to remove all choices
+#'     if (is.null(x))
+#'       x <- character(0)
 #'
 #'     # Can also set the label and select items
 #'     updateCheckboxGroupInput(session, "inCheckboxGroup2",
-#'       label = paste("checkboxgroup label", x),
-#'       choices = cb_options,
-#'       selected = sprintf("option-%d-2", x)
+#'       label = paste("Checkboxgroup label", length(x)),
+#'       choices = x,
+#'       selected = x
 #'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateCheckboxGroupInput <- function(session, inputId, label = NULL,
@@ -372,29 +524,31 @@ updateCheckboxGroupInput <- function(session, inputId, label = NULL,
 #' @seealso \code{\link{radioButtons}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   p("The first radio button group controls the second"),
+#'   radioButtons("inRadioButtons", "Input radio buttons",
+#'     c("Item A", "Item B", "Item C")),
+#'   radioButtons("inRadioButtons2", "Input radio buttons 2",
+#'     c("Item A", "Item B", "Item C"))
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # We'll use the input$controller variable multiple times, so save it as x
-#'     # for convenience.
-#'     x <- input$controller
+#'     x <- input$inRadioButtons
 #'
-#'     r_options <- list()
-#'     r_options[[sprintf("option label %d 1", x)]] <- sprintf("option-%d-1", x)
-#'     r_options[[sprintf("option label %d 2", x)]] <- sprintf("option-%d-2", x)
-#'
-#'     # Change values for input$inRadio
-#'     updateRadioButtons(session, "inRadio", choices = r_options)
-#'
-#'     # Can also set the label and select an item
-#'     updateRadioButtons(session, "inRadio2",
-#'       label = paste("Radio label", x),
-#'       choices = r_options,
-#'       selected = sprintf("option-%d-2", x)
+#'     # Can also set the label and select items
+#'     updateRadioButtons(session, "inRadioButtons2",
+#'       label = paste("radioButtons label", x),
+#'       choices = x,
+#'       selected = x
 #'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateRadioButtons <- function(session, inputId, label = NULL, choices = NULL,
@@ -413,32 +567,35 @@ updateRadioButtons <- function(session, inputId, label = NULL, choices = NULL,
 #' @seealso \code{\link{selectInput}}
 #'
 #' @examples
-#' \dontrun{
-#' shinyServer(function(input, output, session) {
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
 #'
+#' ui <- fluidPage(
+#'   p("The checkbox group controls the select input"),
+#'   checkboxGroupInput("inCheckboxGroup", "Input checkbox",
+#'     c("Item A", "Item B", "Item C")),
+#'   selectInput("inSelect", "Select input",
+#'     c("Item A", "Item B", "Item C"))
+#' )
+#'
+#' server <- function(input, output, session) {
 #'   observe({
-#'     # We'll use the input$controller variable multiple times, so save it as x
-#'     # for convenience.
-#'     x <- input$controller
+#'     x <- input$inCheckboxGroup
 #'
-#'     # Create a list of new options, where the name of the items is something
-#'     # like 'option label x 1', and the values are 'option-x-1'.
-#'     s_options <- list()
-#'     s_options[[sprintf("option label %d 1", x)]] <- sprintf("option-%d-1", x)
-#'     s_options[[sprintf("option label %d 2", x)]] <- sprintf("option-%d-2", x)
+#'     # Can use character(0) to remove all choices
+#'     if (is.null(x))
+#'       x <- character(0)
 #'
-#'     # Change values for input$inSelect
-#'     updateSelectInput(session, "inSelect", choices = s_options)
-#'
-#'     # Can also set the label and select an item (or more than one if it's a
-#'     # multi-select)
-#'     updateSelectInput(session, "inSelect2",
-#'       label = paste("Select label", x),
-#'       choices = s_options,
-#'       selected = sprintf("option-%d-2", x)
+#'     # Can also set the label and select items
+#'     updateSelectInput(session, "inSelect",
+#'       label = paste("Select input label", length(x)),
+#'       choices = x,
+#'       selected = tail(x, 1)
 #'     )
 #'   })
-#' })
+#' }
+#'
+#' shinyApp(ui, server)
 #' }
 #' @export
 updateSelectInput <- function(session, inputId, label = NULL, choices = NULL,
@@ -475,6 +632,7 @@ updateSelectizeInput <- function(session, inputId, label = NULL, choices = NULL,
     return(updateSelectInput(session, inputId, label, choices, selected))
   }
   value <- unname(selected)
+  attr(choices, 'selected_value') <- value
   message <- dropNulls(list(
     label = label,
     value = value,
@@ -492,6 +650,8 @@ selectizeJSON <- function(data, req) {
   key <- unique(strsplit(tolower(query$query), '\\s+')[[1]])
   if (identical(key, '')) key <- character(0)
   mop <- as.numeric(query$maxop)
+  vfd <- query$value  # the value field name
+  sel <- attr(data, 'selected_value', exact = TRUE)
 
   # convert a single vector to a data frame so it returns {label: , value: }
   # later in JSON; other objects return arbitrary JSON {x: , y: , foo: , ...}
@@ -515,6 +675,11 @@ selectizeJSON <- function(data, req) {
   }
   # only return the first n rows (n = maximum options in configuration)
   idx <- utils::head(if (length(key)) which(idx) else seq_along(idx), mop)
+  # make sure the selected value is in the data
+  if (length(sel)) {
+    i <- stats::na.omit(match(sel, data[, vfd]))
+    if (length(i)) idx <- sort(utils::head(unique(c(i, idx)), mop))
+  }
   data <- data[idx, ]
 
   res <- toJSON(columnToRowData(data))

R/utils.R

@@ -23,7 +23,6 @@ NULL
 #' rnormA(3)  # [1]  1.8285879 -0.7468041 -0.4639111
 #' rnormA(5)  # [1]  1.8285879 -0.7468041 -0.4639111 -1.6510126 -1.4686924
 #' rnormB(5)  # [1] -0.7946034  0.2568374 -0.6567597  1.2451387 -0.8375699
-#'
 #' @export
 repeatable <- function(rngfunc, seed = stats::runif(1, 0, .Machine$integer.max)) {
   force(seed)
@@ -155,6 +154,20 @@ dropNullsOrEmpty <- function(x) {
   x[!vapply(x, nullOrEmpty, FUN.VALUE=logical(1))]
 }
 
+# Given a vector/list, return TRUE if any elements are named, FALSE otherwise.
+anyNamed <- function(x) {
+  # Zero-length vector
+  if (length(x) == 0) return(FALSE)
+
+  nms <- names(x)
+
+  # List with no name attribute
+  if (is.null(nms)) return(FALSE)
+
+  # List with name attribute; check for any ""
+  any(nzchar(nms))
+}
+
 # Given a vector/list, return TRUE if any elements are unnamed, FALSE otherwise.
 anyUnnamed <- function(x) {
   # Zero-length vector
@@ -169,6 +182,21 @@ anyUnnamed <- function(x) {
   any(!nzchar(nms))
 }
 
+# Given two named vectors, join them together, and keep only the last element
+# with a given name in the resulting vector. If b has any elements with the same
+# name as elements in a, the element in a is dropped. Also, if there are any
+# duplicated names in a or b, only the last one with that name is kept.
+mergeVectors <- function(a, b) {
+  if (anyUnnamed(a) || anyUnnamed(b)) {
+    stop("Vectors must be either NULL or have names for all elements")
+  }
+
+  x <- c(a, b)
+  drop_idx <- duplicated(names(x), fromLast = TRUE)
+  x[!drop_idx]
+}
+
+
 # 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(...) {
@@ -211,6 +239,12 @@ find.file.ci <- function(...) {
   return(matches[1])
 }
 
+# The function base::dir.exists was added in R 3.2.0, but for backward
+# compatibility we need to add this function
+dirExists <- function(paths) {
+  file.exists(paths) & file.info(paths)$isdir
+}
+
 # Attempt to join a path and relative path, and turn the result into a
 # (normalized) absolute path. The result will only be returned if it is an
 # existing file/directory and is a descendant of dir.
@@ -248,23 +282,49 @@ download <- function(url, ...) {
   # First, check protocol. If http or https, check platform:
   if (grepl('^https?://', url)) {
 
-    # If Windows, call setInternet2, then use download.file with defaults.
-    if (isWindows()) {
-      # If we directly use setInternet2, R CMD CHECK gives a Note on Mac/Linux
-      mySI2 <- `::`(utils, 'setInternet2')
-      # Store initial settings
-      internet2_start <- mySI2(NA)
-      on.exit(mySI2(internet2_start))
+    # Check whether we are running R 3.2
+    isR32 <- getRversion() >= "3.2"
 
-      # Needed for https
-      mySI2(TRUE)
-      utils::download.file(url, ...)
+    # Windows
+    if (.Platform$OS.type == "windows") {
+
+      if (isR32) {
+        method <- "wininet"
+      } else {
+
+        # If we directly use setInternet2, R CMD CHECK gives a Note on Mac/Linux
+        seti2 <- `::`(utils, 'setInternet2')
+
+        # Check whether we are already using internet2 for internal
+        internet2_start <- seti2(NA)
+
+        # If not then temporarily set it
+        if (!internet2_start) {
+          # Store initial settings, and restore on exit
+          on.exit(suppressWarnings(seti2(internet2_start)))
+
+          # Needed for https. Will get warning if setInternet2(FALSE) already run
+          # and internet routines are used. But the warnings don't seem to matter.
+          suppressWarnings(seti2(TRUE))
+        }
+
+        method <- "internal"
+      }
+
+      # download.file will complain about file size with something like:
+      #       Warning message:
+      #         In download.file(url, ...) : downloaded length 19457 != reported length 200
+      # because apparently it compares the length with the status code returned (?)
+      # so we supress that
+      suppressWarnings(utils::download.file(url, method = method, ...))
 
     } else {
-      # If non-Windows, check for curl/wget/lynx, then call download.file with
+      # If non-Windows, check for libcurl/curl/wget/lynx, then call download.file with
       # appropriate method.
 
-      if (nzchar(Sys.which("wget")[1])) {
+      if (isR32 && capabilities("libcurl")) {
+        method <- "libcurl"
+      } else if (nzchar(Sys.which("wget")[1])) {
         method <- "wget"
       } else if (nzchar(Sys.which("curl")[1])) {
         method <- "curl"
@@ -317,8 +377,6 @@ makeFunction <- function(args = pairlist(), body, env = parent.frame()) {
 #' @param env The desired environment for the function. Defaults to the
 #'   calling environment two steps back.
 #' @param quoted Is the expression quoted?
-#' @param caller_offset If specified, the offset in the callstack of the
-#'   functiont to be treated as the caller.
 #'
 #' @examples
 #' # Example of a new renderer, similar to renderText
@@ -352,35 +410,14 @@ makeFunction <- function(args = pairlist(), body, env = parent.frame()) {
 #'
 #' isolate(tripleA())
 #' # "text, text, text"
-#'
 #' @export
-exprToFunction <- function(expr, env=parent.frame(2), quoted=FALSE,
-                           caller_offset=1) {
-  # Get the quoted expr from two calls back
-  expr_sub <- eval(substitute(substitute(expr)), parent.frame(caller_offset))
-
-  # Check if expr is a function, making sure not to evaluate expr, in case it
-  # is actually an unquoted expression.
-  # If expr is a single token, then indexing with [[ will error; if it has multiple
-  # tokens, then [[ works. In the former case it will be a name object; in the
-  # latter, it will be a language object.
-  if (!is.null(expr_sub) && !is.name(expr_sub) && expr_sub[[1]] == as.name('function')) {
-    # Get name of function that called this function
-    called_fun <- sys.call(-1 * caller_offset)[[1]]
-
-    shinyDeprecated(msg = paste("Passing functions to '", called_fun,
-      "' is deprecated. Please use expressions instead. See ?", called_fun,
-      " for more information.", sep=""))
-    return(expr)
+exprToFunction <- function(expr, env=parent.frame(), quoted=FALSE) {
+  if (!quoted) {
+    expr <- eval(substitute(substitute(expr)), parent.frame())
   }
 
-  if (quoted) {
-    # expr is a quoted expression
-    makeFunction(body=expr, env=env)
-  } else {
-    # expr is an unquoted expression
-    makeFunction(body=expr_sub, env=env)
-  }
+  # expr is a quoted expression
+  makeFunction(body=expr, env=env)
 }
 
 #' Install an expression as a function
@@ -404,15 +441,32 @@ exprToFunction <- function(expr, env=parent.frame(2), quoted=FALSE,
 #' @param assign.env The environment in which the function should be assigned.
 #' @param label A label for the object to be shown in the debugger. Defaults to
 #'   the name of the calling function.
-#'
+#' @param wrappedWithLabel,..stacktraceon Advanced use only. For stack manipulation purposes; see
+#'   \code{\link{stacktrace}}.
 #' @export
 installExprFunction <- function(expr, name, eval.env = parent.frame(2),
                                 quoted = FALSE,
                                 assign.env = parent.frame(1),
-                                label = as.character(sys.call(-1)[[1]])) {
-  func <- exprToFunction(expr, eval.env, quoted, 2)
+                                label = deparse(sys.call(-1)[[1]]),
+                                wrappedWithLabel = TRUE,
+                                ..stacktraceon = FALSE) {
+  if (!quoted) {
+    quoted <- TRUE
+    expr <- eval(substitute(substitute(expr)), parent.frame())
+  }
+
+  func <- exprToFunction(expr, eval.env, quoted)
+  if (length(label) > 1) {
+    # Just in case the deparsed code is more complicated than we imagine. If we
+    # have a label with length > 1 it causes warnings in wrapFunctionLabel.
+    label <- paste0(label, collapse = "\n")
+  }
+  if (wrappedWithLabel) {
+    func <- wrapFunctionLabel(func, label, ..stacktraceon = ..stacktraceon)
+  } else {
+    registerDebugHook(name, assign.env, label)
+  }
   assign(name, func, envir = assign.env)
-  registerDebugHook(name, assign.env, label)
 }
 
 #' Parse a GET query string from a URL
@@ -432,7 +486,7 @@ installExprFunction <- function(expr, name, eval.env = parent.frame(2),
 #'
 #' \dontrun{
 #' # Example of usage within a Shiny app
-#' shinyServer(function(input, output, session) {
+#' function(input, output, session) {
 #'
 #'   output$queryText <- renderText({
 #'     query <- parseQueryString(session$clientData$url_search)
@@ -448,7 +502,7 @@ installExprFunction <- function(expr, name, eval.env = parent.frame(2),
 #'     # Return a string with key-value pairs
 #'     paste(names(query), query, sep = "=", collapse=", ")
 #'   })
-#' })
+#' }
 #' }
 #'
 parseQueryString <- function(str, nested = FALSE) {
@@ -460,6 +514,8 @@ parseQueryString <- function(str, nested = FALSE) {
     str <- substr(str, 2, nchar(str))
 
   pairs <- strsplit(str, '&', fixed = TRUE)[[1]]
+  # Drop any empty items (if there's leading/trailing/consecutive '&' chars)
+  pairs <- pairs[pairs != ""]
   pairs <- strsplit(pairs, '=', fixed = TRUE)
 
   keys   <- vapply(pairs, function(x) x[1], FUN.VALUE = character(1))
@@ -498,11 +554,18 @@ assignNestedList <- function(x = list(), idx, value) {
 
 # decide what to do in case of errors; it is customizable using the shiny.error
 # option (e.g. we can set options(shiny.error = recover))
+#' @include conditions.R
 shinyCallingHandlers <- function(expr) {
-  withCallingHandlers(expr, error = function(e) {
-    handle <- getOption('shiny.error')
-    if (is.function(handle)) handle()
-  })
+  withCallingHandlers(captureStackTraces(expr),
+    error = function(e) {
+      # Don't intercept shiny.silent.error (i.e. validation errors)
+      if (inherits(e, "shiny.silent.error"))
+        return()
+
+      handle <- getOption('shiny.error')
+      if (is.function(handle)) handle()
+    }
+  )
 }
 
 #' Print message for deprecated functions in Shiny
@@ -568,7 +631,10 @@ Callbacks <- R6Class(
     .callbacks = 'Map',
 
     initialize = function() {
-      .nextId <<- as.integer(.Machine$integer.max)
+      # NOTE: we avoid using '.Machine$integer.max' directly
+      # as R 3.3.0's 'radixsort' could segfault when sorting
+      # an integer vector containing this value
+      .nextId <<- as.integer(.Machine$integer.max - 1L)
       .callbacks <<- Map$new()
     },
     register = function(callback) {
@@ -579,16 +645,28 @@ Callbacks <- R6Class(
         .callbacks$remove(id)
       })
     },
-    invoke = function(..., onError=NULL) {
+    invoke = function(..., onError=NULL, ..stacktraceon = FALSE) {
       # Ensure that calls are invoked in the order that they were registered
       keys <- as.character(sort(as.integer(.callbacks$keys()), decreasing = TRUE))
       callbacks <- .callbacks$mget(keys)
 
       for (callback in callbacks) {
         if (is.null(onError)) {
-          callback(...)
+          if (..stacktraceon) {
+            ..stacktraceon..(callback(...))
+          } else {
+            callback(...)
+          }
         } else {
-          tryCatch(callback(...), error = onError)
+          tryCatch(
+            captureStackTraces(
+              if (..stacktraceon)
+                ..stacktraceon..(callback(...))
+              else
+                callback(...)
+            ),
+            error = onError
+          )
         }
       }
     },
@@ -606,6 +684,21 @@ dataTablesJSON <- function(data, req) {
   q <- parseQueryString(params, nested = TRUE)
   ci <- q$search[['caseInsensitive']] == 'true'
 
+  # data may have been replaced/updated in the new table while the Ajax request
+  # from the previous table is still on its way, so it is possible that the old
+  # request asks for more columns than the current data, in which case we should
+  # discard this request and return empty data; the next Ajax request from the
+  # new table will retrieve the correct number of columns of data
+  if (length(q$columns) != ncol(data)) {
+    res <- toJSON(list(
+      draw = as.integer(q$draw),
+      recordsTotal = n,
+      recordsFiltered = 0,
+      data = NULL
+    ))
+    return(httpResponse(200, 'application/json', enc2utf8(res)))
+  }
+
   # global searching
   i <- seq_len(n)
   if (length(q$search[['value']]) && q$search[['value']] != '') {
@@ -806,6 +899,143 @@ columnToRowData <- function(data) {
   )
 }
 
+#' Declare an error safe for the user to see
+#'
+#' This should be used when you want to let the user see an error
+#' message even if the default is to sanitize all errors. If you have an
+#' error \code{e} and call \code{stop(safeError(e))}, then Shiny will
+#' ignore the value of \code{getOption("shiny.sanitize.errors")} and always
+#' display the error in the app itself.
+#'
+#' @param error Either an "error" object or a "character" object (string).
+#' In the latter case, the string will become the message of the error
+#' returned by \code{safeError}.
+#'
+#' @return An "error" object
+#'
+#' @details An error generated by \code{safeError} has priority over all
+#' other Shiny errors. This can be dangerous. For example, if you have set
+#' \code{options(shiny.sanitize.errors = TRUE)}, then by default all error
+#' messages are omitted in the app, and replaced by a generic error message.
+#' However, this does not apply to \code{safeError}: whatever you pass
+#' through \code{error} will be displayed to the user. So, this should only
+#' be used when you are sure that your error message does not contain any
+#' sensitive information. In those situations, \code{safeError} can make
+#' your users' lives much easier by giving them a hint as to where the
+#' error occurred.
+#'
+#' @seealso \code{\link{shiny-options}}
+#'
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' # uncomment the desired line to experiment with shiny.sanitize.errors
+#' # options(shiny.sanitize.errors = TRUE)
+#' # options(shiny.sanitize.errors = FALSE)
+#'
+#' # Define UI
+#' ui <- fluidPage(
+#'   textInput('number', 'Enter your favorite number from 1 to 10', '5'),
+#'   textOutput('normalError'),
+#'   textOutput('safeError')
+#' )
+#'
+#' # Server logic
+#' server <- function(input, output) {
+#'   output$normalError <- renderText({
+#'     number <- input$number
+#'     if (number %in% 1:10) {
+#'       return(paste('You chose', number, '!'))
+#'     } else {
+#'       stop(
+#'         paste(number, 'is not a number between 1 and 10')
+#'       )
+#'     }
+#'   })
+#'   output$safeError <- renderText({
+#'     number <- input$number
+#'     if (number %in% 1:10) {
+#'       return(paste('You chose', number, '!'))
+#'     } else {
+#'       stop(safeError(
+#'         paste(number, 'is not a number between 1 and 10')
+#'       ))
+#'     }
+#'   })
+#' }
+#'
+#' # Complete app with UI and server components
+#' shinyApp(ui, server)
+#' }
+#' @export
+safeError <- function(error) {
+  if (inherits(error, "character")) {
+    error <- simpleError(error)
+  }
+  if (!inherits(error, "error")) {
+    stop("The class of the `error` parameter must be either 'error' or 'character'")
+  }
+  class(error) <- c("shiny.custom.error", class(error))
+  error
+}
+
+#***********************************************************************#
+#**** Keep this function internal for now, may chnage in the future ****#
+#***********************************************************************#
+# #' Propagate an error through Shiny, but catch it before it throws
+# #'
+# #' Throws a type of exception that is caught by observers. When such an
+# #' exception is triggered, all reactive links are broken. So, essentially,
+# #' \code{reactiveStop()} behaves just like \code{stop()}, except that
+# #' instead of ending the session, it is silently swalowed by Shiny.
+# #'
+# #' This function should be used when you want to disrupt the reactive
+# #' links in a reactive chain, but do not want to end the session. For
+# #' example, this enables you to disallow certain inputs, but get back
+# #' to business as usual when valid inputs are re-entered.
+# #' \code{reactiveStop} is also called internally by Shiny to create
+# #' special errors, such as the ones generated by \code{\link{validate}()},
+# #' \code{\link{req}()} and \code{\link{cancelOutput}()}.
+# #'
+# #' @param message An optional error message.
+# #' @param class An optional class to add to the error.
+# #' @export
+# #' @examples
+# #' ## Note: the breaking of the reactive chain that happens in the app
+# #' ## below (when input$txt = 'bad' and input$allowBad = 'FALSE') is
+# #' ## easily visualized with `showReactLog()`
+# #'
+# #' ## Only run examples in interactive R sessions
+# #' if (interactive()) {
+# #'
+# #' ui <- fluidPage(
+# #'   textInput('txt', 'Enter some text...'),
+# #'   selectInput('allowBad', 'Allow the string \'bad\'?',
+# #'               c('TRUE', 'FALSE'), selected = 'FALSE')
+# #' )
+# #'
+# #' server <- function(input, output) {
+# #'   val <- reactive({
+# #'     if (!(as.logical(input$allowBad))) {
+# #'       if (identical(input$txt, "bad")) {
+# #'         reactiveStop()
+# #'       }
+# #'     }
+## '   })
+# #'
+# #'   observe({
+# #'     val()
+# #'   })
+# #' }
+# #'
+# #' shinyApp(ui, server)
+# #' }
+# #' @export
+reactiveStop <- function(message = "", class = NULL) {
+  stopWithCondition(c("shiny.silent.error", class), message)
+}
+
 #' Validate input values and other conditions
 #'
 #' For an output rendering function (e.g. \code{\link{renderPlot}()}), you may
@@ -862,15 +1092,16 @@ columnToRowData <- function(data) {
 #'   \code{shiny-output-error-} prepended to this value.
 #' @export
 #' @examples
-#' # in ui.R
-#' fluidPage(
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'
+#' ui <- fluidPage(
 #'   checkboxGroupInput('in1', 'Check some letters', choices = head(LETTERS)),
 #'   selectizeInput('in2', 'Select a state', choices = state.name),
 #'   plotOutput('plot')
 #' )
 #'
-#' # in server.R
-#' function(input, output) {
+#' server <- function(input, output) {
 #'   output$plot <- renderPlot({
 #'     validate(
 #'       need(input$in1, 'Check at least one letter!'),
@@ -879,6 +1110,10 @@ columnToRowData <- function(data) {
 #'     plot(1:10, main = paste(c(input$in1, input$in2), collapse = ', '))
 #'   })
 #' }
+#'
+#' shinyApp(ui, server)
+#'
+#' }
 validate <- function(..., errorClass = character(0)) {
   results <- sapply(list(...), function(x) {
     # Detect NULL or NA
@@ -899,8 +1134,7 @@ validate <- function(..., errorClass = character(0)) {
   # There may be empty strings remaining; these are message-less failures that
   # started as FALSE
   results <- results[nzchar(results)]
-
-  stopWithCondition(c("validation", errorClass), paste(results, collapse="\n"))
+  reactiveStop(paste(results, collapse="\n"), c(errorClass, "validation"))
 }
 
 #' @param expr An expression to test. The condition will pass if the expression
@@ -923,6 +1157,202 @@ need <- function(expr, message = paste(label, "must be provided"), label) {
     return(invisible(NULL))
 }
 
+#' Check for required values
+#'
+#' Ensure that values are available ("truthy"--see Details) before proceeding
+#' with a calculation or action. If any of the given values is not truthy, the
+#' operation is stopped by raising a "silent" exception (not logged by Shiny,
+#' nor displayed in the Shiny app's UI).
+#'
+#' The \code{req} function was designed to be used in one of two ways. The first
+#' is to call it like a statement (ignoring its return value) before attempting
+#' operations using the required values:
+#'
+#' \preformatted{rv <- reactiveValues(state = FALSE)
+#' r <- reactive({
+#'   req(input$a, input$b, rv$state)
+#'   # Code that uses input$a, input$b, and/or rv$state...
+#' })}
+#'
+#' In this example, if \code{r()} is called and any of \code{input$a},
+#' \code{input$b}, and \code{rv$state} are \code{NULL}, \code{FALSE}, \code{""},
+#' etc., then the \code{req} call will trigger an error that propagates all the
+#' way up to whatever render block or observer is executing.
+#'
+#' The second is to use it to wrap an expression that must be truthy:
+#'
+#' \preformatted{output$plot <- renderPlot({
+#'   if (req(input$plotType) == "histogram") {
+#'     hist(dataset())
+#'   } else if (input$plotType == "scatter") {
+#'     qplot(dataset(), aes(x = x, y = y))
+#'   }
+#' })}
+#'
+#' In this example, \code{req(input$plotType)} first checks that
+#' \code{input$plotType} is truthy, and if so, returns it. This is a convenient
+#' way to check for a value "inline" with its first use.
+#'
+#' \strong{Truthy and falsy values}
+#'
+#' The terms "truthy" and "falsy" generally indicate whether a value, when
+#' coerced to a \code{\link{logical}}, is \code{TRUE} or \code{FALSE}. We use
+#' the term a little loosely here; our usage tries to match the intuitive
+#' notions of "Is this value missing or available?", or "Has the user provided
+#' an answer?", or in the case of action buttons, "Has the button been
+#' clicked?".
+#'
+#' For example, a \code{textInput} that has not been filled out by the user has
+#' a value of \code{""}, so that is considered a falsy value.
+#'
+#' To be precise, \code{req} considers a value truthy \emph{unless} it is one
+#' of:
+#'
+#' \itemize{
+#'   \item{\code{FALSE}}
+#'   \item{\code{NULL}}
+#'   \item{\code{""}}
+#'   \item{An empty atomic vector}
+#'   \item{An atomic vector that contains only missing values}
+#'   \item{A logical vector that contains all \code{FALSE} or missing values}
+#'   \item{An object of class \code{"try-error"}}
+#'   \item{A value that represents an unclicked \code{\link{actionButton}}}
+#' }
+#'
+#' Note in particular that the value \code{0} is considered truthy, even though
+#' \code{as.logical(0)} is \code{FALSE}.
+#'
+#' If the built-in rules for truthiness do not match your requirements, you can
+#' always work around them. Since \code{FALSE} is falsy, you can simply provide
+#' the results of your own checks to \code{req}:
+#'
+#' \code{req(input$a != 0)}
+#'
+#' \strong{Using \code{req(FALSE)}}
+#'
+#' You can use \code{req(FALSE)} (i.e. no condition) if you've already performed
+#' all the checks you needed to by that point and just want to stop the reactive
+#' chain now. There is no advantange to this, except perhaps ease of readibility
+#' if you have a complicated condition to check for (or perhaps if you'd like to
+#' divide your condition into nested \code{if} statements).
+#'
+#' \strong{Using \code{cancelOutput = TRUE}}
+#'
+#' When \code{req(..., cancelOutput = TRUE)} is used, the "silent" exception is
+#' also raised, but it is treated slightly differently if one or more outputs are
+#' currently being evaluated. In those cases, the reactive chain does not proceed
+#' or update, but the output(s) are left is whatever state they happen to be in
+#' (whatever was their last valid state).
+#'
+#' Note that this is always going to be the case if
+#' this is used inside an output context (e.g. \code{output$txt <- ...}). It may
+#' or may not be the case if it is used inside a non-output context (e.g.
+#' \code{\link{reactive}}, \code{\link{observe}} or \code{\link{observeEvent}})
+#' -- depending on whether or not there is an \code{output$...} that is triggered
+#' as a result of those calls. See the examples below for concrete scenarios.
+#'
+#' @param ... Values to check for truthiness.
+#' @param cancelOutput If \code{TRUE} and an output is being evaluated, stop
+#'   processing as usual but instead of clearing the output, leave it in
+#'   whatever state it happens to be in.
+#' @param x An expression whose truthiness value we want to determine
+#' @return The first value that was passed in.
+#' @export
+#' @examples
+#' ## Only run examples in interactive R sessions
+#' if (interactive()) {
+#'   ui <- fluidPage(
+#'     textInput('data', 'Enter a dataset from the "datasets" package', 'cars'),
+#'     p('(E.g. "cars", "mtcars", "pressure", "faithful")'), hr(),
+#'     tableOutput('tbl')
+#'   )
+#'
+#'   server <- function(input, output) {
+#'     output$tbl <- renderTable({
+#'
+#'       ## to require that the user types something, use: `req(input$data)`
+#'       ## but better: require that input$data is valid and leave the last
+#'       ## valid table up
+#'       req(exists(input$data, "package:datasets", inherits = FALSE),
+#'           cancelOutput = TRUE)
+#'
+#'       head(get(input$data, "package:datasets", inherits = FALSE))
+#'     })
+#'   }
+#'
+#'   shinyApp(ui, server)
+#' }
+req <- function(..., cancelOutput = FALSE) {
+  dotloop(function(item) {
+    if (!isTruthy(item)) {
+      if (isTRUE(cancelOutput)) {
+        cancelOutput()
+      } else {
+        reactiveStop(class = "validation")
+      }
+    }
+  }, ...)
+
+  if (!missing(..1))
+    ..1
+  else
+    invisible()
+}
+
+#***********************************************************************#
+#**** Keep this function internal for now, may chnage in the future ****#
+#***********************************************************************#
+# #' Cancel processing of the current output
+# #'
+# #' Signals an error that Shiny treats specially if an output is currently being
+# #' evaluated. Execution will stop, but rather than clearing the output (as
+# #' \code{\link{req}} does) or showing an error message (as \code{\link{stop}}
+# #' does), the output simply remains unchanged.
+# #'
+# #' If \code{cancelOutput} is called in any non-output context (like in an
+# #' \code{\link{observe}} or \code{\link{observeEvent}}), the effect is the same
+# #' as \code{\link{req}(FALSE)}.
+# #' @export
+# #' @examples
+# #' ## Only run examples in interactive R sessions
+# #' if (interactive()) {
+# #'
+# #' # uncomment the desired line to experiment with cancelOutput() vs. req()
+# #'
+# #' ui <- fluidPage(
+# #'   textInput('txt', 'Enter text'),
+# #'   textOutput('check')
+# #' )
+# #'
+# #' server <- function(input, output) {
+# #'   output$check <- renderText({
+# #'     # req(input$txt)
+# #'     if (input$txt == 'hi') return('hi')
+# #'     else if (input$txt == 'bye') return('bye')
+# #'     # else cancelOutput()
+# #'   })
+# #' }
+# #'
+# #' shinyApp(ui, server)
+# #' }
+cancelOutput <- function() {
+  reactiveStop(class = "shiny.output.cancel")
+}
+
+# Execute a function against each element of ..., but only evaluate each element
+# after the previous element has been passed to fun_. The return value of fun_
+# is discarded, and only invisible() is returned from dotloop.
+#
+# Can be used to facilitate short-circuit eval on dots.
+dotloop <- function(fun_, ...) {
+  for (i in 1:(nargs()-1)) {
+    fun_(eval(as.symbol(paste0("..", i))))
+  }
+  invisible()
+}
+
+#' @export
+#' @rdname req
 isTruthy <- function(x) {
   if (inherits(x, 'try-error'))
     return(FALSE)
@@ -951,7 +1381,7 @@ isTruthy <- function(x) {
 stopWithCondition <- function(class, message) {
   cond <- structure(
     list(message = message),
-    class = c(class, 'shiny.silent.error', 'error', 'condition')
+    class = c(class, 'error', 'condition')
   )
   stop(cond)
 }
@@ -1002,6 +1432,10 @@ checkEncoding <- function(file) {
             'http://shiny.rstudio.com/articles/unicode.html for more info.')
     return('UTF-8-BOM')
   }
+  x <- readChar(file, size, useBytes = TRUE)
+  if (is.na(iconv(x, 'UTF-8', 'UTF-8'))) {
+    warning('The input file ', file, ' does not seem to be encoded in UTF8')
+  }
   'UTF-8'
 }
 
@@ -1027,19 +1461,38 @@ sourceUTF8 <- function(file, envir = globalenv()) {
   enc <- if (any(Encoding(lines) == 'UTF-8')) 'UTF-8' else 'unknown'
   src <- srcfilecopy(file, lines, isFile = TRUE)  # source reference info
   # oddly, parse(file) does not work when file contains multibyte chars that
-  # **can** be encoded natively on Windows (might be a bug in base R); we fall
-  # back to parse(text) in this case
-  exprs <- tryCatch(
-    parse(file, keep.source = FALSE, srcfile = src, encoding = enc),
-    error = function(e) {
-      parse(text = lines, keep.source = FALSE, srcfile = src, encoding = enc)
-    }
-  )
+  # **can** be encoded natively on Windows (might be a bug in base R); we
+  # rewrite the source code in a natively encoded temp file and parse it in this
+  # case (the source reference is still pointed to the original file, though)
+  if (isWindows() && enc == 'unknown') {
+    file <- tempfile(); on.exit(unlink(file), add = TRUE)
+    writeLines(lines, file)
+  }
+  exprs <- try(parse(file, keep.source = FALSE, srcfile = src, encoding = enc))
+  if (inherits(exprs, "try-error")) {
+    diagnoseCode(file)
+    stop("Error sourcing ", file)
+  }
+
+  # Wrap the exprs in first `{`, then ..stacktraceon..(). It's only really the
+  # ..stacktraceon..() that we care about, but the `{` is needed to make that
+  # possible.
+  exprs <- makeCall(`{`, exprs)
+  # Need to wrap exprs in a list because we want it treated as a single argument
+  exprs <- makeCall(..stacktraceon.., list(exprs))
+
   eval(exprs, envir)
 }
 
+# @param func Name of function, in unquoted form
+# @param args An evaluated list of unevaluated argument expressions
+makeCall <- function(func, args) {
+  as.call(c(list(substitute(func)), args))
+}
+
 # a workaround for https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16264
-if (getRversion() <= '3.2.2') srcfilecopy <- function(filename, lines, ...) {
+srcfilecopy <- function(filename, lines, ...) {
+  if (getRversion() > '3.2.2') return(base::srcfilecopy(filename, lines, ...))
   src <- base::srcfilecopy(filename, lines = '', ...)
   src$lines <- lines
   src
@@ -1062,20 +1515,38 @@ URLencode <- function(value, reserved = FALSE) {
 # function which calls the original function using the specified name. This can
 # be helpful for profiling, because the specified name will show up on the stack
 # trace.
-wrapFunctionLabel <- function(func, name) {
+wrapFunctionLabel <- function(func, name, ..stacktraceon = FALSE) {
   if (name == "name" || name == "func" || name == "relabelWrapper") {
     stop("Invalid name for wrapFunctionLabel: ", name)
   }
   assign(name, func, environment())
+  registerDebugHook(name, environment(), name)
 
   relabelWrapper <- eval(substitute(
     function(...) {
       # This `f` gets renamed to the value of `name`. Note that it may not
       # print as the new name, because of source refs stored in the function.
-      f(...)
+      if (..stacktraceon)
+        ..stacktraceon..(f(...))
+      else
+        f(...)
     },
     list(f = as.name(name))
   ))
 
   relabelWrapper
 }
+
+
+# This is a very simple mutable object which only stores one value
+# (which we can set and get). Using this class is sometimes useful
+# when communicating persistent changes across functions.
+Mutable <- R6Class("Mutable",
+  private = list(
+    value = NULL
+  ),
+  public = list(
+    set = function(value) { private$value <- value },
+    get = function() { private$value }
+  )
+)

README.md

@@ -1,6 +1,8 @@
 # Shiny
 
-[![Build Status](https://travis-ci.org/rstudio/shiny.svg?branch=master)](https://travis-ci.org/rstudio/shiny)
+*Travis:* [![Travis Build Status](https://travis-ci.org/rstudio/shiny.svg?branch=master)](https://travis-ci.org/rstudio/shiny)
+
+*AppVeyor:* [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/rstudio/shiny?branch=master&svg=true)](https://ci.appveyor.com/project/rstudio/shiny)
 
 Shiny is a new package from RStudio that makes it incredibly easy to build interactive web applications with R.
 

appveyor.yml

@@ -0,0 +1,45 @@
+# DO NOT CHANGE the "init" and "install" sections below
+
+# Download script file from GitHub
+init:
+  ps: |
+        $ErrorActionPreference = "Stop"
+        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
+        Import-Module '..\appveyor-tool.ps1'
+
+install:
+  ps: Bootstrap
+
+cache:
+  - C:\RLibrary
+
+# Adapt as necessary starting from here
+
+build_script:
+  - travis-tool.sh install_deps
+
+test_script:
+  - travis-tool.sh run_tests
+
+on_failure:
+  - 7z a failure.zip *.Rcheck\*
+  - appveyor PushArtifact failure.zip
+
+artifacts:
+  - path: '*.Rcheck\**\*.log'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.out'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.fail'
+    name: Logs
+
+  - path: '*.Rcheck\**\*.Rout'
+    name: Logs
+
+  - path: '\*_*.tar.gz'
+    name: Bits
+
+  - path: '\*_*.zip'
+    name: Bits

inst/examples/01_hello/rsconnect/localhost/admin/01_hello.dcf

@@ -1,6 +0,0 @@
-name: 01_hello
-account: admin
-server: localhost
-bundleId: 1
-url: http://localhost:3939/admin/01_hello/
-when: 1436550957.65385

inst/examples/01_hello/server.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define server logic required to draw a histogram
-shinyServer(function(input, output) {
+function(input, output) {
 
   # Expression that generates a histogram. The expression is
   # wrapped in a call to renderPlot to indicate that:
@@ -18,4 +18,4 @@ shinyServer(function(input, output) {
     hist(x, breaks = bins, col = 'darkgray', border = 'white')
   })
 
-})
+}

inst/examples/01_hello/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for application that draws a histogram
-shinyUI(fluidPage(
+fluidPage(
 
   # Application title
   titlePanel("Hello Shiny!"),
@@ -21,4 +21,4 @@ shinyUI(fluidPage(
       plotOutput("distPlot")
     )
   )
-))
+)

inst/examples/02_text/server.R

@@ -3,7 +3,7 @@ library(datasets)
 
 # Define server logic required to summarize and view the selected
 # dataset
-shinyServer(function(input, output) {
+function(input, output) {
   
   # Return the requested dataset
   datasetInput <- reactive({
@@ -23,4 +23,4 @@ shinyServer(function(input, output) {
   output$view <- renderTable({
     head(datasetInput(), n = input$obs)
   })
-})
+}

inst/examples/02_text/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for dataset viewer application
-shinyUI(fluidPage(
+fluidPage(
   
   # Application title
   titlePanel("Shiny Text"),
@@ -24,4 +24,4 @@ shinyUI(fluidPage(
       tableOutput("view")
     )
   )
-))
+)

inst/examples/03_reactivity/server.R

@@ -3,7 +3,7 @@ library(datasets)
 
 # Define server logic required to summarize and view the selected
 # dataset
-shinyServer(function(input, output) {
+function(input, output) {
 
   # By declaring datasetInput as a reactive expression we ensure 
   # that:
@@ -50,4 +50,4 @@ shinyServer(function(input, output) {
   output$view <- renderTable({
     head(datasetInput(), n = input$obs)
   })
-})
+}

inst/examples/03_reactivity/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for dataset viewer application
-shinyUI(fluidPage(
+fluidPage(
   
   # Application title
   titlePanel("Reactivity"),
@@ -31,4 +31,4 @@ shinyUI(fluidPage(
       tableOutput("view")
     )
   )
-))
+)

inst/examples/04_mpg/server.R

@@ -11,7 +11,7 @@ mpgData$am <- factor(mpgData$am, labels = c("Automatic", "Manual"))
 
 # Define server logic required to plot various variables against
 # mpg
-shinyServer(function(input, output) {
+function(input, output) {
 
   # Compute the formula text in a reactive expression since it is
   # shared by the output$caption and output$mpgPlot functions
@@ -31,4 +31,4 @@ shinyServer(function(input, output) {
             data = mpgData,
             outline = input$outliers)
   })
-})
+}

inst/examples/04_mpg/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for miles per gallon application
-shinyUI(fluidPage(
+fluidPage(
   
   # Application title
   titlePanel("Miles Per Gallon"),
@@ -26,4 +26,4 @@ shinyUI(fluidPage(
       plotOutput("mpgPlot")
     )
   )
-))
+)

inst/examples/05_sliders/server.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define server logic for slider examples
-shinyServer(function(input, output) {
+function(input, output) {
   
   # Reactive expression to compose a data frame containing all of
   # the values
@@ -26,4 +26,4 @@ shinyServer(function(input, output) {
   output$values <- renderTable({
     sliderValues()
   })
-})
+}

inst/examples/05_sliders/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for slider demo application
-shinyUI(fluidPage(
+fluidPage(
 
   #  Application title
   titlePanel("Sliders"),
@@ -40,4 +40,4 @@ shinyUI(fluidPage(
       tableOutput("values")
     )
   )
-))
+)

inst/examples/06_tabsets/server.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define server logic for random distribution application
-shinyServer(function(input, output) {
+function(input, output) {
   
   # Reactive expression to generate the requested distribution.
   # This is called whenever the inputs change. The output
@@ -41,4 +41,4 @@ shinyServer(function(input, output) {
     data.frame(x=data())
   })
   
-})
+}

inst/examples/06_tabsets/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for random distribution application 
-shinyUI(fluidPage(
+fluidPage(
     
   # Application title
   titlePanel("Tabsets"),
@@ -35,4 +35,4 @@ shinyUI(fluidPage(
       )
     )
   )
-))
+)

inst/examples/07_widgets/server.R

@@ -3,7 +3,7 @@ library(datasets)
 
 # Define server logic required to summarize and view the 
 # selected dataset
-shinyServer(function(input, output) {
+function(input, output) {
   
   # Return the requested dataset
   datasetInput <- reactive({
@@ -23,4 +23,4 @@ shinyServer(function(input, output) {
   output$view <- renderTable({
     head(datasetInput(), n = input$obs)
   })
-})
+}

inst/examples/07_widgets/ui.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define UI for dataset viewer application
-shinyUI(fluidPage(
+fluidPage(
   
   # Application title.
   titlePanel("More Widgets"),
@@ -40,4 +40,4 @@ shinyUI(fluidPage(
       tableOutput("view")
     )
   )
-))
+)

inst/examples/08_html/server.R

@@ -1,7 +1,7 @@
 library(shiny)
 
 # Define server logic for random distribution application
-shinyServer(function(input, output) {
+function(input, output) {
   
   # Reactive expression to generate the requested distribution. This is 
   # called whenever the inputs change. The output expressions defined 
@@ -39,4 +39,4 @@ shinyServer(function(input, output) {
     data.frame(x=data())
   })
   
-})
+}

inst/examples/09_upload/server.R

@@ -1,6 +1,6 @@
 library(shiny)
 
-shinyServer(function(input, output) {
+function(input, output) {
   output$contents <- renderTable({
     
     # input$file1 will be NULL initially. After the user selects
@@ -17,4 +17,4 @@ shinyServer(function(input, output) {
     read.csv(inFile$datapath, header=input$header, sep=input$sep, 
 				 quote=input$quote)
   })
-})
+}

inst/examples/09_upload/ui.R

@@ -1,6 +1,6 @@
 library(shiny)
 
-shinyUI(fluidPage(
+fluidPage(
   titlePanel("Uploading Files"),
   sidebarLayout(
     sidebarPanel(
@@ -25,4 +25,4 @@ shinyUI(fluidPage(
       tableOutput('contents')
     )
   )
-))
+)

inst/examples/10_download/server.R

@@ -1,4 +1,4 @@
-shinyServer(function(input, output) {
+function(input, output) {
   datasetInput <- reactive({
     switch(input$dataset,
            "rock" = rock,
@@ -18,4 +18,4 @@ shinyServer(function(input, output) {
       write.csv(datasetInput(), file)
     }
   )
-})
+}

inst/examples/10_download/ui.R

@@ -1,4 +1,4 @@
-shinyUI(fluidPage(
+fluidPage(
   titlePanel('Downloading Data'),
   sidebarLayout(
     sidebarPanel(
@@ -10,4 +10,4 @@ shinyUI(fluidPage(
       tableOutput('table')
     )
   )
-))
+)

inst/examples/11_timer/server.R

@@ -1,6 +1,6 @@
-shinyServer(function(input, output, session) {
+function(input, output, session) {
   output$currentTime <- renderText({
     invalidateLater(1000, session)
     paste("The current time is", Sys.time())
   })
-})
+}

inst/examples/11_timer/ui.R

@@ -1,3 +1,3 @@
-shinyUI(fluidPage(
+fluidPage(
   textOutput("currentTime")
-))
+)

inst/staticdocs/index.r

@@ -5,6 +5,8 @@ sd_section("UI Layout",
     "bootstrapPage",
     "column",
     "conditionalPanel",
+    "fillPage",
+    "fillRow",
     "fixedPage",
     "fluidPage",
     "headerPanel",
@@ -42,7 +44,10 @@ sd_section("UI Inputs",
     "sliderInput",
     "submitButton",
     "textInput",
+    "textAreaInput",
     "passwordInput",
+    "modalButton",
+    "updateActionButton",
     "updateCheckboxGroupInput",
     "updateCheckboxInput",
     "updateDateInput",
@@ -52,7 +57,9 @@ sd_section("UI Inputs",
     "updateSelectInput",
     "updateSliderInput",
     "updateTabsetPanel",
-    "updateTextInput"
+    "updateTextInput",
+    "updateTextAreaInput",
+    "updateQueryString"
   )
 )
 sd_section("UI Outputs",
@@ -66,7 +73,11 @@ sd_section("UI Outputs",
     "verbatimTextOutput",
     "downloadButton",
     "Progress",
-    "withProgress"
+    "withProgress",
+    "modalDialog",
+    "urlModal",
+    "showModal",
+    "showNotification"
   )
 )
 sd_section("Interface builder functions",
@@ -78,7 +89,12 @@ sd_section("Interface builder functions",
     "singleton",
     "tag",
     "validateCssUnit",
-    "withTags"
+    "withTags",
+    "htmlTemplate",
+    "bootstrapLib",
+    "suppressDependencies",
+    "insertUI",
+    "removeUI"
   )
 )
 sd_section("Rendering functions",
@@ -114,6 +130,7 @@ sd_section("Reactive constructs",
     "reactiveTimer",
     "reactiveValues",
     "reactiveValuesToList",
+    "freezeReactiveValue",
     "domains",
     "showReactLog"
   )
@@ -129,9 +146,22 @@ sd_section("Running",
   "Functions that are used to run or stop Shiny applications.",
   c(
     "runApp",
+    "runGadget",
     "runExample",
+    "runGadget",
     "runUrl",
-    "stopApp"
+    "stopApp",
+    "viewer"
+  )
+)
+sd_section("Bookmarking state",
+  "Functions that are used for bookmarking and restoring state.",
+  c(
+    "bookmarkButton",
+    "enableBookmarking",
+    "setBookmarkExclude",
+    "showBookmarkUrlModal",
+    "onBookmark"
   )
 )
 sd_section("Extending Shiny",
@@ -147,8 +177,14 @@ sd_section("Extending Shiny",
 sd_section("Utility functions",
   "Miscellaneous utilities that may be useful to advanced users or when extending Shiny.",
   c(
+    "req",
     "validate",
     "session",
+    "shinyOptions",
+    "safeError",
+    "onFlush",
+    "restoreInput",
+    "applyInputHandlers",
     "exprToFunction",
     "installExprFunction",
     "parseQueryString",

inst/template/default.html

@@ -0,0 +1,7 @@
+<!DOCTYPE html>
+<html>
+<head>
+{{ headContent() }}
+</head>
+{{ body }}
+</html>

inst/tests/test-staticdocs.R

@@ -1,35 +0,0 @@
-context("staticdocs")
-
-test_that("All man pages have an entry in staticdocs/index.r", {
-  if (!all(file.exists(c('../../inst/staticdocs', '../../man')))) {
-    # This test works only when run against a package directory
-    return()
-  }
-  # Known not to be indexed
-  known_unindexed <- c("shiny-package", "knitr_methods", "knitr_methods_htmltools")
-
-  indexed_topics <- local({
-    result <- character(0)
-    sd_section <- function(dummy1, dummy2, section_topics) {
-      result <<- c(result, section_topics)
-    }
-    source("../../inst/staticdocs/index.r", local = TRUE)
-    result
-  })
-
-  all_topics <- sub("\\.Rd", "", list.files("../../man", pattern = "*.Rd"))
-
-  # This test ensures that every documented topic is included in
-  # staticdocs/index.r, unless explicitly waived by specifying it
-  # in the known_unindexed variable above.
-  missing <- setdiff(sort(all_topics), sort(c(known_unindexed, indexed_topics)))
-  unknown <- setdiff(sort(c(known_unindexed, indexed_topics)), sort(all_topics))
-  expect_equal(length(missing), 0,
-    info = paste("Functions missing from index:\n",
-      paste("  ", missing, sep = "", collapse = "\n"),
-      sep = ""))
-  expect_equal(length(unknown), 0,
-    info = paste("Unrecognized functions in index.r:\n",
-      paste("  ", unknown, sep = "", collapse = "\n"),
-      sep = ""))
-})

inst/www/shared/bootstrap/css/bootstrap-theme.css

@@ -1,9 +1,8 @@
 /*!
- * Bootstrap v3.3.1 (http://getbootstrap.com)
- * Copyright 2011-2014 Twitter, Inc.
+ * Bootstrap v3.3.7 (http://getbootstrap.com)
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  */
-
 .btn-default,
 .btn-primary,
 .btn-success,
@@ -29,6 +28,27 @@
   -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
           box-shadow: inset 0 3px 5px rgba(0, 0, 0, .125);
 }
+.btn-default.disabled,
+.btn-primary.disabled,
+.btn-success.disabled,
+.btn-info.disabled,
+.btn-warning.disabled,
+.btn-danger.disabled,
+.btn-default[disabled],
+.btn-primary[disabled],
+.btn-success[disabled],
+.btn-info[disabled],
+.btn-warning[disabled],
+.btn-danger[disabled],
+fieldset[disabled] .btn-default,
+fieldset[disabled] .btn-primary,
+fieldset[disabled] .btn-success,
+fieldset[disabled] .btn-info,
+fieldset[disabled] .btn-warning,
+fieldset[disabled] .btn-danger {
+  -webkit-box-shadow: none;
+          box-shadow: none;
+}
 .btn-default .badge,
 .btn-primary .badge,
 .btn-success .badge,
@@ -63,8 +83,24 @@
   background-color: #e0e0e0;
   border-color: #dbdbdb;
 }
-.btn-default:disabled,
-.btn-default[disabled] {
+.btn-default.disabled,
+.btn-default[disabled],
+fieldset[disabled] .btn-default,
+.btn-default.disabled:hover,
+.btn-default[disabled]:hover,
+fieldset[disabled] .btn-default:hover,
+.btn-default.disabled:focus,
+.btn-default[disabled]:focus,
+fieldset[disabled] .btn-default:focus,
+.btn-default.disabled.focus,
+.btn-default[disabled].focus,
+fieldset[disabled] .btn-default.focus,
+.btn-default.disabled:active,
+.btn-default[disabled]:active,
+fieldset[disabled] .btn-default:active,
+.btn-default.disabled.active,
+.btn-default[disabled].active,
+fieldset[disabled] .btn-default.active {
   background-color: #e0e0e0;
   background-image: none;
 }
@@ -88,8 +124,24 @@
   background-color: #265a88;
   border-color: #245580;
 }
-.btn-primary:disabled,
-.btn-primary[disabled] {
+.btn-primary.disabled,
+.btn-primary[disabled],
+fieldset[disabled] .btn-primary,
+.btn-primary.disabled:hover,
+.btn-primary[disabled]:hover,
+fieldset[disabled] .btn-primary:hover,
+.btn-primary.disabled:focus,
+.btn-primary[disabled]:focus,
+fieldset[disabled] .btn-primary:focus,
+.btn-primary.disabled.focus,
+.btn-primary[disabled].focus,
+fieldset[disabled] .btn-primary.focus,
+.btn-primary.disabled:active,
+.btn-primary[disabled]:active,
+fieldset[disabled] .btn-primary:active,
+.btn-primary.disabled.active,
+.btn-primary[disabled].active,
+fieldset[disabled] .btn-primary.active {
   background-color: #265a88;
   background-image: none;
 }
@@ -113,8 +165,24 @@
   background-color: #419641;
   border-color: #3e8f3e;
 }
-.btn-success:disabled,
-.btn-success[disabled] {
+.btn-success.disabled,
+.btn-success[disabled],
+fieldset[disabled] .btn-success,
+.btn-success.disabled:hover,
+.btn-success[disabled]:hover,
+fieldset[disabled] .btn-success:hover,
+.btn-success.disabled:focus,
+.btn-success[disabled]:focus,
+fieldset[disabled] .btn-success:focus,
+.btn-success.disabled.focus,
+.btn-success[disabled].focus,
+fieldset[disabled] .btn-success.focus,
+.btn-success.disabled:active,
+.btn-success[disabled]:active,
+fieldset[disabled] .btn-success:active,
+.btn-success.disabled.active,
+.btn-success[disabled].active,
+fieldset[disabled] .btn-success.active {
   background-color: #419641;
   background-image: none;
 }
@@ -138,8 +206,24 @@
   background-color: #2aabd2;
   border-color: #28a4c9;
 }
-.btn-info:disabled,
-.btn-info[disabled] {
+.btn-info.disabled,
+.btn-info[disabled],
+fieldset[disabled] .btn-info,
+.btn-info.disabled:hover,
+.btn-info[disabled]:hover,
+fieldset[disabled] .btn-info:hover,
+.btn-info.disabled:focus,
+.btn-info[disabled]:focus,
+fieldset[disabled] .btn-info:focus,
+.btn-info.disabled.focus,
+.btn-info[disabled].focus,
+fieldset[disabled] .btn-info.focus,
+.btn-info.disabled:active,
+.btn-info[disabled]:active,
+fieldset[disabled] .btn-info:active,
+.btn-info.disabled.active,
+.btn-info[disabled].active,
+fieldset[disabled] .btn-info.active {
   background-color: #2aabd2;
   background-image: none;
 }
@@ -163,8 +247,24 @@
   background-color: #eb9316;
   border-color: #e38d13;
 }
-.btn-warning:disabled,
-.btn-warning[disabled] {
+.btn-warning.disabled,
+.btn-warning[disabled],
+fieldset[disabled] .btn-warning,
+.btn-warning.disabled:hover,
+.btn-warning[disabled]:hover,
+fieldset[disabled] .btn-warning:hover,
+.btn-warning.disabled:focus,
+.btn-warning[disabled]:focus,
+fieldset[disabled] .btn-warning:focus,
+.btn-warning.disabled.focus,
+.btn-warning[disabled].focus,
+fieldset[disabled] .btn-warning.focus,
+.btn-warning.disabled:active,
+.btn-warning[disabled]:active,
+fieldset[disabled] .btn-warning:active,
+.btn-warning.disabled.active,
+.btn-warning[disabled].active,
+fieldset[disabled] .btn-warning.active {
   background-color: #eb9316;
   background-image: none;
 }
@@ -188,8 +288,24 @@
   background-color: #c12e2a;
   border-color: #b92c28;
 }
-.btn-danger:disabled,
-.btn-danger[disabled] {
+.btn-danger.disabled,
+.btn-danger[disabled],
+fieldset[disabled] .btn-danger,
+.btn-danger.disabled:hover,
+.btn-danger[disabled]:hover,
+fieldset[disabled] .btn-danger:hover,
+.btn-danger.disabled:focus,
+.btn-danger[disabled]:focus,
+fieldset[disabled] .btn-danger:focus,
+.btn-danger.disabled.focus,
+.btn-danger[disabled].focus,
+fieldset[disabled] .btn-danger.focus,
+.btn-danger.disabled:active,
+.btn-danger[disabled]:active,
+fieldset[disabled] .btn-danger:active,
+.btn-danger.disabled.active,
+.btn-danger[disabled].active,
+fieldset[disabled] .btn-danger.active {
   background-color: #c12e2a;
   background-image: none;
 }
@@ -254,6 +370,7 @@
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
+  border-radius: 4px;
 }
 .navbar-inverse .navbar-nav > .open > a,
 .navbar-inverse .navbar-nav > .active > a {

inst/www/shared/bootstrap/fonts/glyphicons-halflings-regular.svg

@@ -6,224 +6,283 @@
 <font id="glyphicons_halflingsregular" horiz-adv-x="1200" >
 <font-face units-per-em="1200" ascent="960" descent="-240" />
 <missing-glyph horiz-adv-x="500" />
-<glyph />
-<glyph />
-<glyph unicode="&#xd;" />
+<glyph horiz-adv-x="0" />
+<glyph horiz-adv-x="400" />
 <glyph unicode=" " />
-<glyph unicode="*" d="M100 500v200h259l-183 183l141 141l183 -183v259h200v-259l183 183l141 -141l-183 -183h259v-200h-259l183 -183l-141 -141l-183 183v-259h-200v259l-183 -183l-141 141l183 183h-259z" />
-<glyph unicode="+" d="M0 400v300h400v400h300v-400h400v-300h-400v-400h-300v400h-400z" />
+<glyph unicode="*" d="M600 1100q15 0 34 -1.5t30 -3.5l11 -1q10 -2 17.5 -10.5t7.5 -18.5v-224l158 158q7 7 18 8t19 -6l106 -106q7 -8 6 -19t-8 -18l-158 -158h224q10 0 18.5 -7.5t10.5 -17.5q6 -41 6 -75q0 -15 -1.5 -34t-3.5 -30l-1 -11q-2 -10 -10.5 -17.5t-18.5 -7.5h-224l158 -158 q7 -7 8 -18t-6 -19l-106 -106q-8 -7 -19 -6t-18 8l-158 158v-224q0 -10 -7.5 -18.5t-17.5 -10.5q-41 -6 -75 -6q-15 0 -34 1.5t-30 3.5l-11 1q-10 2 -17.5 10.5t-7.5 18.5v224l-158 -158q-7 -7 -18 -8t-19 6l-106 106q-7 8 -6 19t8 18l158 158h-224q-10 0 -18.5 7.5 t-10.5 17.5q-6 41 -6 75q0 15 1.5 34t3.5 30l1 11q2 10 10.5 17.5t18.5 7.5h224l-158 158q-7 7 -8 18t6 19l106 106q8 7 19 6t18 -8l158 -158v224q0 10 7.5 18.5t17.5 10.5q41 6 75 6z" />
+<glyph unicode="+" d="M450 1100h200q21 0 35.5 -14.5t14.5 -35.5v-350h350q21 0 35.5 -14.5t14.5 -35.5v-200q0 -21 -14.5 -35.5t-35.5 -14.5h-350v-350q0 -21 -14.5 -35.5t-35.5 -14.5h-200q-21 0 -35.5 14.5t-14.5 35.5v350h-350q-21 0 -35.5 14.5t-14.5 35.5v200q0 21 14.5 35.5t35.5 14.5 h350v350q0 21 14.5 35.5t35.5 14.5z" />
 <glyph unicode="&#xa0;" />
-<glyph unicode="&#x2000;" horiz-adv-x="652" />
-<glyph unicode="&#x2001;" horiz-adv-x="1304" />
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-<glyph unicode="&#x2007;" horiz-adv-x="217" />
-<glyph unicode="&#x2008;" horiz-adv-x="163" />
+<glyph unicode="&#xa5;" d="M825 1100h250q10 0 12.5 -5t-5.5 -13l-364 -364q-6 -6 -11 -18h268q10 0 13 -6t-3 -14l-120 -160q-6 -8 -18 -14t-22 -6h-125v-100h275q10 0 13 -6t-3 -14l-120 -160q-6 -8 -18 -14t-22 -6h-125v-174q0 -11 -7.5 -18.5t-18.5 -7.5h-148q-11 0 -18.5 7.5t-7.5 18.5v174 h-275q-10 0 -13 6t3 14l120 160q6 8 18 14t22 6h125v100h-275q-10 0 -13 6t3 14l120 160q6 8 18 14t22 6h118q-5 12 -11 18l-364 364q-8 8 -5.5 13t12.5 5h250q25 0 43 -18l164 -164q8 -8 18 -8t18 8l164 164q18 18 43 18z" />
+<glyph unicode="&#x2000;" horiz-adv-x="650" />
+<glyph unicode="&#x2001;" horiz-adv-x="1300" />
+<glyph unicode="&#x2002;" horiz-adv-x="650" />
+<glyph unicode="&#x2003;" horiz-adv-x="1300" />
+<glyph unicode="&#x2004;" horiz-adv-x="433" />
+<glyph unicode="&#x2005;" horiz-adv-x="325" />
+<glyph unicode="&#x2006;" horiz-adv-x="216" />
+<glyph unicode="&#x2007;" horiz-adv-x="216" />
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+<glyph unicode="&#x205f;" horiz-adv-x="325" />
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