Disable reactlog from reactives.R

.Rbuildignore

@@ -20,4 +20,3 @@
 ^revdep$
 ^TODO-promises.md$
 ^manualtests$
-^\.github$

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,40 +0,0 @@
----
-name  : Bug report
-about : Report a bug in Shiny.
----
-
-<!--
-This issue tracker is for bugs and feature requests in the Shiny package. If you're having trouble with Shiny Server or a related package, please file an issue in the appropriate repository. 
-
-If you're having trouble with shinyapps.io, and you have a paid account (Starter, Basic, Standard, or Pro), please file a support ticket via https://support.rstudio.com. If you have a Free account, please post to the RStudio Community with the shinyappsio tag: https://community.rstudio.com/tags/shinyappsio.
-
-Finally, if you are an RStudio customer and are having trouble with one of our Pro products, get in touch with our support team at support@rstudio.com.
-
-Before you file an issue, please upgrade to the latest version of Shiny from CRAN and confirm that the problem persists.
-
-# First, restart R.
-# To install latest shiny from CRAN:
-install.packages("shiny")
-
-See our guide to writing good bug reports for further guidance: https://github.com/rstudio/shiny/wiki/Writing-Good-Bug-Reports. The better your report is, the likelier we are to be able to reproduce and ultimately solve it.
--->
-
-### System details
-
-Browser Version: <!-- If applicable -->
-
-Output of `sessionInfo()`:
-
-```
-# sessionInfo() output goes here
-```
-
-### Example application *or* steps to reproduce the problem
-
-<!-- If you're able to create one, a reproducible example is extremely helpful to us. For instructions on how to create one, please see: https://github.com/rstudio/shiny/wiki/Creating-a-Reproducible-Example --> 
-
-```R
-# Minimal, self-contained example app code goes here
-```
-
-### Describe the problem in detail

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,17 +0,0 @@
----
-name  : Feature request
-about : Request a new feature.
----
-
-<!--
-
-Thanks for taking the time to file a feature request! Please take the time to search for an existing feature request, to avoid creating duplicate requests. If you find an existing feature request, please give it a thumbs-up reaction, as we'll use these reactions to help prioritize the implementation of these features in the future.
-
-If the feature has not yet been filed, then please describe the feature you'd like to see become a part of Shiny. See:
-
-https://github.com/rstudio/shiny/wiki/Writing-Good-Feature-Requests
-
-for a guide on how to write good feature requests.
-
--->
-

.github/ISSUE_TEMPLATE/question.md

@@ -1,7 +0,0 @@
----
-name  : Ask a Question
-about : The issue tracker is not for questions -- please ask questions at https://community.rstudio.com/c/shiny.
----
-
-The issue tracker is not for questions. If you have a question, please feel free to ask it on our community site, at https://community.rstudio.com/c/shiny.
-

.travis.yml

@@ -1,31 +1,11 @@
 language: r
-matrix:
-  include:
-    - name: "Roxygen check"
-      r: release
-      r_packages:
-        - devtools
-        - rprojroot
-      script: ./tools/documentation/checkDocsCurrent.sh
-      env:
-        # GITHUB_PAT for gh::gh calls
-        - secure: "Hk4piVNtDobLT1dQPnCOcM7sOlwNGJOU5cpvbRvOxYSgxP+Bj2MyRZMe825rdHkHbFez0h8w3tJOBf9DDBH7PC1BhhNll2+WM/WxGlkNleg8vsoH/Xopffl+2YgtWbAYZjQ2j0QYdgNn0e/TY86/ggk9qit6+gpsZ7z/HmWQuVY="
-
-    - name: "Javascript check"
-      language: node_js
-      cache: yarn
-      script: ./tools/checkJSCurrent.sh
-      node_js:
-        - "12"
-    - r: 3.2
-    - r: 3.3
-    - r: 3.4
-    - r: 3.5
-    - r: release
-    - r: devel
-
+r:
+  - oldrel
+  - release
+  - devel
 sudo: false
 cache: packages
+
 notifications:
   email:
     on_success: change

CONTRIBUTING.md

@@ -2,15 +2,13 @@ We welcome contributions to the **shiny** package. To submit a contribution:
 
 1. [Fork](https://github.com/rstudio/shiny/fork) the repository and make your changes.
 
-2. Submit a [pull request](https://help.github.com/articles/using-pull-requests).
+2. Ensure that you have signed the [individual](https://rstudioblog.files.wordpress.com/2017/05/rstudio_individual_contributor_agreement.pdf) or [corporate](https://rstudioblog.files.wordpress.com/2017/05/rstudio_corporate_contributor_agreement.pdf) contributor agreement as appropriate. You can send the signed copy to jj@rstudio.com.
 
-3. Ensure that you have signed the contributor license agreement. It will appear as a "Check"
-   on your PR and a comment from "CLAassistant" will also appear explaining whether you have
-   yet to sign. After you sign, you can click the "Recheck" link in that comment and the check
-   will flip to reflect that you've signed.
+3. Submit a [pull request](https://help.github.com/articles/using-pull-requests).
 
 We generally do not merge pull requests that update included web libraries (such as Bootstrap or jQuery) because it is difficult for us to verify that the update is done correctly; we prefer to update these libraries ourselves.
 
+
 ## How to make changes
 
 Before you submit a pull request, please do the following:

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: shiny
 Type: Package
 Title: Web Application Framework for R
-Version: 1.4.0.9002
+Version: 1.3.2.9000
 Authors@R: c(
     person("Winston", "Chang", role = c("aut", "cre"), email = "winston@rstudio.com"),
     person("Joe", "Cheng", role = "aut", email = "joe@rstudio.com"),
@@ -65,49 +65,39 @@ Depends:
 Imports:
     utils,
     grDevices,
-    httpuv (>= 1.5.2),
+    httpuv (>= 1.5.0),
     mime (>= 0.3),
     jsonlite (>= 0.9.16),
     xtable,
     digest,
-    htmltools (>= 0.4.0.9001),
+    htmltools (>= 0.3.6),
     R6 (>= 2.0),
     sourcetools,
-    later (>= 1.0.0),
-    promises (>= 1.1.0),
+    later (>= 0.7.2),
+    promises (>= 1.0.1),
     tools,
     crayon,
-    rlang (>= 0.4.0),
-    fastmap (>= 1.0.0),
-    withr,
-    commonmark (>= 1.7),
-    glue (>= 1.3.2)
+    rlang,
+    fastmap
 Suggests:
     datasets,
     Cairo (>= 1.5-5),
-    testthat (>= 2.1.1),
+    testthat (>= 2.2.1),
     knitr (>= 1.6),
     markdown,
     rmarkdown,
     ggplot2,
     reactlog (>= 1.0.0),
-    magrittr,
-    shinytest,
-    yaml,
-    future,
-    dygraphs
+    magrittr
 Remotes:
-    rstudio/htmltools,
-    rstudio/shinytest
+    wch/fastmap
 URL: http://shiny.rstudio.com
 BugReports: https://github.com/rstudio/shiny/issues
 Collate:
     'app.R'
-    'app_template.R'
     'bookmark-state-local.R'
     'stack.R'
     'bookmark-state.R'
-    'bootstrap-deprecated.R'
     'bootstrap-layout.R'
     'globals.R'
     'conditions.R'
@@ -151,15 +141,12 @@ Collate:
     'jqueryui.R'
     'middleware-shiny.R'
     'middleware.R'
-    'timer.R'
-    'mock-session.R'
     'modal.R'
     'modules.R'
     'notifications.R'
     'priorityqueue.R'
     'progress.R'
     'react.R'
-    'reexports.R'
     'render-cached-plot.R'
     'render-plot.R'
     'render-table.R'
@@ -175,9 +162,7 @@ Collate:
     'snapshot.R'
     'tar.R'
     'test-export.R'
-    'test-server.R'
-    'test.R'
+    'timer.R'
     'update-input.R'
-RoxygenNote: 7.1.0
+RoxygenNote: 6.1.1
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)

LICENSE

@@ -25,7 +25,7 @@ these components are included below):
 jQuery license and license for included components from jQuery UI
 ----------------------------------------------------------------------
 
-Copyright JS Foundation and other contributors, https://js.foundation/
+Copyright jQuery Foundation and other contributors, https://jquery.org/
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the
@@ -51,7 +51,7 @@ Bootstrap License
 ----------------------------------------------------------------------
 The MIT License (MIT)
 
-Copyright (c) 2011-2019 Twitter, Inc.
+Copyright (c) 2011-2014 Twitter, Inc
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

NAMESPACE

@@ -1,18 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("$",mockclientdata)
 S3method("$",reactivevalues)
 S3method("$",session_proxy)
 S3method("$",shinyoutput)
 S3method("$<-",reactivevalues)
 S3method("$<-",session_proxy)
 S3method("$<-",shinyoutput)
-S3method("[",mockclientdata)
 S3method("[",reactivevalues)
 S3method("[",shinyoutput)
 S3method("[<-",reactivevalues)
 S3method("[<-",shinyoutput)
-S3method("[[",mockclientdata)
 S3method("[[",reactivevalues)
 S3method("[[",session_proxy)
 S3method("[[",shinyoutput)
@@ -28,16 +25,14 @@ S3method(as.tags,shiny.render.function)
 S3method(format,reactiveExpr)
 S3method(format,reactiveVal)
 S3method(names,reactivevalues)
+S3method(print,key_missing)
 S3method(print,reactive)
-S3method(print,reactivevalues)
 S3method(print,shiny.appobj)
-S3method(print,shiny.render.function)
 S3method(str,reactivevalues)
 export("conditionStackTrace<-")
 export(..stacktraceoff..)
 export(..stacktraceon..)
 export(HTML)
-export(MockShinySession)
 export(NS)
 export(Progress)
 export(a)
@@ -138,17 +133,19 @@ export(isRunning)
 export(isTruthy)
 export(isolate)
 export(key_missing)
-export(loadSupport)
+export(knit_print.html)
+export(knit_print.reactive)
+export(knit_print.shiny.appobj)
+export(knit_print.shiny.render.function)
+export(knit_print.shiny.tag)
+export(knit_print.shiny.tag.list)
 export(mainPanel)
 export(makeReactiveBinding)
 export(markRenderFunction)
-export(markdown)
 export(maskReactiveContext)
 export(memoryCache)
-export(migrateLegacyShinytest)
 export(modalButton)
 export(modalDialog)
-export(moduleServer)
 export(navbarMenu)
 export(navbarPage)
 export(navlistPanel)
@@ -199,7 +196,6 @@ export(registerInputHandler)
 export(removeInputHandler)
 export(removeModal)
 export(removeNotification)
-export(removeResourcePath)
 export(removeTab)
 export(removeUI)
 export(renderCachedPlot)
@@ -212,14 +208,12 @@ export(renderText)
 export(renderUI)
 export(repeatable)
 export(req)
-export(resourcePaths)
 export(restoreInput)
 export(runApp)
 export(runExample)
 export(runGadget)
 export(runGist)
 export(runGitHub)
-export(runTests)
 export(runUrl)
 export(safeError)
 export(selectInput)
@@ -231,7 +225,6 @@ export(setSerializer)
 export(shinyApp)
 export(shinyAppDir)
 export(shinyAppFile)
-export(shinyAppTemplate)
 export(shinyOptions)
 export(shinyServer)
 export(shinyUI)
@@ -255,19 +248,15 @@ export(strong)
 export(submitButton)
 export(suppressDependencies)
 export(tabPanel)
-export(tabPanelBody)
 export(tableOutput)
 export(tabsetPanel)
 export(tag)
 export(tagAppendAttributes)
 export(tagAppendChild)
 export(tagAppendChildren)
-export(tagGetAttribute)
-export(tagHasAttribute)
 export(tagList)
 export(tagSetChildren)
 export(tags)
-export(testServer)
 export(textAreaInput)
 export(textInput)
 export(textOutput)
@@ -275,7 +264,6 @@ export(throttle)
 export(titlePanel)
 export(uiOutput)
 export(updateActionButton)
-export(updateActionLink)
 export(updateCheckboxGroupInput)
 export(updateCheckboxInput)
 export(updateDateInput)
@@ -314,47 +302,5 @@ import(methods)
 import(mime)
 import(xtable)
 importFrom(fastmap,fastmap)
-importFrom(fastmap,is.key_missing)
-importFrom(fastmap,key_missing)
 importFrom(grDevices,dev.cur)
 importFrom(grDevices,dev.set)
-importFrom(htmltools,HTML)
-importFrom(htmltools,a)
-importFrom(htmltools,br)
-importFrom(htmltools,code)
-importFrom(htmltools,div)
-importFrom(htmltools,em)
-importFrom(htmltools,h1)
-importFrom(htmltools,h2)
-importFrom(htmltools,h3)
-importFrom(htmltools,h4)
-importFrom(htmltools,h5)
-importFrom(htmltools,h6)
-importFrom(htmltools,hr)
-importFrom(htmltools,htmlTemplate)
-importFrom(htmltools,img)
-importFrom(htmltools,includeCSS)
-importFrom(htmltools,includeHTML)
-importFrom(htmltools,includeMarkdown)
-importFrom(htmltools,includeScript)
-importFrom(htmltools,includeText)
-importFrom(htmltools,is.singleton)
-importFrom(htmltools,p)
-importFrom(htmltools,pre)
-importFrom(htmltools,singleton)
-importFrom(htmltools,span)
-importFrom(htmltools,strong)
-importFrom(htmltools,suppressDependencies)
-importFrom(htmltools,tag)
-importFrom(htmltools,tagAppendAttributes)
-importFrom(htmltools,tagAppendChild)
-importFrom(htmltools,tagAppendChildren)
-importFrom(htmltools,tagGetAttribute)
-importFrom(htmltools,tagHasAttribute)
-importFrom(htmltools,tagList)
-importFrom(htmltools,tagSetChildren)
-importFrom(htmltools,tags)
-importFrom(htmltools,validateCssUnit)
-importFrom(htmltools,withTags)
-importFrom(promises,"%...!%")
-importFrom(promises,"%...>%")

NEWS.md

@@ -1,129 +1,29 @@
-shiny 1.4.0.9001
-===========
-
-## Full changelog
-
-### Breaking changes
-
-### New features
-
-* The new `shinyAppTemplate()` function creates a new template Shiny application, where components are optional, such as helper files in an R/ subdirectory, a module, and various kinds of tests. ([#2704](https://github.com/rstudio/shiny/pull/2704))
-
-* `runTests()` is a new function that behaves much like R CMD check. `runTests()` invokes all of the top-level R files in the tests/ directory inside an application, in that application's environment. ([#2585](https://github.com/rstudio/shiny/pull/2585))
-
-* `testServer()` and `testModule()` are two new functions for testing reactive behavior inside server functions and modules, respectively. ([#2682](https://github.com/rstudio/shiny/pull/2682), [#2764](https://github.com/rstudio/shiny/pull/2764))
-
-* The new `moduleServer` function provides a simpler interface for creating and using modules. ([#2773](https://github.com/rstudio/shiny/pull/2773))
-
-* Resolved [#2732](https://github.com/rstudio/shiny/issues/2732): `markdown()` is a new function for writing Markdown with Github extensions directly in Shiny UIs. Markdown rendering is performed by the [commonmark](https://github.com/jeroen/commonmark) package. ([#2737](https://github.com/rstudio/shiny/pull/2737))
-
-### Minor new features and improvements
-
-* Fixed [#2042](https://github.com/rstudio/shiny/issues/2042), [#2628](https://github.com/rstudio/shiny/issues/2628): In a `dateInput` and `dateRangeInput`, disabled months and years are now a lighter gray, to make it easier to see that they are disabled. ([#2690](https://github.com/rstudio/shiny/pull/2690))
-
-* `getCurrentOutputInfo()` previously threw an error when called from outside of an output; now it returns `NULL`. ([#2707](https://github.com/rstudio/shiny/pull/2707))
-
-* Added a label to observer that auto-reloads `R/` directory to avoid confusion when using `reactlog`. ([#58](https://github.com/rstudio/reactlog/issues/58))
-
-* `getDefaultReactiveDomain()` can now be called inside a `session$onSessionEnded` callback and will return the calling `session` information. ([#2757](https://github.com/rstudio/shiny/pull/2757))
-
-* Added a `'function'` class to `reactive()` and `reactiveVal()` objects. ([#2793](https://github.com/rstudio/shiny/pull/2793))
-
-* Added a new option (`type = "hidden"`) to `tabsetPanel()`, making it easier to set the active tab via other input controls (e.g., `radioButtons()`) rather than tabs or pills. Use this option in conjunction with `updateTabsetPanel()` and the new `tabsetPanelBody()` function (see `help(tabsetPanel)` for an example and more details).  ([#2814](https://github.com/rstudio/shiny/pull/2814))
-
-* Added function `updateActionLink()` to update an `actionLink()` label and/or icon value. ([#2811](https://github.com/rstudio/shiny/pull/2811))
-
-### Bug fixes
-
-* Fixed [#2606](https://github.com/rstudio/shiny/issues/2606): `debounce()` would not work properly if the code in the reactive expression threw an error on the first run. ([#2652](https://github.com/rstudio/shiny/pull/2652))
-
-* Fixed [#2653](https://github.com/rstudio/shiny/issues/2653): The `dataTableOutput()` could have incorrect output if certain characters were in the column names. ([#2658](https://github.com/rstudio/shiny/pull/2658))
-
-### Documentation Updates
-
-
-shiny 1.4.0.2
-===========
-
-Minor patch release: fixed some timing-dependent tests failed intermittently on CRAN build machines.
-
-
-shiny 1.4.0.1
-===========
-
-Minor patch release to account for changes to the grid package that will be upcoming in the R 4.0 release ([#2776](https://github.com/rstudio/shiny/pull/2776)).
-
-
-shiny 1.4.0
-===========
-
-## Full changelog
-
-### Breaking changes
-
-* Resolved [#2554](https://github.com/rstudio/shiny/issues/2554): Upgraded jQuery from v.1.12.4 to v3.4.1 and bootstrap from v3.3.7 to v3.4.1. ([#2557](https://github.com/rstudio/shiny/pull/2557)). Since the jQuery upgrade may introduce breaking changes to user code, there is an option to switch back to the old version by setting `options(shiny.jquery.version = 1)`. If you've hard-coded `shared/jquery[.min].js` in the HTML of your Shiny app, in order to downgrade, you'll have to change that filepath to `shared/legacy/jquery[.min].js`.
+shiny 1.3.2.9000
+=======
 
 ### Improvements
 
-* Resolved [#1433](https://github.com/rstudio/shiny/issues/1433): `plotOutput()`'s coordmap info now includes discrete axis limits for **ggplot2** plots. As a result, any **shinytest** tests that contain **ggplot2** plots with discrete axes (that were recorded before this change) will now report differences that can safely be updated. This new coordmap info was added to correctly infer what data points are within an input brush and/or near input click/hover in scenarios where a non-trivial discrete axis scale is involved (e.g., whenever `scale_[x/y]_discrete(limits = ...)` and/or free scales across multiple discrete axes are used). ([#2410](https://github.com/rstudio/shiny/pull/2410))
-
-* Resolved [#2402](https://github.com/rstudio/shiny/issues/2402): An informative warning is now thrown for mis-specified (date) strings in `dateInput()`, `updateDateInput()`, `dateRangeInput()`, and `updateDateRangeInput()`. ([#2403](https://github.com/rstudio/shiny/pull/2403))
-
-* If the `shiny.autoload.r` option is set to `TRUE`, all files ending in `.r` or `.R` contained in a directory named `R/` adjacent to your application are sourced when your app is started. This will become the default Shiny behavior in a future release ([#2547](https://github.com/rstudio/shiny/pull/2547))
-
-* Resolved [#2442](https://github.com/rstudio/shiny/issues/2442): The `shiny:inputchanged` JavaScript event now triggers on the related input element instead of `document`. Existing event listeners bound to `document` will still detect the event due to event bubbling. ([#2446](https://github.com/rstudio/shiny/pull/2446))
-
-* Fixed [#1393](https://github.com/rstudio/shiny/issues/1393), [#2223](https://github.com/rstudio/shiny/issues/2223): For plots with any interactions enabled, the image is no longer draggable. ([#2460](https://github.com/rstudio/shiny/pull/2460))
-
-* Resolved [#2469](https://github.com/rstudio/shiny/issues/2469): `renderText` now takes a `sep` argument that is passed to `cat`. ([#2497](https://github.com/rstudio/shiny/pull/2497))
-
-* Added `resourcePaths()` and `removeResourcePaths()` functions. ([#2459](https://github.com/rstudio/shiny/pull/2459))
-
-* Resolved [#2433](https://github.com/rstudio/shiny/issues/2433): An informative warning is now thrown if subdirectories of the app's `www/` directory are masked by other resource prefixes and/or the same resource prefix is mapped to different local file paths. ([#2434](https://github.com/rstudio/shiny/pull/2434))
-
-* Resolved [#2478](https://github.com/rstudio/shiny/issues/2478): `cmd + shift + f3` and `ctrl + shift + f3` can now be used to add a reactlog mark. If reactlog keybindings are used and the reactlog is not enabled, an error page is displayed showing how to enable reactlog recordings. ([#2560](https://github.com/rstudio/shiny/pull/2560))
+* Resolved ([#2402](https://github.com/rstudio/shiny/issues/2402)): An informative warning is now thrown for mis-specified (date) strings in `dateInput()`, `updateDateInput()`, `dateRangeInput()`, and `updateDateRangeInput()`. ([#2403](https://github.com/rstudio/shiny/pull/2403))
 
 ### Bug fixes
 
-* Partially resolved [#2423](https://github.com/rstudio/shiny/issues/2423): Reactivity in Shiny leaked some memory, because R can leak memory whenever a new symbols is interned, which happens whenever a new name/key is used in an environment. R now uses the fastmap package, which avoids this problem. ([#2429](https://github.com/rstudio/shiny/pull/2429))
-
-* Fixed [#2267](https://github.com/rstudio/shiny/issues/2267): Fixed a memory leak with `invalidateLater`. ([#2555](https://github.com/rstudio/shiny/pull/2555))
-
-* Fixed [#1548](https://github.com/rstudio/shiny/issues/1548): The `reactivePoll` function leaked an observer; that is the observer would continue to exist even if the `reactivePoll` object was no longer accessible. [#2522](https://github.com/rstudio/shiny/pull/2522)
-
-* Fixed [#2116](https://github.com/rstudio/shiny/issues/2116): Fixed an issue where dynamic tabs could not be added when on a hosted platform. ([#2545](https://github.com/rstudio/shiny/pull/2545))
-
-* Resolved [#2515](https://github.com/rstudio/shiny/issues/2515): `selectInput()` and `selectizeInput()` now deal appropriately with named factors. Note that `updateSelectInput()` and `updateSelectizeInput()` **do not** yet handle factors; their behavior is unchanged. ([#2524](https://github.com/rstudio/shiny/pull/2524), [#2540](https://github.com/rstudio/shiny/pull/2540), [#2625](https://github.com/rstudio/shiny/pull/2625))
-
-* Resolved [#2471](https://github.com/rstudio/shiny/issues/2471): Large file uploads to a Windows computer were slow. ([#2579](https://github.com/rstudio/shiny/pull/2579))
-
 * Fixed [#2387](https://github.com/rstudio/shiny/issues/2387): Updating a `sliderInput()`'s type from numeric to date no longer changes the rate policy from debounced to immediate. More generally, updating an input binding with a new type should (no longer) incorrectly alter the input rate policy. ([#2404](https://github.com/rstudio/shiny/pull/2404))
 
 * Fixed [#868](https://github.com/rstudio/shiny/issues/868): If an input is initialized with a `NULL` label, it can now be updated with a string. Moreover, if an input label is initialized with a string, it can now be removed by updating with `label=character(0)` (similar to how `choices` and `selected` can be cleared in `updateSelectInput()`). ([#2406](https://github.com/rstudio/shiny/pull/2406))
 
 * Fixed [#2250](https://github.com/rstudio/shiny/issues/2250): `updateSliderInput()` now works with un-specified (or zero-length) `min`, `max`, and `value`. ([#2416](https://github.com/rstudio/shiny/pull/2416))
 
-* Fixed [#2396](https://github.com/rstudio/shiny/issues/2396): `selectInput("myID", ...)` resulting in an extra `myID-selectized` input (introduced in v1.2.0). ([#2418](https://github.com/rstudio/shiny/pull/2418))
-
 * Fixed [#2233](https://github.com/rstudio/shiny/issues/2233): `verbatimTextOutput()` produced wrapped text on Safari, but the text should not be wrapped. ([#2353](https://github.com/rstudio/shiny/pull/2353))
-
-* Fixed [#2335](https://github.com/rstudio/shiny/issues/2335): When `dateInput()`'s `value` was unspecified, and `max` and/or `min` was set to `Sys.Date()`, the value was not being set properly. ([#2526](https://github.com/rstudio/shiny/pull/2526))
-
-* Fixed [#2591](https://github.com/rstudio/shiny/issues/2591): Providing malformed date-strings to `min` or `max` no longer results in JS errors for `dateInput()` and `dateRangeInput()`. ([#2592](https://github.com/rstudio/shiny/pull/2592))
-
 * Fixed [rstudio/reactlog#36](https://github.com/rstudio/reactlog/issues/36): Changes to reactive values not displaying accurately in reactlog. ([#2424](https://github.com/rstudio/shiny/pull/2424))
 
-* Fixed [#2598](https://github.com/rstudio/shiny/issues/2598): Showcase files don't appear with a wide window. ([#2582](https://github.com/rstudio/shiny/pull/2582))
-
 * Fixed [#2329](https://github.com/rstudio/shiny/issues/2329), [#1817](https://github.com/rstudio/shiny/issues/1817): These bugs were reported as fixed in Shiny 1.3.0 but were not actually fixed because some JavaScript changes were accidentally not included in the release. The fix resolves issues that occur when `withProgressBar()` or bookmarking are combined with the [networkD3](https://christophergandrud.github.io/networkD3/) package's Sankey plot.
 
-
 shiny 1.3.2
 ===========
 
 ### Bug fixes
 
-* Fixed [#2385](https://github.com/rstudio/shiny/issues/2385): Static CSS/JS resources in subapps in R Markdown documents did not render properly. ([#2386](https://github.com/rstudio/shiny/pull/2386))
+* Fixed [#2285](https://github.com/rstudio/shiny/issues/2285), [#2288](https://github.com/rstudio/shiny/issues/2288): Static CSS/JS resources in subapps in R Markdown documents did not render properly. ([#2386](https://github.com/rstudio/shiny/pull/2386))
 
 * Fixed [#2280](https://github.com/rstudio/shiny/issues/2280): Shiny applications that used a www/index.html file did not serve up the index file. ([#2382](https://github.com/rstudio/shiny/pull/2382))
 
@@ -215,8 +115,6 @@ This release features plot caching, an important new tool for improving performa
 
 * Fixed [#2138](https://github.com/rstudio/shiny/issues/2138): Inputs that are part of a `renderUI` were no longer restoring correctly from bookmarked state. [#2139](https://github.com/rstudio/shiny/pull/2139)
 
-* The `knit_print` methods from htmltools are no longer imported into shiny and then exported. Also, shiny's `knit_print` methods are no longer exported. [#2166](https://github.com/rstudio/shiny/pull/2166)
-
 * Fixed [#2093](https://github.com/rstudio/shiny/issues/2093): Make sure bookmark scope directory does not exist before trying to create it. [#2168](https://github.com/rstudio/shiny/pull/2168)
 
 * Fixed [#2177](https://github.com/rstudio/shiny/issues/2177): The session name is now being recorded when exiting a context.  Multiple sessions can now view their respective reactlogs. [#2180](https://github.com/rstudio/shiny/pull/2180)
@@ -687,7 +585,7 @@ There are many more minor features, small improvements, and bug fixes than we ca
 
 *    **Code Diagnostics**: if there is an error parsing `ui.R`, `server.R`, `app.R`, or `global.R`, Shiny will search the code for missing commas, extra commas, and unmatched braces, parens, and brackets, and will print out messages pointing out those problems. ([#1126](https://github.com/rstudio/shiny/pull/1126))
 
-*    **Reactlog visualization**: by default, the [`showReactLog()` function](http://shiny.rstudio.com/reference/shiny/latest/reactlog.html) (which brings up the reactive graph) also displays the time that each reactive and observer were active for:
+*    **Reactlog visualization**: by default, the [`showReactLog()` function](http://shiny.rstudio.com/reference/shiny/latest/showReactLog.html) (which brings up the reactive graph) also displays the time that each reactive and observer were active for:
 
       <p align="center">
       <img src="http://shiny.rstudio.com/images/reactlog.png" alt="modal-dialog" width="75%"/>

R/app.R

@@ -3,41 +3,40 @@
 #' Create a Shiny app object
 #'
 #' These functions create Shiny app objects from either an explicit UI/server
-#' pair (`shinyApp`), or by passing the path of a directory that contains a
-#' Shiny app (`shinyAppDir`).
+#' pair (\code{shinyApp}), or by passing the path of a directory that contains a
+#' Shiny app (\code{shinyAppDir}). You generally shouldn't need to use these
+#' functions to create/run applications; they are intended for interoperability
+#' purposes, such as embedding Shiny apps inside a \pkg{knitr} document.
 #'
 #' Normally when this function is used at the R console, the Shiny app object is
-#' automatically passed to the `print()` function, which runs the app. If
+#' automatically passed to the \code{print()} function, which runs the app. If
 #' this is called in the middle of a function, the value will not be passed to
-#' `print()` and the app will not be run. To make the app run, pass the app
-#' object to `print()` or [runApp()].
+#' \code{print()} and the app will not be run. To make the app run, pass the app
+#' object to \code{print()} or \code{\link{runApp}()}.
 #'
 #' @param ui The UI definition of the app (for example, a call to
-#'   `fluidPage()` with nested controls).
-#'
-#'    If bookmarking is enabled (see `enableBookmarking`), this must be
-#'    a single argument function that returns the UI definition.
-#' @param server A function with three parameters: `input`, `output`, and
-#'   `session`. The function is called once for each session ensuring that each
-#'   app is independent.
+#'   \code{fluidPage()} with nested controls)
+#' @param server A server function
 #' @param onStart A function that will be called before the app is actually run.
-#'   This is only needed for `shinyAppObj`, since in the `shinyAppDir`
-#'   case, a `global.R` file can be used for this purpose.
-#' @param options Named options that should be passed to the `runApp` call
+#'   This is only needed for \code{shinyAppObj}, since in the \code{shinyAppDir}
+#'   case, a \code{global.R} file can be used for this purpose.
+#' @param options Named options that should be passed to the \code{runApp} call
 #'   (these can be any of the following: "port", "launch.browser", "host", "quiet",
-#'   "display.mode" and "test.mode"). You can also specify `width` and
-#'   `height` parameters which provide a hint to the embedding environment
+#'   "display.mode" and "test.mode"). You can also specify \code{width} and
+#'   \code{height} parameters which provide a hint to the embedding environment
 #'   about the ideal height/width for the app.
-#' @param uiPattern A regular expression that will be applied to each `GET`
-#'   request to determine whether the `ui` should be used to handle the
+#' @param uiPattern A regular expression that will be applied to each \code{GET}
+#'   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 `"url"`, `"server"`, or
-#'   `"disable"`. The default value, `NULL`, will respect the setting from
-#'   any previous calls to  [enableBookmarking()]. See [enableBookmarking()]
-#'   for more information on bookmarking your app.
+#' @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 [runApp()] will run the app.
+#'   to \code{\link{runApp}} will run the app.
 #'
 #' @examples
 #' ## Only run this example in interactive R sessions
@@ -71,10 +70,10 @@
 #'   runApp(app)
 #' }
 #' @export
-shinyApp <- function(ui, server, onStart=NULL, options=list(),
+shinyApp <- function(ui=NULL, server=NULL, onStart=NULL, options=list(),
                      uiPattern="/", enableBookmarking=NULL) {
-  if (!is.function(server)) {
-    stop("`server` must be a function", call. = FALSE)
+  if (is.null(server)) {
+    stop("`server` missing from shinyApp")
   }
 
   # Ensure that the entire path is a match
@@ -142,21 +141,10 @@ shinyAppFile <- function(appFile, options=list()) {
 
 # This reads in an app dir in the case that there's a server.R (and ui.R/www)
 # present, and returns a shiny.appobj.
-# appDir must be a normalized (absolute) path, not a relative one
 shinyAppDir_serverR <- function(appDir, options=list()) {
   # Most of the complexity here comes from needing to hot-reload if the .R files
   # change on disk, or are created, or are removed.
 
-  # In an upcoming version of shiny, this option will go away.
-  if (getOption("shiny.autoload.r", TRUE)) {
-    # Create a child env which contains all the helpers and will be the shared parent
-    # of the ui.R and server.R load.
-    sharedEnv <- new.env(parent = globalenv())
-  } else {
-    # old behavior
-    sharedEnv <- globalenv()
-  }
-
   # uiHandlerSource is a function that returns an HTTP handler for serving up
   # ui.R as a webpage. The "cachedFuncWithFile" call makes sure that the closure
   # we're creating here only gets executed when ui.R's contents change.
@@ -167,7 +155,7 @@ shinyAppDir_serverR <- function(appDir, options=list()) {
         # If not, then take the last expression that's returned from ui.R.
         .globals$ui <- NULL
         on.exit(.globals$ui <- NULL, add = FALSE)
-        ui <- sourceUTF8(uiR, envir = new.env(parent = sharedEnv))
+        ui <- sourceUTF8(uiR, envir = new.env(parent = globalenv()))
         if (!is.null(.globals$ui)) {
           ui <- .globals$ui[[1]]
         }
@@ -197,7 +185,7 @@ shinyAppDir_serverR <- function(appDir, options=list()) {
       # server.R.
       .globals$server <- NULL
       on.exit(.globals$server <- NULL, add = TRUE)
-      result <- sourceUTF8(serverR, envir = new.env(parent = sharedEnv))
+      result <- sourceUTF8(serverR, envir = new.env(parent = globalenv()))
       if (!is.null(.globals$server)) {
         result <- .globals$server[[1]]
       }
@@ -227,24 +215,14 @@ shinyAppDir_serverR <- function(appDir, options=list()) {
   onStart <- function() {
     oldwd <<- getwd()
     setwd(appDir)
-    # TODO: we should support hot reloading on global.R and R/*.R changes.
-    if (getOption("shiny.autoload.r", TRUE)) {
-      loadSupport(appDir, renv=sharedEnv, globalrenv=globalenv())
-    }  else {
-      if (file.exists(file.path.ci(appDir, "global.R")))
-        sourceUTF8(file.path.ci(appDir, "global.R"))
-    }
     monitorHandle <<- initAutoReloadMonitor(appDir)
+    if (file.exists(file.path.ci(appDir, "global.R")))
+      sourceUTF8(file.path.ci(appDir, "global.R"))
   }
   onStop <- function() {
     setwd(oldwd)
-    # It is possible that while calling appObj()$onStart() or loadingSupport, an error occured
-    # This will cause `onStop` to be called.
-    #   The `oldwd` will exist, but `monitorHandle` is not a function yet.
-    if (is.function(monitorHandle)) {
-      monitorHandle()
-      monitorHandle <<- NULL
-    }
+    monitorHandle()
+    monitorHandle <<- NULL
   }
 
   structure(
@@ -289,8 +267,7 @@ initAutoReloadMonitor <- function(dir) {
     ".*\\.(r|html?|js|css|png|jpe?g|gif)$")
 
   lastValue <- NULL
-  observeLabel <- paste0("File Auto-Reload - '", basename(dir), "'")
-  obs <- observe(label = observeLabel, {
+  obs <- observe({
     files <- sort(list.files(dir, pattern = filePattern, recursive = TRUE,
       ignore.case = TRUE))
     times <- file.info(files)$mtime
@@ -302,104 +279,29 @@ initAutoReloadMonitor <- function(dir) {
     } else if (!identical(lastValue, times)) {
       # We've changed!
       lastValue <<- times
-      autoReloadCallbacks$invoke()
+      for (session in appsByToken$values()) {
+        session$reload()
+      }
     }
 
     invalidateLater(getOption("shiny.autoreload.interval", 500))
   })
 
-  onStop(obs$destroy)
-
   obs$destroy
 }
 
-#' Load an app's supporting R files
-#'
-#' Loads all of the supporting R files of a Shiny application. Specifically,
-#' this function loads any top-level supporting `.R` files in the `R/` directory
-#' adjacent to the `app.R`/`server.R`/`ui.R` files.
-#'
-#' Since Shiny 1.5.0, this function is called by default when running an
-#' application. If it causes problems, there are two ways to opt out. You can
-#' either place a file named `_disable_autoload.R` in your R/ directory, or
-#' set `options(shiny.autoload.r=FALSE)`. If you set this option, it will
-#' affect any application that runs later in the same R session, potentially
-#' breaking it, so after running your application, you should unset option with
-#' `options(shiny.autoload.r=NULL)`
-#'
-#' @details The files are sourced in alphabetical order (as determined by
-#'   [list.files]). `global.R` is evaluated before the supporting R files in the
-#'   `R/` directory.
-#' @param appDir The application directory. If `appDir` is `NULL` or
-#'   not supplied, the nearest enclosing directory that is a Shiny app, starting
-#'   with the current directory, is used.
-#' @param renv The environmeny in which the files in the `R/` directory should
-#'   be evaluated.
-#' @param globalrenv The environment in which `global.R` should be evaluated. If
-#'   `NULL`, `global.R` will not be evaluated at all.
-#' @export
-loadSupport <- function(appDir=NULL, renv=new.env(parent=globalenv()), globalrenv=globalenv()){
-  require(shiny)
-
-  if (is.null(appDir)) {
-    appDir <- findEnclosingApp(".")
-  }
-
-  if (!is.null(globalrenv)){
-    # Evaluate global.R, if it exists.
-    globalPath <- file.path.ci(appDir, "global.R")
-    if (file.exists(globalPath)){
-      withr::with_dir(appDir, {
-        sourceUTF8(basename(globalPath), envir=globalrenv)
-      })
-    }
-  }
-
-
-  helpersDir <- file.path(appDir, "R")
-
-  disabled <- list.files(helpersDir, pattern="^_disable_autoload\\.r$", recursive=FALSE, ignore.case=TRUE)
-  if (length(disabled) > 0){
-    return(invisible(renv))
-  }
-
-  helpers <- list.files(helpersDir, pattern="\\.[rR]$", recursive=FALSE, full.names=TRUE)
-  # Ensure files in R/ are sorted according to the 'C' locale before sourcing.
-  # This convention is based on the default for packages. For details, see:
-  # https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file
-  helpers <- sort(helpers, method = "radix")
-  helpers <- normalizePath(helpers)
-
-  withr::with_dir(appDir, {
-    lapply(helpers, sourceUTF8, envir=renv)
-  })
-
-  invisible(renv)
-}
-
 # This reads in an app dir for a single-file application (e.g. app.R), and
 # returns a shiny.appobj.
-# appDir must be a normalized (absolute) path, not a relative one
 shinyAppDir_appR <- function(fileName, appDir, options=list())
 {
   fullpath <- file.path.ci(appDir, fileName)
 
-  # In an upcoming version of shiny, this option will go away.
-  if (getOption("shiny.autoload.r", TRUE)) {
-    # Create a child env which contains all the helpers and will be the shared parent
-    # of the ui.R and server.R load.
-    sharedEnv <- new.env(parent = globalenv())
-  } else {
-    sharedEnv <- globalenv()
-  }
-
-
   # This sources app.R and caches the content. When appObj() is called but
   # app.R hasn't changed, it won't re-source the file. But if called and
   # app.R has changed, it'll re-source the file and return the result.
   appObj <- cachedFuncWithFile(appDir, fileName, case.sensitive = FALSE,
     function(appR) {
-      result <- sourceUTF8(fullpath, envir = new.env(parent = sharedEnv))
+      result <- sourceUTF8(fullpath, envir = new.env(parent = globalenv()))
 
       if (!is.shiny.appobj(result))
         stop("app.R did not return a shiny.appobj object.")
@@ -442,23 +344,13 @@ shinyAppDir_appR <- function(fileName, appDir, options=list())
   onStart <- function() {
     oldwd <<- getwd()
     setwd(appDir)
-    # TODO: we should support hot reloading on R/*.R changes.
-    if (getOption("shiny.autoload.r", TRUE)) {
-      loadSupport(appDir, renv=sharedEnv, globalrenv=NULL)
-    }
-    if (!is.null(appObj()$onStart)) appObj()$onStart()
     monitorHandle <<- initAutoReloadMonitor(appDir)
-    invisible()
+    if (!is.null(appObj()$onStart)) appObj()$onStart()
   }
   onStop <- function() {
     setwd(oldwd)
-    # It is possible that while calling appObj()$onStart() or loadingSupport, an error occured
-    # This will cause `onStop` to be called.
-    #   The `oldwd` will exist, but `monitorHandle` is not a function yet.
-    if (is.function(monitorHandle)) {
-      monitorHandle()
-      monitorHandle <<- NULL
-    }
+    monitorHandle()
+    monitorHandle <<- NULL
   }
 
   structure(
@@ -486,34 +378,26 @@ shinyAppDir_appR <- function(fileName, appDir, options=list())
 }
 
 
-#' Shiny App object
-#'
-#' Internal methods for the `shiny.appobj` S3 class.
-#'
-#' @keywords internal
-#' @name shiny.appobj
-NULL
-
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @param x Object to convert to a Shiny app.
 #' @export
 as.shiny.appobj <- function(x) {
   UseMethod("as.shiny.appobj", x)
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @export
 as.shiny.appobj.shiny.appobj <- function(x) {
   x
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @export
 as.shiny.appobj.list <- function(x) {
   shinyApp(ui = x$ui, server = x$server)
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @export
 as.shiny.appobj.character <- function(x) {
   if (identical(tolower(tools::file_ext(x)), "r"))
@@ -522,13 +406,13 @@ as.shiny.appobj.character <- function(x) {
     shinyAppDir(x)
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @export
 is.shiny.appobj <- function(x) {
   inherits(x, "shiny.appobj")
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @param ... Additional parameters to be passed to print.
 #' @export
 print.shiny.appobj <- function(x, ...) {
@@ -543,7 +427,7 @@ print.shiny.appobj <- function(x, ...) {
   do.call("runApp", args)
 }
 
-#' @rdname shiny.appobj
+#' @rdname shinyApp
 #' @method as.tags shiny.appobj
 #' @export
 as.tags.shiny.appobj <- function(x, ...) {
@@ -597,6 +481,7 @@ shiny_rmd_warning <- function() {
 }
 
 #' @rdname knitr_methods
+#' @export
 knit_print.shiny.appobj <- function(x, ...) {
   opts <- x$options %OR% list()
   width <- if (is.null(opts$width)) "100%" else opts$width
@@ -633,6 +518,7 @@ knit_print.shiny.appobj <- function(x, ...) {
 # calling output$value <- renderFoo(...) and fooOutput().
 #' @rdname knitr_methods
 #' @param inline Whether the object is printed inline.
+#' @export
 knit_print.shiny.render.function <- function(x, ..., inline = FALSE) {
   x <- htmltools::as.tags(x, inline = inline)
   output <- knitr::knit_print(tagList(x))
@@ -645,6 +531,7 @@ knit_print.shiny.render.function <- function(x, ..., inline = FALSE) {
 # 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({

R/app_template.R

@@ -1,283 +0,0 @@
-#' Generate a Shiny application from a template
-#'
-#' This function populates a directory with files for a Shiny application.
-#'
-#' In an interactive R session, this function will, by default, prompt the user
-#' which components to add to the application.
-#'
-#' The full example application includes the following files and directories:
-#'
-#' ```
-#' appdir/
-#' |- app.R
-#' |- R
-#' |   |- my-module.R
-#' |   `- sort.R
-#' `- tests
-#'     |- shinytest.R
-#'     |- shinytest
-#'     |   `- mytest.R
-#'     |- testthat.R
-#'     `- testthat
-#'         |- helper-load.R
-#'         |- test-mymodule.R
-#'         |- test-server.R
-#'         `- test-sort.R
-#' ```
-#'
-#' Some notes about these files:
-#' * `app.R` is the main application file.
-#' * All files in the `R/` subdirectory are automatically sourced when the
-#'   application is run.
-#' * `R/sort.R` and `R/my-module.R` are automatically sourced when
-#'   the application is run. The first contains a function `lexical_sort()`,
-#'   and the second contains code for a [Shiny module](moduleServer()) which
-#'   is used in the application.
-#' * `tests/` contains various tests for the application. You may
-#'   choose to use or remove any of them. They can be executed by the
-#'   [runTests()] function.
-#' * `tests/shinytest.R` is a test runner for test files in the
-#'   `tests/shinytest/` directory.
-#' * `tests/shinytest/mytest.R` is a test that uses the
-#'   [shinytest](https://rstudio.github.io/shinytest/) package to do
-#'   snapshot-based testing.
-#' * `tests/testthat.R` is a test runner for test files in the
-#'   `tests/testthat/` directory using the [testthat](https://testthat.r-lib.org/) package.
-#' * `tests/testthat/test-mymodule.R` is a test for an application's module server function.
-#' * `tests/testthat/test-server.R` is a test for the application's server code
-#' * `tests/testthat/test-sort.R` is a test for a supporting function in the `R/` directory.
-#'
-#' @param path Path to create new shiny application template.
-#' @param examples Either one of "default", "ask", "all", or any combination of
-#'   "app", "rdir", "module", "shinytest", and "testthat". In an
-#'   interactive session, "default" falls back to "ask"; in a non-interactive
-#'   session, "default" falls back to "all". With "ask", this function will
-#'   prompt the user to select which template items will be added to the new app
-#'   directory. With "all", all template items will be added to the app
-#'   directory.
-#' @param dryrun If `TRUE`, don't actually write any files; just print out which
-#'   files would be written.
-#'
-#' @export
-shinyAppTemplate <- function(path = NULL, examples = "default", dryrun = FALSE)
-{
-  if (is.null(path)) {
-    stop("Please provide a `path`.")
-  }
-
-  # =======================================================
-  # Option handling
-  # =======================================================
-
-  choices <- c(
-    app       = "app.R            : Main application file",
-    rdir      = "R/sort.R         : Helper file with R code",
-    module    = "R/my-module.R    : Example module",
-    shinytest = "tests/shinytest/ : Tests using shinytest package",
-    testthat  = "tests/testthat/  : Tests using testthat"
-  )
-
-  if (identical(examples, "default")) {
-    if (interactive()) {
-      examples <- "ask"
-    } else {
-      examples <- "all"
-    }
-  }
-
-  if (!identical(examples, "ask") &&
-      !identical(examples, "all") &&
-      any(! examples %in% names(choices)))
-  {
-    stop('`examples` must be one of "default", "ask", "all", or any combination of "',
-      paste(names(choices), collapse = '", "'), '".')
-  }
-
-  if (identical(examples, "ask")) {
-    response <- select_menu(
-      c(all = "All", choices),
-      title = paste0(
-        "Select which of the following to add at ", path, "/ :"
-      ),
-      msg = "Enter one or more numbers (with spaces), or an empty line to exit: \n"
-    )
-
-    examples <- names(response)
-  }
-
-  examples <- unique(examples)
-
-  if ("all" %in% examples) {
-    examples <- names(choices)
-  }
-
-  if (length(examples) == 0) {
-    return(invisible())
-  }
-
-  if ("shinytest" %in% examples) {
-    if (system.file(package = "shinytest") != "" &&
-        utils::packageVersion("shinytest") <= "1.3.1.9000")
-    {
-      message(
-        "The tests/shinytest directory needs shinytest 1.4.0 or later to work properly.\n",
-      )
-      if (system.file(package = "shinytest") != "") {
-        message("You currently have shinytest ",
-                utils::packageVersion("shinytest"), " installed.")
-      }
-
-    }
-  }
-
-  # =======================================================
-  # Utility functions
-  # =======================================================
-
-  # Check if a directory is empty, ignoring certain files
-  dir_is_empty <- function(path) {
-    files <- list.files(path, all.files = TRUE, no.. = TRUE)
-    # Ignore .DS_Store files, which are sometimes automatically created on macOS
-    files <- setdiff(files, ".DS_Store")
-    return(length(files) != 0)
-  }
-
-  # Helper to resolve paths relative to our template
-  template_path <- function(...) {
-    system.file("app_template", ..., package = "shiny")
-  }
-
-  # Resolve path relative to destination
-  dest_path <- function(...) {
-    file.path(path, ...)
-  }
-
-  mkdir <- function(path) {
-    if (!dirExists(path)) {
-      message("Creating ", ensure_trailing_slash(path))
-      if (!dryrun) {
-        dir.create(path, recursive = TRUE)
-      }
-    }
-  }
-
-  # Copy a file from the template directory to the destination directory. If the
-  # file has templating code (it contains `{{` in the text), then run it through
-  # the htmlTemplate().
-  copy_file_one <- function(name) {
-    from <- template_path(name)
-    to <- dest_path(name)
-
-    message("Creating ", to)
-    if (file.exists(to)) {
-      stop(to, " already exists. Please remove it and try again.", call. = FALSE)
-    }
-
-    if (!dryrun) {
-      is_template <- any(grepl("{{", readLines(from), fixed = TRUE))
-
-      if (is_template) {
-        writeChar(
-          as.character(htmlTemplate(
-            from,
-            rdir = "rdir" %in% examples,
-            module = "module" %in% examples
-          )),
-          con = to,
-          eos = NULL
-        )
-      } else {
-        file.copy(from, to)
-      }
-    }
-  }
-
-  # Copy multiple files from template to destination.
-  copy_file <- function(names) {
-    for (name in names) {
-      copy_file_one(name)
-    }
-  }
-
-  # Copy the files for a tests/ subdirectory
-  copy_test_dir <- function(name) {
-    files <- dir(template_path("tests"), recursive = TRUE)
-    # Note: This is not the same as using dir(pattern = "^shinytest"), since
-    # that will not match files inside of shinytest/.
-    files <- files[grepl(paste0("^", name), files)]
-
-    # Filter out files that are not module files in the R directory.
-    if (! "rdir" %in% examples) {
-      # find all files in the testthat folder that are not module or server files
-      is_r_folder_file <- (!grepl("module|server", basename(files))) & (dirname(files) == "testthat")
-      files <- files[!is_r_folder_file]
-    }
-
-    # Filter out module files, if applicable.
-    if (! "module" %in% examples) {
-      files <- files[!grepl("module", files)]
-    }
-
-    mkdir(dest_path("tests"))
-
-    # Create any subdirectories if needed
-    dirs <- setdiff(unique(dirname(files)), ".")
-    for (dir in dirs) {
-      mkdir(dest_path("tests", dir))
-    }
-
-    copy_file(file.path("tests", files))
-  }
-
-  # =======================================================
-  # Main function
-  # =======================================================
-
-  if (is.null(path)) {
-    stop("`path` is missing.")
-  }
-  if (file.exists(path) && !dirExists(path)) {
-    stop(path, " exists but is not a directory.")
-  }
-
-  if (dirExists(path) && dir_is_empty(path)) {
-    if (interactive()) {
-      response <- readline(paste0(
-        ensure_trailing_slash(path),
-        " is not empty. Do you want to create a Shiny app in this directory anyway? [y/n] "
-      ))
-      if (tolower(response) != "y") {
-        return(invisible())
-      }
-    }
-  } else {
-    mkdir(path)
-  }
-
-  if ("app" %in% examples) {
-    copy_file("app.R")
-  }
-
-  # R/ dir with non-module files
-  if ("rdir" %in% examples) {
-    non_module_files <- dir(template_path("R"), pattern = "[^(module)].R$")
-    mkdir(dest_path("R"))
-    copy_file(file.path("R", non_module_files))
-  }
-
-  # R/ dir with module files
-  if ("module" %in% examples) {
-    module_files <- dir(template_path("R"), pattern = "module.R$")
-    mkdir(dest_path("R"))
-    copy_file(file.path("R", module_files))
-  }
-
-  # tests/ dir
-  if ("shinytest" %in% examples) {
-    copy_test_dir("shinytest")
-  }
-  if ("testthat" %in% examples) {
-    copy_test_dir("testthat")
-  }
-  invisible()
-}

R/bookmark-state.R

@@ -479,7 +479,7 @@ getCurrentRestoreContext <- function() {
 #' Restore an input value
 #'
 #' This restores an input value from the current restore context. It should be
-#' called early on inside of input functions (like [textInput()]).
+#' called early on inside of input functions (like \code{\link{textInput}}).
 #'
 #' @param id Name of the input value to restore.
 #' @param default A default value to use, if there's no value to restore.
@@ -509,23 +509,23 @@ restoreInput <- function(id, default) {
 #' It typically is called from an observer. Note that this will not work in
 #' Internet Explorer 9 and below.
 #'
-#' For `mode = "push"`, only three updates are currently allowed:
+#' For \code{mode = "push"}, only three updates are currently allowed:
 #' \enumerate{
-#'   \item the query string (format: `?param1=val1&param2=val2`)
-#'   \item the hash (format: `#hash`)
+#'   \item the query string (format: \code{?param1=val1&param2=val2})
+#'   \item the hash (format: \code{#hash})
 #'   \item both the query string and the hash
-#'     (format: `?param1=val1&param2=val2#hash`)
+#'     (format: \code{?param1=val1&param2=val2#hash})
 #' }
 #'
-#' In other words, if `mode = "push"`, the `queryString` must start
-#' with either `?` or with `#`.
+#' In other words, if \code{mode = "push"}, the \code{queryString} must start
+#' with either \code{?} or with \code{#}.
 #'
 #' A technical curiosity: under the hood, this function is calling the HTML5
-#' history API (which is where the names for the `mode` argument come from).
-#' When `mode = "replace"`, the function called is
-#' `window.history.replaceState(null, null, queryString)`.
-#' When `mode = "push"`, the function called is
-#' `window.history.pushState(null, null, queryString)`.
+#' history API (which is where the names for the \code{mode} argument come from).
+#' When \code{mode = "replace"}, the function called is
+#' \code{window.history.replaceState(null, null, queryString)}.
+#' When \code{mode = "push"}, the function called is
+#' \code{window.history.pushState(null, null, queryString)}.
 #'
 #' @param queryString The new query string to show in the location bar.
 #' @param mode When the query string is updated, should the the current history
@@ -534,7 +534,7 @@ restoreInput <- function(id, default) {
 #'   context. The latter is useful if you want to navigate between states using
 #'   the browser's back and forward buttons. See Examples.
 #' @param session A Shiny session object.
-#' @seealso [enableBookmarking()], [getQueryString()]
+#' @seealso \code{\link{enableBookmarking}}, \code{\link{getQueryString}}
 #' @examples
 #' ## Only run these examples in interactive sessions
 #' if (interactive()) {
@@ -597,7 +597,7 @@ updateQueryString <- function(queryString, mode = c("replace", "push"),
 
 #' Create a button for bookmarking/sharing
 #'
-#' A `bookmarkButton` is a [actionButton()] with a default label
+#' A \code{bookmarkButton} is a \code{\link{actionButton}} with a default label
 #' that consists of a link icon and the text "Bookmark...". It is meant to be
 #' used for bookmarking state.
 #'
@@ -607,10 +607,10 @@ updateQueryString <- function(queryString, mode = c("replace", "push"),
 #' @param id An ID for the bookmark button. The only time it is necessary to set
 #'   the ID unless you have more than one bookmark button in your application.
 #'   If you specify an input ID, it should be excluded from bookmarking with
-#'   [setBookmarkExclude()], and you must create an observer that
+#'   \code{\link{setBookmarkExclude}}, and you must create an observer that
 #'   does the bookmarking when the button is pressed. See the examples below.
 #'
-#' @seealso [enableBookmarking()] for more examples.
+#' @seealso \code{\link{enableBookmarking}} for more examples.
 #'
 #' @examples
 #' ## Only run these examples in interactive sessions
@@ -660,10 +660,10 @@ bookmarkButton <- function(label = "Bookmark...",
 
 #' Generate a modal dialog that displays a URL
 #'
-#' The modal dialog generated by `urlModal` will display the URL in a
+#' The modal dialog generated by \code{urlModal} will display the URL in a
 #' textarea input, and the URL text will be selected so that it can be easily
-#' copied. The result from `urlModal` should be passed to the
-#' [showModal()] function to display it in the browser.
+#' copied. The result from \code{urlModal} should be passed to the
+#' \code{\link{showModal}} function to display it in the browser.
 #'
 #' @param url A URL to display in the dialog box.
 #' @param title A title for the dialog box.
@@ -719,8 +719,8 @@ urlModal <- function(url, title = "Bookmarked application link", subtitle = NULL
 
 #' Display a modal dialog for bookmarking
 #'
-#' This is a wrapper function for [urlModal()] that is automatically
-#' called if an application is bookmarked but no other [onBookmark()]
+#' This is a wrapper function for \code{\link{urlModal}} that is automatically
+#' called if an application is bookmarked but no other \code{\link{onBookmark}}
 #' callback was set. It displays a modal dialog with the bookmark URL, along
 #' with a subtitle that is appropriate for the type of bookmarking used ("url"
 #' or "server").
@@ -761,8 +761,8 @@ showBookmarkUrlModal <- function(url) {
 #' @details
 #'
 #' For restoring state to work properly, the UI must be a function that takes
-#' one argument, `request`. In most Shiny applications, the UI is not a
-#' function; it might have the form `fluidPage(....)`. Converting it to a
+#' one argument, \code{request}. In most Shiny applications, the UI is not a
+#' function; it might have the form \code{fluidPage(....)}. Converting it to a
 #' function is as simple as wrapping it in a function, as in
 #' \code{function(request) \{ fluidPage(....) \}}.
 #'
@@ -771,17 +771,17 @@ showBookmarkUrlModal <- function(url) {
 #' but not if the state is encoded in a URL.
 #'
 #' When bookmarking state, arbitrary values can be stored, by passing a function
-#' as the `onBookmark` argument. That function will be passed a
-#' `ShinySaveState` object. The `values` field of the object is a list
+#' as the \code{onBookmark} argument. That function will be passed a
+#' \code{ShinySaveState} object. The \code{values} field of the object is a list
 #' which can be manipulated to save extra information. Additionally, if the
-#' state is being saved on the server, and the `dir` field of that object
+#' state is being saved on the server, and the \code{dir} field of that object
 #' can be used to save extra information to files in that directory.
 #'
 #' For saved-to-server state, this is how the state directory is chosen:
 #' \itemize{
 #'   \item If running in a hosting environment such as Shiny Server or
 #'     Connect, the hosting environment will choose the directory.
-#'   \item If running an app in a directory with [runApp()], the
+#'   \item If running an app in a directory with \code{\link{runApp}()}, the
 #'     saved states will be saved in a subdirectory of the app called
 #'    shiny_bookmarks.
 #'   \item If running a Shiny app object that is generated from code (not run
@@ -789,22 +789,22 @@ showBookmarkUrlModal <- function(url) {
 #'     the current working directory called shiny_bookmarks.
 #' }
 #'
-#' When used with [shinyApp()], this function must be called before
-#' `shinyApp()`, or in the `shinyApp()`'s `onStart` function. An
-#' alternative to calling the `enableBookmarking()` function is to use the
-#' `enableBookmarking` *argument* for `shinyApp()`. See examples
+#' When used with \code{\link{shinyApp}()}, this function must be called before
+#' \code{shinyApp()}, or in the \code{shinyApp()}'s \code{onStart} function. An
+#' alternative to calling the \code{enableBookmarking()} function is to use the
+#' \code{enableBookmarking} \emph{argument} for \code{shinyApp()}. See examples
 #' below.
 #'
-#' @param store Either `"url"`, which encodes all of the relevant values in
-#'   a URL, `"server"`, which saves to disk on the server, or
-#'   `"disable"`, which disables any previously-enabled bookmarking.
+#' @param store Either \code{"url"}, which encodes all of the relevant values in
+#'   a URL, \code{"server"}, which saves to disk on the server, or
+#'   \code{"disable"}, which disables any previously-enabled bookmarking.
 #'
-#' @seealso [onBookmark()], [onBookmarked()],
-#'   [onRestore()], and [onRestored()] for registering
+#' @seealso \code{\link{onBookmark}}, \code{\link{onBookmarked}},
+#'   \code{\link{onRestore}}, and \code{\link{onRestored}} for registering
 #'   callback functions that are invoked when the state is bookmarked or
 #'   restored.
 #'
-#'   Also see [updateQueryString()].
+#'   Also see \code{\link{updateQueryString}}.
 #'
 #' @export
 #' @examples
@@ -983,7 +983,7 @@ enableBookmarking <- function(store = c("url", "server", "disable")) {
 #' @param names A character vector containing names of inputs to exclude from
 #'   bookmarking.
 #' @param session A shiny session object.
-#' @seealso [enableBookmarking()] for examples.
+#' @seealso \code{\link{enableBookmarking}} for examples.
 #' @export
 setBookmarkExclude <- function(names = character(0), session = getDefaultReactiveDomain()) {
   session$setBookmarkExclude(names)
@@ -998,17 +998,17 @@ setBookmarkExclude <- function(names = character(0), session = getDefaultReactiv
 #' should be called within an application's server function.
 #'
 #' \itemize{
-#'   \item `onBookmark` registers a function that will be called just
+#'   \item \code{onBookmark} registers a function that will be called just
 #'     before Shiny bookmarks state.
-#'   \item `onBookmarked` registers a function that will be called just
+#'   \item \code{onBookmarked} registers a function that will be called just
 #'     after Shiny bookmarks state.
-#'   \item `onRestore` registers a function that will be called when a
+#'   \item \code{onRestore} registers a function that will be called when a
 #'     session is restored, after the server function executes, but before all
 #'     other reactives, observers and render functions are run.
-#'   \item `onRestored` registers a function that will be called after a
-#'     session is restored. This is similar to `onRestore`, but it will be
+#'   \item \code{onRestored} registers a function that will be called after a
+#'     session is restored. This is similar to \code{onRestore}, but it will be
 #'     called after all reactives, observers, and render functions run, and
-#'     after results are sent to the client browser. `onRestored`
+#'     after results are sent to the client browser. \code{onRestored}
 #'     callbacks can be useful for sending update messages to the client
 #'     browser.
 #' }
@@ -1019,25 +1019,25 @@ setBookmarkExclude <- function(names = character(0), session = getDefaultReactiv
 #' arguments to cancel the registration.
 #'
 #' The callback function that is passed to these functions should take one
-#' argument, typically named "state" (for `onBookmark`, `onRestore`,
-#' and `onRestored`) or "url" (for `onBookmarked`).
+#' argument, typically named "state" (for \code{onBookmark}, \code{onRestore},
+#' and \code{onRestored}) or "url" (for \code{onBookmarked}).
 #'
-#' For `onBookmark`, the state object has three relevant fields. The
-#' `values` field is an environment which can be used to save arbitrary
+#' For \code{onBookmark}, the state object has three relevant fields. The
+#' \code{values} field is an environment which can be used to save arbitrary
 #' values (see examples). If the state is being saved to disk (as opposed to
-#' being encoded in a URL), the `dir` field contains the name of a
+#' being encoded in a URL), the \code{dir} field contains the name of a
 #' directory which can be used to store extra files. Finally, the state object
-#' has an `input` field, which is simply the application's `input`
+#' has an \code{input} field, which is simply the application's \code{input}
 #' object. It can be read, but not modified.
 #'
-#' For `onRestore` and `onRestored`, the state object is a list. This
-#' list contains `input`, which is a named list of input values to restore,
-#' `values`, which is an environment containing arbitrary values that were
-#' saved in `onBookmark`, and `dir`, the name of the directory that
+#' For \code{onRestore} and \code{onRestored}, the state object is a list. This
+#' list contains \code{input}, which is a named list of input values to restore,
+#' \code{values}, which is an environment containing arbitrary values that were
+#' saved in \code{onBookmark}, and \code{dir}, the name of the directory that
 #' the state is being restored from, and which could have been used to save
 #' extra files.
 #'
-#' For `onBookmarked`, the callback function receives a string with the
+#' For \code{onBookmarked}, the callback function receives a string with the
 #' bookmark URL. This callback function should be used to display UI in the
 #' client browser with the bookmark URL. If no callback function is registered,
 #' then Shiny will by default display a modal dialog with the bookmark URL.

R/bootstrap-deprecated.R

@@ -1,47 +0,0 @@
-#' Create a page with a sidebar
-#'
-#' **DEPRECATED**: use [fluidPage()] and [sidebarLayout()] instead.
-#'
-#' @param headerPanel The [headerPanel] with the application title
-#' @param sidebarPanel The [sidebarPanel] containing input controls
-#' @param mainPanel The [mainPanel] containing outputs
-#' @keywords internal
-#' @return A UI defintion that can be passed to the [shinyUI] function
-#' @export
-pageWithSidebar <- function(headerPanel,
-                            sidebarPanel,
-                            mainPanel) {
-
-  bootstrapPage(
-    # basic application container divs
-    div(
-      class="container-fluid",
-      div(class="row",
-          headerPanel
-      ),
-      div(class="row",
-          sidebarPanel,
-          mainPanel
-      )
-    )
-  )
-}
-
-#' Create a header panel
-#'
-#' **DEPRECATED**: use [titlePanel()] instead.
-#'
-#' @param title An application title to display
-#' @param windowTitle The title that should be displayed by the browser window.
-#'   Useful if `title` is not a string.
-#' @return A headerPanel that can be passed to [pageWithSidebar]
-#' @keywords internal
-#' @export
-headerPanel <- function(title, windowTitle=title) {
-  tagList(
-    tags$head(tags$title(windowTitle)),
-    div(class="col-sm-12",
-      h1(title)
-    )
-  )
-}

R/bootstrap-layout.R

@@ -10,26 +10,25 @@
 #'
 #' @param ... Elements to include within the page
 #' @param title The browser window title (defaults to the host URL of the page).
-#'   Can also be set as a side effect of the [titlePanel()] function.
+#'   Can also be set as a side effect of the \code{\link{titlePanel}} function.
 #' @param responsive This option is deprecated; it is no longer optional with
 #'   Bootstrap 3.
 #' @param theme Alternative Bootstrap stylesheet (normally a css file within the
 #'   www directory). For example, to use the theme located at
-#'   `www/bootstrap.css` you would use `theme = "bootstrap.css"`.
+#'   \code{www/bootstrap.css} you would use \code{theme = "bootstrap.css"}.
 #'
-#' @return A UI defintion that can be passed to the [shinyUI] function.
+#' @return A UI defintion that can be passed to the \link{shinyUI} function.
 #'
-#' @details To create a fluid page use the `fluidPage` function and include
-#'   instances of `fluidRow` and [column()] within it. As an
+#' @details To create a fluid page use the \code{fluidPage} function and include
+#'   instances of \code{fluidRow} and \code{\link{column}} within it. As an
 #'   alternative to low-level row and column functions you can also use
-#'   higher-level layout functions like [sidebarLayout()].
+#'   higher-level layout functions like \code{\link{sidebarLayout}}.
 #'
-#' @note See the [
-#'   Shiny-Application-Layout-Guide](http://shiny.rstudio.com/articles/layout-guide.html) for additional details on laying out fluid
+#' @note See the \href{http://shiny.rstudio.com/articles/layout-guide.html}{
+#'   Shiny-Application-Layout-Guide} for additional details on laying out fluid
 #'   pages.
 #'
-#' @family layout functions
-#' @seealso [column()]
+#' @seealso \code{\link{column}}, \code{\link{sidebarLayout}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -117,23 +116,21 @@ fluidRow <- function(...) {
 #'   Bootstrap 3.
 #' @param theme Alternative Bootstrap stylesheet (normally a css file within the
 #'   www directory). For example, to use the theme located at
-#'   `www/bootstrap.css` you would use `theme = "bootstrap.css"`.
+#'   \code{www/bootstrap.css} you would use \code{theme = "bootstrap.css"}.
 #'
-#' @return A UI defintion that can be passed to the [shinyUI] function.
+#' @return A UI defintion that can be passed to the \link{shinyUI} function.
 #'
-#' @details To create a fixed page use the `fixedPage` function and include
-#'   instances of `fixedRow` and [column()] within it. Note that
-#'   unlike [fluidPage()], fixed pages cannot make use of higher-level
-#'   layout functions like `sidebarLayout`, rather, all layout must be done
-#'   with `fixedRow` and `column`.
+#' @details To create a fixed page use the \code{fixedPage} function and include
+#'   instances of \code{fixedRow} and \code{\link{column}} within it. Note that
+#'   unlike \code{\link{fluidPage}}, fixed pages cannot make use of higher-level
+#'   layout functions like \code{sidebarLayout}, rather, all layout must be done
+#'   with \code{fixedRow} and \code{column}.
 #'
-#' @note See the [
-#'   Shiny Application Layout Guide](http://shiny.rstudio.com/articles/layout-guide.html) for additional details on laying out fixed
+#' @note See the \href{http://shiny.rstudio.com/articles/layout-guide.html}{
+#'   Shiny Application Layout Guide} for additional details on laying out fixed
 #'   pages.
 #'
-#' @family layout functions
-#'
-#' @seealso [column()]
+#' @seealso \code{\link{column}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -172,8 +169,8 @@ fixedRow <- function(...) {
 
 #' Create a column within a UI definition
 #'
-#' Create a column for use within a  [fluidRow()] or
-#' [fixedRow()]
+#' Create a column for use within a  \code{\link{fluidRow}} or
+#' \code{\link{fixedRow}}
 #'
 #' @param width The grid width of the column (must be between 1 and 12)
 #' @param ... Elements to include within the column
@@ -181,10 +178,10 @@ fixedRow <- function(...) {
 #'   previous column.
 #'
 #' @return A column that can be included within a
-#'   [fluidRow()] or [fixedRow()].
+#'   \code{\link{fluidRow}} or \code{\link{fixedRow}}.
 #'
 #'
-#' @seealso [fluidRow()], [fixedRow()].
+#' @seealso \code{\link{fluidRow}}, \code{\link{fixedRow}}.
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -231,12 +228,8 @@ column <- function(width, ..., offset = 0) {
     stop("column width must be between 1 and 12")
 
   colClass <- paste0("col-sm-", width)
-  if (offset > 0) {
-    # offset-md-x is for bootstrap 4 forward compat
-    # (every size tier has been bumped up one level)
-    # https://github.com/twbs/bootstrap/blob/74b8fe7/docs/4.3/migration/index.html#L659
-    colClass <- paste0(colClass, " offset-md-", offset, " col-sm-offset-", offset)
-  }
+  if (offset > 0)
+    colClass <- paste0(colClass, " col-sm-offset-", offset)
   div(class = colClass, ...)
 }
 
@@ -247,9 +240,10 @@ column <- function(width, ..., offset = 0) {
 #' @param windowTitle The title that should be displayed by the browser window.
 #'
 #' @details Calling this function has the side effect of including a
-#'   `title` tag within the head. You can also specify a page title
+#'   \code{title} tag within the head. You can also specify a page title
 #'   explicitly using the `title` parameter of the top-level page function.
 #'
+#'
 #' @examples
 #' ## Only run examples in interactive R sessions
 #' if (interactive()) {
@@ -269,23 +263,16 @@ titlePanel <- function(title, windowTitle=title) {
 
 #' Layout a sidebar and main area
 #'
-#' Create a layout (`sidebarLayout()`) with a sidebar (`sidebarPanel()`) and
-#' main area (`mainPanel()`). The sidebar is displayed with a distinct
-#' background color and typically contains input controls. The main
+#' Create a layout with a sidebar and main area. The sidebar is displayed with a
+#' distinct background color and typically contains input controls. The main
 #' area occupies 2/3 of the horizontal width and typically contains outputs.
 #'
-#' @param sidebarPanel The `sidebarPanel()` containing input controls.
-#' @param mainPanel The `mainPanel()` containing outputs.
+#' @param sidebarPanel The \link{sidebarPanel} containing input controls
+#' @param mainPanel The \link{mainPanel} containing outputs
 #' @param position The position of the sidebar relative to the main area ("left"
-#'   or "right").
-#' @param fluid `TRUE` to use fluid layout; `FALSE` to use fixed
+#'   or "right")
+#' @param fluid \code{TRUE} to use fluid layout; \code{FALSE} to use fixed
 #'   layout.
-#' @param width The width of the sidebar and main panel. By default, the
-#'   sidebar takes up 1/3 of the width, and the main panel 2/3. The total
-#'   width must be 12 or less.
-#' @param ... Output elements to include in the sidebar/main panel.
-#'
-#' @family layout functions
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -350,34 +337,16 @@ sidebarLayout <- function(sidebarPanel,
     fixedRow(firstPanel, secondPanel)
 }
 
-#' @export
-#' @rdname sidebarLayout
-sidebarPanel <- function(..., width = 4) {
-  div(class=paste0("col-sm-", width),
-    tags$form(class="well",
-      ...
-    )
-  )
-}
-
-#' @export
-#' @rdname sidebarLayout
-mainPanel <- function(..., width = 8) {
-  div(class=paste0("col-sm-", width),
-    ...
-  )
-}
-
 #' Lay out UI elements vertically
 #'
 #' Create a container that includes one or more rows of content (each element
 #' passed to the container will appear on it's own line in the UI)
 #'
 #' @param ... Elements to include within the container
-#' @param fluid `TRUE` to use fluid layout; `FALSE` to use fixed
+#' @param fluid \code{TRUE} to use fluid layout; \code{FALSE} to use fixed
 #'   layout.
 #'
-#' @family layout functions
+#' @seealso \code{\link{fluidPage}}, \code{\link{flowLayout}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -408,14 +377,14 @@ verticalLayout <- function(..., fluid = TRUE) {
 #' Lays out elements in a left-to-right, top-to-bottom arrangement. The elements
 #' on a given row will be top-aligned with each other. This layout will not work
 #' well with elements that have a percentage-based width (e.g.
-#' [plotOutput()] at its default setting of `width = "100%"`).
+#' \code{\link{plotOutput}} at its default setting of \code{width = "100\%"}).
 #'
 #' @param ... Unnamed arguments will become child elements of the layout. Named
 #'   arguments will become HTML attributes on the outermost tag.
 #' @param cellArgs Any additional attributes that should be used for each cell
 #'   of the layout.
 #'
-#' @family layout functions
+#' @seealso \code{\link{verticalLayout}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -446,7 +415,7 @@ flowLayout <- function(..., cellArgs = list()) {
 
 #' Input panel
 #'
-#' A [flowLayout()] with a grey border and light grey background,
+#' A \code{\link{flowLayout}} with a grey border and light grey background,
 #' suitable for wrapping inputs.
 #'
 #' @param ... Input controls or other HTML elements.
@@ -466,13 +435,11 @@ inputPanel <- function(...) {
 #'   arguments will become HTML attributes on the outermost tag.
 #' @param cellWidths Character or numeric vector indicating the widths of the
 #'   individual cells. Recycling will be used if needed. Character values will
-#'   be interpreted as CSS lengths (see [validateCssUnit()]), numeric
+#'   be interpreted as CSS lengths (see \code{\link{validateCssUnit}}), numeric
 #'   values as pixels.
 #' @param cellArgs Any additional attributes that should be used for each cell
 #'   of the layout.
 #'
-#' @family layout functions
-#'
 #' @examples
 #' ## Only run examples in interactive R sessions
 #' if (interactive()) {
@@ -542,41 +509,41 @@ splitLayout <- function(..., cellWidths = NULL, cellArgs = list()) {
 #'
 #' 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. **Warning:** Flex Box is not well supported
+#' 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 `fillRow` and `fillCol` inside of other
-#'   Shiny containers, such as [sidebarLayout()],
-#'   [navbarPage()], or even `tags$div`, you will probably find
-#'   that they will not appear. This is due to `fillRow` and `fillCol`
-#'   defaulting to `height="100%"`, which will only work inside of
+#' @details If you try to use \code{fillRow} and \code{fillCol} inside of other
+#'   Shiny containers, such as \code{\link{sidebarLayout}},
+#'   \code{\link{navbarPage}}, or even \code{tags$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 `fillRow`/`fillCol` inside of `fillPage`,
-#'       `fillRow`, or `fillCol`
-#'     \item provide an explicit `height` argument to
-#'       `fillRow`/`fillCol`
+#'     \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
-#'   [tagList()] or [div()] to combine them.) Named
-#'   arguments will be used as attributes on the `div` element that
+#'   \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 `1` or `2` to evenly distribute the available
+#'   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,
-#'   `flex = c(2, 3)` would cause the space to be split 40%/60% between
+#'   \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 `"100%"` to be
-#'   effective, the parent must be `fillPage`, another
-#'   `fillRow`/`fillCol`, or some other HTML element whose height is
+#'   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

R/bootstrap.R

@@ -4,27 +4,27 @@ NULL
 #' Create a Bootstrap page
 #'
 #' Create a Shiny UI page that loads the CSS and JavaScript for
-#' [Bootstrap](http://getbootstrap.com/), and has no content in the page
+#' \href{http://getbootstrap.com/}{Bootstrap}, and has no content in the page
 #' body (other than what you provide).
 #'
 #' This function is primarily intended for users who are proficient in HTML/CSS,
 #' and know how to lay out pages in Bootstrap. Most applications should use
-#' [fluidPage()] along with layout functions like
-#' [fluidRow()] and [sidebarLayout()].
+#' \code{\link{fluidPage}} along with layout functions like
+#' \code{\link{fluidRow}} and \code{\link{sidebarLayout}}.
 #'
 #' @param ... The contents of the document body.
 #' @param title The browser window title (defaults to the host URL of the page)
 #' @param responsive This option is deprecated; it is no longer optional with
 #'   Bootstrap 3.
 #' @param theme Alternative Bootstrap stylesheet (normally a css file within the
-#'   www directory, e.g. `www/bootstrap.css`)
+#'   www directory, e.g. \code{www/bootstrap.css})
 #'
-#' @return A UI defintion that can be passed to the [shinyUI] function.
+#' @return A UI defintion that can be passed to the \link{shinyUI} function.
 #'
-#' @note The `basicPage` function is deprecated, you should use the
-#'   [fluidPage()] function instead.
+#' @note The \code{basicPage} function is deprecated, you should use the
+#'   \code{\link{fluidPage}} function instead.
 #'
-#' @seealso [fluidPage()], [fixedPage()]
+#' @seealso \code{\link{fluidPage}}, \code{\link{fixedPage}}
 #' @export
 bootstrapPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
 
@@ -52,15 +52,15 @@ bootstrapPage <- function(..., title = NULL, responsive = NULL, theme = NULL) {
 #' components in a web page.
 #'
 #' It isn't necessary to call this function if you use
-#' [bootstrapPage()] or others which use `bootstrapPage`, such
-#' [basicPage()], [fluidPage()], [fillPage()],
-#' [pageWithSidebar()], and [navbarPage()], because they
+#' \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", "3.4.1",
+  htmlDependency("bootstrap", "3.3.7",
     c(
       href = "shared/bootstrap",
       file = system.file("www/shared/bootstrap", package = "shiny")
@@ -85,34 +85,34 @@ basicPage <- function(...) {
 
 #' Create a page that fills the window
 #'
-#' `fillPage` creates a page whose height and width always fill the
+#' \code{fillPage} creates a page whose height and width always fill the
 #' available area of the browser window.
 #'
-#' The [fluidPage()] and [fixedPage()] functions are used
+#' 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.
 #'
-#' `fillPage` is designed to latch the document body's size to the size of
+#' \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, `fluidPage(plotOutput("plot", height = "100%"))` will not
-#' work as expected; the plot element's effective height will be `0`,
-#' because the plot's containing elements (`<div>` and `<body>`) have
-#' *automatic* height; that is, they determine their own height based on
+#' 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,
-#' `fillPage(plotOutput("plot", height = "100%"))` will work because
-#' `fillPage` fixes the `<body>` height at 100% of the window height.
+#' \code{fillPage(plotOutput("plot", height = "100\%"))} will work because
+#' \code{fillPage} fixes the \code{<body>} height at 100\% of the window height.
 #'
-#' Note that `fillPage(plotOutput("plot"))` will not cause the plot to fill
-#' the page. Like most Shiny output widgets, `plotOutput`'s default height
-#' is a fixed number of pixels. You must explicitly set `height = "100%"`
+#' 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
-#' `fillPage` and the plots/widgets. Any container that has an automatic
-#' height will cause children with `height = "100%"` to misbehave. Stick
+#' \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.
 #'
@@ -127,11 +127,9 @@ basicPage <- function(...) {
 #'   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 `TRUE`, load the Bootstrap CSS library.
+#' @param bootstrap If \code{TRUE}, load the Bootstrap CSS library.
 #' @param theme URL to alternative Bootstrap stylesheet.
 #'
-#' @family layout functions
-#'
 #' @examples
 #' fillPage(
 #'   tags$style(type = "text/css",
@@ -180,62 +178,115 @@ collapseSizes <- function(padding) {
     collapse = " ")
 }
 
+#' Create a page with a sidebar
+#'
+#' Create a Shiny UI that contains a header with the application title, a
+#' sidebar for input controls, and a main area for output.
+#'
+#' @param headerPanel The \link{headerPanel} with the application title
+#' @param sidebarPanel The \link{sidebarPanel} containing input controls
+#' @param mainPanel The \link{mainPanel} containing outputs
+
+#' @return A UI defintion that can be passed to the \link{shinyUI} function
+#'
+#' @note This function is deprecated. You should use \code{\link{fluidPage}}
+#' along with \code{\link{sidebarLayout}} to implement a page with a sidebar.
+#'
+#' @examples
+#' # Define UI
+#' pageWithSidebar(
+#'
+#'   # Application title
+#'   headerPanel("Hello Shiny!"),
+#'
+#'   # Sidebar with a slider input
+#'   sidebarPanel(
+#'     sliderInput("obs",
+#'                 "Number of observations:",
+#'                 min = 0,
+#'                 max = 1000,
+#'                 value = 500)
+#'   ),
+#'
+#'   # Show a plot of the generated distribution
+#'   mainPanel(
+#'     plotOutput("distPlot")
+#'   )
+#' )
+#' @export
+pageWithSidebar <- function(headerPanel,
+                            sidebarPanel,
+                            mainPanel) {
+
+  bootstrapPage(
+    # basic application container divs
+    div(
+      class="container-fluid",
+      div(class="row",
+          headerPanel
+      ),
+      div(class="row",
+          sidebarPanel,
+          mainPanel
+      )
+    )
+  )
+}
+
 #' Create a page with a top level navigation bar
 #'
 #' Create a page that contains a top level navigation bar that can be used to
-#' toggle a set of [tabPanel()] elements.
+#' toggle a set of \code{\link{tabPanel}} elements.
 #'
 #' @param title The title to display in the navbar
-#' @param ... [tabPanel()] elements to include in the page. The
-#'   `navbarMenu` function also accepts strings, which will be used as menu
-#'   section headers. If the string is a set of dashes like `"----"` a
+#' @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 `input$`*`id`* in your
+#' @param id If provided, you can use \code{input$}\emph{\code{id}} in your
 #'   server logic to determine which of the current tabs is active. The value
-#'   will correspond to the `value` argument that is passed to
-#'   [tabPanel()].
-#' @param selected The `value` (or, if none was supplied, the `title`)
-#'   of the tab that should be selected by default. If `NULL`, the first
+#'   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 (`"static-top"`), pinned at
-#'   the top (`"fixed-top"`), or pinned at the bottom
-#'   (`"fixed-bottom"`). Note that using `"fixed-top"` or
-#'   `"fixed-bottom"` will cause the navbar to overlay your body content,
+#'   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;}")}
 #' @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
 #'   tabPanels
-#' @param inverse `TRUE` to use a dark background and light text for the
+#' @param inverse \code{TRUE} to use a dark background and light text for the
 #'   navigation bar
-#' @param collapsible `TRUE` to automatically collapse the navigation
+#' @param collapsible \code{TRUE} to automatically collapse the navigation
 #'   elements into a menu when the width of the browser is less than 940 pixels
 #'   (useful for viewing on smaller touchscreen device)
-#' @param collapsable Deprecated; use `collapsible` instead.
-#' @param fluid `TRUE` to use a fluid layout. `FALSE` to use a fixed
+#' @param collapsable Deprecated; use \code{collapsible} instead.
+#' @param fluid \code{TRUE} to use a fluid layout. \code{FALSE} to use a fixed
 #'   layout.
 #' @param responsive This option is deprecated; it is no longer optional with
 #'   Bootstrap 3.
 #' @param theme Alternative Bootstrap stylesheet (normally a css file within the
 #'   www directory). For example, to use the theme located at
-#'   `www/bootstrap.css` you would use `theme = "bootstrap.css"`.
+#'   \code{www/bootstrap.css} you would use \code{theme = "bootstrap.css"}.
 #' @param windowTitle The title that should be displayed by the browser window.
-#'   Useful if `title` is not a string.
-#' @param icon Optional icon to appear on a `navbarMenu` tab.
+#'   Useful if \code{title} is not a string.
+#' @param icon Optional icon to appear on a \code{navbarMenu} tab.
 #'
-#' @return A UI defintion that can be passed to the [shinyUI] function.
+#' @return A UI defintion that can be passed to the \link{shinyUI} function.
 #'
-#' @details The `navbarMenu` function can be used to create an embedded
+#' @details The \code{navbarMenu} function can be used to create an embedded
 #'   menu within the navbar that in turns includes additional tabPanels (see
 #'   example below).
 #'
-#' @seealso [tabPanel()], [tabsetPanel()],
-#'   [updateNavbarPage()], [insertTab()],
-#'   [showTab()]
-#'
-#' @family layout functions
+#' @seealso \code{\link{tabPanel}}, \code{\link{tabsetPanel}},
+#'   \code{\link{updateNavbarPage}}, \code{\link{insertTab}},
+#'   \code{\link{showTab}}
 #'
 #' @examples
 #' navbarPage("App Title",
@@ -343,9 +394,9 @@ navbarPage <- function(title,
   )
 }
 
-#' @param menuName A name that identifies this `navbarMenu`. This
+#' @param menuName A name that identifies this \code{navbarMenu}. This
 #'   is needed if you want to insert/remove or show/hide an entire
-#'   `navbarMenu`.
+#'   \code{navbarMenu}.
 #'
 #' @rdname navbarPage
 #' @export
@@ -357,10 +408,31 @@ navbarMenu <- function(title, ..., menuName = title, icon = NULL) {
             class = "shiny.navbarmenu")
 }
 
+#' Create a header panel
+#'
+#' Create a header panel containing an application title.
+#'
+#' @param title An application title to display
+#' @param windowTitle The title that should be displayed by the browser window.
+#'   Useful if \code{title} is not a string.
+#' @return A headerPanel that can be passed to \link{pageWithSidebar}
+#'
+#' @examples
+#' headerPanel("Hello Shiny!")
+#' @export
+headerPanel <- function(title, windowTitle=title) {
+  tagList(
+    tags$head(tags$title(windowTitle)),
+    div(class="col-sm-12",
+      h1(title)
+    )
+  )
+}
+
 #' Create a well panel
 #'
 #' Creates a panel with a slightly inset border and grey background. Equivalent
-#' to Bootstrap's `well` CSS class.
+#' to Bootstrap's \code{well} CSS class.
 #'
 #' @param ... UI elements to include inside the panel.
 #' @return The newly created panel.
@@ -369,28 +441,81 @@ wellPanel <- function(...) {
   div(class="well", ...)
 }
 
+#' Create a sidebar panel
+#'
+#' Create a sidebar panel containing input controls that can in turn be passed
+#' to \code{\link{sidebarLayout}}.
+#'
+#' @param ... UI elements to include on the sidebar
+#' @param width The width of the sidebar. For fluid layouts this is out of 12
+#'   total units; for fixed layouts it is out of whatever the width of the
+#'   sidebar's parent column is.
+#' @return A sidebar that can be passed to \code{\link{sidebarLayout}}
+#'
+#' @examples
+#' # Sidebar with controls to select a dataset and specify
+#' # the number of observations to view
+#' sidebarPanel(
+#'   selectInput("dataset", "Choose a dataset:",
+#'               choices = c("rock", "pressure", "cars")),
+#'
+#'   numericInput("obs", "Observations:", 10)
+#' )
+#' @export
+sidebarPanel <- function(..., width = 4) {
+  div(class=paste0("col-sm-", width),
+    tags$form(class="well",
+      ...
+    )
+  )
+}
+
+#' Create a main panel
+#'
+#' Create a main panel containing output elements that can in turn be passed to
+#' \code{\link{sidebarLayout}}.
+#'
+#' @param ... Output elements to include in the main panel
+#' @param width The width of the main panel. For fluid layouts this is out of 12
+#'   total units; for fixed layouts it is out of whatever the width of the main
+#'   panel's parent column is.
+#' @return A main panel that can be passed to \code{\link{sidebarLayout}}.
+#'
+#' @examples
+#' # Show the caption and plot of the requested variable against mpg
+#' mainPanel(
+#'    h3(textOutput("caption")),
+#'    plotOutput("mpgPlot")
+#' )
+#' @export
+mainPanel <- function(..., width = 8) {
+  div(class=paste0("col-sm-", width),
+    ...
+  )
+}
+
 #' Conditional Panel
 #'
 #' Creates a panel that is visible or not, depending on the value of a
 #' JavaScript expression. The JS expression is evaluated once at startup and
 #' whenever Shiny detects a relevant change in input/output.
 #'
-#' In the JS expression, you can refer to `input` and `output`
+#' In the JS expression, you can refer to \code{input} and \code{output}
 #' JavaScript objects that contain the current values of input and output. For
-#' example, if you have an input with an id of `foo`, then you can use
-#' `input.foo` to read its value. (Be sure not to modify the input/output
+#' example, if you have an input with an id of \code{foo}, then you can use
+#' \code{input.foo} to read its value. (Be sure not to modify the input/output
 #' objects, as this may cause unpredictable behavior.)
 #'
 #' @param condition A JavaScript expression that will be evaluated repeatedly to
 #'   determine whether the panel should be displayed.
-#' @param ns The [`namespace()`][NS] object of the current module, if
+#' @param ns The \code{\link[=NS]{namespace}} object of the current module, if
 #'   any.
 #' @param ... Elements to include in the panel.
 #'
 #' @note You are not recommended to use special JavaScript characters such as a
-#'   period `.` in the input id's, but if you do use them anyway, for
-#'   example, `inputId = "foo.bar"`, you will have to use
-#'   `input["foo.bar"]` instead of `input.foo.bar` to read the input
+#'   period \code{.} in the input id's, but if you do use them anyway, for
+#'   example, \code{inputId = "foo.bar"}, you will have to use
+#'   \code{input["foo.bar"]} instead of \code{input.foo.bar} to read the input
 #'   value.
 #' @examples
 #' ## Only run this example in interactive R sessions
@@ -464,17 +589,18 @@ helpText <- function(...) {
 
 #' Create a tab panel
 #'
+#' Create a tab panel that can be included within a \code{\link{tabsetPanel}}.
 #'
 #' @param title Display title for tab
 #' @param ... UI elements to include within the tab
-#' @param value The value that should be sent when `tabsetPanel` reports
-#'   that this tab is selected. If omitted and `tabsetPanel` has an
-#'   `id`, then the title will be used..
+#' @param value The value that should be sent when \code{tabsetPanel} reports
+#'   that this tab is selected. If omitted and \code{tabsetPanel} has an
+#'   \code{id}, then the title will be used..
 #' @param icon Optional icon to appear on the tab. This attribute is only
-#' valid when using a `tabPanel` within a [navbarPage()].
-#' @return A tab that can be passed to [tabsetPanel()]
+#' valid when using a \code{tabPanel} within a \code{\link{navbarPage}}.
+#' @return A tab that can be passed to \code{\link{tabsetPanel}}
 #'
-#' @seealso [tabsetPanel()]
+#' @seealso \code{\link{tabsetPanel}}
 #'
 #' @examples
 #' # Show a tabset that includes a plot, summary, and
@@ -487,49 +613,35 @@ helpText <- function(...) {
 #'   )
 #' )
 #' @export
-#' @describeIn tabPanel Create a tab panel that can be included within a [tabsetPanel()] or a [navbarPage()].
 tabPanel <- function(title, ..., value = title, icon = NULL) {
-  div(
-    class = "tab-pane",
-    title = title,
-    `data-value` = value,
-    `data-icon-class` = iconClass(icon),
-    ...
-  )
-}
-#' @export
-#' @describeIn tabPanel Create a tab panel that drops the title argument.
-#'   This function should be used within `tabsetPanel(type = "hidden")`. See [tabsetPanel()] for example usage.
-tabPanelBody <- function(..., value = NULL, icon = NULL) {
-  tabPanel(title = NULL, ..., value = value, icon = icon)
+  divTag <- div(class="tab-pane",
+                title=title,
+                `data-value`=value,
+                `data-icon-class` = iconClass(icon),
+                ...)
 }
 
 #' Create a tabset panel
 #'
-#' Create a tabset that contains [tabPanel()] elements. Tabsets are
+#' Create a tabset that contains \code{\link{tabPanel}} elements. Tabsets are
 #' useful for dividing output into multiple independently viewable sections.
 #'
-#' @param ... [tabPanel()] elements to include in the tabset
-#' @param id If provided, you can use `input$`*`id`* in your
+#' @param ... \code{\link{tabPanel}} elements to include in the tabset
+#' @param id If provided, you can use \code{input$}\emph{\code{id}} in your
 #'   server logic to determine which of the current tabs is active. The value
-#'   will correspond to the `value` argument that is passed to
-#'   [tabPanel()].
-#' @param selected The `value` (or, if none was supplied, the `title`)
-#'   of the tab that should be selected by default. If `NULL`, the first
+#'   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 type  \describe{
-#'   \item{`"tabs"`}{Standard tab look}
-#'   \item{`"pills"`}{Selected tabs use the background fill color}
-#'   \item{`"hidden"`}{Hides the selectable tabs. Use `type = "hidden"` in
-#'   conjunction with [tabPanelBody()] and [updateTabsetPanel()] to control the
-#'   active tab via other input controls. (See example below)}
-#' }
+#' @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 This argument is deprecated; it has been discontinued in
 #'   Bootstrap 3.
-#' @return A tabset that can be passed to [mainPanel()]
+#' @return A tabset that can be passed to \code{\link{mainPanel}}
 #'
-#' @seealso [tabPanel()], [updateTabsetPanel()],
-#'   [insertTab()], [showTab()]
+#' @seealso \code{\link{tabPanel}}, \code{\link{updateTabsetPanel}},
+#'   \code{\link{insertTab}}, \code{\link{showTab}}
 #'
 #' @examples
 #' # Show a tabset that includes a plot, summary, and
@@ -541,40 +653,11 @@ tabPanelBody <- function(..., value = NULL, icon = NULL) {
 #'     tabPanel("Table", tableOutput("table"))
 #'   )
 #' )
-#'
-#' ui <- fluidPage(
-#'   sidebarLayout(
-#'     sidebarPanel(
-#'       radioButtons("controller", "Controller", 1:3, 1)
-#'     ),
-#'     mainPanel(
-#'       tabsetPanel(
-#'         id = "hidden_tabs",
-#'         # Hide the tab values.
-#'         # Can only switch tabs by using `updateTabsetPanel()`
-#'         type = "hidden",
-#'         tabPanelBody(value = "panel1", "Panel 1 content"),
-#'         tabPanelBody(value = "panel2", "Panel 2 content"),
-#'         tabPanelBody(value = "panel3", "Panel 3 content")
-#'       )
-#'     )
-#'   )
-#' )
-#'
-#' server <- function(input, output, session) {
-#'   observeEvent(input$controller, {
-#'     updateTabsetPanel(session, "hidden_tabs", selected = paste0("panel", input$controller))
-#'   })
-#' }
-#'
-#' if (interactive()) {
-#'   shinyApp(ui, server)
-#' }
 #' @export
 tabsetPanel <- function(...,
                         id = NULL,
                         selected = NULL,
-                        type = c("tabs", "pills", "hidden"),
+                        type = c("tabs", "pills"),
                         position = NULL) {
   if (!is.null(position)) {
     shinyDeprecated(msg = paste("tabsetPanel: argument 'position' is deprecated;",
@@ -604,29 +687,29 @@ tabsetPanel <- function(...,
 #' Create a navigation list panel that provides a list of links on the left
 #' which navigate to a set of tabPanels displayed to the right.
 #'
-#' @param ... [tabPanel()] elements to include in the navlist
-#' @param id If provided, you can use `input$`*`id`* in your
+#' @param ... \code{\link{tabPanel}} elements to include in the navlist
+#' @param id If provided, you can use \code{input$}\emph{\code{id}} in your
 #'   server logic to determine which of the current navlist items is active. The
-#'   value will correspond to the `value` argument that is passed to
-#'   [tabPanel()].
-#' @param selected The `value` (or, if none was supplied, the `title`)
-#'   of the navigation item that should be selected by default. If `NULL`,
+#'   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 navigation item that should be selected by default. If \code{NULL},
 #'   the first navigation will be selected.
-#' @param well `TRUE` to place a well (gray rounded rectangle) around the
+#' @param well \code{TRUE} to place a well (gray rounded rectangle) around the
 #'   navigation list.
-#' @param fluid `TRUE` to use fluid layout; `FALSE` to use fixed
+#' @param fluid \code{TRUE} to use fluid layout; \code{FALSE} to use fixed
 #'   layout.
 #' @param widths Column withs of the navigation list and tabset content areas
 #'   respectively.
 #'
-#' @details You can include headers within the `navlistPanel` by including
+#' @details You can include headers within the \code{navlistPanel} by including
 #'   plain text elements in the list. Versions of Shiny before 0.11 supported
 #'   separators with "------", but as of 0.11, separators were no longer
 #'   supported. This is because version 0.11 switched to Bootstrap 3, which
 #'   doesn't support separators.
 #'
-#' @seealso [tabPanel()], [updateNavlistPanel()],
-#'    [insertTab()], [showTab()]
+#' @seealso \code{\link{tabPanel}}, \code{\link{updateNavlistPanel}},
+#'    \code{\link{insertTab}}, \code{\link{showTab}}
 #'
 #' @examples
 #' fluidPage(
@@ -834,43 +917,50 @@ buildTabItem <- function(index, tabsetId, foundSelected, tabs = NULL,
 
 #' Create a text output element
 #'
-#' Render a reactive output variable as text within an application page.
-#' `textOutput()` is usually paired with [renderText()] and puts regular text
-#' in `<div>` or `<span>`; `verbatimTextOutput()` is usually paired with
-#' [renderPrint()] and provudes fixed-width text in a `<pre>`.
-#'
-#' In both funtions, text is HTML-escaped prior to rendering.
-#'
+#' Render a reactive output variable as text within an application page. The
+#' text will be included within an HTML \code{div} tag by default.
 #' @param outputId output variable to read the value from
 #' @param container a function to generate an HTML element to contain the text
-#' @param inline use an inline (`span()`) or block container (`div()`)
+#' @param inline use an inline (\code{span()}) or block container (\code{div()})
 #'   for the output
-#' @return A output element for use in UI.
+#' @return A text output element that can be included in a panel
+#' @details Text is HTML-escaped prior to rendering. This element is often used
+#'   to display \link{renderText} output variables.
+#' @examples
+#' h3(textOutput("caption"))
+#' @export
+textOutput <- function(outputId, container = if (inline) span else div, inline = FALSE) {
+  container(id = outputId, class = "shiny-text-output")
+}
+
+#' Create a verbatim text output element
+#'
+#' Render a reactive output variable as verbatim text within an
+#' application page. The text will be included within an HTML \code{pre} tag.
+#' @param outputId output variable to read the value from
+#' @param placeholder if the output is empty or \code{NULL}, should an empty
+#'   rectangle be displayed to serve as a placeholder? (does not affect
+#'   behavior when the the output in nonempty)
+#' @return A verbatim text output element that can be included in a panel
+#' @details Text is HTML-escaped prior to rendering. This element is often used
+#'   with the \link{renderPrint} function to preserve fixed-width formatting
+#'   of printed objects.
 #' @examples
 #' ## Only run this example in interactive R sessions
 #' if (interactive()) {
 #'   shinyApp(
 #'     ui = basicPage(
 #'       textInput("txt", "Enter the text to display below:"),
-#'       textOutput("text"),
-#'       verbatimTextOutput("verb")
+#'       verbatimTextOutput("default"),
+#'       verbatimTextOutput("placeholder", placeholder = TRUE)
 #'     ),
 #'     server = function(input, output) {
-#'       output$text <- renderText({ input$txt })
-#'       output$verb <- renderText({ input$txt })
+#'       output$default <- renderText({ input$txt })
+#'       output$placeholder <- renderText({ input$txt })
 #'     }
 #'   )
 #' }
 #' @export
-textOutput <- function(outputId, container = if (inline) span else div, inline = FALSE) {
-  container(id = outputId, class = "shiny-text-output")
-}
-
-#' @param placeholder if the output is empty or `NULL`, should an empty
-#'   rectangle be displayed to serve as a placeholder? (does not affect
-#'   behavior when the the output in nonempty)
-#' @export
-#' @rdname textOutput
 verbatimTextOutput <- function(outputId, placeholder = FALSE) {
   pre(id = outputId,
       class = paste(c("shiny-text-output", if (!placeholder) "noplaceholder"),
@@ -883,9 +973,42 @@ verbatimTextOutput <- function(outputId, placeholder = FALSE) {
 #' @rdname plotOutput
 #' @export
 imageOutput <- function(outputId, width = "100%", height="400px",
-                        click = NULL, dblclick = NULL, hover = NULL, brush = NULL,
+                        click = NULL, dblclick = NULL,
+                        hover = NULL, hoverDelay = NULL, hoverDelayType = NULL,
+                        brush = NULL,
+                        clickId = NULL, hoverId = NULL,
                         inline = FALSE) {
 
+  if (!is.null(clickId)) {
+    shinyDeprecated(
+      msg = paste("The 'clickId' argument is deprecated. ",
+                  "Please use 'click' instead. ",
+                  "See ?imageOutput or ?plotOutput for more information."),
+      version = "0.11.1"
+    )
+    click <- clickId
+  }
+
+  if (!is.null(hoverId)) {
+    shinyDeprecated(
+      msg = paste("The 'hoverId' argument is deprecated. ",
+                  "Please use 'hover' instead. ",
+                  "See ?imageOutput or ?plotOutput for more information."),
+      version = "0.11.1"
+    )
+    hover <- hoverId
+  }
+
+  if (!is.null(hoverDelay) || !is.null(hoverDelayType)) {
+    shinyDeprecated(
+      msg = paste("The 'hoverDelay'and 'hoverDelayType' arguments are deprecated. ",
+                  "Please use 'hoverOpts' instead. ",
+                  "See ?imageOutput or ?plotOutput for more information."),
+      version = "0.11.1"
+    )
+    hover <- hoverOpts(id = hover, delay = hoverDelay, delayType = hoverDelayType)
+  }
+
   style <- if (!inline) {
     paste("width:", validateCssUnit(width), ";", "height:", validateCssUnit(height))
   }
@@ -943,77 +1066,86 @@ imageOutput <- function(outputId, width = "100%", height="400px",
 
 #' Create an plot or image output element
 #'
-#' Render a [renderPlot()] or [renderImage()] within an
+#' Render a \code{\link{renderPlot}} or \code{\link{renderImage}} within an
 #' application page.
 #'
 #' @section Interactive plots:
 #'
 #'   Plots and images in Shiny support mouse-based interaction, via clicking,
 #'   double-clicking, hovering, and brushing. When these interaction events
-#'   occur, the mouse coordinates will be sent to the server as `input$`
-#'   variables, as specified by `click`, `dblclick`, `hover`, or
-#'   `brush`.
+#'   occur, the mouse coordinates will be sent to the server as \code{input$}
+#'   variables, as specified by \code{click}, \code{dblclick}, \code{hover}, or
+#'   \code{brush}.
 #'
-#'   For `plotOutput`, the coordinates will be sent scaled to the data
+#'   For \code{plotOutput}, the coordinates will be sent scaled to the data
 #'   space, if possible. (At the moment, plots generated by base graphics and
 #'   ggplot2 support this scaling, although plots generated by lattice and
 #'   others do not.) If scaling is not possible, the raw pixel coordinates will
-#'   be sent. For `imageOutput`, the coordinates will be sent in raw pixel
+#'   be sent. For \code{imageOutput}, the coordinates will be sent in raw pixel
 #'   coordinates.
 #'
-#'   With ggplot2 graphics, the code in `renderPlot` should return a ggplot
+#'   With ggplot2 graphics, the code in \code{renderPlot} should return a ggplot
 #'   object; if instead the code prints the ggplot2 object with something like
-#'   `print(p)`, then the coordinates for interactive graphics will not be
+#'   \code{print(p)}, then the coordinates for interactive graphics will not be
 #'   properly scaled to the data space.
 #'
 #' @param outputId output variable to read the plot/image from.
 #' @param width,height Image width/height. Must be a valid CSS unit (like
-#'   `"100%"`, `"400px"`, `"auto"`) or a number, which will be
-#'   coerced to a string and have `"px"` appended. These two arguments are
-#'   ignored when `inline = TRUE`, in which case the width/height of a plot
-#'   must be specified in `renderPlot()`. Note that, for height, using
-#'   `"auto"` or `"100%"` generally will not work as expected,
+#'   \code{"100\%"}, \code{"400px"}, \code{"auto"}) or a number, which will be
+#'   coerced to a string and have \code{"px"} appended. These two arguments are
+#'   ignored when \code{inline = TRUE}, in which case the width/height of a plot
+#'   must be specified in \code{renderPlot()}. Note that, for height, using
+#'   \code{"auto"} or \code{"100\%"} generally will not work as expected,
 #'   because of how height is computed with HTML/CSS.
-#' @param click This can be `NULL` (the default), a string, or an object
-#'   created by the [clickOpts()] function. If you use a value like
-#'   `"plot_click"` (or equivalently, `clickOpts(id="plot_click")`),
+#' @param click This can be \code{NULL} (the default), a string, or an object
+#'   created by the \code{\link{clickOpts}} function. If you use a value like
+#'   \code{"plot_click"} (or equivalently, \code{clickOpts(id="plot_click")}),
 #'   the plot will send coordinates to the server whenever it is clicked, and
-#'   the value will be accessible via `input$plot_click`. The value will be
-#'   a named list  with `x` and `y` elements indicating the mouse
+#'   the value will be accessible via \code{input$plot_click}. The value will be
+#'   a named list  with \code{x} and \code{y} elements indicating the mouse
 #'   position.
-#' @param dblclick This is just like the `click` argument, but for
+#' @param dblclick This is just like the \code{click} argument, but for
 #'   double-click events.
-#' @param hover Similar to the `click` argument, this can be `NULL`
+#' @param hover Similar to the \code{click} argument, this can be \code{NULL}
 #'   (the default), a string, or an object created by the
-#'   [hoverOpts()] function. If you use a value like
-#'   `"plot_hover"` (or equivalently, `hoverOpts(id="plot_hover")`),
+#'   \code{\link{hoverOpts}} function. If you use a value like
+#'   \code{"plot_hover"} (or equivalently, \code{hoverOpts(id="plot_hover")}),
 #'   the plot will send coordinates to the server pauses on the plot, and the
-#'   value will be accessible via `input$plot_hover`. The value will be a
-#'   named list with `x` and `y` elements indicating the mouse
+#'   value will be accessible via \code{input$plot_hover}. The value will be a
+#'   named list with \code{x} and \code{y} elements indicating the mouse
 #'   position. To control the hover time or hover delay type, you must use
-#'   [hoverOpts()].
-#' @param brush Similar to the `click` argument, this can be `NULL`
+#'   \code{\link{hoverOpts}}.
+#' @param clickId Deprecated; use \code{click} instead. Also see the
+#'   \code{\link{clickOpts}} function.
+#' @param hoverId Deprecated; use \code{hover} instead. Also see the
+#'   \code{\link{hoverOpts}} function.
+#' @param hoverDelay Deprecated; use \code{hover} instead. Also see the
+#'   \code{\link{hoverOpts}} function.
+#' @param hoverDelayType Deprecated; use \code{hover} instead. Also see the
+#'   \code{\link{hoverOpts}} function.
+#' @param brush Similar to the \code{click} argument, this can be \code{NULL}
 #'   (the default), a string, or an object created by the
-#'   [brushOpts()] function. If you use a value like
-#'   `"plot_brush"` (or equivalently, `brushOpts(id="plot_brush")`),
+#'   \code{\link{brushOpts}} function. If you use a value like
+#'   \code{"plot_brush"} (or equivalently, \code{brushOpts(id="plot_brush")}),
 #'   the plot will allow the user to "brush" in the plotting area, and will send
 #'   information about the brushed area to the server, and the value will be
-#'   accessible via `input$plot_brush`. Brushing means that the user will
+#'   accessible via \code{input$plot_brush}. Brushing means that the user will
 #'   be able to draw a rectangle in the plotting area and drag it around. The
-#'   value will be a named list with `xmin`, `xmax`, `ymin`, and
-#'   `ymax` elements indicating the brush area. To control the brush
-#'   behavior, use [brushOpts()]. Multiple
-#'   `imageOutput`/`plotOutput` calls may share the same `id`
+#'   value will be a named list with \code{xmin}, \code{xmax}, \code{ymin}, and
+#'   \code{ymax} elements indicating the brush area. To control the brush
+#'   behavior, use \code{\link{brushOpts}}. Multiple
+#'   \code{imageOutput}/\code{plotOutput} calls may share the same \code{id}
 #'   value; brushing one image or plot will cause any other brushes with the
-#'   same `id` to disappear.
+#'   same \code{id} to disappear.
 #' @inheritParams textOutput
-#' @note The arguments `clickId` and `hoverId` only work for R base graphics
-#'   (see the \pkg{\link[graphics:graphics-package]{graphics}} package). They do
-#'   not work for \pkg{\link[grid:grid-package]{grid}}-based graphics, such as
-#'   \pkg{ggplot2}, \pkg{lattice}, and so on.
+#' @note The arguments \code{clickId} and \code{hoverId} only work for R base
+#'   graphics (see the \pkg{\link[graphics:graphics-package]{graphics}} package). They do not work for
+#'   \pkg{\link[grid:grid-package]{grid}}-based graphics, such as \pkg{ggplot2},
+#'   \pkg{lattice}, and so on.
+#'
 #' @return A plot or image output element that can be included in a panel.
-#' @seealso For the corresponding server-side functions, see [renderPlot()] and
-#'   [renderImage()].
+#' @seealso For the corresponding server-side functions, see
+#'   \code{\link{renderPlot}} and  \code{\link{renderImage}}.
 #'
 #' @examples
 #' # Only run these examples in interactive R sessions
@@ -1175,12 +1307,16 @@ imageOutput <- function(outputId, width = "100%", height="400px",
 #' }
 #' @export
 plotOutput <- function(outputId, width = "100%", height="400px",
-                       click = NULL, dblclick = NULL, hover = NULL, brush = NULL,
+                       click = NULL, dblclick = NULL,
+                       hover = NULL, hoverDelay = NULL, hoverDelayType = NULL,
+                       brush = NULL,
+                       clickId = NULL, hoverId = NULL,
                        inline = FALSE) {
 
   # Result is the same as imageOutput, except for HTML class
   res <- imageOutput(outputId, width, height, click, dblclick,
-                     hover, brush, inline)
+                     hover, hoverDelay, hoverDelayType, brush,
+                     clickId, hoverId, inline)
 
   res$attribs$class <- "shiny-plot-output"
   res
@@ -1188,15 +1324,15 @@ plotOutput <- function(outputId, width = "100%", height="400px",
 
 #' Create a table output element
 #'
-#' Render a [renderTable()] or [renderDataTable()] within an
-#' application page. `renderTable` uses a standard HTML table, while
-#' `renderDataTable` uses the DataTables Javascript library to create an
+#' Render a \code{\link{renderTable}} or \code{\link{renderDataTable}} within an
+#' application page. \code{renderTable} uses a standard HTML table, while
+#' \code{renderDataTable} uses the DataTables Javascript library to create an
 #' interactive table with more features.
 #'
 #' @param outputId output variable to read the table from
 #' @return A table output element that can be included in a panel
 #'
-#' @seealso [renderTable()], [renderDataTable()].
+#' @seealso \code{\link{renderTable}}, \code{\link{renderDataTable}}.
 #' @examples
 #' ## Only run this example in interactive R sessions
 #' if (interactive()) {
@@ -1258,11 +1394,11 @@ dataTableOutput <- function(outputId) {
 #' Create an HTML output element
 #'
 #' Render a reactive output variable as HTML within an application page. The
-#' text will be included within an HTML `div` tag, and is presumed to
+#' text will be included within an HTML \code{div} tag, and is presumed to
 #' contain HTML content which should not be escaped.
 #'
-#' `uiOutput` is intended to be used with `renderUI` on the server
-#' side. It is currently just an alias for `htmlOutput`.
+#' \code{uiOutput} is intended to be used with \code{renderUI} on the server
+#' side. It is currently just an alias for \code{htmlOutput}.
 #'
 #' @param outputId output variable to read the value from
 #' @param ... Other arguments to pass to the container tag function. This is
@@ -1294,10 +1430,10 @@ uiOutput <- htmlOutput
 #'
 #' Use these functions to create a download button or link; when clicked, it
 #' will initiate a browser download. The filename and contents are specified by
-#' the corresponding [downloadHandler()] defined in the server
+#' the corresponding \code{\link{downloadHandler}} defined in the server
 #' function.
 #'
-#' @param outputId The name of the output slot that the `downloadHandler`
+#' @param outputId The name of the output slot that the \code{downloadHandler}
 #'   is assigned to.
 #' @param label The label that should appear on the button.
 #' @param class Additional CSS classes to apply to the tag, if any.
@@ -1320,7 +1456,7 @@ uiOutput <- htmlOutput
 #' }
 #'
 #' @aliases downloadLink
-#' @seealso [downloadHandler()]
+#' @seealso \code{\link{downloadHandler}}
 #' @export
 downloadButton <- function(outputId,
                            label="Download",
@@ -1349,26 +1485,26 @@ downloadLink <- function(outputId, label="Download", class=NULL, ...) {
 #' Create an icon
 #'
 #' Create an icon for use within a page. Icons can appear on their own, inside
-#' of a button, or as an icon for a [tabPanel()] within a
-#' [navbarPage()].
+#' of a button, or as an icon for a \code{\link{tabPanel}} within a
+#' \code{\link{navbarPage}}.
 #'
 #' @param name Name of icon. Icons are drawn from the
-#'   [Font Awesome Free](https://fontawesome.com/) (currently icons from
+#'   \href{https://fontawesome.com/}{Font Awesome Free} (currently icons from
 #'   the v5.3.1 set are supported with the v4 naming convention) and
-#'   [Glyphicons](http://getbootstrap.com/components/#glyphicons)
+#'   \href{http://getbootstrap.com/components/#glyphicons}{Glyphicons}
 #'   libraries. Note that the "fa-" and "glyphicon-" prefixes should not be used
 #'   in icon names (i.e. the "fa-calendar" icon should be referred to as
 #'   "calendar")
 #' @param class Additional classes to customize the style of the icon (see the
-#'   [usage examples](http://fontawesome.io/examples/) for details on
+#'   \href{http://fontawesome.io/examples/}{usage examples} for details on
 #'   supported styles).
 #' @param lib Icon library to use ("font-awesome" or "glyphicon")
 #'
 #' @return An icon element
 #'
 #' @seealso For lists of available icons, see
-#'   [http://fontawesome.io/icons/](http://fontawesome.io/icons/) and
-#'   [http://getbootstrap.com/components/#glyphicons](http://getbootstrap.com/components/#glyphicons).
+#'   \href{http://fontawesome.io/icons/}{http://fontawesome.io/icons/} and
+#'   \href{http://getbootstrap.com/components/#glyphicons}{http://getbootstrap.com/components/#glyphicons}.
 #'
 #'
 #' @examples

R/cache-disk.R

@@ -1,44 +1,44 @@
 #' Create a disk cache object
 #'
 #' A disk cache object is a key-value store that saves the values as files in a
-#' directory on disk. Objects can be stored and retrieved using the `get()`
-#' and `set()` methods. Objects are automatically pruned from the cache
-#' according to the parameters `max_size`, `max_age`, `max_n`,
-#' and `evict`.
+#' directory on disk. Objects can be stored and retrieved using the \code{get()}
+#' and \code{set()} methods. Objects are automatically pruned from the cache
+#' according to the parameters \code{max_size}, \code{max_age}, \code{max_n},
+#' and \code{evict}.
 #'
 #'
 #' @section Missing Keys:
 #'
-#'   The `missing` and `exec_missing` parameters controls what happens
-#'   when `get()` is called with a key that is not in the cache (a cache
-#'   miss). The default behavior is to return a [key_missing()]
-#'   object. This is a *sentinel value* that indicates that the key was not
+#'   The \code{missing} and \code{exec_missing} parameters controls what happens
+#'   when \code{get()} is called with a key that is not in the cache (a cache
+#'   miss). The default behavior is to return a \code{\link{key_missing}}
+#'   object. This is a \emph{sentinel value} that indicates that the key was not
 #'   present in the cache. You can test if the returned value represents a
-#'   missing key by using the [is.key_missing()] function. You can
-#'   also have `get()` return a different sentinel value, like `NULL`.
+#'   missing key by using the \code{\link{is.key_missing}} function. You can
+#'   also have \code{get()} return a different sentinel value, like \code{NULL}.
 #'   If you want to throw an error on a cache miss, you can do so by providing a
-#'   function for `missing` that takes one argument, the key, and also use
-#'   `exec_missing=TRUE`.
+#'   function for \code{missing} that takes one argument, the key, and also use
+#'   \code{exec_missing=TRUE}.
 #'
-#'   When the cache is created, you can supply a value for `missing`, which
+#'   When the cache is created, you can supply a value for \code{missing}, which
 #'   sets the default value to be returned for missing values. It can also be
-#'   overridden when `get()` is called, by supplying a `missing`
-#'   argument. For example, if you use `cache$get("mykey", missing =
-#'   NULL)`, it will return `NULL` if the key is not in the cache.
+#'   overridden when \code{get()} is called, by supplying a \code{missing}
+#'   argument. For example, if you use \code{cache$get("mykey", missing =
+#'   NULL)}, it will return \code{NULL} if the key is not in the cache.
 #'
-#'   If your cache is configured so that `get()` returns a sentinel value
-#'   to represent a cache miss, then `set` will also not allow you to store
+#'   If your cache is configured so that \code{get()} returns a sentinel value
+#'   to represent a cache miss, then \code{set} will also not allow you to store
 #'   the sentinel value in the cache. It will throw an error if you attempt to
 #'   do so.
 #'
 #'   Instead of returning the same sentinel value each time there is cache miss,
-#'   the cache can execute a function each time `get()` encounters missing
-#'   key. If the function returns a value, then `get()` will in turn return
+#'   the cache can execute a function each time \code{get()} encounters missing
+#'   key. If the function returns a value, then \code{get()} will in turn return
 #'   that value. However, a more common use is for the function to throw an
-#'   error. If an error is thrown, then `get()` will not return a value.
+#'   error. If an error is thrown, then \code{get()} will not return a value.
 #'
-#'   To do this, pass a one-argument function to `missing`, and use
-#'   `exec_missing=TRUE`. For example, if you want to throw an error that
+#'   To do this, pass a one-argument function to \code{missing}, and use
+#'   \code{exec_missing=TRUE}. For example, if you want to throw an error that
 #'   prints the missing key, you could do this:
 #'
 #'   \preformatted{
@@ -50,58 +50,58 @@
 #'   )
 #'   }
 #'
-#'   If you use this, the code that calls `get()` should be wrapped with
-#'   [tryCatch()] to gracefully handle missing keys.
+#'   If you use this, the code that calls \code{get()} should be wrapped with
+#'   \code{\link{tryCatch}()} to gracefully handle missing keys.
 #'
 #' @section Cache pruning:
 #'
-#'   Cache pruning occurs when `set()` is called, or it can be invoked
-#'   manually by calling `prune()`.
+#'   Cache pruning occurs when \code{set()} is called, or it can be invoked
+#'   manually by calling \code{prune()}.
 #'
 #'   The disk cache will throttle the pruning so that it does not happen on
-#'   every call to `set()`, because the filesystem operations for checking
+#'   every call to \code{set()}, because the filesystem operations for checking
 #'   the status of files can be slow. Instead, it will prune once in every 20
-#'   calls to `set()`, or if at least 5 seconds have elapsed since the last
+#'   calls to \code{set()}, or if at least 5 seconds have elapsed since the last
 #'   prune occurred, whichever is first. These parameters are currently not
 #'   customizable, but may be in the future.
 #'
 #'   When a pruning occurs, if there are any objects that are older than
-#'   `max_age`, they will be removed.
+#'   \code{max_age}, they will be removed.
 #'
-#'   The `max_size` and `max_n` parameters are applied to the cache as
-#'   a whole, in contrast to `max_age`, which is applied to each object
+#'   The \code{max_size} and \code{max_n} parameters are applied to the cache as
+#'   a whole, in contrast to \code{max_age}, which is applied to each object
 #'   individually.
 #'
-#'   If the number of objects in the cache exceeds `max_n`, then objects
+#'   If the number of objects in the cache exceeds \code{max_n}, then objects
 #'   will be removed from the cache according to the eviction policy, which is
-#'   set with the `evict` parameter. Objects will be removed so that the
-#'   number of items is `max_n`.
+#'   set with the \code{evict} parameter. Objects will be removed so that the
+#'   number of items is \code{max_n}.
 #'
-#'   If the size of the objects in the cache exceeds `max_size`, then
+#'   If the size of the objects in the cache exceeds \code{max_size}, then
 #'   objects will be removed from the cache. Objects will be removed from the
-#'   cache so that the total size remains under `max_size`. Note that the
+#'   cache so that the total size remains under \code{max_size}. Note that the
 #'   size is calculated using the size of the files, not the size of disk space
-#'   used by the files --- these two values can differ because of files are
+#'   used by the files -- these two values can differ because of files are
 #'   stored in blocks on disk. For example, if the block size is 4096 bytes,
 #'   then a file that is one byte in size will take 4096 bytes on disk.
 #'
 #'   Another time that objects can be removed from the cache is when
-#'   `get()` is called. If the target object is older than `max_age`,
+#'   \code{get()} is called. If the target object is older than \code{max_age},
 #'   it will be removed and the cache will report it as a missing value.
 #'
 #' @section Eviction policies:
 #'
-#' If `max_n` or `max_size` are used, then objects will be removed
+#' If \code{max_n} or \code{max_size} are used, then objects will be removed
 #' from the cache according to an eviction policy. The available eviction
 #' policies are:
 #'
 #'   \describe{
-#'     \item{`"lru"`}{
+#'     \item{\code{"lru"}}{
 #'       Least Recently Used. The least recently used objects will be removed.
 #'       This uses the filesystem's mtime property. When "lru" is used, each
-#'       `get()` is called, it will update the file's mtime.
+#'       \code{get()} is called, it will update the file's mtime.
 #'     }
-#'     \item{`"fifo"`}{
+#'     \item{\code{"fifo"}}{
 #'       First-in-first-out. The oldest objects will be removed.
 #'     }
 #'   }
@@ -126,17 +126,17 @@
 #' Redis, SQLite, mySQL, or similar.
 #'
 #' When multiple processes share a cache directory, there are some potential
-#' race conditions. For example, if your code calls `exists(key)` to check
-#' if an object is in the cache, and then call `get(key)`, the object may
-#' be removed from the cache in between those two calls, and `get(key)`
+#' race conditions. For example, if your code calls \code{exists(key)} to check
+#' if an object is in the cache, and then call \code{get(key)}, the object may
+#' be removed from the cache in between those two calls, and \code{get(key)}
 #' will throw an error. Instead of calling the two functions, it is better to
-#' simply call `get(key)`, and use `tryCatch()` to handle the error
+#' simply call \code{get(key)}, and use \code{tryCatch()} to handle the error
 #' that is thrown if the object is not in the cache. This effectively tests for
 #' existence and gets the object in one operation.
 #'
 #' It is also possible for one processes to prune objects at the same time that
 #' another processes is trying to prune objects. If this happens, you may see
-#' a warning from `file.remove()` failing to remove a file that has
+#' a warning from \code{file.remove()} failing to remove a file that has
 #' already been deleted.
 #'
 #'
@@ -145,72 +145,72 @@
 #'  A disk cache object has the following methods:
 #'
 #'   \describe{
-#'     \item{`get(key, missing, exec_missing)`}{
-#'       Returns the value associated with `key`. If the key is not in the
-#'       cache, then it returns the value specified by `missing` or,
-#'       `missing` is a function and `exec_missing=TRUE`, then
-#'       executes `missing`. The function can throw an error or return the
+#'     \item{\code{get(key, missing, exec_missing)}}{
+#'       Returns the value associated with \code{key}. If the key is not in the
+#'       cache, then it returns the value specified by \code{missing} or,
+#'       \code{missing} is a function and \code{exec_missing=TRUE}, then
+#'       executes \code{missing}. The function can throw an error or return the
 #'       value. If either of these parameters are specified here, then they
 #'       will override the defaults that were set when the DiskCache object was
 #'       created. See section Missing Keys for more information.
 #'     }
-#'     \item{`set(key, value)`}{
-#'       Stores the `key`-`value` pair in the cache.
+#'     \item{\code{set(key, value)}}{
+#'       Stores the \code{key}-\code{value} pair in the cache.
 #'     }
-#'     \item{`exists(key)`}{
-#'       Returns `TRUE` if the cache contains the key, otherwise
-#'       `FALSE`.
+#'     \item{\code{exists(key)}}{
+#'       Returns \code{TRUE} if the cache contains the key, otherwise
+#'       \code{FALSE}.
 #'     }
-#'     \item{`size()`}{
+#'     \item{\code{size()}}{
 #'       Returns the number of items currently in the cache.
 #'     }
-#'     \item{`keys()`}{
+#'     \item{\code{keys()}}{
 #'       Returns a character vector of all keys currently in the cache.
 #'     }
-#'     \item{`reset()`}{
+#'     \item{\code{reset()}}{
 #'       Clears all objects from the cache.
 #'     }
-#'     \item{`destroy()`}{
+#'     \item{\code{destroy()}}{
 #'       Clears all objects in the cache, and removes the cache directory from
 #'       disk.
 #'     }
-#'     \item{`prune()`}{
-#'       Prunes the cache, using the parameters specified by `max_size`,
-#'       `max_age`, `max_n`, and `evict`.
+#'     \item{\code{prune()}}{
+#'       Prunes the cache, using the parameters specified by \code{max_size},
+#'       \code{max_age}, \code{max_n}, and \code{evict}.
 #'     }
 #'   }
 #'
-#' @param dir Directory to store files for the cache. If `NULL` (the
+#' @param dir Directory to store files for the cache. If \code{NULL} (the
 #'   default) it will create and use a temporary directory.
 #' @param max_age Maximum age of files in cache before they are evicted, in
-#'   seconds. Use `Inf` for no age limit.
+#'   seconds. Use \code{Inf} for no age limit.
 #' @param max_size Maximum size of the cache, in bytes. If the cache exceeds
 #'   this size, cached objects will be removed according to the value of the
-#'   `evict`. Use `Inf` for no size limit.
+#'   \code{evict}. Use \code{Inf} for no size limit.
 #' @param max_n Maximum number of objects in the cache. If the number of objects
 #'   exceeds this value, then cached objects will be removed according to the
-#'   value of `evict`. Use `Inf` for no limit of number of items.
+#'   value of \code{evict}. Use \code{Inf} for no limit of number of items.
 #' @param evict The eviction policy to use to decide which objects are removed
-#'   when a cache pruning occurs. Currently, `"lru"` and `"fifo"` are
+#'   when a cache pruning occurs. Currently, \code{"lru"} and \code{"fifo"} are
 #'   supported.
-#' @param destroy_on_finalize If `TRUE`, then when the DiskCache object is
+#' @param destroy_on_finalize If \code{TRUE}, then when the DiskCache object is
 #'   garbage collected, the cache directory and all objects inside of it will be
-#'   deleted from disk. If `FALSE` (the default), it will do nothing when
+#'   deleted from disk. If \code{FALSE} (the default), it will do nothing when
 #'   finalized.
 #' @param missing A value to return or a function to execute when
-#'   `get(key)` is called but the key is not present in the cache. The
-#'   default is a [key_missing()] object. If it is a function to
+#'   \code{get(key)} is called but the key is not present in the cache. The
+#'   default is a \code{\link{key_missing}} object. If it is a function to
 #'   execute, the function must take one argument (the key), and you must also
-#'   use `exec_missing = TRUE`. If it is a function, it is useful in most
+#'   use \code{exec_missing = TRUE}. If it is a function, it is useful in most
 #'   cases for it to throw an error, although another option is to return a
 #'   value. If a value is returned, that value will in turn be returned by
-#'   `get()`. See section Missing keys for more information.
-#' @param exec_missing If `FALSE` (the default), then treat `missing`
-#'   as a value to return when `get()` results in a cache miss. If
-#'   `TRUE`, treat `missing` as a function to execute when
-#'   `get()` results in a cache miss.
+#'   \code{get()}. See section Missing keys for more information.
+#' @param exec_missing If \code{FALSE} (the default), then treat \code{missing}
+#'   as a value to return when \code{get()} results in a cache miss. If
+#'   \code{TRUE}, treat \code{missing} as a function to execute when
+#'   \code{get()} results in a cache miss.
 #' @param logfile An optional filename or connection object to where logging
-#'   information will be written. To log to the console, use `stdout()`.
+#'   information will be written. To log to the console, use \code{stdout()}.
 #'
 #' @export
 diskCache <- function(

R/cache-memory.R

@@ -1,50 +1,50 @@
 #' Create a memory cache object
 #'
 #' A memory cache object is a key-value store that saves the values in an
-#' environment. Objects can be stored and retrieved using the `get()` and
-#' `set()` methods. Objects are automatically pruned from the cache
-#' according to the parameters `max_size`, `max_age`, `max_n`,
-#' and `evict`.
+#' environment. Objects can be stored and retrieved using the \code{get()} and
+#' \code{set()} methods. Objects are automatically pruned from the cache
+#' according to the parameters \code{max_size}, \code{max_age}, \code{max_n},
+#' and \code{evict}.
 #'
-#' In a `MemoryCache`, R objects are stored directly in the cache; they are
-#' not *not* serialized before being stored in the cache. This contrasts
-#' with other cache types, like [diskCache()], where objects are
+#' In a \code{MemoryCache}, R objects are stored directly in the cache; they are
+#' not \emph{not} serialized before being stored in the cache. This contrasts
+#' with other cache types, like \code{\link{diskCache}}, where objects are
 #' serialized, and the serialized object is cached. This can result in some
 #' differences of behavior. For example, as long as an object is stored in a
 #' MemoryCache, it will not be garbage collected.
 #'
 #'
 #' @section Missing keys:
-#'   The `missing` and `exec_missing` parameters controls what happens
-#'   when `get()` is called with a key that is not in the cache (a cache
-#'   miss). The default behavior is to return a [key_missing()]
-#'   object. This is a *sentinel value* that indicates that the key was not
+#'   The \code{missing} and \code{exec_missing} parameters controls what happens
+#'   when \code{get()} is called with a key that is not in the cache (a cache
+#'   miss). The default behavior is to return a \code{\link{key_missing}}
+#'   object. This is a \emph{sentinel value} that indicates that the key was not
 #'   present in the cache. You can test if the returned value represents a
-#'   missing key by using the [is.key_missing()] function. You can
-#'   also have `get()` return a different sentinel value, like `NULL`.
+#'   missing key by using the \code{\link{is.key_missing}} function. You can
+#'   also have \code{get()} return a different sentinel value, like \code{NULL}.
 #'   If you want to throw an error on a cache miss, you can do so by providing a
-#'   function for `missing` that takes one argument, the key, and also use
-#'   `exec_missing=TRUE`.
+#'   function for \code{missing} that takes one argument, the key, and also use
+#'   \code{exec_missing=TRUE}.
 #'
-#'   When the cache is created, you can supply a value for `missing`, which
+#'   When the cache is created, you can supply a value for \code{missing}, which
 #'   sets the default value to be returned for missing values. It can also be
-#'   overridden when `get()` is called, by supplying a `missing`
-#'   argument. For example, if you use `cache$get("mykey", missing =
-#'   NULL)`, it will return `NULL` if the key is not in the cache.
+#'   overridden when \code{get()} is called, by supplying a \code{missing}
+#'   argument. For example, if you use \code{cache$get("mykey", missing =
+#'   NULL)}, it will return \code{NULL} if the key is not in the cache.
 #'
-#'   If your cache is configured so that `get()` returns a sentinel value
-#'   to represent a cache miss, then `set` will also not allow you to store
+#'   If your cache is configured so that \code{get()} returns a sentinel value
+#'   to represent a cache miss, then \code{set} will also not allow you to store
 #'   the sentinel value in the cache. It will throw an error if you attempt to
 #'   do so.
 #'
 #'   Instead of returning the same sentinel value each time there is cache miss,
-#'   the cache can execute a function each time `get()` encounters missing
-#'   key. If the function returns a value, then `get()` will in turn return
+#'   the cache can execute a function each time \code{get()} encounters missing
+#'   key. If the function returns a value, then \code{get()} will in turn return
 #'   that value. However, a more common use is for the function to throw an
-#'   error. If an error is thrown, then `get()` will not return a value.
+#'   error. If an error is thrown, then \code{get()} will not return a value.
 #'
-#'   To do this, pass a one-argument function to `missing`, and use
-#'   `exec_missing=TRUE`. For example, if you want to throw an error that
+#'   To do this, pass a one-argument function to \code{missing}, and use
+#'   \code{exec_missing=TRUE}. For example, if you want to throw an error that
 #'   prints the missing key, you could do this:
 #'
 #'   \preformatted{
@@ -56,53 +56,53 @@
 #'   )
 #'   }
 #'
-#'   If you use this, the code that calls `get()` should be wrapped with
-#'   [tryCatch()] to gracefully handle missing keys.
+#'   If you use this, the code that calls \code{get()} should be wrapped with
+#'   \code{\link{tryCatch}()} to gracefully handle missing keys.
 #'
 #' @section Cache pruning:
 #'
-#'   Cache pruning occurs when `set()` is called, or it can be invoked
-#'   manually by calling `prune()`.
+#'   Cache pruning occurs when \code{set()} is called, or it can be invoked
+#'   manually by calling \code{prune()}.
 #'
 #'   When a pruning occurs, if there are any objects that are older than
-#'   `max_age`, they will be removed.
+#'   \code{max_age}, they will be removed.
 #'
-#'   The `max_size` and `max_n` parameters are applied to the cache as
-#'   a whole, in contrast to `max_age`, which is applied to each object
+#'   The \code{max_size} and \code{max_n} parameters are applied to the cache as
+#'   a whole, in contrast to \code{max_age}, which is applied to each object
 #'   individually.
 #'
-#'   If the number of objects in the cache exceeds `max_n`, then objects
+#'   If the number of objects in the cache exceeds \code{max_n}, then objects
 #'   will be removed from the cache according to the eviction policy, which is
-#'   set with the `evict` parameter. Objects will be removed so that the
-#'   number of items is `max_n`.
+#'   set with the \code{evict} parameter. Objects will be removed so that the
+#'   number of items is \code{max_n}.
 #'
-#'   If the size of the objects in the cache exceeds `max_size`, then
+#'   If the size of the objects in the cache exceeds \code{max_size}, then
 #'   objects will be removed from the cache. Objects will be removed from the
-#'   cache so that the total size remains under `max_size`. Note that the
+#'   cache so that the total size remains under \code{max_size}. Note that the
 #'   size is calculated using the size of the files, not the size of disk space
-#'   used by the files --- these two values can differ because of files are
+#'   used by the files -- these two values can differ because of files are
 #'   stored in blocks on disk. For example, if the block size is 4096 bytes,
 #'   then a file that is one byte in size will take 4096 bytes on disk.
 #'
 #'   Another time that objects can be removed from the cache is when
-#'   `get()` is called. If the target object is older than `max_age`,
+#'   \code{get()} is called. If the target object is older than \code{max_age},
 #'   it will be removed and the cache will report it as a missing value.
 #'
 #' @section Eviction policies:
 #'
-#' If `max_n` or `max_size` are used, then objects will be removed
+#' If \code{max_n} or \code{max_size} are used, then objects will be removed
 #' from the cache according to an eviction policy. The available eviction
 #' policies are:
 #'
 #'   \describe{
-#'     \item{`"lru"`}{
+#'     \item{\code{"lru"}}{
 #'       Least Recently Used. The least recently used objects will be removed.
 #'       This uses the filesystem's atime property. Some filesystems do not
 #'       support atime, or have a very low atime resolution. The DiskCache will
 #'       check for atime support, and if the filesystem does not support atime,
 #'       a warning will be issued and the "fifo" policy will be used instead.
 #'     }
-#'     \item{`"fifo"`}{
+#'     \item{\code{"fifo"}}{
 #'       First-in-first-out. The oldest objects will be removed.
 #'     }
 #'   }
@@ -112,38 +112,38 @@
 #'  A disk cache object has the following methods:
 #'
 #'   \describe{
-#'     \item{`get(key, missing, exec_missing)`}{
-#'       Returns the value associated with `key`. If the key is not in the
-#'       cache, then it returns the value specified by `missing` or,
-#'       `missing` is a function and `exec_missing=TRUE`, then
-#'       executes `missing`. The function can throw an error or return the
+#'     \item{\code{get(key, missing, exec_missing)}}{
+#'       Returns the value associated with \code{key}. If the key is not in the
+#'       cache, then it returns the value specified by \code{missing} or,
+#'       \code{missing} is a function and \code{exec_missing=TRUE}, then
+#'       executes \code{missing}. The function can throw an error or return the
 #'       value. If either of these parameters are specified here, then they
 #'       will override the defaults that were set when the DiskCache object was
 #'       created. See section Missing Keys for more information.
 #'     }
-#'     \item{`set(key, value)`}{
-#'       Stores the `key`-`value` pair in the cache.
+#'     \item{\code{set(key, value)}}{
+#'       Stores the \code{key}-\code{value} pair in the cache.
 #'     }
-#'     \item{`exists(key)`}{
-#'       Returns `TRUE` if the cache contains the key, otherwise
-#'       `FALSE`.
+#'     \item{\code{exists(key)}}{
+#'       Returns \code{TRUE} if the cache contains the key, otherwise
+#'       \code{FALSE}.
 #'     }
-#'     \item{`size()`}{
+#'     \item{\code{size()}}{
 #'       Returns the number of items currently in the cache.
 #'     }
-#'     \item{`keys()`}{
+#'     \item{\code{keys()}}{
 #'       Returns a character vector of all keys currently in the cache.
 #'     }
-#'     \item{`reset()`}{
+#'     \item{\code{reset()}}{
 #'       Clears all objects from the cache.
 #'     }
-#'     \item{`destroy()`}{
+#'     \item{\code{destroy()}}{
 #'       Clears all objects in the cache, and removes the cache directory from
 #'       disk.
 #'     }
-#'     \item{`prune()`}{
-#'       Prunes the cache, using the parameters specified by `max_size`,
-#'       `max_age`, `max_n`, and `evict`.
+#'     \item{\code{prune()}}{
+#'       Prunes the cache, using the parameters specified by \code{max_size},
+#'       \code{max_age}, \code{max_n}, and \code{evict}.
 #'     }
 #'   }
 #'
@@ -239,7 +239,7 @@ MemoryCache <- R6Class("MemoryCache",
 
     exists = function(key) {
       validate_key(key)
-      private$cache$has(key)
+      private$cache$exists(key)
     },
 
     keys = function() {

R/cache-utils.R

@@ -1,3 +1,27 @@
+#' A Key Missing object
+#'
+#' A \code{key_missing} object represents a cache miss.
+#'
+#' @param x An object to test.
+#'
+#' @seealso \code{\link{diskCache}}, \code{\link{memoryCache}}.
+#'
+#' @export
+key_missing <- function() {
+  structure(list(), class = "key_missing")
+}
+
+#' @rdname key_missing
+#' @export
+is.key_missing <- function(x) {
+  inherits(x, "key_missing")
+}
+
+#' @export
+print.key_missing <- function(x, ...) {
+  cat("<Key Missing>\n")
+}
+
 
 validate_key <- function(key) {
   if (!is.character(key) || length(key) != 1 || nchar(key) == 0) {

R/conditions.R

@@ -3,9 +3,9 @@
 #' Advanced (borderline internal) functions for capturing, printing, and
 #' manipulating stack traces.
 #'
-#' @return `printError` and `printStackTrace` return
-#'   `invisible()`. The other functions pass through the results of
-#'   `expr`.
+#' @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
@@ -106,17 +106,17 @@ getCallCategories <- function(calls) {
   }, character(1))
 }
 
-#' @details `captureStackTraces` runs the given `expr` and if any
-#'   *uncaught* errors occur, annotates them with stack trace info for use
-#'   by `printError` and `printStackTrace`. It is not necessary to use
-#'   `captureStackTraces` around the same expression as
-#'   `withLogErrors`, as the latter includes a call to the former. Note
-#'   that if `expr` contains calls (either directly or indirectly) to
-#'   `try`, or `tryCatch` with an error handler, stack traces therein
-#'   cannot be captured unless another `captureStackTraces` call is
-#'   inserted in the interior of the `try` or `tryCatch`. This is
+#' @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 `captureStackTraces`.
+#'   condition handler installed by \code{captureStackTraces}.
 #'
 #' @param expr The expression to wrap.
 #' @rdname stacktrace
@@ -209,11 +209,11 @@ doCaptureStack <- function(e) {
   stop(e)
 }
 
-#' @details `withLogErrors` captures stack traces and logs errors that
-#'   occur in `expr`, but does allow errors to propagate beyond this point
+#' @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
-#'   `captureStackTraces` with regard to `try`/`tryCatch` apply
-#'   to `withLogErrors`.
+#'   \code{captureStackTraces} with regard to \code{try}/\code{tryCatch} apply
+#'   to \code{withLogErrors}.
 #' @rdname stacktrace
 #' @export
 withLogErrors <- function(expr,
@@ -247,19 +247,19 @@ withLogErrors <- function(expr,
   )
 }
 
-#' @details `printError` prints the error and stack trace (if any) using
-#'   `warning(immediate.=TRUE)`. `printStackTrace` prints the stack
+#' @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 `TRUE`, then every element of `sys.calls()` will be
-#'   included in the stack trace. By default (`FALSE`), calls that Shiny
+#' @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 `TRUE` (the default), srcrefs will be reassigned from
+#' @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 `FALSE`, srcrefs will be
+#'   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
@@ -361,10 +361,10 @@ printStackTrace <- function(cond,
   invisible()
 }
 
-#' @details `extractStackTrace` takes a list of calls (e.g. as returned
-#'   from `conditionStackTrace(cond)`) and returns a data frame with one
-#'   row for each stack frame and the columns `num` (stack frame number),
-#'   `call` (a function name or similar), and `loc` (source file path
+#' @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). It was deprecated after shiny 1.0.5 because
 #'   it doesn't support deep stack traces.
 #' @rdname stacktrace
@@ -537,7 +537,7 @@ offsetSrcrefs <- function(calls, offset = TRUE) {
   calls
 }
 
-#' @details `formatStackTrace` is similar to `extractStackTrace`, but
+#' @details \code{formatStackTrace} is similar to \code{extractStackTrace}, but
 #'   it returns a preformatted character vector instead of a data frame. It was
 #'   deprecated after shiny 1.0.5 because it doesn't support deep stack traces.
 #' @param indent A string to prefix every line of the stack trace.
@@ -588,11 +588,11 @@ stripStackTrace <- function(cond) {
   conditionStackTrace(cond) <- NULL
 }
 
-#' @details `conditionStackTrace` and `conditionStackTrace<-` are
+#' @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
-#'   `captureStackTraces` (or `withLogErrors`).
+#'   \code{captureStackTraces} (or \code{withLogErrors}).
 #' @rdname stacktrace
 #' @export
 conditionStackTrace <- function(cond) {
@@ -607,8 +607,8 @@ conditionStackTrace <- function(cond) {
   invisible(cond)
 }
 
-#' @details The two functions `..stacktraceon..` and
-#'   `..stacktraceoff..` have no runtime behavior during normal execution;
+#' @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
@@ -624,4 +624,4 @@ conditionStackTrace <- function(cond) {
 #' @export
 ..stacktraceoff.. <- function(expr) expr
 
-..stacktracefloor.. <- function(expr) expr
+..stacktracefloor.. <- function(expr) expr

R/globals.R

@@ -1,78 +1,29 @@
 # A scope where we can put mutable global state
 .globals <- new.env(parent = emptyenv())
 
-register_s3_method <- function(pkg, generic, class, fun = NULL) {
-  stopifnot(is.character(pkg), length(pkg) == 1)
-  stopifnot(is.character(generic), length(generic) == 1)
-  stopifnot(is.character(class), length(class) == 1)
-
-  if (is.null(fun)) {
-    fun <- get(paste0(generic, ".", class), envir = parent.frame())
-  } else {
-    stopifnot(is.function(fun))
-  }
-
-  if (pkg %in% loadedNamespaces()) {
-    registerS3method(generic, class, fun, envir = asNamespace(pkg))
-  }
-
-  # Always register hook in case pkg is loaded at some
-  # point the future (or, potentially, but less commonly,
-  # unloaded & reloaded)
-  setHook(
-    packageEvent(pkg, "onLoad"),
-    function(...) {
-      registerS3method(generic, class, fun, envir = asNamespace(pkg))
-    }
-  )
-}
-
-register_upgrade_message <- function(pkg, version) {
-  # Is an out-dated version of this package installed?
-  needs_upgrade <- function() {
-    if (system.file(package = pkg) == "")
-      return(FALSE)
-    if (utils::packageVersion(pkg) >= version)
-      return(FALSE)
-    TRUE
-  }
-
-  msg <- sprintf(
-    "This version of Shiny is designed to work with '%s' >= %s.
-    Please upgrade via install.packages('%s').",
-    pkg, version, pkg
-  )
-
-  if (pkg %in% loadedNamespaces() && needs_upgrade()) {
-    packageStartupMessage(msg)
-  }
-
-  # Always register hook in case pkg is loaded at some
-  # point the future (or, potentially, but less commonly,
-  # unloaded & reloaded)
-  setHook(
-    packageEvent(pkg, "onLoad"),
-    function(...) {
-      if (needs_upgrade()) packageStartupMessage(msg)
-    }
-  )
-}
-
 .onLoad <- function(libname, pkgname) {
   # R's lazy-loading package scheme causes the private seed to be cached in the
   # package itself, making our PRNG completely deterministic. This line resets
   # the private seed during load.
   withPrivateSeed(set.seed(NULL))
 
-  # Make sure these methods are available to knitr if shiny is loaded but not
-  # attached.
-  register_s3_method("knitr", "knit_print", "reactive")
-  register_s3_method("knitr", "knit_print", "shiny.appobj")
-  register_s3_method("knitr", "knit_print", "shiny.render.function")
-
-  # Shiny 1.4.0 bumps jQuery 1.x to 3.x, which caused a problem
-  # with static-rendering of htmlwidgets, and htmlwidgets 1.5
-  # includes a fix for this problem
-  # https://github.com/rstudio/shiny/issues/2630
-  register_upgrade_message("htmlwidgets", 1.5)
+  appsByToken <<- Map$new()
+  appsNeedingFlush <<- Map$new()
+  timerCallbacks <<- TimerCallbacks$new()
+  initializeInputHandlers()
+  .globals$onStopCallbacks <<- Callbacks$new()
+}
+
+.onAttach <- function(libname, pkgname) {
+  # Check for htmlwidgets version, if installed. As of Shiny 0.12.0 and
+  # htmlwidgets 0.4, both packages switched from RJSONIO to jsonlite. Because of
+  # this change, Shiny 0.12.0 will work only with htmlwidgets >= 0.4, and vice
+  # versa.
+  if (system.file(package = "htmlwidgets") != "" &&
+      utils::packageVersion("htmlwidgets") < "0.4") {
+    packageStartupMessage(
+      "This version of Shiny is designed to work with htmlwidgets >= 0.4. ",
+      "Please upgrade your version of htmlwidgets."
+    )
+  }
 }

R/graph.R

@@ -59,8 +59,8 @@ reactIdStr <- function(num) {
 #' dependencies and execution in your application.
 #'
 #' To use the reactive log visualizer, start with a fresh R session and
-#' run the command `options(shiny.reactlog=TRUE)`; then launch your
-#' application in the usual way (e.g. using [runApp()]). At
+#' run the command \code{options(shiny.reactlog=TRUE)}; then launch your
+#' application in the usual way (e.g. using \code{\link{runApp}}). At
 #' any time you can hit Ctrl+F3 (or for Mac users, Command+F3) in your
 #' web browser to launch the reactive log visualization.
 #'
@@ -75,14 +75,14 @@ reactIdStr <- function(num) {
 #'
 #' As an alternative to pressing Ctrl/Command+F3--for example, if you
 #' are using reactives outside of the context of a Shiny
-#' application--you can run the `reactlogShow` function, which will
+#' application--you can run the \code{reactlogShow} function, which will
 #' generate the reactive log visualization as a static HTML file and
 #' launch it in your default browser. In this case, refreshing your
 #' browser will not load new activity into the report; you will need to
-#' call `reactlogShow()` explicitly.
+#' call \code{reactlogShow()} explicitly.
 #'
 #' For security and performance reasons, do not enable
-#' `shiny.reactlog` in production environments. When the option is
+#' \code{shiny.reactlog} in production environments. When the option is
 #' 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.
 #'
@@ -91,7 +91,7 @@ NULL
 
 
 #' @describeIn reactlog Return a list of reactive information.  Can be used in conjunction with
-#'   [reactlog::reactlog_show] to later display the reactlog graph.
+#'   \code{reactlog::\link[reactlog]{reactlog_show}} to later display the reactlog graph.
 #' @export
 reactlog <- function() {
   rLog$asList()
@@ -104,7 +104,7 @@ reactlogShow <- function(time = TRUE) {
   check_reactlog()
   reactlog::reactlog_show(reactlog(), time = time)
 }
-#' @describeIn reactlog This function is deprecated. You should use [reactlogShow()]
+#' @describeIn reactlog This function is deprecated. You should use \code{\link{reactlogShow}}
 #' @export
 # legacy purposes
 showReactLog <- function(time = TRUE) {

R/history.R

@@ -15,21 +15,21 @@ NULL
 #' the conditional on an input or a calculated reactive, you can base it on the
 #' query string). However, note that, if you're changing the query string / hash
 #' programatically from within the server code, you must use
-#' `updateQueryString(_yourNewQueryString_, mode = "push")`. The default
-#' `mode` for `updateQueryString` is `"replace"`, which doesn't
+#' \code{updateQueryString(_yourNewQueryString_, mode = "push")}. The default
+#' \code{mode} for \code{updateQueryString} is \code{"replace"}, which doesn't
 #' raise any events, so any observers or reactives that depend on it will
-#' *not* get triggered. However, if you're changing the query string / hash
+#' \emph{not} get triggered. However, if you're changing the query string / hash
 #' directly by typing directly in the browser and hitting enter, you don't have
 #' to worry about this.
 #'
 #' @param session	A Shiny session object.
 #'
-#' @return For `getQueryString`, a named list. For example, the query
-#'   string `?param1=value1&param2=value2` becomes `list(param1 =
-#'   value1, param2 = value2)`. For `getUrlHash`, a character vector with
-#'   the hash (including the leading `#` symbol).
+#' @return For \code{getQueryString}, a named list. For example, the query
+#'   string \code{?param1=value1&param2=value2} becomes \code{list(param1 =
+#'   value1, param2 = value2)}. For \code{getUrlHash}, a character vector with
+#'   the hash (including the leading \code{#} symbol).
 #'
-#' @seealso [updateQueryString()]
+#' @seealso \code{\link{updateQueryString}}
 #'
 #' @examples
 #' ## Only run this example in interactive R sessions

R/html-deps.R

@@ -2,20 +2,20 @@
 #'
 #' Ensure that a file-based HTML dependency (from the htmltools package) can be
 #' served over Shiny's HTTP server. This function works by using
-#' [addResourcePath()] to map the HTML dependency's directory to a
+#' \code{\link{addResourcePath}} to map the HTML dependency's directory to a
 #' URL.
 #'
 #' @param dependency A single HTML dependency object, created using
-#'   [htmltools::htmlDependency()]. If the `src` value is named,
-#'   then `href` and/or `file` names must be present.
-#' @param scrubFile If TRUE (the default), remove `src$file` for the
+#'   \code{\link[htmltools]{htmlDependency}}. If the \code{src} value is named,
+#'   then \code{href} and/or \code{file} names must be present.
+#' @param scrubFile If TRUE (the default), remove \code{src$file} for the
 #'   dependency. This prevents the local file path from being sent to the client
 #'   when dynamic web dependencies are used. If FALSE, don't remove
-#'   `src$file`. Setting it to FALSE should be needed only in very unusual
+#'   \code{src$file}. Setting it to FALSE should be needed only in very unusual
 #'   cases.
 #'
-#' @return A single HTML dependency object that has an `href`-named element
-#'   in its `src`.
+#' @return A single HTML dependency object that has an \code{href}-named element
+#'   in its \code{src}.
 #' @export
 createWebDependency <- function(dependency, scrubFile = TRUE) {
   if (is.null(dependency))

R/htmltools.R

@@ -1,11 +1,8 @@
-#' @import htmltools
-#' @export tags p h1 h2 h3 h4 h5 h6 a br div span pre code img strong em hr
-#' @export tag tagList tagAppendAttributes tagHasAttribute tagGetAttribute tagAppendChild tagAppendChildren tagSetChildren
-#' @export HTML
-#' @export includeHTML includeText includeMarkdown includeCSS includeScript
-#' @export singleton is.singleton
+#' @export a br code div em h1 h2 h3 h4 h5 h6 hr HTML img p pre span strong
+#' @export includeCSS includeHTML includeMarkdown includeScript includeText
+#' @export is.singleton singleton
+#' @export tag tagAppendAttributes tagAppendChild tagAppendChildren tagList tags tagSetChildren withTags
 #' @export validateCssUnit
-#' @export htmlTemplate
-#' @export suppressDependencies
-#' @export withTags
+#' @export knit_print.html knit_print.shiny.tag knit_print.shiny.tag.list
+#' @export htmlTemplate suppressDependencies
 NULL

R/image-interact-opts.R

@@ -1,16 +1,16 @@
 #' Create an object representing click options
 #'
 #' This generates an object representing click options, to be passed as the
-#' `click` argument of [imageOutput()] or
-#' [plotOutput()].
+#' \code{click} argument of \code{\link{imageOutput}} or
+#' \code{\link{plotOutput}}.
 #'
-#' @param id Input value name. For example, if the value is `"plot_click"`,
-#'   then the click coordinates will be available as `input$plot_click`.
+#' @param id Input value name. For example, if the value is \code{"plot_click"},
+#'   then the click coordinates will be available as \code{input$plot_click}.
 #' @param clip Should the click area be clipped to the plotting area? If FALSE,
 #'   then the server will receive click events even when the mouse is outside
 #'   the plotting area, as long as it is still inside the image.
 #' @export
-clickOpts <- function(id, clip = TRUE) {
+clickOpts <- function(id = NULL, clip = TRUE) {
   if (is.null(id))
     stop("id must not be NULL")
 
@@ -24,19 +24,19 @@ clickOpts <- function(id, clip = TRUE) {
 #' Create an object representing double-click options
 #'
 #' This generates an object representing dobule-click options, to be passed as
-#' the `dblclick` argument of [imageOutput()] or
-#' [plotOutput()].
+#' the \code{dblclick} argument of \code{\link{imageOutput}} or
+#' \code{\link{plotOutput}}.
 #'
 #' @param id Input value name. For example, if the value is
-#'   `"plot_dblclick"`, then the click coordinates will be available as
-#'   `input$plot_dblclick`.
+#'   \code{"plot_dblclick"}, then the click coordinates will be available as
+#'   \code{input$plot_dblclick}.
 #' @param clip Should the click area be clipped to the plotting area? If FALSE,
 #'   then the server will receive double-click events even when the mouse is
 #'   outside the plotting area, as long as it is still inside the image.
 #' @param delay Maximum delay (in ms) between a pair clicks for them to be
 #'   counted as a double-click.
 #' @export
-dblclickOpts <- function(id, clip = TRUE, delay = 400) {
+dblclickOpts <- function(id = NULL, clip = TRUE, delay = 400) {
   if (is.null(id))
     stop("id must not be NULL")
 
@@ -50,26 +50,26 @@ dblclickOpts <- function(id, clip = TRUE, delay = 400) {
 #' Create an object representing hover options
 #'
 #' This generates an object representing hovering options, to be passed as the
-#' `hover` argument of [imageOutput()] or
-#' [plotOutput()].
+#' \code{hover} argument of \code{\link{imageOutput}} or
+#' \code{\link{plotOutput}}.
 #'
-#' @param id Input value name. For example, if the value is `"plot_hover"`,
-#'   then the hover coordinates will be available as `input$plot_hover`.
+#' @param id Input value name. For example, if the value is \code{"plot_hover"},
+#'   then the hover coordinates will be available as \code{input$plot_hover}.
 #' @param delay How long to delay (in milliseconds) when debouncing or
 #'   throttling, before sending the mouse location to the server.
 #' @param delayType The type of algorithm for limiting the number of hover
-#'   events. Use `"throttle"` to limit the number of hover events to one
-#'   every `delay` milliseconds. Use `"debounce"` to suspend events
+#'   events. Use \code{"throttle"} to limit the number of hover events to one
+#'   every \code{delay} milliseconds. Use \code{"debounce"} to suspend events
 #'   while the cursor is moving, and wait until the cursor has been at rest for
-#'   `delay` milliseconds before sending an event.
+#'   \code{delay} milliseconds before sending an event.
 #' @param clip Should the hover area be clipped to the plotting area? If FALSE,
 #'   then the server will receive hover events even when the mouse is outside
 #'   the plotting area, as long as it is still inside the image.
-#' @param nullOutside If `TRUE` (the default), the value will be set to
-#'   `NULL` when the mouse exits the plotting area. If `FALSE`, the
+#' @param nullOutside If \code{TRUE} (the default), the value will be set to
+#'   \code{NULL} when the mouse exits the plotting area. If \code{FALSE}, the
 #'   value will stop changing when the cursor exits the plotting area.
 #' @export
-hoverOpts <- function(id, delay = 300,
+hoverOpts <- function(id = NULL, delay = 300,
                       delayType = c("debounce", "throttle"), clip = TRUE,
                       nullOutside = TRUE) {
   if (is.null(id))
@@ -87,37 +87,37 @@ hoverOpts <- function(id, delay = 300,
 #' Create an object representing brushing options
 #'
 #' This generates an object representing brushing options, to be passed as the
-#' `brush` argument of [imageOutput()] or
-#' [plotOutput()].
+#' \code{brush} argument of \code{\link{imageOutput}} or
+#' \code{\link{plotOutput}}.
 #'
-#' @param id Input value name. For example, if the value is `"plot_brush"`,
-#'   then the coordinates will be available as `input$plot_brush`. Multiple
-#'   `imageOutput`/`plotOutput` calls may share the same `id`
+#' @param id Input value name. For example, if the value is \code{"plot_brush"},
+#'   then the coordinates will be available as \code{input$plot_brush}. Multiple
+#'   \code{imageOutput}/\code{plotOutput} calls may share the same \code{id}
 #'   value; brushing one image or plot will cause any other brushes with the
-#'   same `id` to disappear.
+#'   same \code{id} to disappear.
 #' @param fill Fill color of the brush.
 #' @param stroke Outline color of the brush.
 #' @param opacity Opacity of the brush
 #' @param delay How long to delay (in milliseconds) when debouncing or
 #'   throttling, before sending the brush data to the server.
 #' @param delayType The type of algorithm for limiting the number of brush
-#'   events. Use `"throttle"` to limit the number of brush events to one
-#'   every `delay` milliseconds. Use `"debounce"` to suspend events
+#'   events. Use \code{"throttle"} to limit the number of brush events to one
+#'   every \code{delay} milliseconds. Use \code{"debounce"} to suspend events
 #'   while the cursor is moving, and wait until the cursor has been at rest for
-#'   `delay` milliseconds before sending an event.
+#'   \code{delay} milliseconds before sending an event.
 #' @param clip Should the brush area be clipped to the plotting area? If FALSE,
 #'   then the user will be able to brush outside the plotting area, as long as
 #'   it is still inside the image.
-#' @param direction The direction for brushing. If `"xy"`, the brush can be
-#'   drawn and moved in both x and y directions. If `"x"`, or `"y"`,
+#' @param direction The direction for brushing. If \code{"xy"}, the brush can be
+#'   drawn and moved in both x and y directions. If \code{"x"}, or \code{"y"},
 #'   the brush wil work horizontally or vertically.
 #' @param resetOnNew When a new image is sent to the browser (via
-#'   [renderImage()]), should the brush be reset? The default,
-#'   `FALSE`, is useful if you want to update the plot while keeping the
-#'   brush. Using `TRUE` is useful if you want to clear the brush whenever
+#'   \code{\link{renderImage}}), should the brush be reset? The default,
+#'   \code{FALSE}, is useful if you want to update the plot while keeping the
+#'   brush. Using \code{TRUE} is useful if you want to clear the brush whenever
 #'   the plot is updated.
 #' @export
-brushOpts <- function(id, fill = "#9cf", stroke = "#036",
+brushOpts <- function(id = NULL, fill = "#9cf", stroke = "#036",
                       opacity = 0.25, delay = 300,
                       delayType = c("debounce", "throttle"), clip = TRUE,
                       direction = c("xy", "x", "y"),

R/image-interact.R

@@ -1,76 +1,59 @@
-#' Find rows of data selected on an interactive plot.
+#' Find rows of data that are selected by a brush
 #'
-#' @description
-#' `brushedPoints()` returns rows from a data frame which are under a brush.
-#' `nearPoints()` returns rows from a data frame which are near a click, hover,
-#' or double-click. Alternatively, set `allRows = TRUE` to return all rows from
-#' the input data with an additional column `selected_` that indicates which
-#' rows of the would be selected.
+#' This function returns rows from a data frame which are under a brush used
+#' with \code{\link{plotOutput}}.
 #'
-#' @section ggplot2:
-#' For plots created with ggplot2, it is not necessary to specify the
-#' column names to `xvar`, `yvar`, `panelvar1`, and `panelvar2` as that
-#' information can be automatically derived from the plot specification.
+#' It is also possible for this function to return all rows from the input data
+#' frame, but with an additional column \code{selected_}, which indicates which
+#' rows of the input data frame are selected by the brush (\code{TRUE} for
+#' selected, \code{FALSE} for not-selected). This is enabled by setting
+#' \code{allRows=TRUE} option.
 #'
-#' Note, however, that this will not work if you use a computed column, like
-#' `aes(speed/2, dist))`. Instead, we recommend that you modify the data
+#' The \code{xvar}, \code{yvar}, \code{panelvar1}, and \code{panelvar2}
+#' arguments specify which columns in the data correspond to the x variable, y
+#' variable, and panel variables of the plot. For example, if your plot is
+#' \code{plot(x=cars$speed, y=cars$dist)}, and your brush is named
+#' \code{"cars_brush"}, then you would use \code{brushedPoints(cars,
+#' input$cars_brush, "speed", "dist")}.
+#'
+#' For plots created with ggplot2, it should not be necessary to specify the
+#' column names; that information will already be contained in the brush,
+#' provided that variables are in the original data, and not computed. For
+#' example, with \code{ggplot(cars, aes(x=speed, y=dist)) + geom_point()}, you
+#' could use \code{brushedPoints(cars, input$cars_brush)}. If, however, you use
+#' a computed column, like \code{ggplot(cars, aes(x=speed/2, y=dist)) +
+#' geom_point()}, then it will not be able to automatically extract column names
+#' and filter on them. If you want to use this function to filter data, it is
+#' recommended that you not use computed columns; instead, modify the data
 #' first, and then make the plot with "raw" columns in the modified data.
 #'
-#' @section Brushing:
-#' If x or y column is a factor, then it will be coerced to an integer vector.
-#' If it is a character vector, then it will be coerced to a factor and then
-#' integer vector. This means that the brush will be considered to cover a
-#' given character/factor value when it covers the center value.
+#' If a specified x or y column is a factor, then it will be coerced to an
+#' integer vector. If it is a character vector, then it will be coerced to a
+#' factor and then integer vector. This means that the brush will be considered
+#' to cover a given character/factor value when it covers the center value.
 #'
 #' If the brush is operating in just the x or y directions (e.g., with
-#' `brushOpts(direction = "x")`, then this function will filter out points
+#' \code{brushOpts(direction = "x")}, then this function will filter out points
 #' using just the x or y variable, whichever is appropriate.
 #'
-#' @returns
-#' A data frame based on `df`, containing the observations selected by the
-#' brush or near the click event. For `nearPoints()`, the rows will be sorted
-#' by distance to the event.
-#'
-#' If `allRows = TRUE`, then all rows will returned, along with a new
-#' `selected_` column that indicates whether or not the point was selected.
-#' The output from `nearPoints()` will no longer be sorted, but you can
-#' set `addDist = TRUE` to get an additional column that gives the pixel
-#' distance to the pointer.
-#'
+#' @param brush The data from a brush, such as \code{input$plot_brush}.
 #' @param df A data frame from which to select rows.
-#' @param brush,coordinfo The data from a brush or click/dblclick/hover event
-#'   e.g. `input$plot_brush`, `input$plot_click`.
-#' @param xvar,yvar A string giving the name of the variable on the x or y axis.
-#'   These are only required for base graphics, and must be the name of
-#'   a column in `df`.
-#' @param panelvar1,panelvar2 A string giving the name of a panel variable.
-#'   For expert use only; in most cases these will be automatically
-#'   derived from the ggplot2 spec.
-#' @param allRows If `FALSE` (the default) return a data frame containing
-#'   the selected rows. If `TRUE`, the input data frame will have a new
-#'   column, `selected_`, which indicates whether the row was selected or not.
-#' @param threshold A maximum distance (in pixels) to the pointer location.
-#'   Rows in the data frame will be selected if the distance to the pointer is
-#'   less than `threshold`.
-#' @param maxpoints Maximum number of rows to return. If `NULL` (the default),
-#'   will return all rows within the threshold distance.
-#' @param addDist If TRUE, add a column named `dist_` that contains the
-#'   distance from the coordinate to the point, in pixels. When no pointer
-#'   event has yet occurred, the value of `dist_` will be `NA`.
-#' @seealso [plotOutput()] for example usage.
+#' @param xvar,yvar A string with the name of the variable on the x or y axis.
+#'   This must also be the name of a column in \code{df}. If absent, then this
+#'   function will try to infer the variable from the brush (only works for
+#'   ggplot2).
+#' @param panelvar1,panelvar2 Each of these is a string with the name of a panel
+#'   variable. For example, if with ggplot2, you facet on a variable called
+#'   \code{cyl}, then you can use \code{"cyl"} here. However, specifying the
+#'   panel variable should not be necessary with ggplot2; Shiny should be able
+#'   to auto-detect the panel variable.
+#' @param allRows If \code{FALSE} (the default) return a data frame containing
+#'   the selected rows. If \code{TRUE}, the input data frame will have a new
+#'   column, \code{selected_}, which indicates whether the row was inside the
+#'   brush (\code{TRUE}) or outside the brush (\code{FALSE}).
+#'
+#' @seealso \code{\link{plotOutput}} for example usage.
 #' @export
-#' @examples
-#' \dontrun{
-#' # Note that in practice, these examples would need to go in reactives
-#' # or observers.
-#'
-#' # This would select all points within 5 pixels of the click
-#' nearPoints(mtcars, input$plot_click)
-#'
-#' # Select just the nearest point within 10 pixels of the click
-#' nearPoints(mtcars, input$plot_click, threshold = 10, maxpoints = 1)
-#'
-#' }
 brushedPoints <- function(df, brush, xvar = NULL, yvar = NULL,
                           panelvar1 = NULL, panelvar2 = NULL,
                           allRows = FALSE) {
@@ -105,14 +88,17 @@ brushedPoints <- function(df, brush, xvar = NULL, yvar = NULL,
       stop("brushedPoints: not able to automatically infer `xvar` from brush")
     if (!(xvar %in% names(df)))
       stop("brushedPoints: `xvar` ('", xvar ,"')  not in names of input")
-    keep_rows <- keep_rows & within_brush(df[[xvar]], brush, "x")
+    # Extract data values from the data frame
+    x <- asNumber(df[[xvar]])
+    keep_rows <- keep_rows & (x >= brush$xmin & x <= brush$xmax)
   }
   if (use_y) {
     if (is.null(yvar))
       stop("brushedPoints: not able to automatically infer `yvar` from brush")
     if (!(yvar %in% names(df)))
       stop("brushedPoints: `yvar` ('", yvar ,"') not in names of input")
-    keep_rows <- keep_rows & within_brush(df[[yvar]], brush, "y")
+    y <- asNumber(df[[yvar]])
+    keep_rows <- keep_rows & (y >= brush$ymin & y <= brush$ymax)
   }
 
   # Find which rows are matches for the panel vars (if present)
@@ -208,8 +194,56 @@ brushedPoints <- function(df, brush, xvar = NULL, yvar = NULL,
 #  $ direction: chr "y"
 
 
-#' @export
-#' @rdname brushedPoints
+#'Find rows of data that are near a click/hover/double-click
+#'
+#'This function returns rows from a data frame which are near a click, hover, or
+#'double-click, when used with \code{\link{plotOutput}}. The rows will be sorted
+#'by their distance to the mouse event.
+#'
+#'It is also possible for this function to return all rows from the input data
+#'frame, but with an additional column \code{selected_}, which indicates which
+#'rows of the input data frame are selected by the brush (\code{TRUE} for
+#'selected, \code{FALSE} for not-selected). This is enabled by setting
+#'\code{allRows=TRUE} option. If this is used, the resulting data frame will not
+#'be sorted by distance to the mouse event.
+#'
+#'The \code{xvar}, \code{yvar}, \code{panelvar1}, and \code{panelvar2} arguments
+#'specify which columns in the data correspond to the x variable, y variable,
+#'and panel variables of the plot. For example, if your plot is
+#'\code{plot(x=cars$speed, y=cars$dist)}, and your click variable is named
+#'\code{"cars_click"}, then you would use \code{nearPoints(cars,
+#'input$cars_brush, "speed", "dist")}.
+#'
+#'@inheritParams brushedPoints
+#'@param coordinfo The data from a mouse event, such as \code{input$plot_click}.
+#'@param threshold A maxmimum distance to the click point; rows in the data
+#'  frame where the distance to the click is less than \code{threshold} will be
+#'  returned.
+#'@param maxpoints Maximum number of rows to return. If NULL (the default),
+#'  return all rows that are within the threshold distance.
+#'@param addDist If TRUE, add a column named \code{dist_} that contains the
+#'  distance from the coordinate to the point, in pixels. When no mouse event
+#'  has yet occured, the value of \code{dist_} will be \code{NA}.
+#'@param allRows If \code{FALSE} (the default) return a data frame containing
+#'  the selected rows. If \code{TRUE}, the input data frame will have a new
+#'  column, \code{selected_}, which indicates whether the row was inside the
+#'  selected by the mouse event (\code{TRUE}) or not (\code{FALSE}).
+#'
+#'@seealso \code{\link{plotOutput}} for more examples.
+#'
+#' @examples
+#' \dontrun{
+#' # Note that in practice, these examples would need to go in reactives
+#' # or observers.
+#'
+#' # This would select all points within 5 pixels of the click
+#' nearPoints(mtcars, input$plot_click)
+#'
+#' # Select just the nearest point within 10 pixels of the click
+#' nearPoints(mtcars, input$plot_click, threshold = 10, maxpoints = 1)
+#'
+#' }
+#'@export
 nearPoints <- function(df, coordinfo, xvar = NULL, yvar = NULL,
                        panelvar1 = NULL, panelvar2 = NULL,
                        threshold = 5, maxpoints = NULL, addDist = FALSE,
@@ -247,8 +281,8 @@ nearPoints <- function(df, coordinfo, xvar = NULL, yvar = NULL,
     stop("nearPoints: `yvar` ('", yvar ,"')  not in names of input")
 
   # Extract data values from the data frame
-  x <- asNumber(df[[xvar]], coordinfo$domain$discrete_limits$x)
-  y <- asNumber(df[[yvar]], coordinfo$domain$discrete_limits$y)
+  x <- asNumber(df[[xvar]])
+  y <- asNumber(df[[yvar]])
 
   # Get the coordinates of the point (in img pixel coordinates)
   point_img <- coordinfo$coords_img
@@ -368,27 +402,11 @@ nearPoints <- function(df, coordinfo, xvar = NULL, yvar = NULL,
 #   ..$ y: NULL
 #  $ .nonce    : num 0.603
 
-# Helper to determine if data values are within the limits of
-# an input brush
-within_brush <- function(vals, brush, var = "x") {
-  var <- match.arg(var, c("x", "y"))
-  vals <- asNumber(vals, brush$domain$discrete_limits[[var]])
-  # It's possible for a non-missing data values to not
-  # map to the axis limits, for example:
-  # https://github.com/rstudio/shiny/pull/2410#issuecomment-488100881
-  !is.na(vals) &
-    vals >= brush[[paste0(var, "min")]] &
-    vals <= brush[[paste0(var, "max")]]
-}
+
 
 # Coerce various types of variables to numbers. This works for Date, POSIXt,
 # characters, and factors. Used because the mouse coords are numeric.
-# The `levels` argument should be used when mapping this variable to
-# a known set of discrete levels, which is needed for ggplot2 since
-# it allows you to control ordering and possible values of a discrete
-# positional scale (#2410)
-asNumber <- function(x, levels = NULL) {
-  if (length(levels)) return(match(x, levels))
+asNumber <- function(x) {
   if (is.character(x)) x <- as.factor(x)
   if (is.factor(x)) x <- as.integer(x)
   as.numeric(x)

R/imageutils.R

@@ -31,29 +31,29 @@ startPNG <- function(filename, width, height, res, ...) {
 #' Run a plotting function and save the output as a PNG
 #'
 #' This function returns the name of the PNG file that it generates. In
-#' essence, it calls `png()`, then `func()`, then `dev.off()`.
-#' So `func` must be a function that will generate a plot when used this
+#' essence, it calls \code{png()}, then \code{func()}, then \code{dev.off()}.
+#' So \code{func} must be a function that will generate a plot when used this
 #' way.
 #'
 #' For output, it will try to use the following devices, in this order:
-#' quartz (via [grDevices::png()]), then [Cairo::CairoPNG()],
-#' and finally [grDevices::png()]. This is in order of quality of
-#' output. Notably, plain `png` output on Linux and Windows may not
+#' quartz (via \code{\link[grDevices]{png}}), then \code{\link[Cairo]{CairoPNG}},
+#' and finally \code{\link[grDevices]{png}}. This is in order of quality of
+#' output. Notably, plain \code{png} output on Linux and Windows may not
 #' antialias some point shapes, resulting in poor quality output.
 #'
-#' In some cases, `Cairo()` provides output that looks worse than
-#' `png()`. To disable Cairo output for an app, use
-#' `options(shiny.usecairo=FALSE)`.
+#' In some cases, \code{Cairo()} provides output that looks worse than
+#' \code{png()}. To disable Cairo output for an app, use
+#' \code{options(shiny.usecairo=FALSE)}.
 #'
 #' @param func A function that generates a plot.
 #' @param filename The name of the output file. Defaults to a temp file with
-#'   extension `.png`.
+#'   extension \code{.png}.
 #' @param width Width in pixels.
 #' @param height Height in pixels.
 #' @param res Resolution in pixels per inch. This value is passed to
-#'   [grDevices::png()]. Note that this affects the resolution of PNG rendering in
+#'   \code{\link[grDevices]{png}}. Note that this affects the resolution of PNG rendering in
 #'   R; it won't change the actual ppi of the browser.
-#' @param ... Arguments to be passed through to [grDevices::png()].
+#' @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'),

R/input-action.R

@@ -6,7 +6,7 @@
 #' @inheritParams textInput
 #' @param label The contents of the button or link--usually a text label, but
 #'   you could also use any other HTML, like an image.
-#' @param icon An optional [icon()] to appear on the button.
+#' @param icon An optional \code{\link{icon}} to appear on the button.
 #' @param ... Named attributes to be applied to the button or link.
 #'
 #' @family input elements
@@ -16,7 +16,7 @@
 #'
 #' ui <- fluidPage(
 #'   sliderInput("obs", "Number of observations", 0, 1000, 500),
-#'   actionButton("goButton", "Go!", class = "btn-success"),
+#'   actionButton("goButton", "Go!"),
 #'   plotOutput("distPlot")
 #' )
 #'
@@ -36,18 +36,7 @@
 #'
 #' }
 #'
-#' ## Example of adding extra class values
-#' actionButton("largeButton", "Large Primary Button", class = "btn-primary btn-lg")
-#' actionLink("infoLink", "Information Link", class = "btn-info")
-#'
-#' @seealso [observeEvent()] and [eventReactive()]
-#'
-#' @section Server value:
-#' An integer of class `"shinyActionButtonValue"`. This class differs from
-#' ordinary integers in that a value of 0 is considered "falsy".
-#' This implies two things:
-#'   * Event handlers (e.g., [observeEvent()], [eventReactive()]) won't execute on initial load.
-#'   * Input validation (e.g., [req()], [need()]) will fail on initial load.
+#' @seealso \code{\link{observeEvent}} and \code{\link{eventReactive}}
 #' @export
 actionButton <- function(inputId, label, icon = NULL, width = NULL, ...) {
 

R/input-checkbox.R

@@ -3,11 +3,11 @@
 #' Create a checkbox that can be used to specify logical values.
 #'
 #' @inheritParams textInput
-#' @param value Initial value (`TRUE` or `FALSE`).
+#' @param value Initial value (\code{TRUE} or \code{FALSE}).
 #' @return A checkbox control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [checkboxGroupInput()], [updateCheckboxInput()]
+#' @seealso \code{\link{checkboxGroupInput}}, \code{\link{updateCheckboxInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -22,10 +22,6 @@
 #' }
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' `TRUE` if checked, `FALSE` otherwise.
-#'
 #' @export
 checkboxInput <- function(inputId, label, value = FALSE, width = NULL) {
 

R/input-checkboxgroup.R

@@ -7,25 +7,25 @@
 #' @inheritParams textInput
 #' @param choices List of values to show checkboxes for. If elements of the list
 #'   are named then that name rather than the value is displayed to the user. If
-#'   this argument is provided, then `choiceNames` and `choiceValues`
+#'   this argument is provided, then \code{choiceNames} and \code{choiceValues}
 #'   must not be provided, and vice-versa. The values should be strings; other
 #'   types (such as logicals and numbers) will be coerced to strings.
 #' @param selected The values that should be initially selected, if any.
-#' @param inline If `TRUE`, render the choices inline (i.e. horizontally)
+#' @param inline If \code{TRUE}, render the choices inline (i.e. horizontally)
 #' @param choiceNames,choiceValues List of names and values, respectively,
 #'   that are displayed to the user in the app and correspond to the each
-#'   choice (for this reason, `choiceNames` and `choiceValues`
+#'   choice (for this reason, \code{choiceNames} and \code{choiceValues}
 #'   must have the same length). If either of these arguments is
-#'   provided, then the other *must* be provided and `choices`
-#'   *must not* be provided. The advantage of using both of these over
-#'   a named list for `choices` is that `choiceNames` allows any
+#'   provided, then the other \emph{must} be provided and \code{choices}
+#'   \emph{must not} be provided. The advantage of using both of these over
+#'   a named list for \code{choices} is that \code{choiceNames} allows any
 #'   type of UI object to be passed through (tag objects, icons, HTML code,
 #'   ...), instead of just simple text. See Examples.
 #'
 #' @return A list of HTML elements that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [checkboxInput()], [updateCheckboxGroupInput()]
+#' @seealso \code{\link{checkboxInput}}, \code{\link{updateCheckboxGroupInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -67,9 +67,6 @@
 #'
 #' shinyApp(ui, server)
 #' }
-#' @section Server value:
-#' Character vector of values corresponding to the boxes that are checked.
-#'
 #' @export
 checkboxGroupInput <- function(inputId, label, choices = NULL, selected = NULL,
   inline = FALSE, width = NULL, choiceNames = NULL, choiceValues = NULL) {

R/input-date.R

@@ -3,32 +3,32 @@
 #' Creates a text input which, when clicked on, brings up a calendar that
 #' the user can click on to select dates.
 #'
-#' The date `format` string specifies how the date will be displayed in
+#' The date \code{format} string specifies how the date will be displayed in
 #' the browser. It allows the following values:
 #'
 #' \itemize{
-#'   \item `yy` Year without century (12)
-#'   \item `yyyy` Year with century (2012)
-#'   \item `mm` Month number, with leading zero (01-12)
-#'   \item `m` Month number, without leading zero (1-12)
-#'   \item `M` Abbreviated month name
-#'   \item `MM` Full month name
-#'   \item `dd` Day of month with leading zero
-#'   \item `d` Day of month without leading zero
-#'   \item `D` Abbreviated weekday name
-#'   \item `DD` Full weekday name
+#'   \item \code{yy} Year without century (12)
+#'   \item \code{yyyy} Year with century (2012)
+#'   \item \code{mm} Month number, with leading zero (01-12)
+#'   \item \code{m} Month number, without leading zero (1-12)
+#'   \item \code{M} Abbreviated month name
+#'   \item \code{MM} Full month name
+#'   \item \code{dd} Day of month with leading zero
+#'   \item \code{d} Day of month without leading zero
+#'   \item \code{D} Abbreviated weekday name
+#'   \item \code{DD} Full weekday name
 #' }
 #'
 #' @inheritParams textInput
 #' @param value The starting date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format. If NULL (the default), will use the current date
+#'   \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
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #' @param format The format of the date to display in the browser. Defaults to
-#'   `"yyyy-mm-dd"`.
+#'   \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 weekstart Which day is the start of the week. Should be an integer
@@ -44,12 +44,12 @@
 #' @param autoclose Whether or not to close the datepicker immediately when a
 #'   date is selected.
 #' @param datesdisabled Which dates should be disabled. Either a Date object,
-#' or a string in `yyyy-mm-dd` format.
+#' or a string in \code{yyyy-mm-dd} format.
 #' @param daysofweekdisabled Days of the week that should be disabled. Should be
 #'   a integer vector with values from 0 (Sunday) to 6 (Saturday).
 #'
 #' @family input elements
-#' @seealso [dateRangeInput()], [updateDateInput()]
+#' @seealso \code{\link{dateRangeInput}}, \code{\link{updateDateInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -86,10 +86,6 @@
 #'
 #' shinyApp(ui, server = function(input, output) { })
 #' }
-#'
-#' @section Server value:
-#' A [Date] vector of length 1.
-#'
 #' @export
 dateInput <- function(inputId, label, value = NULL, min = NULL, max = NULL,
   format = "yyyy-mm-dd", startview = "month", weekstart = 0,

R/input-daterange.R

@@ -3,33 +3,33 @@
 #' Creates a pair of text inputs which, when clicked on, bring up calendars that
 #' the user can click on to select dates.
 #'
-#' The date `format` string specifies how the date will be displayed in
+#' The date \code{format} string specifies how the date will be displayed in
 #' the browser. It allows the following values:
 #'
 #' \itemize{
-#'   \item `yy` Year without century (12)
-#'   \item `yyyy` Year with century (2012)
-#'   \item `mm` Month number, with leading zero (01-12)
-#'   \item `m` Month number, without leading zero (1-12)
-#'   \item `M` Abbreviated month name
-#'   \item `MM` Full month name
-#'   \item `dd` Day of month with leading zero
-#'   \item `d` Day of month without leading zero
-#'   \item `D` Abbreviated weekday name
-#'   \item `DD` Full weekday name
+#'   \item \code{yy} Year without century (12)
+#'   \item \code{yyyy} Year with century (2012)
+#'   \item \code{mm} Month number, with leading zero (01-12)
+#'   \item \code{m} Month number, without leading zero (1-12)
+#'   \item \code{M} Abbreviated month name
+#'   \item \code{MM} Full month name
+#'   \item \code{dd} Day of month with leading zero
+#'   \item \code{d} Day of month without leading zero
+#'   \item \code{D} Abbreviated weekday name
+#'   \item \code{DD} Full weekday name
 #' }
 #'
 #' @inheritParams dateInput
 #' @param start The initial start date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format. If NULL (the default), will use the current
+#'   \code{yyyy-mm-dd} format. If NULL (the default), will use the current
 #'   date in the client's time zone.
 #' @param end The initial end date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format. If NULL (the default), will use the current
+#'   \code{yyyy-mm-dd} format. If NULL (the default), will use the current
 #'   date in the client's time zone.
 #' @param separator String to display between the start and end input boxes.
 #'
 #' @family input elements
-#' @seealso [dateInput()], [updateDateRangeInput()]
+#' @seealso \code{\link{dateInput}}, \code{\link{updateDateRangeInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -70,10 +70,6 @@
 #'
 #' shinyApp(ui, server = function(input, output) { })
 #' }
-#'
-#' @section Server value:
-#' A [Date] vector of length 2.
-#'
 #' @export
 dateRangeInput <- function(inputId, label, start = NULL, end = NULL,
     min = NULL, max = NULL, format = "yyyy-mm-dd", startview = "month",
@@ -96,9 +92,9 @@ dateRangeInput <- function(inputId, label, start = NULL, end = NULL,
 
       shinyInputLabel(inputId, label),
       # input-daterange class is needed for dropdown behavior
-      div(class = "input-daterange input-group input-group-sm",
+      div(class = "input-daterange input-group",
         tags$input(
-          class = "form-control",
+          class = "input-sm form-control",
           type = "text",
           `data-date-language` = language,
           `data-date-week-start` = weekstart,
@@ -109,14 +105,9 @@ dateRangeInput <- function(inputId, label, start = NULL, end = NULL,
           `data-initial-date` = start,
           `data-date-autoclose` = if (autoclose) "true" else "false"
         ),
-        # input-group-prepend and input-group-append are for bootstrap 4 forward compat
-        span(class = "input-group-addon input-group-prepend input-group-append",
-          span(class = "input-group-text",
-            separator
-          )
-        ),
+        span(class = "input-group-addon", separator),
         tags$input(
-          class = "form-control",
+          class = "input-sm form-control",
           type = "text",
           `data-date-language` = language,
           `data-date-week-start` = weekstart,

R/input-file.R

@@ -3,23 +3,30 @@
 #' Create a file upload control that can be used to upload one or more files.
 #'
 #' Whenever a file upload completes, the corresponding input variable is set
-#' to a dataframe. See the `Server value` section.
+#' to a dataframe. This dataframe contains one row for each selected file, and
+#' the following columns:
+#' \describe{
+#'   \item{\code{name}}{The filename provided by the web browser. This is
+#'   \strong{not} the path to read to get at the actual data that was uploaded
+#'   (see
+#'   \code{datapath} column).}
+#'   \item{\code{size}}{The size of the uploaded data, in
+#'   bytes.}
+#'   \item{\code{type}}{The MIME type reported by the browser (for example,
+#'   \code{text/plain}), or empty string if the browser didn't know.}
+#'   \item{\code{datapath}}{The path to a temp file that contains the data that was
+#'   uploaded. This file may be deleted if the user performs another upload
+#'   operation.}
+#' }
 #'
 #' @family input elements
 #'
 #' @inheritParams textInput
 #' @param multiple Whether the user should be allowed to select and upload
-#'   multiple files at once. **Does not work on older browsers, including
-#'   Internet Explorer 9 and earlier.**
-#' @param accept A character vector of "unique file type specifiers" which
-#'   gives the browser a hint as to the type of file the server expects.
-#'   Many browsers use this prevent the user from selecting an invalid file.
-#'
-#'   A unique file type specifier can be:
-#'   * A case insensitive extension like `.csv` or `.rds`.
-#'   * A valid MIME type, like `text/plain` or `application/pdf`
-#'   * One of `audio/*`, `video/*`, or `image/*` meaning any audio, video,
-#'     or image type, respectively.
+#'   multiple files at once. \bold{Does not work on older browsers, including
+#'   Internet Explorer 9 and earlier.}
+#' @param accept A character vector of MIME types; gives the browser a hint of
+#'   what kind of files the server is expecting.
 #' @param buttonLabel The label used on the button. Can be text or an HTML tag
 #'   object.
 #' @param placeholder The text to show before a file has been uploaded.
@@ -31,7 +38,13 @@
 #' ui <- fluidPage(
 #'   sidebarLayout(
 #'     sidebarPanel(
-#'       fileInput("file1", "Choose CSV File", accept = ".csv"),
+#'       fileInput("file1", "Choose CSV File",
+#'         accept = c(
+#'           "text/csv",
+#'           "text/comma-separated-values,text/plain",
+#'           ".csv")
+#'         ),
+#'       tags$hr(),
 #'       checkboxInput("header", "Header", TRUE)
 #'     ),
 #'     mainPanel(
@@ -42,35 +55,22 @@
 #'
 #' server <- function(input, output) {
 #'   output$contents <- renderTable({
-#'     file <- input$file1
-#'     ext <- tools::file_ext(file$datapath)
+#'     # 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
 #'
-#'     req(file)
-#'     validate(need(ext == "csv", "Please upload a csv file"))
+#'     if (is.null(inFile))
+#'       return(NULL)
 #'
-#'     read.csv(file$datapath, header = input$header)
+#'     read.csv(inFile$datapath, header = input$header)
 #'   })
 #' }
 #'
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' A `data.frame` that contains one row for each selected file, and following columns:
-#' \describe{
-#'   \item{`name`}{The filename provided by the web browser. This is
-#'   **not** the path to read to get at the actual data that was uploaded
-#'   (see
-#'   `datapath` column).}
-#'   \item{`size`}{The size of the uploaded data, in
-#'   bytes.}
-#'   \item{`type`}{The MIME type reported by the browser (for example,
-#'   `text/plain`), or empty string if the browser didn't know.}
-#'   \item{`datapath`}{The path to a temp file that contains the data that was
-#'   uploaded. This file may be deleted if the user performs another upload
-#'   operation.}
-#' }
-#'
 #' @export
 fileInput <- function(inputId, label, multiple = FALSE, accept = NULL,
   width = NULL, buttonLabel = "Browse...", placeholder = "No file selected") {
@@ -106,8 +106,7 @@ fileInput <- function(inputId, label, multiple = FALSE, accept = NULL,
     shinyInputLabel(inputId, label),
 
     div(class = "input-group",
-      # input-group-prepend is for bootstrap 4 compat
-      tags$label(class = "input-group-btn input-group-prepend",
+      tags$label(class = "input-group-btn",
         span(class = "btn btn-default btn-file",
           buttonLabel,
           inputTag
@@ -120,7 +119,7 @@ fileInput <- function(inputId, label, multiple = FALSE, accept = NULL,
 
     tags$div(
       id=paste(inputId, "_progress", sep=""),
-      class="progress active shiny-file-input-progress",
+      class="progress progress-striped active shiny-file-input-progress",
       tags$div(class="progress-bar")
     )
   )

R/input-numeric.R

@@ -9,7 +9,7 @@
 #' @return A numeric input control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [updateNumericInput()]
+#' @seealso \code{\link{updateNumericInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -24,10 +24,6 @@
 #' }
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' A numeric vector of length 1.
-#'
 #' @export
 numericInput <- function(inputId, label, value, min = NA, max = NA, step = NA,
   width = NULL) {

R/input-password.R

@@ -6,11 +6,7 @@
 #' @return A text input control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [updateTextInput()]
-#'
-#' @section Server value:
-#' A character string of the password input. The default value is `""`
-#' unless `value` is provided.
+#' @seealso \code{\link{updateTextInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions

R/input-radiobuttons.R

@@ -3,33 +3,33 @@
 #' Create a set of radio buttons used to select an item from a list.
 #'
 #' If you need to represent a "None selected" state, it's possible to default
-#' the radio buttons to have no options selected by using `selected =
-#' character(0)`. However, this is not recommended, as it gives the user no way
+#' the radio buttons to have no options selected by using \code{selected =
+#' character(0)}. However, this is not recommended, as it gives the user no way
 #' to return to that state once they've made a selection. Instead, consider
-#' having the first of your choices be `c("None selected" = "")`.
+#' having the first of your choices be \code{c("None selected" = "")}.
 #'
 #' @inheritParams textInput
 #' @param choices List of values to select from (if elements of the list are
 #'   named then that name rather than the value is displayed to the user). If
-#'   this argument is provided, then `choiceNames` and `choiceValues`
+#'   this argument is provided, then \code{choiceNames} and \code{choiceValues}
 #'   must not be provided, and vice-versa. The values should be strings; other
 #'   types (such as logicals and numbers) will be coerced to strings.
 #' @param selected The initially selected value (if not specified then defaults
 #'   to the first value)
-#' @param inline If `TRUE`, render the choices inline (i.e. horizontally)
+#' @param inline If \code{TRUE}, render the choices inline (i.e. horizontally)
 #' @return A set of radio buttons that can be added to a UI definition.
 #' @param choiceNames,choiceValues List of names and values, respectively, that
 #'   are displayed to the user in the app and correspond to the each choice (for
-#'   this reason, `choiceNames` and `choiceValues` must have the same
+#'   this reason, \code{choiceNames} and \code{choiceValues} must have the same
 #'   length). If either of these arguments is provided, then the other
-#'   *must* be provided and `choices` *must not* be provided. The
-#'   advantage of using both of these over a named list for `choices` is
-#'   that `choiceNames` allows any type of UI object to be passed through
+#'   \emph{must} be provided and \code{choices} \emph{must not} be provided. The
+#'   advantage of using both of these over a named list for \code{choices} is
+#'   that \code{choiceNames} allows any type of UI object to be passed through
 #'   (tag objects, icons, HTML code, ...), instead of just simple text. See
 #'   Examples.
 #'
 #' @family input elements
-#' @seealso [updateRadioButtons()]
+#' @seealso \code{\link{updateRadioButtons}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -80,10 +80,6 @@
 #'
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' A character string containing the value of the selected button.
-#'
 #' @export
 radioButtons <- function(inputId, label, choices = NULL, selected = NULL,
   inline = FALSE, width = NULL, choiceNames = NULL, choiceValues = NULL) {

R/input-select.R

@@ -3,36 +3,37 @@
 #' Create a select list that can be used to choose a single or multiple items
 #' from a list of values.
 #'
-#' By default, `selectInput()` and `selectizeInput()` use the JavaScript library
-#' \pkg{selectize.js} (<https://github.com/selectize/selectize.js>) instead of
-#' the basic select input element. To use the standard HTML select input
-#' element, use `selectInput()` with `selectize=FALSE`.
+#' By default, \code{selectInput()} and \code{selectizeInput()} use the
+#' JavaScript library \pkg{selectize.js}
+#' (\url{https://github.com/selectize/selectize.js}) instead of the basic
+#' select input element. To use the standard HTML select input element, use
+#' \code{selectInput()} with \code{selectize=FALSE}.
 #'
-#' In selectize mode, if the first element in `choices` has a value of `""`, its
-#' name will be treated as a placeholder prompt. For example:
-#' `selectInput("letter", "Letter", c("Choose one" = "", LETTERS))`
+#' In selectize mode, if the first element in \code{choices} has a value of
+#' \code{""}, its name will be treated as a placeholder prompt. For example:
+#' \code{selectInput("letter", "Letter", c("Choose one" = "", LETTERS))}
 #'
 #' @inheritParams textInput
 #' @param choices List of values to select from. If elements of the list are
-#'   named, then that name --- rather than the value --- is displayed to the
-#'   user. It's also possible to group related inputs by providing a named list
-#'   whose elements are (either named or unnamed) lists, vectors, or factors. In
-#'   this case, the outermost names will be used as the group labels (leveraging
-#'   the `<optgroup>` HTML tag) for the elements in the respective sublist. See
-#'   the example section for a small demo of this feature.
-#' @param selected The initially selected value (or multiple values if `multiple
-#'   = TRUE`). If not specified then defaults to the first value for
-#'   single-select lists and no values for multiple select lists.
+#'   named, then that name rather than the value is displayed to the user.
+#'   This can also be a named list whose elements are (either named or
+#'   unnamed) lists or vectors. If this is the case, the outermost names
+#'   will be used as the "optgroup" label for the elements in the respective
+#'   sublist. This allows you to group and label similar choices. See the
+#'   example section for a small demo of this feature.
+#' @param selected The initially selected value (or multiple values if
+#'   \code{multiple = TRUE}). If not specified then defaults to the first value
+#'   for single-select lists and no values for multiple select lists.
 #' @param multiple Is selection of multiple items allowed?
 #' @param selectize Whether to use \pkg{selectize.js} or not.
 #' @param size Number of items to show in the selection box; a larger number
-#'   will result in a taller box. Not compatible with `selectize=TRUE`.
-#'   Normally, when `multiple=FALSE`, a select input will be a drop-down list,
-#'   but when `size` is set, it will be a box instead.
+#'   will result in a taller box. Not compatible with \code{selectize=TRUE}.
+#'   Normally, when \code{multiple=FALSE}, a select input will be a drop-down
+#'   list, but when \code{size} is set, it will be a box instead.
 #' @return A select list control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [updateSelectInput()] [varSelectInput()]
+#' @seealso \code{\link{updateSelectInput}} \code{\link{varSelectInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -54,7 +55,7 @@
 #'   }
 #' )
 #'
-#' # demoing group support in the `choices` arg
+#' # demoing optgroup support in the `choices` arg
 #' shinyApp(
 #'   ui = fluidPage(
 #'     selectInput("state", "Choose a state:",
@@ -71,11 +72,6 @@
 #'   }
 #' )
 #' }
-#'
-#' @section Server value: A vector of character strings, usually of length
-#'   1, with the value of the selected items. When `multiple=TRUE` and
-#'   nothing is selected, this value will be `NULL`.
-#'
 #' @export
 selectInput <- function(inputId, label, choices, selected = NULL,
   multiple = FALSE, selectize = TRUE, width = NULL,
@@ -157,21 +153,21 @@ needOptgroup <- function(choices) {
 }
 
 #' @rdname selectInput
-#' @param ... Arguments passed to `selectInput()`.
+#' @param ... Arguments passed to \code{selectInput()}.
 #' @param options A list of options. See the documentation of \pkg{selectize.js}
-#'   for possible options (character option values inside [base::I()] will
-#'   be treated as literal JavaScript code; see [renderDataTable()]
+#'   for possible options (character option values inside \code{\link[base]{I}()} will
+#'   be treated as literal JavaScript code; see \code{\link{renderDataTable}()}
 #'   for details).
-#' @param width The width of the input, e.g. `'400px'`, or `'100%'`;
-#'   see [validateCssUnit()].
-#' @note The selectize input created from `selectizeInput()` allows
+#' @param width The width of the input, e.g. \code{'400px'}, or \code{'100\%'};
+#'   see \code{\link{validateCssUnit}}.
+#' @note The selectize input created from \code{selectizeInput()} allows
 #'   deletion of the selected option even in a single select input, which will
 #'   return an empty string as its value. This is the default behavior of
 #'   \pkg{selectize.js}. However, the selectize input created from
-#'   `selectInput(..., selectize = TRUE)` will ignore the empty string
+#'   \code{selectInput(..., selectize = TRUE)} will ignore the empty string
 #'   value when it is a single choice input and the empty string is not in the
-#'   `choices` argument. This is to keep compatibility with
-#'   `selectInput(..., selectize = FALSE)`.
+#'   \code{choices} argument. This is to keep compatibility with
+#'   \code{selectInput(..., selectize = FALSE)}.
 #' @export
 selectizeInput <- function(inputId, ..., options = NULL, width = NULL) {
   selectizeIt(
@@ -229,31 +225,30 @@ selectizeIt <- function(inputId, select, options, nonempty = FALSE) {
 #' Create a select list that can be used to choose a single or multiple items
 #' from the column names of a data frame.
 #'
-#' By default, `varSelectInput()` and `selectizeInput()` use the
+#' The resulting server \code{input} value will be returned as:
+#' \itemize{
+#'   \item a symbol if \code{multiple = FALSE}.  The \code{input} value should be
+#'         used with rlang's \code{\link[rlang]{!!}}. For example,
+#'         \code{ggplot2::aes(!!input$variable)}.
+#'   \item a list of symbols if \code{multiple = TRUE}. The \code{input} value
+#'         should be used with rlang's \code{\link[rlang]{!!!}} to expand
+#'         the symbol list as individual arguments. For example,
+#'         \code{dplyr::select(mtcars, !!!input$variabls)} which is
+#'         equivalent to \code{dplyr::select(mtcars, !!input$variabls[[1]], !!input$variabls[[2]], ..., !!input$variabls[[length(input$variabls)]])}.
+#' }
+#'
+#' By default, \code{varSelectInput()} and \code{selectizeInput()} use the
 #' JavaScript library \pkg{selectize.js}
-#' (<https://github.com/selectize/selectize.js>) to instead of the basic
+#' (\url{https://github.com/selectize/selectize.js}) to instead of the basic
 #' select input element. To use the standard HTML select input element, use
-#' `selectInput()` with `selectize=FALSE`.
+#' \code{selectInput()} with \code{selectize=FALSE}.
 #'
 #' @inheritParams selectInput
-#' @param data A data frame. Used to retrieve the column names as choices for a [selectInput()]
+#' @param data A data frame. Used to retrieve the column names as choices for a \code{\link{selectInput}}
 #' @return A variable select list control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [updateSelectInput()]
-#'
-#' @section Server value:
-#' The resulting server `input` value will be returned as:
-#'
-#'  * A symbol if `multiple = FALSE`. The `input` value should be
-#'  used with rlang's [rlang::!!()]. For example,
-#'  `ggplot2::aes(!!input$variable)`.
-#'  * A list of symbols if `multiple = TRUE`. The `input` value
-#'  should be used with rlang's [rlang::!!!()] to expand
-#'  the symbol list as individual arguments. For example,
-#'  `dplyr::select(mtcars, !!!input$variabls)` which is
-#'  equivalent to `dplyr::select(mtcars, !!input$variabls[[1]], !!input$variabls[[2]], ..., !!input$variabls[[length(input$variabls)]])`.
-#'
+#' @seealso \code{\link{updateSelectInput}}
 #' @examples
 #'
 #' ## Only run examples in interactive R sessions
@@ -326,21 +321,21 @@ varSelectInput <- function(
 
 
 #' @rdname varSelectInput
-#' @param ... Arguments passed to `varSelectInput()`.
+#' @param ... Arguments passed to \code{varSelectInput()}.
 #' @param options A list of options. See the documentation of \pkg{selectize.js}
-#'   for possible options (character option values inside [base::I()] will
-#'   be treated as literal JavaScript code; see [renderDataTable()]
+#'   for possible options (character option values inside \code{\link[base]{I}()} will
+#'   be treated as literal JavaScript code; see \code{\link{renderDataTable}()}
 #'   for details).
-#' @param width The width of the input, e.g. `'400px'`, or `'100%'`;
-#'   see [validateCssUnit()].
-#' @note The variable selectize input created from `varSelectizeInput()` allows
+#' @param width The width of the input, e.g. \code{'400px'}, or \code{'100\%'};
+#'   see \code{\link{validateCssUnit}}.
+#' @note The variable selectize input created from \code{varSelectizeInput()} allows
 #'   deletion of the selected option even in a single select input, which will
 #'   return an empty string as its value. This is the default behavior of
 #'   \pkg{selectize.js}. However, the selectize input created from
-#'   `selectInput(..., selectize = TRUE)` will ignore the empty string
+#'   \code{selectInput(..., selectize = TRUE)} will ignore the empty string
 #'   value when it is a single choice input and the empty string is not in the
-#'   `choices` argument. This is to keep compatibility with
-#'   `selectInput(..., selectize = FALSE)`.
+#'   \code{choices} argument. This is to keep compatibility with
+#'   \code{selectInput(..., selectize = FALSE)}.
 #' @export
 varSelectizeInput <- function(inputId, ..., options = NULL, width = NULL) {
   selectizeIt(

R/input-slider.R

@@ -8,45 +8,45 @@
 #' @param value The initial value of the slider. A numeric vector of length one
 #'   will create a regular slider; a numeric vector of length two will create a
 #'   double-ended range slider. A warning will be issued if the value doesn't
-#'   fit between `min` and `max`.
+#'   fit between \code{min} and \code{max}.
 #' @param step Specifies the interval between each selectable value on the
-#'   slider (if `NULL`, a heuristic is used to determine the step size). If
-#'   the values are dates, `step` is in days; if the values are times
-#'   (POSIXt), `step` is in seconds.
-#' @param round `TRUE` to round all values to the nearest integer;
-#'   `FALSE` if no rounding is desired; or an integer to round to that
+#'   slider (if \code{NULL}, a heuristic is used to determine the step size). If
+#'   the values are dates, \code{step} is in days; if the values are times
+#'   (POSIXt), \code{step} is in seconds.
+#' @param round \code{TRUE} to round all values to the nearest integer;
+#'   \code{FALSE} if no rounding is desired; or an integer to round to that
 #'   number of digits (for example, 1 will round to the nearest 10, and -2 will
 #'   round to the nearest .01). Any rounding will be applied after snapping to
 #'   the nearest step.
 #' @param format Deprecated.
 #' @param locale Deprecated.
-#' @param ticks `FALSE` to hide tick marks, `TRUE` to show them
+#' @param ticks \code{FALSE} to hide tick marks, \code{TRUE} to show them
 #'   according to some simple heuristics.
-#' @param animate `TRUE` to show simple animation controls with default
-#'   settings; `FALSE` not to; or a custom settings list, such as those
-#'   created using [animationOptions()].
+#' @param animate \code{TRUE} to show simple animation controls with default
+#'   settings; \code{FALSE} not to; or a custom settings list, such as those
+#'   created using \code{\link{animationOptions}}.
 #' @param sep Separator between thousands places in numbers.
 #' @param pre A prefix string to put in front of the value.
 #' @param post A suffix string to put after the value.
 #' @param dragRange This option is used only if it is a range slider (with two
-#'   values). If `TRUE` (the default), the range can be dragged. In other
-#'   words, the min and max can be dragged together. If `FALSE`, the range
+#'   values). If \code{TRUE} (the default), the range can be dragged. In other
+#'   words, the min and max can be dragged together. If \code{FALSE}, the range
 #'   cannot be dragged.
 #' @param timeFormat Only used if the values are Date or POSIXt objects. A time
 #'   format string, to be passed to the Javascript strftime library. See
-#'   <https://github.com/samsonjs/strftime> for more details. The allowed
+#'   \url{https://github.com/samsonjs/strftime} for more details. The allowed
 #'   format specifications are very similar, but not identical, to those for R's
-#'   [base::strftime()] function. For Dates, the default is `"%F"`
-#'   (like `"2015-07-01"`), and for POSIXt, the default is `"%F %T"`
-#'   (like `"2015-07-01 15:32:10"`).
+#'   \code{\link[base]{strftime}} function. For Dates, the default is \code{"\%F"}
+#'   (like \code{"2015-07-01"}), and for POSIXt, the default is \code{"\%F \%T"}
+#'   (like \code{"2015-07-01 15:32:10"}).
 #' @param timezone Only used if the values are POSIXt objects. A string
 #'   specifying the time zone offset for the displayed times, in the format
-#'   `"+HHMM"` or `"-HHMM"`. If `NULL` (the default), times will
-#'   be displayed in the browser's time zone. The value `"+0000"` will
+#'   \code{"+HHMM"} or \code{"-HHMM"}. If \code{NULL} (the default), times will
+#'   be displayed in the browser's time zone. The value \code{"+0000"} will
 #'   result in UTC time.
 #' @inheritParams selectizeInput
 #' @family input elements
-#' @seealso [updateSliderInput()]
+#' @seealso \code{\link{updateSliderInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -70,10 +70,6 @@
 #' # Complete app with UI and server components
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' A number, or in the case of slider range, a vector of two numbers.
-#'
 #' @export
 sliderInput <- function(inputId, label, min, max, value, step = NULL,
                         round = FALSE, format = NULL, locale = NULL,
@@ -257,13 +253,13 @@ findStepSize <- function(min, max, step) {
 #' @rdname sliderInput
 #'
 #' @param interval The interval, in milliseconds, between each animation step.
-#' @param loop `TRUE` to automatically restart the animation when it
+#' @param loop \code{TRUE} to automatically restart the animation when it
 #'   reaches the end.
 #' @param playButton Specifies the appearance of the play button. Valid values
 #'   are a one-element character vector (for a simple text label), an HTML tag
-#'   or list of tags (using [tag()] and friends), or raw HTML (using
-#'   [HTML()]).
-#' @param pauseButton Similar to `playButton`, but for the pause button.
+#'   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-submit.R

@@ -3,30 +3,30 @@
 #' Create a submit button for an app. Apps that include a submit
 #' button do not automatically update their outputs when inputs change,
 #' rather they wait until the user explicitly clicks the submit button.
-#' The use of `submitButton` is generally discouraged in favor of
-#' the more versatile [actionButton()] (see details below).
+#' The use of \code{submitButton} is generally discouraged in favor of
+#' the more versatile \code{\link{actionButton}} (see details below).
 #'
 #' Submit buttons are unusual Shiny inputs, and we recommend using
-#' [actionButton()] instead of `submitButton` when you
+#' \code{\link{actionButton}} instead of \code{submitButton} when you
 #' want to delay a reaction.
-#' See [this
-#' article](http://shiny.rstudio.com/articles/action-buttons.html) for more information (including a demo of how to "translate"
-#' code using a `submitButton` to code using an `actionButton`).
+#' See \href{http://shiny.rstudio.com/articles/action-buttons.html}{this
+#' article} for more information (including a demo of how to "translate"
+#' code using a \code{submitButton} to code using an \code{actionButton}).
 #'
 #' In essence, the presence of a submit button stops all inputs from
 #' sending their values automatically to the server. This means, for
-#' instance, that if there are *two* submit buttons in the same app,
+#' instance, that if there are \emph{two} submit buttons in the same app,
 #' clicking either one will cause all inputs in the app to send their
 #' values to the server. This is probably not what you'd want, which is
 #' why submit button are unwieldy for all but the simplest apps. There
 #' are other problems with submit buttons: for example, dynamically
-#' created submit buttons (for example, with [renderUI()]
-#' or [insertUI()]) will not work.
+#' created submit buttons (for example, with \code{\link{renderUI}}
+#' or \code{\link{insertUI}}) will not work.
 #'
 #' @param text Button caption
-#' @param icon Optional [icon()] to appear on the button
-#' @param width The width of the button, e.g. `'400px'`, or `'100%'`;
-#'   see [validateCssUnit()].
+#' @param icon Optional \code{\link{icon}} to appear on the button
+#' @param width The width of the button, e.g. \code{'400px'}, or \code{'100\%'};
+#'   see \code{\link{validateCssUnit}}.
 #' @return A submit button that can be added to a UI definition.
 #'
 #' @family input elements

R/input-text.R

@@ -2,18 +2,18 @@
 #'
 #' Create an input control for entry of unstructured text values
 #'
-#' @param inputId The `input` slot that will be used to access the value.
-#' @param label Display label for the control, or `NULL` for no label.
+#' @param inputId The \code{input} slot that will be used to access the value.
+#' @param label Display label for the control, or \code{NULL} for no label.
 #' @param value Initial value.
-#' @param width The width of the input, e.g. `'400px'`, or `'100%'`;
-#'   see [validateCssUnit()].
+#' @param width The width of the input, e.g. \code{'400px'}, or \code{'100\%'};
+#'   see \code{\link{validateCssUnit}}.
 #' @param placeholder A character string giving the user a hint as to what can
 #'   be entered into the control. Internet Explorer 8 and 9 do not support this
 #'   option.
 #' @return A text input control that can be added to a UI definition.
 #'
 #' @family input elements
-#' @seealso [updateTextInput()]
+#' @seealso \code{\link{updateTextInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -28,11 +28,6 @@
 #' }
 #' shinyApp(ui, server)
 #' }
-#'
-#' @section Server value:
-#' A character string of the text input. The default value is `""`
-#' unless `value` is provided.
-#'
 #' @export
 textInput <- function(inputId, label, value = "", width = NULL,
   placeholder = NULL) {

R/input-textarea.R

@@ -3,23 +3,22 @@
 #' Create a textarea input control for entry of unstructured text values.
 #'
 #' @inheritParams textInput
-#' @param height The height of the input, e.g. `'400px'`, or `'100%'`; see
-#'   [validateCssUnit()].
-#' @param cols Value of the visible character columns of the input, e.g. `80`.
-#'   This argument will only take effect if there is not a CSS `width` rule
-#'   defined for this element; such a rule could come from the `width` argument
-#'   of this function or from a containing page layout such as
-#'   [fluidPage()].
-#' @param rows The value of the visible character rows of the input, e.g. `6`.
-#'   If the `height` argument is specified, `height` will take precedence in the
-#'   browser's rendering.
+#' @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
-#'   `"both"`, `"none"`, `"vertical"`, and `"horizontal"`. The default, `NULL`,
-#'   will use the client browser's default setting for resizing textareas.
+#'   \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 [updateTextAreaInput()]
+#' @seealso \code{\link{updateTextAreaInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -35,11 +34,6 @@
 #' shinyApp(ui, server)
 #'
 #' }
-#'
-#' @section Server value:
-#' A character string of the text input. The default value is `""`
-#' unless `value` is provided.
-#'
 #' @export
 textAreaInput <- function(inputId, label, value = "", width = NULL, height = NULL,
   cols = NULL, rows = NULL, placeholder = NULL, resize = NULL) {

R/input-utils.R

@@ -90,83 +90,45 @@ generateOptions <- function(inputId, selected, inline, type = 'checkbox',
   div(class = "shiny-options-group", options)
 }
 
-# True when a choice list item represents a group of related inputs.
-isGroup <- function(choice) {
-  is.list(choice) ||
-    !is.null(names(choice)) ||
-    length(choice) > 1 ||
-    length(choice) == 0
-}
 
-# True when choices is a list and contains at least one group of related inputs.
-hasGroups <- function(choices) {
-  is.list(choices) && any(vapply(choices, isGroup, logical(1)))
-}
-
-# Assigns empty names to x if it's unnamed, and then fills any empty names with
-# the corresponding value coerced to a character(1).
-setDefaultNames <- function(x) {
-  x <- asNamed(x)
-  emptyNames <- names(x) == ""
-  names(x)[emptyNames] <- as.character(x)[emptyNames]
-  x
-}
-
-# Makes a character vector out of x in a way that preserves names.
-asCharacter <- function(x) {
-  stats::setNames(as.character(x), names(x))
-}
-
-# Processes a "flat" set of choices, or a collection of choices not containing
-# any named groups. choices should be a list without any list children, or an
-# atomic vector. choices may be named or unnamed. Any empty names are replaced
-# with the corresponding value coerced to a character.
-processFlatChoices <- function(choices) {
-  choices <- setDefaultNames(asCharacter(choices))
-  as.list(choices)
-}
-
-# Processes a "nested" set of choices, or a collection of choices that contains
-# one or more named groups of related choices and zero or more "flat" choices.
-# choices should be a named list, and any choice group must have a non-empty
-# name. Empty names of remaining "flat" choices are replaced with that choice's
-# value coerced to a character.
-processGroupedChoices <- function(choices) {
-  # We assert choices is a list, since only a list may contain a group.
-  stopifnot(is.list(choices))
-  # The list might be unnamed by this point. We add default names of "" so that
-  # names(choices) is not zero-length and mapply can work. Within mapply, we
-  # error if any group's name is ""
-  choices <- asNamed(choices)
-  choices <- mapply(function(name, choice) {
-    choiceIsGroup <- isGroup(choice)
-    if (choiceIsGroup && name == "") {
-      # If the choice is a group, and if its name is empty, produce an error. We
-      # error here because the composite nature of the choice prevents us from
-      # meaningfully automatically naming it. Note that while not documented,
-      # groups are not necessarily lists (aka generic vectors) but can also be
-      # any named atomic vector, or any atomic vector of length > 1.
-      stop('All sub-lists in "choices" must be named.')
-    } else if (choiceIsGroup) {
-      # The choice is a group, but it is named. Process it using the same
-      # function we use for "top level" choices.
-      processFlatChoices(choice)
-    } else {
-      # The choice was not named and is not a group; it is a "leaf".
-      as.character(choice)
-    }
-  }, names(choices), choices, SIMPLIFY = FALSE)
-  # By this point, any leaves in the choices list might still have empty names,
-  # so we're sure to automatically name them.
-  setDefaultNames(choices)
-}
-
-# Takes a vector/list/factor, and adds names (same as the value) to any entries
+# Takes a vector or list, and adds names (same as the value) to any entries
 # without names. Coerces all leaf nodes to `character`.
 choicesWithNames <- function(choices) {
-  if (hasGroups(choices)) {
-    processGroupedChoices(choices)
-  } else {
-    processFlatChoices(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,
+  # convert it to a named list with blank names.
+  listify <- function(obj) {
+    # If a list/vector is unnamed, give it blank names
+    makeNamed <- function(x) {
+      if (is.null(names(x))) names(x) <- character(length(x))
+      x
+    }
+
+    res <- lapply(obj, function(val) {
+      if (is.list(val))
+        listify(val)
+      else if (length(val) == 1 && is.null(names(val)))
+        as.character(val)
+      else
+        makeNamed(as.list(val))
+    })
+
+    makeNamed(res)
   }
+
+  choices <- listify(choices)
+  if (length(choices) == 0) return(choices)
+
+  # Recurse into any subgroups
+  choices <- mapply(choices, names(choices), FUN = function(choice, name) {
+    if (!is.list(choice)) return(choice)
+    if (name == "") stop('All sub-lists in "choices" must be named.')
+    choicesWithNames(choice)
+  }, SIMPLIFY = FALSE)
+
+  # default missing names to choice values
+  missing <- names(choices) == ""
+  names(choices)[missing] <- as.character(choices)[missing]
+
+  choices
 }

R/insert-tab.R

@@ -1,43 +1,43 @@
 #' Dynamically insert/remove a tabPanel
 #'
-#' Dynamically insert or remove a [tabPanel()] (or a
-#' [navbarMenu()]) from an existing [tabsetPanel()],
-#' [navlistPanel()] or [navbarPage()].
+#' Dynamically insert or remove a \code{\link{tabPanel}} (or a
+#' \code{\link{navbarMenu}}) from an existing \code{\link{tabsetPanel}},
+#' \code{\link{navlistPanel}} or \code{\link{navbarPage}}.
 #'
 #' When you want to insert a new tab before or after an existing tab, you
-#' should use `insertTab`. When you want to prepend a tab (i.e. add a
-#' tab to the beginning of the `tabsetPanel`), use `prependTab`.
+#' should use \code{insertTab}. When you want to prepend a tab (i.e. add a
+#' tab to the beginning of the \code{tabsetPanel}), use \code{prependTab}.
 #' When you want to append a tab (i.e. add a tab to the end of the
-#' `tabsetPanel`), use `appendTab`.
+#' \code{tabsetPanel}), use \code{appendTab}.
 #'
-#' For `navbarPage`, you can insert/remove conventional
-#' `tabPanel`s (whether at the top level or nested inside a
-#' `navbarMenu`), as well as an entire [navbarMenu()].
-#' For the latter case, `target` should be the `menuName` that
-#' you gave your `navbarMenu` when you first created it (by default,
-#' this is equal to the value of the `title` argument).
+#' For \code{navbarPage}, you can insert/remove conventional
+#' \code{tabPanel}s (whether at the top level or nested inside a
+#' \code{navbarMenu}), as well as an entire \code{\link{navbarMenu}}.
+#' For the latter case, \code{target} should be the \code{menuName} that
+#' you gave your \code{navbarMenu} when you first created it (by default,
+#' this is equal to the value of the \code{title} argument).
 #'
-#' @param inputId The `id` of the `tabsetPanel` (or
-#'   `navlistPanel` or `navbarPage`) into which `tab` will
+#' @param inputId The \code{id} of the \code{tabsetPanel} (or
+#'   \code{navlistPanel} or \code{navbarPage}) into which \code{tab} will
 #'   be inserted/removed.
 #'
-#' @param tab The item to be added (must be created with `tabPanel`,
-#'   or with `navbarMenu`).
+#' @param tab The item to be added (must be created with \code{tabPanel},
+#'   or with \code{navbarMenu}).
 #'
-#' @param target If inserting: the `value` of an existing
-#'   `tabPanel`, next to which `tab` will be added.
-#'   If removing: the `value` of the `tabPanel` that
+#' @param target If inserting: the \code{value} of an existing
+#'   \code{tabPanel}, next to which \code{tab} will be added.
+#'   If removing: the \code{value} of the \code{tabPanel} that
 #'   you want to remove. See Details if you want to insert next to/remove
-#'   an entire `navbarMenu` instead.
+#'   an entire \code{navbarMenu} instead.
 #'
-#' @param position Should `tab` be added before or after the
-#'   `target` tab?
+#' @param position Should \code{tab} be added before or after the
+#'   \code{target} tab?
 #'
-#' @param select Should `tab` be selected upon being inserted?
+#' @param select Should \code{tab} be selected upon being inserted?
 #'
 #' @param session The shiny session within which to call this function.
 #'
-#' @seealso [showTab()]
+#' @seealso \code{\link{showTab}}
 #'
 #' @examples
 #' ## Only run this example in interactive R sessions
@@ -144,16 +144,16 @@ insertTab <- function(inputId, tab, target,
 }
 
 #' @param menuName This argument should only be used when you want to
-#'   prepend (or append) `tab` to the beginning (or end) of an
-#'   existing [navbarMenu()] (which must itself be part of
-#'   an existing [navbarPage()]). In this case, this argument
-#'   should be the `menuName` that you gave your `navbarMenu`
+#'   prepend (or append) \code{tab} to the beginning (or end) of an
+#'   existing \code{\link{navbarMenu}} (which must itself be part of
+#'   an existing \code{\link{navbarPage}}). In this case, this argument
+#'   should be the \code{menuName} that you gave your \code{navbarMenu}
 #'   when you first created it (by default, this is equal to the value
-#'   of the `title` argument). Note that you still need to set the
-#'   `inputId` argument to whatever the `id` of the parent
-#'   `navbarPage` is. If `menuName` is left as `NULL`,
-#'   `tab` will be prepended (or appended) to whatever
-#'   `inputId` is.
+#'   of the \code{title} argument). Note that you still need to set the
+#'   \code{inputId} argument to whatever the \code{id} of the parent
+#'   \code{navbarPage} is. If \code{menuName} is left as \code{NULL},
+#'   \code{tab} will be prepended (or appended) to whatever
+#'   \code{inputId} is.
 #'
 #' @rdname insertTab
 #' @export
@@ -221,30 +221,30 @@ removeTab <- function(inputId, target,
 
 #' Dynamically hide/show a tabPanel
 #'
-#' Dynamically hide or show a [tabPanel()] (or a
-#' [navbarMenu()])from an existing [tabsetPanel()],
-#' [navlistPanel()] or [navbarPage()].
+#' Dynamically hide or show a \code{\link{tabPanel}} (or a
+#' \code{\link{navbarMenu}})from an existing \code{\link{tabsetPanel}},
+#' \code{\link{navlistPanel}} or \code{\link{navbarPage}}.
 #'
-#' For `navbarPage`, you can hide/show conventional
-#' `tabPanel`s (whether at the top level or nested inside a
-#' `navbarMenu`), as well as an entire [navbarMenu()].
-#' For the latter case, `target` should be the `menuName` that
-#' you gave your `navbarMenu` when you first created it (by default,
-#' this is equal to the value of the `title` argument).
+#' For \code{navbarPage}, you can hide/show conventional
+#' \code{tabPanel}s (whether at the top level or nested inside a
+#' \code{navbarMenu}), as well as an entire \code{\link{navbarMenu}}.
+#' For the latter case, \code{target} should be the \code{menuName} that
+#' you gave your \code{navbarMenu} when you first created it (by default,
+#' this is equal to the value of the \code{title} argument).
 #'
-#' @param inputId The `id` of the `tabsetPanel` (or
-#'   `navlistPanel` or `navbarPage`) in which to find
-#'   `target`.
+#' @param inputId The \code{id} of the \code{tabsetPanel} (or
+#'   \code{navlistPanel} or \code{navbarPage}) in which to find
+#'   \code{target}.
 #'
-#' @param target The `value` of the `tabPanel` to be
+#' @param target The \code{value} of the \code{tabPanel} to be
 #'   hidden/shown. See Details if you want to hide/show an entire
-#'   `navbarMenu` instead.
+#'   \code{navbarMenu} instead.
 #'
-#' @param select Should `target` be selected upon being shown?
+#' @param select Should \code{target} be selected upon being shown?
 #'
 #' @param session The shiny session within which to call this function.
 #'
-#' @seealso [insertTab()]
+#' @seealso \code{\link{insertTab}}
 #'
 #' @examples
 #' ## Only run this example in interactive R sessions

R/insert-ui.R

@@ -1,54 +1,55 @@
-#' Insert and remove UI objects
+#' Insert UI objects
 #'
-#' These functions allow you to dynamically add and remove arbirary UI
-#' into your app, whenever you want, as many times as you want.
-#' Unlike [renderUI()], the UI generated with `insertUI()` is persistent:
-#' once it's created, it stays there until removed by `removeUI()`. Each
-#' new call to `insertUI()` creates more UI objects, in addition to
+#' 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 `render` function or a customized `reactive`
-#' function.
+#' appropriate \code{render} function or a customized \code{reactive}
+#' function. To remove any part of your UI, use \code{\link{removeUI}}.
 #'
-#' It's particularly useful to pair `removeUI` with `insertUI()`, but there is
-#' no restriction on what you can use 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{$(s)} jQuery call). This selector
+#' will determine the element(s) relative to which you want to insert your
+#' UI object.
 #'
-#' @param selector A string that is accepted by jQuery's selector
-#'   (i.e. the string `s` to be placed in a `$(s)` jQuery call).
-#'
-#'   For `insertUI()` this determines the element(s) relative to which you
-#'   want to insert your UI object. For `removeUI()` this 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 `<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 `<div>` with an id.)
 #' @param where Where your UI object should go relative to the selector:
-#'   \describe{
-#'     \item{`beforeBegin`}{Before the selector element itself}
-#'     \item{`afterBegin`}{Just inside the selector element, before its
-#'     first child}
-#'     \item{`beforeEnd`}{Just inside the selector element, after its
-#'     last child (default)}
-#'     \item{`afterEnd`}{After the selector element itself}
-#'   }
-#'   Adapted from <https://developer.mozilla.org/en-US/docs/Web/API/Element/insertAdjacentHTML>.
+#' \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 `ui` function. If you're inserting
-#'   multiple elements in one call, make sure to wrap them in either a
-#'   `tagList()` or a `tags$div()` (the latter option has the
-#'   advantage that you can give it an `id` to make it easier to
-#'   reference or remove it later on). If you want to insert raw html, use
-#'   `ui = HTML()`.
+#' you usually put inside your apps's \code{ui} function. If you're inserting
+#' multiple elements in one call, make sure to wrap them in either a
+#' \code{tagList()} or a \code{tags$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,
-#'   `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
-#'   or removed, or whether Shiny should wait until all outputs have been
-#'   updated and all observers have been run (default).
-#' @param session The shiny session. Advanced use only.
+#' \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()) {
@@ -72,26 +73,6 @@
 #' # Complete app with UI and server components
 #' shinyApp(ui, server)
 #' }
-#'
-#' 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
 insertUI <- function(selector,
   where = c("beforeBegin", "afterBegin", "beforeEnd", "afterEnd"),
@@ -119,7 +100,60 @@ insertUI <- function(selector,
 }
 
 
-#' @rdname insertUI
+#' 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,

R/jqueryui.R

@@ -2,32 +2,32 @@
 #'
 #' Creates a panel whose contents are absolutely positioned.
 #'
-#' The `absolutePanel` function creates a `<div>` tag whose CSS
-#' position is set to `absolute` (or fixed if `fixed = TRUE`). The way
+#' The \code{absolutePanel} function creates a \code{<div>} tag whose CSS
+#' position is set to \code{absolute} (or fixed if \code{fixed = TRUE}). The way
 #' absolute positioning works in HTML is that absolute coordinates are specified
 #' relative to its nearest parent element whose position is not set to
-#' `static` (which is the default), and if no such parent is found, then
+#' \code{static} (which is the default), and if no such parent is found, then
 #' relative to the page borders. If you're not sure what that means, just keep
-#' in mind that you may get strange results if you use `absolutePanel` from
+#' in mind that you may get strange results if you use \code{absolutePanel} from
 #' inside of certain types of panels.
 #'
-#' The `fixedPanel` function is the same as `absolutePanel` with
-#' `fixed = TRUE`.
+#' The \code{fixedPanel} function is the same as \code{absolutePanel} with
+#' \code{fixed = TRUE}.
 #'
-#' The position (`top`, `left`, `right`, `bottom`) and size
-#' (`width`, `height`) parameters are all optional, but you should
-#' specify exactly two of `top`, `bottom`, and `height` and
-#' exactly two of `left`, `right`, and `width` for predictable
+#' The position (\code{top}, \code{left}, \code{right}, \code{bottom}) and size
+#' (\code{width}, \code{height}) parameters are all optional, but you should
+#' specify exactly two of \code{top}, \code{bottom}, and \code{height} and
+#' exactly two of \code{left}, \code{right}, and \code{width} for predictable
 #' results.
 #'
 #' Like most other distance parameters in Shiny, the position and size
 #' parameters take a number (interpreted as pixels) or a valid CSS size string,
-#' such as `"100px"` (100 pixels) or `"25%"`.
+#' such as \code{"100px"} (100 pixels) or \code{"25\%"}.
 #'
 #' For arcane HTML reasons, to have the panel fill the page or parent you should
-#' specify `0` for `top`, `left`, `right`, and `bottom`
-#' rather than the more obvious `width = "100%"` and `height =
-#' "100%"`.
+#' specify \code{0} for \code{top}, \code{left}, \code{right}, and \code{bottom}
+#' rather than the more obvious \code{width = "100\%"} and \code{height =
+#' "100\%"}.
 #'
 #' @param ... Attributes (named arguments) or children (unnamed arguments) that
 #'   should be included in the panel.
@@ -42,16 +42,16 @@
 #'   page or parent container.
 #' @param width Width of the panel.
 #' @param height Height of the panel.
-#' @param draggable If `TRUE`, allows the user to move the panel by
+#' @param draggable If \code{TRUE}, allows the user to move the panel by
 #'   clicking and dragging.
 #' @param fixed Positions the panel relative to the browser window and prevents
 #'   it from being scrolled with the rest of the page.
 #' @param cursor The type of cursor that should appear when the user mouses over
-#'   the panel. Use `"move"` for a north-east-south-west icon,
-#'   `"default"` for the usual cursor arrow, or `"inherit"` for the
+#'   the panel. Use \code{"move"} for a north-east-south-west icon,
+#'   \code{"default"} for the usual cursor arrow, or \code{"inherit"} for the
 #'   usual cursor behavior (including changing to an I-beam when the cursor is
-#'   over text). The default is `"auto"`, which is equivalent to
-#'   `ifelse(draggable, "move", "inherit")`.
+#'   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(...,

R/map.R

@@ -35,7 +35,7 @@ Map <- R6Class(
       map$mset(...)
     },
     remove = function(key) {
-      if (!map$has(key))
+      if (!map$exists(key))
         return(NULL)
 
       result <- map$get(key)
@@ -43,13 +43,13 @@ Map <- R6Class(
       result
     },
     containsKey = function(key) {
-      map$has(key)
+      map$exists(key)
     },
-    keys = function(sort = FALSE) {
-      map$keys(sort = sort)
+    keys = function() {
+      map$keys()
     },
-    values = function(sort = FALSE) {
-      map$as_list(sort = sort)
+    values = function() {
+      map$as_list()
     },
     clear = function() {
       map$reset()

R/middleware-shiny.R

@@ -3,27 +3,7 @@ NULL
 
 reactLogHandler <- function(req) {
   if (! rLog$isLogging()) {
-    if (
-      identical(req$PATH_INFO, "/reactlog/mark") ||
-      identical(req$PATH_INFO, "/reactlog")
-    ) {
-      # is not logging, but is a reactlog path...
-
-      return(
-        httpResponse(
-          # Not Implemented
-          # - The server either does not recognize the request method, or it lacks the ability to fulfil the request.
-          status = 501,
-          content_type = "text/plain; charset=utf-8",
-          content = "To enable reactlog, set the following option before running the application: \n\noptions(shiny.reactlog = TRUE)"
-        )
-      )
-
-    } else {
-      # continue on like normal
-      return(NULL)
-    }
-
+    return(NULL)
   }
 
   if (identical(req$PATH_INFO, "/reactlog/mark")) {
@@ -57,7 +37,6 @@ reactLogHandler <- function(req) {
     ))
 
   } else {
-    # continue on like normal
     return(NULL)
   }
 }

R/middleware.R

@@ -199,9 +199,6 @@ staticHandler <- function(root) {
     if (path == '/')
       path <- '/index.html'
 
-    if (grepl('\\', path, fixed = TRUE))
-      return(NULL)
-
     abs.path <- resolve(root, path)
     if (is.null(abs.path))
       return(NULL)
@@ -311,32 +308,16 @@ HandlerManager <- R6Class("HandlerManager",
         },
         call = .httpServer(
           function (req) {
-            hybrid_chain(
-              hybrid_chain(
-                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)
-                    }
-                  }
-                ),
-                catch = function(err) {
-                  httpResponse(status = 500L,
-                    content_type = "text/html",
-                    content = as.character(htmltools::htmlTemplate(
-                      system.file("template", "error.html", package = "shiny"),
-                      message = conditionMessage(err)
-                    ))
-                  )
+            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)
                 }
-              ),
-              function(resp) {
-                maybeInjectAutoreload(resp)
               }
             )
           },
@@ -406,22 +387,6 @@ HandlerManager <- R6Class("HandlerManager",
   )
 )
 
-maybeInjectAutoreload <- function(resp) {
-  if (getOption("shiny.autoreload", FALSE) &&
-      isTRUE(grepl("^text/html($|;)", resp$content_type)) &&
-      is.character(resp$content)) {
-
-    resp$content <- gsub(
-      "</head>",
-      "<script src=\"shared/shiny-autoreload.js\"></script>\n</head>",
-      resp$content,
-      fixed = TRUE
-    )
-  }
-
-  resp
-}
-
 # Safely get the Content-Length of a Rook response, or NULL if the length cannot
 # be determined for whatever reason (probably malformed response$content).
 # If deleteOwnedContent is TRUE, then the function should delete response

R/mock-session.R

@@ -1,466 +0,0 @@
-# Promise helpers taken from:
-#   https://github.com/rstudio/promises/blob/master/tests/testthat/common.R
-# Block until all pending later tasks have executed
-wait_for_it <- function() {
-  while (!later::loop_empty()) {
-    later::run_now(0.1)
-  }
-}
-
-# Block until the promise is resolved/rejected. If resolved, return the value.
-# If rejected, throw (yes throw, not return) the error.
-#' @importFrom promises %...!%
-#' @importFrom promises %...>%
-extract <- function(promise) {
-  promise_value <- NULL
-  error <- NULL
-  promise %...>%
-    (function(value) promise_value <<- value) %...!%
-    (function(reason) error <<- reason)
-
-  wait_for_it()
-  if (!is.null(error))
-    stop(error)
-  else
-    promise_value
-}
-
-# TODO: is there a way to get this behavior without exporting these functions? R6?
-# TODO: clientData is documented as a reactiveValues, which this is not. Is it possible that
-#   users are currently assigning into clientData? That would not work as expected here.
-#' @noRd
-#' @export
-`$.mockclientdata` <- function(x, name) {
-  if (name == "allowDataUriScheme") { return(TRUE) }
-  if (name == "pixelratio") { return(1) }
-  if (name == "url_protocol") { return("http:") }
-  if (name == "url_hostname") { return("mocksession") }
-  if (name == "url_port") { return(1234) }
-  if (name == "url_pathname") { return("/mockpath") }
-  if (name == "url_hash") { return("#mockhash") }
-  if (name == "url_hash_initial") { return("#mockhash") }
-  if (name == "url_search") { return("?mocksearch=1") }
-
-  clientRE <- "^output_(.+)_([^_]+)$"
-  if(grepl(clientRE, name)) {
-    # TODO: use proper regex group matching here instead of redundantly parsing
-    el <- sub(clientRE, "\\1", name)
-    att <- sub(clientRE, "\\2", name)
-
-    if (att == "width") {
-      return(600)
-    } else if (att == "height") {
-      return(400)
-    } else if (att == "hidden") {
-      return(FALSE)
-    }
-  }
-  warning("Unexpected clientdata attribute accessed: ", name)
-  return(NULL)
-}
-
-#' @noRd
-#' @export
-`[[.mockclientdata` <- `$.mockclientdata`
-
-#' @noRd
-#' @export
-`[.mockclientdata` <- function(values, name) {
-  stop("Single-bracket indexing of mockclientdata is not allowed.")
-}
-
-#' @noRd
-mapNames <- function(func, vals) {
-  names(vals) <- vapply(names(vals), func, character(1))
-  vals
-}
-
-#' Mock Shiny Session
-#'
-#' @description
-#' An R6 class suitable for testing that simulates the `session` parameter
-#' provided to Shiny server functions or modules.
-#'
-#' @include timer.R
-#' @export
-MockShinySession <- R6Class(
-  'MockShinySession',
-  portable = FALSE,
-  public = list(
-    #' @field env The environment associated with the session.
-    env = NULL,
-    #' @field returned The value returned by the module.
-    returned = NULL,
-    #' @field singletons Hardcoded as empty. Needed for rendering HTML (i.e. renderUI)
-    singletons = character(0),
-    #' @field clientData Mock client data that always returns a size for plots
-    clientData = structure(list(), class="mockclientdata"),
-    #' @description No-op
-    #' @param logEntry Not used
-    reactlog = function(logEntry){},
-    #' @description No-op
-    incrementBusyCount = function(){},
-    #' @field output The shinyoutputs associated with the session
-    output = NULL,
-    #' @field input The reactive inputs associated with the session
-    input = NULL,
-    #' @field userData An environment initialized as empty.
-    userData = NULL,
-    #' @field progressStack A stack of progress objects
-    progressStack = 'Stack',
-
-    #' @description Create a new MockShinySession
-    initialize = function() {
-      private$.input <- ReactiveValues$new(dedupe = FALSE, label = "input")
-      private$flushCBs <- Callbacks$new()
-      private$flushedCBs <- Callbacks$new()
-      private$endedCBs <- Callbacks$new()
-      private$timer <- MockableTimerCallbacks$new()
-      self$progressStack <- Stack$new()
-
-      self$userData <- new.env(parent=emptyenv())
-
-      # create output
-      out <- .createOutputWriter(self)
-      class(out) <- "shinyoutput"
-      self$output <- out
-
-      # Create a read-only copy of the inputs reactive.
-      self$input <- .createReactiveValues(private$.input, readonly = TRUE)
-    },
-    #' @description Define a callback to be invoked before a reactive flush
-    #' @param fun The function to invoke
-    #' @param once If `TRUE`, will only run once. Otherwise, will run every time reactives are flushed.
-    onFlush = function(fun, once=TRUE) {
-      if (!isTRUE(once)) {
-        return(private$flushCBs$register(fun))
-      } else {
-        dereg <- private$flushCBs$register(function() {
-          dereg()
-          fun()
-        })
-        return(dereg)
-      }
-    },
-    #' @description Define a callback to be invoked after a reactive flush
-    #' @param fun The function to invoke
-    #' @param once If `TRUE`, will only run once. Otherwise, will run every time reactives are flushed.
-    onFlushed = function(fun, once=TRUE) {
-      if (!isTRUE(once)) {
-        return(private$flushedCBs$register(fun))
-      } else {
-        dereg <- private$flushedCBs$register(function() {
-          dereg()
-          fun()
-        })
-        return(dereg)
-      }
-    },
-    #' @description Define a callback to be invoked when the session ends
-    #' @param sessionEndedCallback The callback to invoke when the session has ended.
-    onEnded = function(sessionEndedCallback) {
-      private$endedCBs$register(sessionEndedCallback)
-    },
-
-    #' @description Returns `FALSE` if the session has not yet been closed
-    isEnded = function(){ private$closed },
-    #' @description Returns `FALSE` if the session has not yet been closed
-    isClosed = function(){ private$closed },
-    #' @description Closes the session
-    close = function(){ private$closed <- TRUE },
-
-    #FIXME: this is wrong. Will need to be more complex.
-    #' @description Unsophisticated mock implementation that merely invokes
-    #'   the given callback immediately.
-    #' @param callback The callback ato be invoked.
-    cycleStartAction = function(callback){ callback() },
-
-    #' @description Base64-encode the given file. Needed for image rendering.
-    #' @param name Not used
-    #' @param file The file to be encoded
-    #' @param contentType The content type of the base64-encoded string
-    fileUrl = function(name, file, contentType='application/octet-stream') {
-      bytes <- file.info(file)$size
-      if (is.na(bytes))
-        return(NULL)
-
-      fileData <- readBin(file, 'raw', n=bytes)
-      b64 <- rawToBase64(fileData)
-      return(paste('data:', contentType, ';base64,', b64, sep=''))
-    },
-
-    #' @description Sets reactive values associated with the `session$inputs`
-    #'   object and flushes the reactives.
-    #' @param ... The inputs to set. These arguments are processed with
-    #'   [rlang::list2()] and so are _[dynamic][rlang::dyn-dots]_. Input names
-    #'   may not be duplicated.
-    #' @examples
-    #' \dontrun{
-    #' session$setInputs(x=1, y=2)
-    #' }
-    setInputs = function(...) {
-      vals <- rlang::dots_list(..., .homonyms = "error")
-      mapply(names(vals), vals, FUN = function(name, value) {
-        private$.input$set(name, value)
-      })
-      private$flush()
-    },
-
-    #' @description An internal method which shouldn't be used by others.
-    #' @param millis The number of milliseconds on which to schedule a callback
-    #' @param callback The function to schedule
-    .scheduleTask = function(millis, callback) {
-      id <- private$timer$schedule(millis, callback)
-
-      # Return a deregistration callback
-      function() {
-        invisible(private$timer$unschedule(id))
-      }
-    },
-
-    #' @description Simulate the passing of time by the given number of milliseconds.
-    #' @param millis The number of milliseconds to advance time.
-    elapse = function(millis) {
-      msLeft <- millis
-
-      while (msLeft > 0){
-        t <- private$timer$timeToNextEvent()
-
-        if (is.infinite(t) || t <= 0 || msLeft < t){
-          # Either there's no good upcoming event or we can't make it to it in the allotted time.
-          break
-        }
-        msLeft <- msLeft - t
-        private$timer$elapse(t)
-
-        # timerCallbacks must run before flushReact.
-        private$timer$executeElapsed()
-        private$flush()
-      }
-
-      private$timer$elapse(msLeft)
-
-      # Run again in case our callbacks resulted in a scheduled
-      # function that needs executing.
-      private$timer$executeElapsed()
-      private$flush()
-    },
-
-    #' @description An internal method which shouldn't be used by others.
-    .now = function() {
-      # Returns elapsed time in milliseconds
-      private$timer$getElapsed()
-    },
-
-    #' @description An internal method which shouldn't be used by others.
-    #' @param name The name of the output
-    #' @param func The render definition
-    #' @param label Not used
-    defineOutput = function(name, func, label) {
-      force(name)
-
-      if (!is.null(private$outs[[name]]$obs)) {
-        private$outs[[name]]$obs$destroy()
-      }
-
-      if (is.null(func)) func <- missingOutput
-
-      if (!is.function(func))
-        stop(paste("Unexpected", class(func), "output for", name))
-
-      obs <- observe({
-        # We could just stash the promise, but we get an "unhandled promise error". This bypasses
-        prom <- NULL
-        tryCatch({
-          v <- func(self, name)
-          if (!promises::is.promise(v)){
-            # Make our sync value into a promise
-            prom <- promises::promise(function(resolve, reject){ resolve(v) })
-          } else {
-            prom <- v
-          }
-        }, error=function(e){
-          # Error running value()
-          prom <<- promises::promise(function(resolve, reject){ reject(e) })
-        })
-
-        private$outs[[name]]$promise <- hybrid_chain(
-          prom,
-          function(v){
-            list(val = v, err = NULL)
-          }, catch=function(e){
-            list(val = NULL, err = e)
-          })
-      })
-      private$outs[[name]] <- list(obs = obs, func = func, promise = NULL)
-    },
-
-    #' @description An internal method which shouldn't be used by others.
-    #' @param name The name of the output
-    getOutput = function(name) {
-      # Unlike the real outputs, we're going to return the last value rather than the unevaluated function
-      if (is.null(private$outs[[name]])) {
-        stop("The test referenced an output that hasn't been defined yet: output$", name)
-      }
-
-      if (is.null(private$outs[[name]]$promise)) {
-        # Means the output was defined but the observer hasn't had a chance to run
-        # yet. Run flushReact() now to force the observer to run.
-        flushReact()
-
-        if (is.null(private$outs[[name]]$promise)) {
-          stop("output$", name, " encountered an unexpected error resolving its promise")
-        }
-      }
-
-      # Make promise return
-      v <- extract(private$outs[[name]]$promise)
-      if (!is.null(v$err)){
-        stop(v$err)
-      } else {
-        v$val
-      }
-    },
-
-    #' @description No-op
-    #' @param name Not used
-    #' @param data Not used
-    #' @param filterFunc Not used
-    registerDataObj = function(name, data, filterFunc) {},
-    #' @description No-op
-    #' @param value Not used
-    allowReconnect = function(value) {},
-    #' @description No-op
-    reload = function() {},
-    #' @description No-op
-    #' @param brushId Not used
-    resetBrush = function(brushId) {
-      warning("session$brush isn't meaningfully mocked on the MockShinySession")
-    },
-    #' @description No-op
-    #' @param type Not used
-    #' @param message Not used
-    sendCustomMessage = function(type, message) {},
-    #' @description No-op
-    #' @param type Not used
-    #' @param message Not used
-    sendBinaryMessage = function(type, message) {},
-    #' @description No-op
-    #' @param inputId Not used
-    #' @param message Not used
-    sendInputMessage = function(inputId, message) {},
-    #' @description No-op
-    #' @param names Not used
-    setBookmarkExclude = function(names) {
-      warning("Bookmarking isn't meaningfully mocked in MockShinySession")
-    },
-    #' @description No-op
-    getBookmarkExclude = function() {
-      warning("Bookmarking isn't meaningfully mocked in MockShinySession")
-    },
-    #' @description No-op
-    #' @param fun Not used
-    onBookmark = function(fun) {},
-    #' @description No-op
-    #' @param fun Not used
-    onBookmarked = function(fun) {},
-    #' @description No-op
-    doBookmark = function() {
-      warning("Bookmarking isn't meaningfully mocked in MockShinySession")
-    },
-    #' @description No-op
-    #' @param fun Not used
-    onRestore = function(fun) {},
-    #' @description No-op
-    #' @param fun Not used
-    onRestored = function(fun) {},
-    #' @description No-op
-    exportTestValues = function() {},
-    #' @description No-op
-    #' @param input Not used
-    #' @param output Not used
-    #' @param export Not used
-    #' @param format Not used
-    getTestSnapshotUrl = function(input=TRUE, output=TRUE, export=TRUE, format="json") {},
-    #' @description Returns the given id prefixed by this namespace's id.
-    #' @param id The id to modify.
-    ns = function(id) {
-      NS(private$nsPrefix, id)
-    },
-    #' @description Trigger a reactive flush right now.
-    flushReact = function(){
-      private$flush()
-    },
-    #' @description Create and return a namespace-specific session proxy.
-    #' @param namespace Character vector indicating a namespace.
-    makeScope = function(namespace) {
-      ns <- NS(namespace)
-      createSessionProxy(
-        self,
-        input = .createReactiveValues(private$.input, readonly = TRUE, ns = ns),
-        output = structure(.createOutputWriter(self, ns = ns), class = "shinyoutput"),
-        makeScope = function(namespace) self$makeScope(ns(namespace)),
-        ns = function(namespace) ns(namespace),
-        setInputs = function(...) {
-          self$setInputs(!!!mapNames(ns, rlang::dots_list(..., .homonyms = "error")))
-        }
-      )
-    },
-    #' @description Set the environment associated with a testServer() call, but
-    #'   only if it has not previously been set. This ensures that only the
-    #'   environment of the outermost module under test is the one retained. In
-    #'   other words, the first assignment wins.
-    #' @param env The environment to retain.
-    setEnv = function(env) {
-      if (is.null(self$env)) {
-        stopifnot(all(c("input", "output", "session") %in% ls(env)))
-        self$env <- env
-      }
-    },
-    #' @description Set the value returned by the module call and proactively
-    #'   flush. Note that this method may be called multiple times if modules
-    #'   are nested. The last assignment, corresponding to an invocation of
-    #'   setReturned() in the outermost module, wins.
-    #' @param value The value returned from the module
-    setReturned = function(value) {
-      self$returned <- value
-      value
-    },
-    #' @description Get the value returned by the module call.
-    getReturned = function() self$returned,
-    #' @description Return a distinct character identifier for use as a proxy
-    #'   namespace.
-    genId = function() {
-      private$idCounter <- private$idCounter + 1
-      paste0("proxy", private$idCounter)
-    }
-  ),
-  private = list(
-    .input = NULL,
-    flushCBs = NULL,
-    flushedCBs = NULL,
-    endedCBs = NULL,
-    timer = NULL,
-    closed = FALSE,
-    outs = list(),
-    nsPrefix = "mock-session",
-    idCounter = 0,
-
-    flush = function(){
-      isolate(private$flushCBs$invoke(..stacktraceon = TRUE))
-      shiny:::flushReact() # namespace to avoid calling our own method
-      isolate(private$flushedCBs$invoke(..stacktraceon = TRUE))
-      later::run_now()
-    }
-  ),
-  active = list(
-    #' @field request An empty environment where the request should be. The request isn't meaningfully mocked currently.
-    request = function(value) {
-      if (!missing(value)){
-        stop("session$request can't be assigned to")
-      }
-      warning("session$request doesn't currently simulate a realistic request on MockShinySession")
-      new.env(parent=emptyenv())
-    }
-  )
-)

R/modal.R

@@ -1,13 +1,13 @@
 #' Show or remove a modal dialog
 #'
 #' This causes a modal dialog to be displayed in the client browser, and is
-#' typically used with [modalDialog()].
+#' typically used with \code{\link{modalDialog}}.
 #'
 #' @param ui UI content to show in the modal.
-#' @param session The `session` object passed to function given to
-#'   `shinyServer`.
+#' @param session The \code{session} object passed to function given to
+#'   \code{shinyServer}.
 #'
-#' @seealso [modalDialog()] for examples.
+#' @seealso \code{\link{modalDialog}} for examples.
 #' @export
 showModal <- function(ui, session = getDefaultReactiveDomain()) {
   res <- processDeps(ui, session)
@@ -35,15 +35,15 @@ removeModal <- function(session = getDefaultReactiveDomain()) {
 #'
 #' @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 `NULL` for no footer.
-#' @param size One of `"s"` for small, `"m"` (the default) for medium,
-#'   or `"l"` for large.
-#' @param easyClose If `TRUE`, the modal dialog can be dismissed by
+#' @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
-#'   `FALSE` (the default), the modal dialog can't be dismissed in those
+#'   \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 [removeModal()] on the server.
-#' @param fade If `FALSE`, the modal dialog will have no fade-in animation
+#'   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
@@ -171,10 +171,10 @@ modalDialog <- function(..., title = NULL, footer = modalButton("Dismiss"),
 
 #' Create a button for a modal dialog
 #'
-#' When clicked, a `modalButton` will dismiss the modal dialog.
+#' When clicked, a \code{modalButton} will dismiss the modal dialog.
 #'
 #' @inheritParams actionButton
-#' @seealso [modalDialog()] for examples.
+#' @seealso \code{\link{modalDialog}} for examples.
 #' @export
 modalButton <- function(label, icon = NULL) {
   tags$button(type = "button", class = "btn btn-default",

R/modules.R

@@ -36,119 +36,25 @@ createSessionProxy <- function(parentSession, ...) {
 
 `[[<-.session_proxy` <- `$<-.session_proxy`
 
-#' Shiny modules
+
+#' Invoke a Shiny module
 #'
 #' Shiny's module feature lets you break complicated UI and server logic into
 #' smaller, self-contained pieces. Compared to large monolithic Shiny apps,
 #' modules are easier to reuse and easier to reason about. See the article at
-#' <http://shiny.rstudio.com/articles/modules.html> to learn more.
+#' \url{http://shiny.rstudio.com/articles/modules.html} to learn more.
 #'
-#' Starting in Shiny 1.5.0, we recommend using `moduleServer` instead of
-#' `callModule`, because the syntax is a little easier to understand, and
-#' modules created with `moduleServer` can be tested with [`testServer()`].
-#'
-#' @param module A Shiny module server function.
+#' @param module A Shiny module server function
 #' @param id An ID string that corresponds with the ID used to call the module's
-#'   UI function.
-#' @param ... For `callModule`, additional parameters to pass to module server
-#'   function.
+#'   UI function
+#' @param ... Additional parameters to pass to module server function
 #' @param session Session from which to make a child scope (the default should
-#'   almost always be used).
+#'   almost always be used)
 #'
 #' @return The return value, if any, from executing the module server function
-#' @seealso <http://shiny.rstudio.com/articles/modules.html>
-#'
-#' @examples
-#' # Define the UI for a module
-#' counterUI <- function(id, label = "Counter") {
-#'   ns <- NS(id)
-#'   tagList(
-#'     actionButton(ns("button"), label = label),
-#'     verbatimTextOutput(ns("out"))
-#'   )
-#' }
-#'
-#' # Define the server logic for a module
-#' counterServer <- function(id) {
-#'   moduleServer(
-#'     id,
-#'     function(input, output, session) {
-#'       count <- reactiveVal(0)
-#'       observeEvent(input$button, {
-#'         count(count() + 1)
-#'       })
-#'       output$out <- renderText({
-#'         count()
-#'       })
-#'       count
-#'     }
-#'   )
-#' }
-#'
-#' # Use the module in an app
-#' ui <- fluidPage(
-#'   counterUI("counter1", "Counter #1"),
-#'   counterUI("counter2", "Counter #2")
-#' )
-#' server <- function(input, output, session) {
-#'   counterServer("counter1")
-#'   counterServer("counter2")
-#' }
-#' if (interactive()) {
-#'   shinyApp(ui, server)
-#' }
-#'
-#'
-#'
-#' # If you want to pass extra parameters to the module's server logic, you can
-#' # add them to your function. In this case `prefix` is text that will be
-#' # printed before the count.
-#' counterServer2 <- function(id, prefix = NULL) {
-#'   moduleServer(
-#'     id,
-#'     function(input, output, session) {
-#'       count <- reactiveVal(0)
-#'       observeEvent(input$button, {
-#'         count(count() + 1)
-#'       })
-#'       output$out <- renderText({
-#'         paste0(prefix, count())
-#'       })
-#'       count
-#'     }
-#'   )
-#' }
-#'
-#' ui <- fluidPage(
-#'   counterUI("counter", "Counter"),
-#' )
-#' server <- function(input, output, session) {
-#'   counterServer2("counter", "The current count is: ")
-#' }
-#' if (interactive()) {
-#'   shinyApp(ui, server)
-#' }
-#'
-#' @export
-moduleServer <- function(id, module, session = getDefaultReactiveDomain()) {
-  if (inherits(session, "MockShinySession")) {
-    body(module) <- rlang::expr({
-      session$setEnv(base::environment())
-      !!body(module)
-    })
-    session$setReturned(callModule(module, id, session = session))
-  } else {
-    callModule(module, id, session = session)
-  }
-}
-
-
-#' @rdname moduleServer
+#' @seealso \url{http://shiny.rstudio.com/articles/modules.html}
 #' @export
 callModule <- function(module, id, ..., session = getDefaultReactiveDomain()) {
-  if (!inherits(session, c("ShinySession", "session_proxy", "MockShinySession"))) {
-    stop("session must be a ShinySession or session_proxy object.")
-  }
   childScope <- session$makeScope(id)
 
   withReactiveDomain(childScope, {

R/notifications.R

@@ -4,21 +4,19 @@
 #'
 #' @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 `ui`
+#'   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 `NULL` to make the message not automatically
+#'   disappears. Use \code{NULL} to make the message not automatically
 #'   disappear.
-#' @param closeButton If `TRUE`, display a button which will make the
-#'   notification disappear when clicked. If `FALSE` do not display.
-#' @param id A unique identifier for the notification.
-#'
-#'   `id` is optional for `showNotification()`: Shiny will automatically create
-#'   one if needed. If you do supply it, Shiny will update an existing
-#'   notification if it exists, otherwise it will create a new one.
-#'
-#'   `id` is required for `removeNotification()`.
+#' @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.
@@ -99,8 +97,10 @@ showNotification <- function(ui, action = NULL, duration = 5,
 
 #' @rdname showNotification
 #' @export
-removeNotification <- function(id, session = getDefaultReactiveDomain()) {
-  force(id)
+removeNotification <- function(id = NULL, session = getDefaultReactiveDomain()) {
+  if (is.null(id)) {
+    stop("id is required.")
+  }
   session$sendNotification("remove", id)
   id
 }

R/progress.R

@@ -3,29 +3,67 @@
 #' Reports progress to the user during long-running operations.
 #'
 #' This package exposes two distinct programming APIs for working with
-#' progress. [withProgress()] and [setProgress()]
+#' progress. \code{\link{withProgress}} and \code{\link{setProgress}}
 #' together provide a simple function-based interface, while the
-#' `Progress` reference class provides an object-oriented API.
+#' \code{Progress} reference class provides an object-oriented API.
 #'
-#' Instantiating a `Progress` object causes a progress panel to be
-#' created, and it will be displayed the first time the `set`
-#' method is called. Calling `close` will cause the progress panel
+#' Instantiating a \code{Progress} object causes a progress panel to be
+#' created, and it will be displayed the first time the \code{set}
+#' method is called. Calling \code{close} will cause the progress panel
 #' to be removed.
 #'
 #' 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 `style="old"` each time you call
-#' `Progress$new()`. If you don't want to set the style each time
-#' `Progress$new` is called, you can instead call
-#' [`shinyOptions(progress.style="old")`][shinyOptions] just once, inside the server
+#' 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)}}{
+#'       Creates a new progress panel (but does not display it).
+#'     }
+#'     \item{\code{set(value = NULL, message = NULL, detail = NULL)}}{
+#'       Updates the progress panel. When called the first time, the
+#'       progress panel is displayed.
+#'     }
+#'     \item{\code{inc(amount = 0.1, message = NULL, detail = NULL)}}{
+#'       Like \code{set}, this updates the progress panel. The difference is
+#'       that \code{inc} increases the progress bar by \code{amount}, instead
+#'       of setting it to a specific value.
+#'     }
+#'     \item{\code{close()}}{
+#'       Removes the progress panel. Future calls to \code{set} and
+#'       \code{close} will be ignored.
+#'     }
+#'   }
+#'
+#' @param session The Shiny session object, as provided by
+#'   \code{shinyServer} to the server function.
+#' @param min The value that represents the starting point of the
+#'   progress bar. Must be less tham \code{max}.
+#' @param max The value that represents the end of the progress bar.
+#'   Must be greater than \code{min}.
 #' @param message A single-element character vector; the message to be
-#'   displayed to the user, or `NULL` to hide the current message (if any).
-#' @param detail A single-element character vector; the detail message to be
-#'   displayed to the user, or `NULL` to hide the current detail message (if
-#'   any). The detail message will be shown with a de-emphasized appearance
-#'   relative to `message`.
+#'   displayed to the user, or \code{NULL} to hide the current message
+#'   (if any).
+#' @param detail A single-element character vector; the detail message
+#'   to be displayed to the user, or \code{NULL} to hide the current
+#'   detail message (if any). The detail message will be shown with a
+#'   de-emphasized appearance relative to \code{message}.
+#' @param value A numeric value at which to set
+#'   the progress bar, relative to \code{min} and \code{max}.
+#' @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.
+#' @param amount For the \code{inc()} method, a numeric value to increment the
+#'   progress bar.
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -53,7 +91,7 @@
 #'
 #' shinyApp(ui, server)
 #' }
-#' @seealso [withProgress()]
+#' @seealso \code{\link{withProgress}}
 #' @format NULL
 #' @usage NULL
 #' @export
@@ -61,17 +99,6 @@ Progress <- R6Class(
   'Progress',
   public = list(
 
-    #' @description Creates a new progress panel (but does not display it).
-    #' @param session The Shiny session object, as provided by `shinyServer` to
-    #'   the server function.
-    #' @param min The value that represents the starting point of the progress
-    #'   bar. Must be less than `max`.
-    #' @param max The value that represents the end of the progress bar. Must be
-    #'   greater than `min`.
-    #' @param style Progress display style. If `"notification"` (the default),
-    #'   the progress indicator will show using Shiny's notification API. If
-    #'   `"old"`, use the same HTML and CSS used in Shiny 0.13.2 and below (this
-    #'   is for backward-compatibility).
     initialize = function(session = getDefaultReactiveDomain(),
       min = 0, max = 1,
       style = getShinyOption("progress.style", default = "notification"))
@@ -90,11 +117,6 @@ Progress <- R6Class(
       session$sendProgress('open', list(id = private$id, style = private$style))
     },
 
-    #' @description Updates the progress panel. When called the first time, the
-    #'   progress panel is displayed.
-    #' @param value Single-element numeric vector; the value at which to set the
-    #'   progress bar, relative to `min` and `max`. `NULL` hides the progress
-    #'   bar, if it is currently visible.
     set = function(value = NULL, message = NULL, detail = NULL) {
       if (private$closed) {
         warning("Attempting to set progress, but progress already closed.")
@@ -121,11 +143,6 @@ Progress <- R6Class(
       private$session$sendProgress('update', data)
     },
 
-    #' @description Like `set`, this updates the progress panel. The difference
-    #'   is that `inc` increases the progress bar by `amount`, instead of
-    #'   setting it to a specific value.
-    #' @param amount For the `inc()` method, a numeric value to increment the
-    #'   progress bar.
     inc = function(amount = 0.1, message = NULL, detail = NULL) {
       if (is.null(private$value))
         private$value <- private$min
@@ -134,17 +151,12 @@ Progress <- R6Class(
       self$set(value, message, detail)
     },
 
-    #' @description Returns the minimum value.
     getMin = function() private$min,
 
-    #' @description Returns the maximum value.
     getMax = function() private$max,
 
-    #' @description Returns the current value.
     getValue = function() private$value,
 
-    #' @description Removes the progress panel. Future calls to `set` and
-    #'   `close` will be ignored.
     close = function() {
       if (private$closed) {
         warning("Attempting to close progress, but progress already closed.")
@@ -174,58 +186,58 @@ Progress <- R6Class(
 #' Reports progress to the user during long-running operations.
 #'
 #' This package exposes two distinct programming APIs for working with progress.
-#' Using `withProgress` with `incProgress` or `setProgress`
-#' provide a simple function-based interface, while the [Progress()]
+#' Using \code{withProgress} with \code{incProgress} or \code{setProgress}
+#' provide a simple function-based interface, while the \code{\link{Progress}}
 #' reference class provides an object-oriented API.
 #'
-#' Use `withProgress` to wrap the scope of your work; doing so will cause a
+#' Use \code{withProgress} to wrap the scope of your work; doing so will cause a
 #' new progress panel to be created, and it will be displayed the first time
-#' `incProgress` or `setProgress` are called. When `withProgress`
+#' \code{incProgress} or \code{setProgress} are called. When \code{withProgress}
 #' exits, the corresponding progress panel will be removed.
 #'
-#' The `incProgress` function increments the status bar by a specified
-#' amount, whereas the `setProgress` function sets it to a specific value,
+#' The \code{incProgress} function increments the status bar by a specified
+#' amount, whereas the \code{setProgress} function sets it to a specific value,
 #' and can also set the text displayed.
 #'
-#' Generally, `withProgress`/`incProgress`/`setProgress` should
+#' Generally, \code{withProgress}/\code{incProgress}/\code{setProgress} should
 #' be sufficient; the exception is if the work to be done is asynchronous (this
 #' is not common) or otherwise cannot be encapsulated by a single scope. In that
-#' case, you can use the `Progress` reference class.
+#' 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 `style="old"` each time you call
-#' `withProgress()`. If you don't want to set the style each time
-#' `withProgress` is called, you can instead call
-#' [`shinyOptions(progress.style="old")`][shinyOptions] just once, inside the server
+#' 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 `shinyServer` to
+#' @param session The Shiny session object, as provided by \code{shinyServer} to
 #'   the server function. The default is to automatically find the session by
 #'   using the current reactive domain.
 #' @param expr The work to be done. This expression should contain calls to
-#'   `setProgress`.
+#'   \code{setProgress}.
 #' @param min The value that represents the starting point of the progress bar.
-#'   Must be less tham `max`. Default is 0.
+#'   Must be less tham \code{max}. Default is 0.
 #' @param max The value that represents the end of the progress bar. Must be
-#'   greater than `min`. Default is 1.
-#' @param amount For `incProgress`, the amount to increment the status bar.
+#'   greater than \code{min}. Default is 1.
+#' @param amount For \code{incProgress}, the amount to increment the status bar.
 #'   Default is 0.1.
-#' @param env The environment in which `expr` should be evaluated.
-#' @param quoted Whether `expr` is a quoted expression (this is not
+#' @param env The environment in which \code{expr} should be evaluated.
+#' @param quoted Whether \code{expr} is a quoted expression (this is not
 #'   common).
 #' @param message A single-element character vector; the message to be displayed
-#'   to the user, or `NULL` to hide the current message (if any).
+#'   to the user, or \code{NULL} to hide the current message (if any).
 #' @param detail A single-element character vector; the detail message to be
-#'   displayed to the user, or `NULL` to hide the current detail message
+#'   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 `message`.
-#' @param style Progress display style. If `"notification"` (the default),
+#'   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
-#'   `"old"`, use the same HTML and CSS used in Shiny 0.13.2 and below
+#'   \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 `min` and `max`.
+#'   progress bar, relative to \code{min} and \code{max}.
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -251,7 +263,7 @@ Progress <- R6Class(
 #'
 #' shinyApp(ui, server)
 #' }
-#' @seealso [Progress()]
+#' @seealso \code{\link{Progress}}
 #' @rdname withProgress
 #' @export
 withProgress <- function(expr, min = 0, max = 1,

R/react.R

@@ -31,13 +31,11 @@ Context <- R6Class(
     .flushCallbacks = list(),
     .domain = NULL,
     .pid = NULL,
-    .weak = NULL,
 
     initialize = function(
       domain, label='', type='other', prevId='',
       reactId = rLog$noReactId,
-      id = .getReactiveEnvironment()$nextId(), # For dummy context
-      weak = FALSE
+      id = .getReactiveEnvironment()$nextId() # For dummy context
     ) {
       id <<- id
       .label <<- label
@@ -45,7 +43,6 @@ Context <- R6Class(
       .pid <<- processId()
       .reactId <<- reactId
       .reactType <<- type
-      .weak <<- weak
       rLog$createContext(id, label, type, prevId, domain)
     },
     run = function(func) {
@@ -111,9 +108,6 @@ Context <- R6Class(
       lapply(.flushCallbacks, function(flushCallback) {
         flushCallback()
       })
-    },
-    isWeak = function() {
-      .weak
     }
   )
 )

R/reactive-domains.R

@@ -168,31 +168,31 @@ onReactiveDomainEnded <- function(domain, callback, failIfNull = FALSE) {
 #' them ends) and error handling.
 #'
 #' At any given time, there can be either a single "default" reactive domain
-#' object, or none (i.e. the reactive domain object is `NULL`). You can
+#' object, or none (i.e. the reactive domain object is \code{NULL}). You can
 #' access the current default reactive domain by calling
-#' `getDefaultReactiveDomain`.
+#' \code{getDefaultReactiveDomain}.
 #'
 #' Unless you specify otherwise, newly created observers and reactive
 #' expressions will be assigned to the current default domain (if any). You can
-#' override this assignment by providing an explicit `domain` argument to
-#' [reactive()] or [observe()].
+#' override this assignment by providing an explicit \code{domain} argument to
+#' \code{\link{reactive}} or \code{\link{observe}}.
 #'
 #' For advanced usage, it's possible to override the default domain using
-#' `withReactiveDomain`. The `domain` argument will be made the
-#' default domain while `expr` is evaluated.
+#' \code{withReactiveDomain}. The \code{domain} argument will be made the
+#' default domain while \code{expr} is evaluated.
 #'
-#' Implementers of new reactive primitives can use `onReactiveDomainEnded`
+#' Implementers of new reactive primitives can use \code{onReactiveDomainEnded}
 #' as a convenience function for registering callbacks. If the reactive domain
-#' is `NULL` and `failIfNull` is `FALSE`, then the callback will
+#' is \code{NULL} and \code{failIfNull} is \code{FALSE}, then the callback will
 #' never be invoked.
 #'
 #' @name domains
 #' @param domain A valid domain object (for example, a Shiny session), or
-#'   `NULL`
-#' @param expr An expression to evaluate under `domain`
+#'   \code{NULL}
+#' @param expr An expression to evaluate under \code{domain}
 #' @param callback A callback function to be invoked
-#' @param failIfNull If `TRUE` then an error is given if the `domain`
-#'   is `NULL`
+#' @param failIfNull If \code{TRUE} then an error is given if the \code{domain}
+#'   is \code{NULL}
 NULL
 
 #

R/reexports.R

@@ -1,195 +0,0 @@
-####
-# Generated by `./tools/updateReexports.R`: do not edit by hand
-# Please call `source('tools/updateReexports.R') from the root folder to update`
-####
-
-
-# fastmap key_missing.Rd -------------------------------------------------------
-
-#' @importFrom fastmap key_missing
-#' @export
-fastmap::key_missing
-
-#' @importFrom fastmap is.key_missing
-#' @export
-fastmap::is.key_missing
-
-
-
-# htmltools builder.Rd ---------------------------------------------------------
-
-#' @importFrom htmltools tags
-#' @export
-htmltools::tags
-
-#' @importFrom htmltools p
-#' @export
-htmltools::p
-
-#' @importFrom htmltools h1
-#' @export
-htmltools::h1
-
-#' @importFrom htmltools h2
-#' @export
-htmltools::h2
-
-#' @importFrom htmltools h3
-#' @export
-htmltools::h3
-
-#' @importFrom htmltools h4
-#' @export
-htmltools::h4
-
-#' @importFrom htmltools h5
-#' @export
-htmltools::h5
-
-#' @importFrom htmltools h6
-#' @export
-htmltools::h6
-
-#' @importFrom htmltools a
-#' @export
-htmltools::a
-
-#' @importFrom htmltools br
-#' @export
-htmltools::br
-
-#' @importFrom htmltools div
-#' @export
-htmltools::div
-
-#' @importFrom htmltools span
-#' @export
-htmltools::span
-
-#' @importFrom htmltools pre
-#' @export
-htmltools::pre
-
-#' @importFrom htmltools code
-#' @export
-htmltools::code
-
-#' @importFrom htmltools img
-#' @export
-htmltools::img
-
-#' @importFrom htmltools strong
-#' @export
-htmltools::strong
-
-#' @importFrom htmltools em
-#' @export
-htmltools::em
-
-#' @importFrom htmltools hr
-#' @export
-htmltools::hr
-
-
-# htmltools tag.Rd -------------------------------------------------------------
-
-#' @importFrom htmltools tag
-#' @export
-htmltools::tag
-
-#' @importFrom htmltools tagList
-#' @export
-htmltools::tagList
-
-#' @importFrom htmltools tagAppendAttributes
-#' @export
-htmltools::tagAppendAttributes
-
-#' @importFrom htmltools tagHasAttribute
-#' @export
-htmltools::tagHasAttribute
-
-#' @importFrom htmltools tagGetAttribute
-#' @export
-htmltools::tagGetAttribute
-
-#' @importFrom htmltools tagAppendChild
-#' @export
-htmltools::tagAppendChild
-
-#' @importFrom htmltools tagAppendChildren
-#' @export
-htmltools::tagAppendChildren
-
-#' @importFrom htmltools tagSetChildren
-#' @export
-htmltools::tagSetChildren
-
-
-# htmltools HTML.Rd ------------------------------------------------------------
-
-#' @importFrom htmltools HTML
-#' @export
-htmltools::HTML
-
-
-# htmltools include.Rd ---------------------------------------------------------
-
-#' @importFrom htmltools includeHTML
-#' @export
-htmltools::includeHTML
-
-#' @importFrom htmltools includeText
-#' @export
-htmltools::includeText
-
-#' @importFrom htmltools includeMarkdown
-#' @export
-htmltools::includeMarkdown
-
-#' @importFrom htmltools includeCSS
-#' @export
-htmltools::includeCSS
-
-#' @importFrom htmltools includeScript
-#' @export
-htmltools::includeScript
-
-
-# htmltools singleton.Rd -------------------------------------------------------
-
-#' @importFrom htmltools singleton
-#' @export
-htmltools::singleton
-
-#' @importFrom htmltools is.singleton
-#' @export
-htmltools::is.singleton
-
-
-# htmltools validateCssUnit.Rd -------------------------------------------------
-
-#' @importFrom htmltools validateCssUnit
-#' @export
-htmltools::validateCssUnit
-
-
-# htmltools htmlTemplate.Rd ----------------------------------------------------
-
-#' @importFrom htmltools htmlTemplate
-#' @export
-htmltools::htmlTemplate
-
-
-# htmltools suppressDependencies.Rd --------------------------------------------
-
-#' @importFrom htmltools suppressDependencies
-#' @export
-htmltools::suppressDependencies
-
-
-# htmltools withTags.Rd --------------------------------------------------------
-
-#' @importFrom htmltools withTags
-#' @export
-htmltools::withTags

R/render-cached-plot.R

@@ -2,29 +2,29 @@
 #'
 #' Renders a reactive plot, with plot images cached to disk.
 #'
-#' `expr` is an expression that generates a plot, similar to that in
-#' `renderPlot`. Unlike with `renderPlot`, this expression does not
+#' \code{expr} is an expression that generates a plot, similar to that in
+#' \code{renderPlot}. Unlike with \code{renderPlot}, this expression does not
 #' take reactive dependencies. It is re-executed only when the cache key
 #' changes.
 #'
-#' `cacheKeyExpr` is an expression which, when evaluated, returns an object
-#' which will be serialized and hashed using the [digest::digest()]
+#' \code{cacheKeyExpr} is an expression which, when evaluated, returns an object
+#' which will be serialized and hashed using the \code{\link[digest]{digest}}
 #' function to generate a string that will be used as a cache key. This key is
 #' used to identify the contents of the plot: if the cache key is the same as a
 #' previous time, it assumes that the plot is the same and can be retrieved from
 #' the cache.
 #'
-#' This `cacheKeyExpr` is reactive, and so it will be re-evaluated when any
+#' This \code{cacheKeyExpr} is reactive, and so it will be re-evaluated when any
 #' upstream reactives are invalidated. This will also trigger re-execution of
-#' the plotting expression, `expr`.
+#' the plotting expression, \code{expr}.
 #'
 #' The key should consist of "normal" R objects, like vectors and lists. Lists
 #' should in turn contain other normal R objects. If the key contains
-#' environments, external pointers, or reference objects --- or even if it has
-#' such objects attached as attributes --- then it is possible that it will
+#' environments, external pointers, or reference objects -- or even if it has
+#' such objects attached as attributes -- then it is possible that it will
 #' change unpredictably even when you do not expect it to. Additionally, because
 #' the entire key is serialized and hashed, if it contains a very large object
-#' --- a large data set, for example --- there may be a noticeable performance
+#' -- a large data set, for example -- there may be a noticeable performance
 #' penalty.
 #'
 #' If you face these issues with the cache key, you can work around them by
@@ -32,12 +32,12 @@
 #' to normal R objects before returning them. Your expression could even
 #' serialize and hash that information in an efficient way and return a string,
 #' which will in turn be hashed (very quickly) by the
-#' [digest::digest()] function.
+#' \code{\link[digest]{digest}} function.
 #'
-#' Internally, the result from `cacheKeyExpr` is combined with the name of
-#' the output (if you assign it to `output$plot1`, it will be combined
-#' with `"plot1"`) to form the actual key that is used. As a result, even
-#' if there are multiple plots that have the same `cacheKeyExpr`, they
+#' Internally, the result from \code{cacheKeyExpr} is combined with the name of
+#' the output (if you assign it to \code{output$plot1}, it will be combined
+#' with \code{"plot1"}) to form the actual key that is used. As a result, even
+#' if there are multiple plots that have the same \code{cacheKeyExpr}, they
 #' will not have cache key collisions.
 #'
 #' @section Cache scoping:
@@ -49,28 +49,28 @@
 #'   cache that persists even after the application is shut down and started
 #'   again.
 #'
-#'   To control the scope of the cache, use the `cache` parameter. There
+#'   To control the scope of the cache, use the \code{cache} parameter. There
 #'   are two ways of having Shiny automatically create and clean up the disk
 #'   cache.
 #'
 #' \describe{
 #'   \item{1}{To scope the cache to one run of a Shiny application (shared
-#'     among possibly multiple user sessions), use `cache="app"`. This
+#'     among possibly multiple user sessions), use \code{cache="app"}. This
 #'     is the default. The cache will be shared across multiple sessions, so
 #'     there is potentially a large performance benefit if there are many users
 #'     of the application. When the application stops running, the cache will
 #'     be deleted. If plots cannot be safely shared across users, this should
 #'     not be used.}
-#'   \item{2}{To scope the cache to one session, use `cache="session"`.
-#'     When a new user session starts --- in other words, when a web browser
-#'     visits the Shiny application --- a new cache will be created on disk
+#'   \item{2}{To scope the cache to one session, use \code{cache="session"}.
+#'     When a new user session starts -- in other words, when a web browser
+#'     visits the Shiny application -- a new cache will be created on disk
 #'     for that session. When the session ends, the cache will be deleted.
 #'     The cache will not be shared across multiple sessions.}
 #'  }
 #'
-#'   If either `"app"` or `"session"` is used, the cache will be 10 MB
+#'   If either \code{"app"} or \code{"session"} is used, the cache will be 10 MB
 #'   in size, and will be stored stored in memory, using a
-#'   [memoryCache()] object. Note that the cache space will be shared
+#'   \code{\link{memoryCache}} object. Note that the cache space will be shared
 #'   among all cached plots within a single application or session.
 #'
 #'   In some cases, you may want more control over the caching behavior. For
@@ -79,7 +79,7 @@
 #'   multiple runs of an application, or even across multiple R processes.
 #'
 #'   To use different settings for an application-scoped cache, you can call
-#'   [shinyOptions()] at the top of your app.R, server.R, or
+#'   \code{\link{shinyOptions}()} at the top of your app.R, server.R, or
 #'   global.R. For example, this will create a cache with 20 MB of space
 #'   instead of the default 10 MB:
 #'   \preformatted{
@@ -87,9 +87,9 @@
 #'   }
 #'
 #'   To use different settings for a session-scoped cache, you can call
-#'   [shinyOptions()] at the top of your server function. To use
-#'   the session-scoped cache, you must also call `renderCachedPlot` with
-#'   `cache="session"`. This will create a 20 MB cache for the session:
+#'   \code{\link{shinyOptions}()} at the top of your server function. To use
+#'   the session-scoped cache, you must also call \code{renderCachedPlot} with
+#'   \code{cache="session"}. This will create a 20 MB cache for the session:
 #'   \preformatted{
 #'   function(input, output, session) {
 #'     shinyOptions(cache = memoryCache(size = 20e6))
@@ -102,7 +102,7 @@
 #'   }
 #'
 #'   If you want to create a cache that is shared across multiple concurrent
-#'   R processes, you can use a [diskCache()]. You can create an
+#'   R processes, you can use a \code{\link{diskCache}}. You can create an
 #'   application-level shared cache by putting this at the top of your app.R,
 #'   server.R, or global.R:
 #'   \preformatted{
@@ -110,7 +110,7 @@
 #'   }
 #'
 #'   This will create a subdirectory in your system temp directory named
-#'   `myapp-cache` (replace `myapp-cache` with a unique name of
+#'   \code{myapp-cache} (replace \code{myapp-cache} with a unique name of
 #'   your choosing). On most platforms, this directory will be removed when
 #'   your system reboots. This cache will persist across multiple starts and
 #'   stops of the R process, as long as you do not reboot.
@@ -126,34 +126,34 @@
 #'   the directory.
 #'
 #'   You can also scope a cache to just one plot, or selected plots. To do that,
-#'   create a [memoryCache()] or [diskCache()], and pass it
-#'   as the `cache` argument of `renderCachedPlot`.
+#'   create a \code{\link{memoryCache}} or \code{\link{diskCache}}, and pass it
+#'   as the \code{cache} argument of \code{renderCachedPlot}.
 #'
 #' @section Interactive plots:
 #'
-#'   `renderCachedPlot` can be used to create interactive plots. See
-#'   [plotOutput()] for more information and examples.
+#'   \code{renderCachedPlot} can be used to create interactive plots. See
+#'   \code{\link{plotOutput}} for more information and examples.
 #'
 #'
 #' @inheritParams renderPlot
 #' @param cacheKeyExpr An expression that returns a cache key. This key should
 #'   be a unique identifier for a plot: the assumption is that if the cache key
 #'   is the same, then the plot will be the same.
-#' @param sizePolicy A function that takes two arguments, `width` and
-#'   `height`, and returns a list with `width` and `height`. The
+#' @param sizePolicy A function that takes two arguments, \code{width} and
+#'   \code{height}, and returns a list with \code{width} and \code{height}. The
 #'   purpose is to round the actual pixel dimensions from the browser to some
 #'   other dimensions, so that this will not generate and cache images of every
-#'   possible pixel dimension. See [sizeGrowthRatio()] for more
+#'   possible pixel dimension. See \code{\link{sizeGrowthRatio}} for more
 #'   information on the default sizing policy.
 #' @param res The resolution of the PNG, in pixels per inch.
 #' @param cache The scope of the cache, or a cache object. This can be
-#'   `"app"` (the default), `"session"`, or a cache object like
-#'   a [diskCache()]. See the Cache Scoping section for more
+#'   \code{"app"} (the default), \code{"session"}, or a cache object like
+#'   a \code{\link{diskCache}}. See the Cache Scoping section for more
 #'   information.
 #'
-#' @seealso See [renderPlot()] for the regular, non-cached version of
+#' @seealso See \code{\link{renderPlot}} for the regular, non-cached version of
 #'   this function. For more about configuring caches, see
-#'   [memoryCache()] and [diskCache()].
+#'   \code{\link{memoryCache}} and \code{\link{diskCache}}.
 #'
 #'
 #' @examples
@@ -379,7 +379,7 @@ renderCachedPlot <- function(expr,
     hybrid_chain(
       # Depend on the user cache key, even though we don't use the value. When
       # it changes, it can cause the drawReactive to re-execute. (Though
-      # drawReactive will not necessarily re-execute --- it must be called from
+      # drawReactive will not necessarily re-execute -- it must be called from
       # renderFunc, which happens only if there's a cache miss.)
       userCacheKey(),
       function(userCacheKeyValue) {
@@ -562,7 +562,7 @@ renderCachedPlot <- function(expr,
 #' @param width,height Base width and height.
 #' @param growthRate Growth rate multiplier.
 #'
-#' @seealso This is to be used with [renderCachedPlot()].
+#' @seealso This is to be used with \code{\link{renderCachedPlot}}.
 #'
 #' @examples
 #' f <- sizeGrowthRatio(500, 500, 1.25)

R/render-plot.R

@@ -1,54 +1,48 @@
 #' Plot Output
 #'
-#' Renders a reactive plot that is suitable for assigning to an `output`
+#' Renders a reactive plot that is suitable for assigning to an \code{output}
 #' slot.
 #'
-#' The corresponding HTML output tag should be `div` or `img` and have
-#' the CSS class name `shiny-plot-output`.
+#' 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 `renderPlot` should return a ggplot
+#'   With ggplot2 graphics, the code in \code{renderPlot} should return a ggplot
 #'   object; if instead the code prints the ggplot2 object with something like
-#'   `print(p)`, then the coordinates for interactive graphics will not be
+#'   \code{print(p)}, then the coordinates for interactive graphics will not be
 #'   properly scaled to the data space.
 #'
-#'   See [plotOutput()] for more information about interactive plots.
+#'   See \code{\link{plotOutput}} for more information about interactive plots.
 #'
 #' @seealso For the corresponding client-side output function, and example
-#'   usage, see [plotOutput()]. For more details on how the plots are
-#'   generated, and how to control the output, see [plotPNG()].
-#'   [renderCachedPlot()] offers a way to cache generated plots to
-#'   expedite the rendering of identical plots.
+#'   usage, see \code{\link{plotOutput}}. For more details on how the plots are
+#'   generated, and how to control the output, see \code{\link{plotPNG}}.
 #'
 #' @param expr An expression that generates a plot.
-#' @param width,height Height and width can be specified in three ways:
-#'   * `"auto"`, the default, uses the size specified by [plotOutput()]
-#'      (i.e. the `offsetWidth`/`offsetHeight`` of the HTML element bound to
-#'      this plot.)
-#'  * An integer, defining the width/height in pixels.
-#'  * A function that returns the width/height in pixels (or `"auto"`).
-#'    The function is executed in a reactive context so that you can refer to
-#'    reactive values and expression to make the width/height reactive.
-#'
-#'   When rendering an inline plot, you must provide numeric values (in pixels)
-#'   to both \code{width} and \code{height}.
+#' @param width,height The width/height of the rendered plot, in pixels; or
+#'   \code{'auto'} to use the \code{offsetWidth}/\code{offsetHeight} of the HTML
+#'   element that is bound to this plot. You can also pass in a function that
+#'   returns the width/height in pixels or \code{'auto'}; in the body of the
+#'   function you may reference reactive values and functions. When rendering an
+#'   inline plot, you must provide numeric values (in pixels) to both
+#'   \code{width} and \code{height}.
 #' @param res Resolution of resulting plot, in pixels per inch. This value is
-#'   passed to [grDevices::png()]. Note that this affects the resolution of PNG
+#'   passed to \code{\link[grDevices]{png}}. Note that this affects the resolution of PNG
 #'   rendering in R; it won't change the actual ppi of the browser.
-#' @param ... Arguments to be passed through to [grDevices::png()].
+#' @param ... Arguments to be passed through to \code{\link[grDevices]{png}}.
 #'   These can be used to set the width, height, background color, etc.
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)? This
+#' @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 execOnResize If `FALSE` (the default), then when a plot is
-#'   resized, Shiny will *replay* the plot drawing commands with
-#'   [grDevices::replayPlot()] instead of re-executing `expr`.
+#' @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 `TRUE`.
+#'   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 [plotOutput()] when `renderPlot` is used in an
+#'   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, ...,
@@ -359,88 +353,62 @@ custom_print.ggplot <- function(x) {
 # With a faceted ggplot2 plot, the outer list contains two objects, each of
 # which represents one panel. In this example, there is one panelvar, but there
 # can be up to two of them.
-# p <- print(ggplot(mpg) + geom_point(aes(fl, cty), alpha = 0.2) + facet_wrap(~drv, scales = "free_x"))
-# str(getGgplotCoordmap(p, 500, 400, 72))
+# mtc <- mtcars
+# mtc$am <- factor(mtc$am)
+# p <- print(ggplot(mtc, aes(wt, mpg)) + geom_point() + facet_wrap(~ am))
+# str(getGgplotCoordmap(p, 400, 300, 72))
 # List of 2
-#  $ panels:List of 3
+#  $ panels:List of 2
 #   ..$ :List of 8
 #   .. ..$ panel     : num 1
 #   .. ..$ row       : int 1
 #   .. ..$ col       : int 1
 #   .. ..$ panel_vars:List of 1
-#   .. .. ..$ panelvar1: chr "4"
+#   .. .. ..$ panelvar1: Factor w/ 2 levels "0","1": 1
 #   .. ..$ log       :List of 2
 #   .. .. ..$ x: NULL
 #   .. .. ..$ y: NULL
-#   .. ..$ domain    :List of 5
-#   .. .. ..$ left           : num 0.4
-#   .. .. ..$ right          : num 4.6
-#   .. .. ..$ bottom         : num 7.7
-#   .. .. ..$ top            : num 36.3
-#   .. .. ..$ discrete_limits:List of 1
-#   .. .. .. ..$ x: chr [1:4] "d" "e" "p" "r"
+#   .. ..$ domain    :List of 4
+#   .. .. ..$ left  : num 1.32
+#   .. .. ..$ right : num 5.62
+#   .. .. ..$ bottom: num 9.22
+#   .. .. ..$ top   : num 35.1
 #   .. ..$ mapping   :List of 3
-#   .. .. ..$ x        : chr "fl"
-#   .. .. ..$ y        : chr "cty"
-#   .. .. ..$ panelvar1: chr "drv"
+#   .. .. ..$ x        : chr "wt"
+#   .. .. ..$ y        : chr "mpg"
+#   .. .. ..$ panelvar1: chr "am"
 #   .. ..$ range     :List of 4
 #   .. .. ..$ left  : num 33.3
-#   .. .. ..$ right : num 177
-#   .. .. ..$ bottom: num 448
+#   .. .. ..$ right : num 191
+#   .. .. ..$ bottom: num 328
 #   .. .. ..$ top   : num 23.1
 #   ..$ :List of 8
 #   .. ..$ panel     : num 2
 #   .. ..$ row       : int 1
 #   .. ..$ col       : int 2
 #   .. ..$ panel_vars:List of 1
-#   .. .. ..$ panelvar1: chr "f"
+#   .. .. ..$ panelvar1: Factor w/ 2 levels "0","1": 2
 #   .. ..$ log       :List of 2
 #   .. .. ..$ x: NULL
 #   .. .. ..$ y: NULL
-#   .. ..$ domain    :List of 5
-#   .. .. ..$ left           : num 0.4
-#   .. .. ..$ right          : num 5.6
-#   .. .. ..$ bottom         : num 7.7
-#   .. .. ..$ top            : num 36.3
-#   .. .. ..$ discrete_limits:List of 1
-#   .. .. .. ..$ x: chr [1:5] "c" "d" "e" "p" ...
+#   .. ..$ domain    :List of 4
+#   .. .. ..$ left  : num 1.32
+#   .. .. ..$ right : num 5.62
+#   .. .. ..$ bottom: num 9.22
+#   .. .. ..$ top   : num 35.1
 #   .. ..$ mapping   :List of 3
-#   .. .. ..$ x        : chr "fl"
-#   .. .. ..$ y        : chr "cty"
-#   .. .. ..$ panelvar1: chr "drv"
+#   .. .. ..$ x        : chr "wt"
+#   .. .. ..$ y        : chr "mpg"
+#   .. .. ..$ panelvar1: chr "am"
 #   .. ..$ range     :List of 4
-#   .. .. ..$ left  : num 182
-#   .. .. ..$ right : num 326
-#   .. .. ..$ bottom: num 448
-#   .. .. ..$ top   : num 23.1
-#   ..$ :List of 8
-#   .. ..$ panel     : num 3
-#   .. ..$ row       : int 1
-#   .. ..$ col       : int 3
-#   .. ..$ panel_vars:List of 1
-#   .. .. ..$ panelvar1: chr "r"
-#   .. ..$ log       :List of 2
-#   .. .. ..$ x: NULL
-#   .. .. ..$ y: NULL
-#   .. ..$ domain    :List of 5
-#   .. .. ..$ left           : num 0.4
-#   .. .. ..$ right          : num 3.6
-#   .. .. ..$ bottom         : num 7.7
-#   .. .. ..$ top            : num 36.3
-#   .. .. ..$ discrete_limits:List of 1
-#   .. .. .. ..$ x: chr [1:3] "e" "p" "r"
-#   .. ..$ mapping   :List of 3
-#   .. .. ..$ x        : chr "fl"
-#   .. .. ..$ y        : chr "cty"
-#   .. .. ..$ panelvar1: chr "drv"
-#   .. ..$ range     :List of 4
-#   .. .. ..$ left  : num 331
-#   .. .. ..$ right : num 475
-#   .. .. ..$ bottom: num 448
+#   .. .. ..$ left  : num 197
+#   .. .. ..$ right : num 355
+#   .. .. ..$ bottom: num 328
 #   .. .. ..$ top   : num 23.1
 #  $ dims  :List of 2
-#   ..$ width : num 500
-#   ..$ height: num 400
+#   ..$ width : num 400
+#   ..$ height: num 300
+
 
 getCoordmap <- function(x, width, height, res) {
   if (inherits(x, "ggplot_build_gtable")) {
@@ -602,9 +570,6 @@ find_panel_info_api <- function(b) {
       domain$bottom <- -domain$bottom
     }
 
-    domain <- add_discrete_limits(domain, xscale, "x")
-    domain <- add_discrete_limits(domain, yscale, "y")
-
     domain
   }
 
@@ -724,9 +689,6 @@ find_panel_info_non_api <- function(b, ggplot_format) {
       domain$bottom <- -domain$bottom
     }
 
-    domain <- add_discrete_limits(domain, xscale, "x")
-    domain <- add_discrete_limits(domain, yscale, "y")
-
     domain
   }
 
@@ -889,14 +851,6 @@ find_panel_info_non_api <- function(b, ggplot_format) {
   })
 }
 
-# Use public API for getting the unit's type (grid::unitType(), added in R 4.0)
-# https://github.com/wch/r-source/blob/f9b8a42/src/library/grid/R/unit.R#L179
-getUnitType <- function(u) {
-  tryCatch(
-    get("unitType", envir = asNamespace("grid"))(u),
-    error = function(e) attr(u, "unit", exact = TRUE)
-  )
-}
 
 # Given a gtable object, return the x and y ranges (in pixel dimensions)
 find_panel_ranges <- function(g, res) {
@@ -912,11 +866,11 @@ find_panel_ranges <- function(g, res) {
     if (inherits(x, "unit.list")) {
       # For ggplot2 <= 1.0.1
       vapply(x, FUN.VALUE = logical(1), function(u) {
-        isTRUE(getUnitType(u) == "null")
+        isTRUE(attr(u, "unit", exact = TRUE) == "null")
       })
     } else {
       # For later versions of ggplot2
-      getUnitType(x) == "null"
+      attr(x, "unit", exact = TRUE) == "null"
     }
   }
 
@@ -956,11 +910,7 @@ find_panel_ranges <- function(g, res) {
 
     # The plotting panels all are 'null' units.
     null_sizes <- rep(NA_real_, length(rel_sizes))
-    # Workaround for `[.unit` forbidding zero-length subsets
-    # https://github.com/wch/r-source/blob/f9b8a42/src/library/grid/R/unit.R#L448-L450
-    if (length(null_idx)) {
-      null_sizes[null_idx] <- as.numeric(rel_sizes[null_idx])
-    }
+    null_sizes[null_idx] <- as.numeric(rel_sizes[null_idx])
 
     # Total size allocated for panels is the total image size minus absolute
     # (non-panel) elements.
@@ -1045,23 +995,3 @@ find_panel_ranges <- function(g, res) {
     )
   })
 }
-
-# Remember the x/y limits of discrete axes. This info is
-# necessary to properly inverse map the numeric (i.e., trained)
-# positions back to the data scale, for example:
-# https://github.com/rstudio/shiny/pull/2410#issuecomment-487783828
-# https://github.com/rstudio/shiny/pull/2410#issuecomment-488100881
-#
-# Eventually, we may want to consider storing the entire ggplot2
-# object server-side and querying information from that object
-# as we need it...that's the only way we'll ever be able to
-# faithfully brush examples like this:
-# https://github.com/rstudio/shiny/issues/2411
-add_discrete_limits <- function(domain, scale, var = "x") {
-  var <- match.arg(var, c("x", "y"))
-  if (!is.function(scale$is_discrete) || !is.function(scale$get_limits)) return(domain)
-  if (scale$is_discrete()) {
-    domain$discrete_limits[[var]] <- scale$get_limits()
-  }
-  domain
-}

R/render-table.R

@@ -1,50 +1,50 @@
 #' Table Output
 #'
-#' Creates a reactive table that is suitable for assigning to an `output`
+#' Creates a reactive table that is suitable for assigning to an \code{output}
 #' slot.
 #'
-#' The corresponding HTML output tag should be `div` and have the CSS
-#' class name `shiny-html-output`.
+#' 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
-#'   [xtable::xtable()].
-#' @param striped,hover,bordered Logicals: if `TRUE`, apply the
+#'   \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 (`xs`
-#'   stands for "extra small", `s` for "small", `m` for "medium"
-#'   and `l` for "large").
+#' @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
-#'   `'l'`, `'c'` or `'r'`, then all columns will be,
-#'   respectively, left-, center- or right-aligned. Otherwise, `align`
+#'   \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
-#'   `rownames = TRUE`, this will be equal to `ncol()+1`), with
-#'   the *i*-th character specifying the alignment for the
-#'   *i*-th column (besides `'l'`, `'c'` and
-#'   `'r'`, `'?'` is also permitted - `'?'` is a placeholder
+#'   \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 `NULL`, then all numeric/integer columns (including
+#'   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 (`align = '?'` produces the
+#'   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 `digits` is set to a negative value, then the numeric
+#'   class). If \code{digits} is set to a negative value, then the numeric
 #'   columns will be displayed in scientific format with a precision of
-#'   `abs(digits)` digits.
+#'   \code{abs(digits)} digits.
 #' @param na The string to use in the table cells whose values are missing
-#'   (i.e. they either evaluate to `NA` or `NaN`).
-#' @param ... Arguments to be passed through to [xtable::xtable()]
-#'   and [xtable::print.xtable()].
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)?
+#'   (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 [tableOutput()] when `renderTable` is
+#'   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,

R/run-url.R

@@ -1,24 +1,24 @@
 #' Run a Shiny application from a URL
 #'
-#' `runUrl()` downloads and launches a Shiny application that is hosted at
+#' \code{runUrl()} downloads and launches a Shiny application that is hosted at
 #' a downloadable URL. The Shiny application must be saved in a .zip, .tar, or
 #' .tar.gz file. The Shiny application files must be contained in the root
 #' directory or a subdirectory in the archive. For example, the files might be
-#' `myapp/server.r` and `myapp/ui.r`. The functions `runGitHub()`
-#' and `runGist()` are based on `runUrl()`, using URL's from GitHub
-#' (<https://github.com>) and GitHub gists (<https://gist.github.com>),
+#' \code{myapp/server.r} and \code{myapp/ui.r}. The functions \code{runGitHub()}
+#' and \code{runGist()} are based on \code{runUrl()}, using URL's from GitHub
+#' (\url{https://github.com}) and GitHub gists (\url{https://gist.github.com}),
 #' respectively.
 #' @param url URL of the application.
-#' @param filetype The file type (`".zip"`, `".tar"`, or
-#'   `".tar.gz"`. Defaults to the file extension taken from the url.
+#' @param filetype The file type (\code{".zip"}, \code{".tar"}, or
+#'   \code{".tar.gz"}. Defaults to the file extension taken from the url.
 #' @param subdir A subdirectory in the repository that contains the app. By
 #'   default, this function will run an app from the top level of the repo, but
-#'   you can use a path such as `"inst/shinyapp"`.
-#' @param destdir Directory to store the downloaded application files. If `NULL`
+#'   you can use a path such as `\code{"inst/shinyapp"}.
+#' @param destdir Directory to store the downloaded application files. If \code{NULL}
 #'   (the default), the application files will be stored in a temporary directory
 #'   and removed when the app exits
-#' @param ... Other arguments to be passed to [runApp()], such as
-#'   `port` and `launch.browser`.
+#' @param ... Other arguments to be passed to \code{\link{runApp}()}, such as
+#'   \code{port} and \code{launch.browser}.
 #' @export
 #' @examples
 #' ## Only run this example in interactive R sessions
@@ -88,8 +88,8 @@ runUrl <- function(url, filetype = NULL, subdir = NULL, destdir = NULL, ...) {
 
 #' @rdname runUrl
 #' @param gist The identifier of the gist. For example, if the gist is
-#'   https://gist.github.com/jcheng5/3239667, then `3239667`,
-#'   `'3239667'`, and `'https://gist.github.com/jcheng5/3239667'` are
+#'   https://gist.github.com/jcheng5/3239667, then \code{3239667},
+#'   \code{'3239667'}, and \code{'https://gist.github.com/jcheng5/3239667'} are
 #'   all valid values.
 #' @export
 #' @examples
@@ -118,10 +118,10 @@ runGist <- function(gist, destdir = NULL, ...) {
 
 #' @rdname runUrl
 #' @param repo Name of the repository.
-#' @param username GitHub username. If `repo` is of the form
-#'   `"username/repo"`, `username` will be taken from `repo`.
+#' @param username GitHub username. If \code{repo} is of the form
+#'   \code{"username/repo"}, \code{username} will be taken from \code{repo}.
 #' @param ref Desired git reference. Could be a commit, tag, or branch name.
-#'   Defaults to `"master"`.
+#'   Defaults to \code{"master"}.
 #' @export
 #' @examples
 #' ## Only run this example in interactive R sessions

R/server-input-handlers.R

@@ -1,38 +1,39 @@
-# Create a map for input handlers and register the defaults.
-inputHandlers <- Map$new()
+# Create a map for input handlers and register the defaults. The Map object is
+# initialized in initializeInputHandlers, which is called from .onLoad().
+inputHandlers <- NULL
 
 #' Register an Input Handler
 #'
 #' Adds an input handler for data of this type. When called, Shiny will use the
 #' function provided to refine the data passed back from the client (after being
-#' deserialized by jsonlite) before making it available in the `input`
-#' variable of the `server.R` file.
+#' deserialized by jsonlite) before making it available in the \code{input}
+#' variable of the \code{server.R} file.
 #'
 #' This function will register the handler for the duration of the R process
-#' (unless Shiny is explicitly reloaded). For that reason, the `type` used
+#' (unless Shiny is explicitly reloaded). For that reason, the \code{type} used
 #' should be very specific to this package to minimize the risk of colliding
 #' with another Shiny package which might use this data type name. We recommend
 #' the format of "packageName.widgetName".
 #'
-#' Currently Shiny registers the following handlers: `shiny.matrix`,
-#' `shiny.number`, and `shiny.date`.
+#' Currently Shiny registers the following handlers: \code{shiny.matrix},
+#' \code{shiny.number}, and \code{shiny.date}.
 #'
-#' The `type` of a custom Shiny Input widget will be deduced using the
-#' `getType()` JavaScript function on the registered Shiny inputBinding.
-#' @param type The type for which the handler should be added --- should be a
+#' The \code{type} of a custom Shiny Input widget will be deduced using the
+#' \code{getType()} JavaScript function on the registered Shiny inputBinding.
+#' @param type The type for which the handler should be added -- should be a
 #' single-element character vector.
 #' @param fun The handler function. This is the function that will be used to
 #'   parse the data delivered from the client before it is available in the
-#'   `input` variable. The function will be called with the following three
+#'   \code{input} variable. The function will be called with the following three
 #'   parameters:
 #'    \enumerate{
 #'      \item{The value of this input as provided by the client, deserialized
 #'      using jsonlite.}
-#'      \item{The `shinysession` in which the input exists.}
+#'      \item{The \code{shinysession} in which the input exists.}
 #'      \item{The name of the input.}
 #'    }
-#' @param force If `TRUE`, will overwrite any existing handler without
-#' warning. If `FALSE`, will throw an error if this class already has
+#' @param force If \code{TRUE}, will overwrite any existing handler without
+#' warning. If \code{FALSE}, will throw an error if this class already has
 #' a handler defined.
 #' @examples
 #' \dontrun{
@@ -48,7 +49,7 @@ inputHandlers <- Map$new()
 #' }
 #'
 #' }
-#' @seealso [removeInputHandler()]
+#' @seealso \code{\link{removeInputHandler}}
 #' @export
 registerInputHandler <- function(type, fun, force=FALSE){
   if (inputHandlers$containsKey(type) && !force){
@@ -63,9 +64,9 @@ registerInputHandler <- function(type, fun, force=FALSE){
 #' for data of this type, the default jsonlite serialization will be used.
 #'
 #' @param type The type for which handlers should be removed.
-#' @return The handler previously associated with this `type`, if one
-#'   existed. Otherwise, `NULL`.
-#' @seealso [registerInputHandler()]
+#' @return The handler previously associated with this \code{type}, if one
+#'   existed. Otherwise, \code{NULL}.
+#' @seealso \code{\link{registerInputHandler}}
 #' @export
 removeInputHandler <- function(type){
   inputHandlers$remove(type)
@@ -103,8 +104,8 @@ applyInputHandler <- function(name, val, shinysession) {
 #' values.
 #'
 #' The raw input values should be in a named list. Some values may have names
-#' like `"x:shiny.date"`. This function would apply the `"shiny.date"`
-#' input handler to the value, and then rename the result to `"x"`, in the
+#' 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.
@@ -128,114 +129,118 @@ applyInputHandlers <- function(inputs, shinysession = getDefaultReactiveDomain()
 }
 
 
-# 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, ...) {
-  if (length(data) == 0)
-    return(matrix(nrow=0, ncol=0))
+initializeInputHandlers <- function() {
+  inputHandlers <<- Map$new()
 
-  m <- matrix(unlist(lapply(data, function(x) {
-    sapply(x, function(y) {
-      ifelse(is.null(y), NA, y)
-    })
-  })), nrow = length(data[[1]]), ncol = length(data))
-  return(m)
-})
+  # 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, ...) {
+    if (length(data) == 0)
+      return(matrix(nrow=0, ncol=0))
 
-
-registerInputHandler("shiny.number", function(val, ...){
-  ifelse(is.null(val), NA, val)
-})
-
-registerInputHandler("shiny.password", function(val, shinysession, name) {
-  # Mark passwords as not serializable
-  setSerializer(name, 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)
-
-  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$message)
-      res <<- as.Date(rep(NA, length(datelist)))
-    }
-  )
-
-  res
-})
-
-registerInputHandler("shiny.datetime", function(val, ...){
-  # First replace NULLs with NA, then convert to POSIXct vector
-  times <- lapply(val, function(x) {
-    if (is.null(x)) NA
-    else x
+    m <- matrix(unlist(lapply(data, function(x) {
+      sapply(x, function(y) {
+        ifelse(is.null(y), NA, y)
+      })
+    })), nrow = length(data[[1]]), ncol = length(data))
+    return(m)
   })
-  as.POSIXct(unlist(times), origin = "1970-01-01", tz = "UTC")
-})
-
-registerInputHandler("shiny.action", function(val, shinysession, name) {
-  # mark up the action button value with a special class so we can recognize it later
-  class(val) <- c(class(val), "shinyActionButtonValue")
-  val
-})
-
-registerInputHandler("shiny.file", function(val, shinysession, name) {
-  # This function is only used when restoring a Shiny fileInput. When a file is
-  # uploaded the usual way, it takes a different code path and won't hit this
-  # function.
-  if (is.null(val))
-    return(NULL)
-
-  # The data will be a named list of lists; convert to a data frame.
-  val <- as.data.frame(lapply(val, unlist), stringsAsFactors = FALSE)
-
-  # `val$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`.
-  setSerializer(name, serializerFileInput)
-
-  snapshotPreprocessInput(name, snapshotPreprocessorFileInput)
-
-  val
-})
 
 
-# to be used with !!!answer
-registerInputHandler("shiny.symbolList", function(val, ...) {
-  if (is.null(val)) {
-    list()
-  } else {
-    lapply(val, as.symbol)
-  }
-})
-# to be used with !!answer
-registerInputHandler("shiny.symbol", function(val, ...) {
-  if (is.null(val) || identical(val, "")) {
-    NULL
-  } else {
-    as.symbol(val)
-  }
-})
+  registerInputHandler("shiny.number", function(val, ...){
+    ifelse(is.null(val), NA, val)
+  })
+
+  registerInputHandler("shiny.password", function(val, shinysession, name) {
+    # Mark passwords as not serializable
+    setSerializer(name, 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)
+
+    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$message)
+        res <<- as.Date(rep(NA, length(datelist)))
+      }
+    )
+
+    res
+  })
+
+  registerInputHandler("shiny.datetime", function(val, ...){
+    # First replace NULLs with NA, then convert to POSIXct vector
+    times <- lapply(val, function(x) {
+      if (is.null(x)) NA
+      else x
+    })
+    as.POSIXct(unlist(times), origin = "1970-01-01", tz = "UTC")
+  })
+
+  registerInputHandler("shiny.action", function(val, shinysession, name) {
+    # mark up the action button value with a special class so we can recognize it later
+    class(val) <- c(class(val), "shinyActionButtonValue")
+    val
+  })
+
+  registerInputHandler("shiny.file", function(val, shinysession, name) {
+    # This function is only used when restoring a Shiny fileInput. When a file is
+    # uploaded the usual way, it takes a different code path and won't hit this
+    # function.
+    if (is.null(val))
+      return(NULL)
+
+    # The data will be a named list of lists; convert to a data frame.
+    val <- as.data.frame(lapply(val, unlist), stringsAsFactors = FALSE)
+
+    # `val$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`.
+    setSerializer(name, serializerFileInput)
+
+    snapshotPreprocessInput(name, snapshotPreprocessorFileInput)
+
+    val
+  })
+
+
+  # to be used with !!!answer
+  registerInputHandler("shiny.symbolList", function(val, ...) {
+    if (is.null(val)) {
+      list()
+    } else {
+      lapply(val, as.symbol)
+    }
+  })
+  # to be used with !!answer
+  registerInputHandler("shiny.symbol", function(val, ...) {
+    if (is.null(val) || identical(val, "")) {
+      NULL
+    } else {
+      as.symbol(val)
+    }
+  })
+}

R/server.R

@@ -1,7 +1,9 @@
 #' @include server-input-handlers.R
 
-appsByToken <- Map$new()
-appsNeedingFlush <- Map$new()
+# These Map objects are initialized in .onLoad() because Maps based on fastmap
+# can't be saved in one R session and loaded in another.
+appsByToken <- NULL
+appsNeedingFlush <- NULL
 
 # Provide a character representation of the WS that can be used
 # as a key in a Map.
@@ -31,46 +33,24 @@ registerClient <- function(client) {
 
 #' Resource Publishing
 #'
-#' Add, remove, or list directory of static resources to Shiny's web server,
-#' with the given path prefix. Primarily intended for package authors to make
-#' supporting JavaScript/CSS files available to their components.
-#'
-#' Shiny provides two ways of serving static files (i.e., resources):
-#'
-#' 1. Static files under the `www/` directory are automatically made available
-#' under a request path that begins with `/`.
-#' 2. `addResourcePath()` makes static files in a `directoryPath` available
-#' under a request path that begins with `prefix`.
-#'
-#' The second approach is primarily intended for package authors to make
-#' supporting JavaScript/CSS files available to their components.
-#'
-#' Tools for managing static resources published by Shiny's web server:
-#'  * `addResourcePath()` adds a directory of static resources.
-#'  * `resourcePaths()` lists the currently active resource mappings.
-#'  * `removeResourcePath()` removes a directory of static resources.
+#' Adds a directory of static resources to Shiny's web server, with the given
+#' path prefix. Primarily intended for package authors to make supporting
+#' JavaScript/CSS files available to their components.
 #'
 #' @param prefix The URL prefix (without slashes). Valid characters are a-z,
-#'   A-Z, 0-9, hyphen, period, and underscore. For example, a value of 'foo'
-#'   means that any request paths that begin with '/foo' will be mapped to the
-#'   given directory.
+#'   A-Z, 0-9, hyphen, period, and underscore.
+#'   For example, a value of 'foo' means that any request paths that begin with
+#'   '/foo' will be mapped to the given directory.
 #' @param directoryPath The directory that contains the static resources to be
 #'   served.
 #'
-#' @rdname resourcePaths
-#' @seealso [singleton()]
+#' @seealso \code{\link{singleton}}
 #'
 #' @examples
 #' addResourcePath('datasets', system.file('data', package='datasets'))
-#' resourcePaths()
-#' removeResourcePath('datasets')
-#' resourcePaths()
-#'
-#' # make sure all resources are removed
-#' lapply(names(resourcePaths()), removeResourcePath)
 #' @export
 addResourcePath <- function(prefix, directoryPath) {
-  if (length(prefix) != 1) stop("prefix must be of length 1")
+  prefix <- prefix[1]
   if (!grepl('^[a-z0-9\\-_][a-z0-9\\-_.]*$', prefix, ignore.case = TRUE, perl = TRUE)) {
     stop("addResourcePath called with invalid prefix; please see documentation")
   }
@@ -85,26 +65,6 @@ addResourcePath <- function(prefix, directoryPath) {
     }
   )
 
-  # # Often times overwriting a resource path is "what you want",
-  # # but sometimes it can lead to difficult to diagnose issues
-  # # (e.g. an implict dependency might set a resource path that
-  # # conflicts with what you, the app author, are trying to register)
-  # # Note that previous versions of shiny used to warn about this case,
-  # # but it was eventually removed since it caused confusion (#567).
-  # # It seems a good compromise is to throw a more information message.
-  # if (getOption("shiny.resourcePathChanges", FALSE) &&
-  #     prefix %in% names(.globals$resourcePaths)) {
-  #   existingPath <- .globals$resourcePaths[[prefix]]$path
-  #   if (normalizedPath != existingPath) {
-  #     message(
-  #       "The resource path '", prefix, "' used to point to ",
-  #       existingPath, ", but it now points to ", normalizedPath, ". ",
-  #       "If your app doesn't work as expected, you may want to ",
-  #       "choose a different prefix name."
-  #     )
-  #   }
-  # }
-
   # If a shiny app is currently running, dynamically register this path with
   # the corresponding httpuv server object.
   if (!is.null(getShinyOption("server")))
@@ -124,33 +84,6 @@ addResourcePath <- function(prefix, directoryPath) {
   )
 }
 
-#' @rdname resourcePaths
-#' @export
-resourcePaths <- function() {
-  urls <- names(.globals$resourcePaths)
-  paths <- vapply(.globals$resourcePaths, function(x) x$path, character(1))
-  stats::setNames(paths, urls)
-}
-
-hasResourcePath <- function(prefix) {
-  prefix %in% names(resourcePaths())
-}
-
-#' @rdname resourcePaths
-#' @export
-removeResourcePath <- function(prefix) {
-  if (length(prefix) > 1) stop("`prefix` must be of length 1.")
-  if (!hasResourcePath(prefix)) {
-    warning("Resource ", prefix, " not found.")
-    return(invisible(FALSE))
-  }
-  .globals$resourcePaths[[prefix]] <- NULL
-  .globals$resources[[prefix]] <- NULL
-  invisible(TRUE)
-}
-
-
-
 # This function handles any GET request with two or more path elements where the
 # first path element matches a prefix that was previously added using
 # addResourcePath().
@@ -201,23 +134,23 @@ resourcePathHandler <- function(req) {
 #'
 #' Defines the server-side logic of the Shiny application. This generally
 #' involves creating functions that map user inputs to various kinds of output.
-#' In older versions of Shiny, it was necessary to call `shinyServer()` in
-#' the `server.R` file, but this is no longer required as of Shiny 0.10.
-#' Now the `server.R` file may simply return the appropriate server
+#' In older versions of Shiny, it was necessary to call \code{shinyServer()} in
+#' the \code{server.R} file, but this is no longer required as of Shiny 0.10.
+#' Now the \code{server.R} file may simply return the appropriate server
 #' function (as the last expression in the code), without calling
-#' `shinyServer()`.
+#' \code{shinyServer()}.
 #'
-#' Call `shinyServer` from your application's `server.R`
+#' Call \code{shinyServer} from your application's \code{server.R}
 #' file, passing in a "server function" that provides the server-side logic of
 #' your application.
 #'
 #' The server function will be called when each client (web browser) first loads
-#' the Shiny application's page. It must take an `input` and an
-#' `output` parameter. Any return value will be ignored. It also takes an
-#' optional `session` parameter, which is used when greater control is
+#' the Shiny application's page. It must take an \code{input} and an
+#' \code{output} parameter. Any return value will be ignored. It also takes an
+#' optional \code{session} parameter, which is used when greater control is
 #' needed.
 #'
-#' See the [tutorial](http://rstudio.github.com/shiny/tutorial/) for more
+#' See the \href{http://rstudio.github.com/shiny/tutorial/}{tutorial} for more
 #' on how to write a server function.
 #'
 #' @param func The server function for this application. See the details section
@@ -244,7 +177,6 @@ resourcePathHandler <- function(req) {
 #' }
 #' }
 #' @export
-#' @keywords internal
 shinyServer <- function(func) {
   .globals$server <- list(func)
   invisible(func)
@@ -279,8 +211,6 @@ decodeMessage <- function(data) {
   return(mainMessage)
 }
 
-autoReloadCallbacks <- Callbacks$new()
-
 createAppHandlers <- function(httpHandlers, serverFuncSource) {
   appvars <- new.env()
   appvars$server <- NULL
@@ -306,22 +236,6 @@ createAppHandlers <- function(httpHandlers, serverFuncSource) {
         return(TRUE)
       }
 
-      if (identical(ws$request$PATH_INFO, "/autoreload/")) {
-        if (!getOption("shiny.autoreload", FALSE)) {
-          ws$close()
-          return(TRUE)
-        }
-
-        callbackHandle <- autoReloadCallbacks$register(function() {
-          ws$send("autoreload")
-          ws$close()
-        })
-        ws$onClose(function() {
-          callbackHandle()
-        })
-        return(TRUE)
-      }
-
       if (!is.null(getOption("shiny.observer.error", NULL))) {
         warning(
           call. = FALSE,
@@ -546,49 +460,6 @@ startApp <- function(appObj, port, host, quiet) {
     ),
     .globals$resourcePaths
   )
-
-  # throw an informative warning if a subdirectory of the
-  # app's www dir conflicts with another resource prefix
-  wwwDir <- httpuvApp$staticPaths[["/"]]$path
-  if (length(wwwDir)) {
-    # although httpuv allows for resource prefixes like 'foo/bar',
-    # we won't worry about conflicts in sub-sub directories since
-    # addResourcePath() currently doesn't allow it
-    wwwSubDirs <- list.dirs(wwwDir, recursive = FALSE, full.names = FALSE)
-    resourceConflicts <- intersect(wwwSubDirs, names(httpuvApp$staticPaths))
-    if (length(resourceConflicts)) {
-      warning(
-        "Found subdirectories of your app's www/ directory that ",
-        "conflict with other resource URL prefixes. ",
-        "Consider renaming these directories: '",
-        paste0("www/", resourceConflicts, collapse = "', '"), "'",
-        call. = FALSE
-      )
-    }
-  }
-
-  # check for conflicts in each pairwise combinations of resource mappings
-  checkResourceConflict <- function(paths) {
-    if (length(paths) < 2) return(NULL)
-    # ensure paths is a named character vector: c(resource_path = local_path)
-    paths <- vapply(paths, function(x) if (inherits(x, "staticPath")) x$path else x, character(1))
-    # get all possible pairwise combinations of paths
-    pair_indices <- utils::combn(length(paths), 2, simplify = FALSE)
-    lapply(pair_indices, function(x) {
-      p1 <- paths[x[1]]
-      p2 <- paths[x[2]]
-      if (identical(names(p1), names(p2)) && (p1 != p2)) {
-        warning(
-          "Found multiple local file paths pointing the same resource prefix: ", names(p1), ". ",
-          "If you run into resource-related issues (e.g. 404 requests), consider ",
-          "using `addResourcePath()` and/or `removeResourcePath()` to manage resource mappings.",
-          call. = FALSE
-        )
-      }
-    })
-  }
-  checkResourceConflict(httpuvApp$staticPaths)
-
   httpuvApp$staticPathOptions <- httpuv::staticPathOptions(
     html_charset = "utf-8",
     headers = list("X-UA-Compatible" = "IE=edge,chrome=1"),
@@ -651,8 +522,8 @@ serviceApp <- function() {
 #'
 #' This function tests whether a Shiny application is currently running.
 #'
-#' @return `TRUE` if a Shiny application is currently running. Otherwise,
-#'   `FALSE`.
+#' @return \code{TRUE} if a Shiny application is currently running. Otherwise,
+#'   \code{FALSE}.
 #' @export
 isRunning <- function() {
   .globals$running
@@ -664,44 +535,44 @@ isRunning <- function() {
 #' to stop the application (usually by pressing Ctrl+C or Esc).
 #'
 #' The host parameter was introduced in Shiny 0.9.0. Its default value of
-#' `"127.0.0.1"` means that, contrary to previous versions of Shiny, only
+#' \code{"127.0.0.1"} means that, contrary to previous versions of Shiny, only
 #' the current machine can access locally hosted Shiny apps. To allow other
-#' clients to connect, use the value `"0.0.0.0"` instead (which was the
+#' clients to connect, use the value \code{"0.0.0.0"} instead (which was the
 #' value that was hard-coded into Shiny in 0.8.0 and earlier).
 #'
 #' @param appDir The application to run. Should be one of the following:
 #'   \itemize{
-#'   \item A directory containing `server.R`, plus, either `ui.R` or
-#'    a `www` directory that contains the file `index.html`.
-#'   \item A directory containing `app.R`.
-#'   \item An `.R` file containing a Shiny application, ending with an
+#'   \item A directory containing \code{server.R}, plus, either \code{ui.R} or
+#'    a \code{www} directory that contains the file \code{index.html}.
+#'   \item A directory containing \code{app.R}.
+#'   \item An \code{.R} file containing a Shiny application, ending with an
 #'    expression that produces a Shiny app object.
-#'   \item A list with `ui` and `server` components.
-#'   \item A Shiny app object created by [shinyApp()].
+#'   \item A list with \code{ui} and \code{server} components.
+#'   \item A Shiny app object created by \code{\link{shinyApp}}.
 #'   }
 #' @param port The TCP port that the application should listen on. If the
-#'   `port` is not specified, and the `shiny.port` option is set (with
-#'   `options(shiny.port = XX)`), then that port will be used. Otherwise,
+#'   \code{port} is not specified, and the \code{shiny.port} option is set (with
+#'   \code{options(shiny.port = XX)}), then that port will be used. Otherwise,
 #'   use a random port.
 #' @param launch.browser If true, the system's default web browser will be
 #'   launched automatically after the app is started. Defaults to true in
 #'   interactive sessions only. This value of this parameter can also be a
 #'   function to call with the application's URL.
 #' @param host The IPv4 address that the application should listen on. Defaults
-#'   to the `shiny.host` option, if set, or `"127.0.0.1"` if not. See
+#'   to the \code{shiny.host} option, if set, or \code{"127.0.0.1"} if not. See
 #'   Details.
 #' @param workerId Can generally be ignored. Exists to help some editions of
 #'   Shiny Server Pro route requests to the correct process.
 #' @param quiet Should Shiny status messages be shown? Defaults to FALSE.
 #' @param display.mode The mode in which to display the application. If set to
-#'   the value `"showcase"`, shows application code and metadata from a
-#'   `DESCRIPTION` file in the application directory alongside the
-#'   application. If set to `"normal"`, displays the application normally.
-#'   Defaults to `"auto"`, which displays the application in the mode given
-#'   in its `DESCRIPTION` file, if any.
+#'   the value \code{"showcase"}, shows application code and metadata from a
+#'   \code{DESCRIPTION} file in the application directory alongside the
+#'   application. If set to \code{"normal"}, displays the application normally.
+#'   Defaults to \code{"auto"}, which displays the application in the mode given
+#'   in its \code{DESCRIPTION} file, if any.
 #' @param test.mode Should the application be launched in test mode? This is
 #'   only used for recording or running automated tests. Defaults to the
-#'   `shiny.testmode` option, or FALSE if the option is not set.
+#'   \code{shiny.testmode} option, or FALSE if the option is not set.
 #'
 #' @examples
 #' \dontrun{
@@ -1005,6 +876,7 @@ runApp <- function(appDir=getwd(),
     captureStackTraces({
       while (!.globals$stopped) {
         ..stacktracefloor..(serviceApp())
+        Sys.sleep(0.001)
       }
     })
   )
@@ -1021,10 +893,10 @@ runApp <- function(appDir=getwd(),
 #' Stop the currently running Shiny app
 #'
 #' Stops the currently running Shiny app, returning control to the caller of
-#' [runApp()].
+#' \code{\link{runApp}}.
 #'
 #' @param returnValue The value that should be returned from
-#'   [runApp()].
+#'   \code{\link{runApp}}.
 #' @export
 stopApp <- function(returnValue = invisible()) {
   # reterror will indicate whether retval is an error (i.e. it should be passed
@@ -1053,7 +925,7 @@ stopApp <- function(returnValue = invisible()) {
 #'
 #' Launch Shiny example applications, and optionally, your system's web browser.
 #'
-#' @param example The name of the example to run, or `NA` (the default) to
+#' @param example The name of the example to run, or \code{NA} (the default) to
 #'   list the available examples.
 #' @param port The TCP port that the application should listen on. Defaults to
 #'   choosing a random port.
@@ -1061,9 +933,9 @@ stopApp <- function(returnValue = invisible()) {
 #'   launched automatically after the app is started. Defaults to true in
 #'   interactive sessions only.
 #' @param host The IPv4 address that the application should listen on. Defaults
-#'   to the `shiny.host` option, if set, or `"127.0.0.1"` if not.
+#'   to the \code{shiny.host} option, if set, or \code{"127.0.0.1"} if not.
 #' @param display.mode The mode in which to display the example. Defaults to
-#'   `showcase`, but may be set to `normal` to see the example without
+#'   \code{showcase}, but may be set to \code{normal} to see the example without
 #'   code or commentary.
 #'
 #' @examples
@@ -1110,21 +982,21 @@ runExample <- function(example=NA,
 
 #' Run a gadget
 #'
-#' Similar to `runApp`, but handles `input$cancel` automatically, and
+#' Similar to \code{runApp}, but handles \code{input$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
-#'   [`shinyApp()`][shiny] et al, or, a UI object.
-#' @param server Ignored if `app` is a Shiny app object; otherwise, passed
-#'   along to `shinyApp` (i.e. `shinyApp(ui = app, server = server)`).
-#' @param port See [`runApp()`][shiny].
+#'   \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
-#'   [viewer()] functions.
-#' @param stopOnCancel If `TRUE` (the default), then an `observeEvent`
-#'   is automatically created that handles `input$cancel` by calling
-#'   `stopApp()` with an error. Pass `FALSE` if you want to handle
-#'   `input$cancel` yourself.
+#'   \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
@@ -1189,10 +1061,10 @@ decorateServerFunc <- function(appobj, serverFunc) {
 #' 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
-#' [utils::browseURL()]).
+#' \code{\link[utils]{browseURL}}).
 #'
-#' @return A function that takes a single `url` parameter, suitable for
-#'   passing as the `viewer` argument of [runGadget()].
+#' @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
@@ -1200,8 +1072,8 @@ 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 `NULL`, use the existing viewer pane
-#'   size. If `"maximize"`, use the maximum available vertical space.
+#'   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) {
@@ -1230,7 +1102,7 @@ dialogViewer <- function(dialogName, width = 600, height = 600) {
   }
 }
 
-#' @param browser See [utils::browseURL()].
+#' @param browser See \code{\link[utils]{browseURL}}.
 #' @rdname viewer
 #' @export
 browserViewer <- function(browser = getOption("browser")) {
@@ -1248,5 +1120,5 @@ inShinyServer <- function() {
 # This check was moved out of the main function body because of an issue with
 # the RStudio debugger. (#1474)
 isEmptyMessage <- function(msg) {
-  identical(as.raw(c(0x03, 0xe9)), msg)
+  identical(charToRaw("\003\xe9"), msg)
 }

R/shiny-options.R

@@ -16,103 +16,20 @@ getShinyOption <- function(name, default = NULL) {
 
 #' Get or set Shiny options
 #'
-#' `getShinyOption()` retrieves the value of a Shiny option. `shinyOptions()`
-#' sets the value of Shiny options; it can also be used to return a list of all
-#' currently-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.
 #'
-#' @section Scope:
-#' There is a global option set which is available by default. When a Shiny
-#' application is run with [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
+#' 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.
 #'
-#' @section Options:
-#' There are a number of global options that affect Shiny's behavior. These can
-#' be set globally with `options()` or locally (for a single app) with
-#' `shinyOptions()`.
+#' @param ... Options to set, with the form \code{name = value}.
 #'
-#' \describe{
-#' \item{shiny.autoreload (defaults to `FALSE`)}{If `TRUE` when a Shiny app is launched, the
-#'   app directory will be continually monitored for changes to files that
-#'   have the extensions: r, htm, html, js, css, png, jpg, jpeg, gif. If any
-#'   changes are detected, all connected Shiny sessions are reloaded. This
-#'   allows for fast feedback loops when tweaking Shiny UI.
-#'
-#'   Since monitoring for changes is expensive (we simply poll for last
-#'   modified times), 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 default polling interval is 500 milliseconds. You can change this
-#'   by setting e.g. `options(shiny.autoreload.interval = 2000)` (every
-#'   two seconds).}
-#' \item{shiny.deprecation.messages (defaults to `TRUE`)}{This controls whether messages for
-#'   deprecated functions in Shiny will be printed. See
-#'   [shinyDeprecated()] for more information.}
-#' \item{shiny.error (defaults to `NULL`)}{This can be a function which is called when an error
-#'   occurs. For example, `options(shiny.error=recover)` will result a
-#'   the debugger prompt when an error occurs.}
-#' \item{shiny.fullstacktrace (defaults to `FALSE`)}{Controls whether "pretty" (`FALSE`) or full
-#'   stack traces (`TRUE`) are dumped to the console when errors occur during Shiny app execution.
-#'   Pretty stack traces attempt to only show user-supplied code, but this pruning can't always
-#'   be done 100% correctly.}
-#' \item{shiny.host (defaults to `"127.0.0.1"`)}{The IP address that Shiny should listen on. See
-#'   [runApp()] for more information.}
-#' \item{shiny.jquery.version (defaults to `3`)}{The major version of jQuery to use.
-#' Currently only values of `3` or `1` are supported. If `1`, then jQuery 1.12.4 is used. If `3`,
-#' then jQuery 3.4.1 is used.}
-#' \item{shiny.json.digits (defaults to `16`)}{The number of digits to use when converting
-#'   numbers to JSON format to send to the client web browser.}
-#' \item{shiny.launch.browser (defaults to `interactive()`)}{A boolean which controls the default behavior
-#'   when an app is run. See [runApp()] for more information.}
-#' \item{shiny.maxRequestSize (defaults to 5MB)}{This is a number which specifies the maximum
-#'   web request size, which serves as a size limit for file uploads.}
-#' \item{shiny.minified (defaults to `TRUE`)}{By default
-#'   Whether or not to include Shiny's JavaScript as a minified (`shiny.min.js`)
-#'   or un-minified (`shiny.js`) file. The un-minified version is larger,
-#'   but can be helpful for development and debugging.}
-#' \item{shiny.port (defaults to a random open port)}{A port number that Shiny will listen on. See
-#'   [runApp()] for more information.}
-#' \item{shiny.reactlog (defaults to `FALSE`)}{If `TRUE`, enable logging of reactive events,
-#'   which can be viewed later with the [reactlogShow()] function.
-#'   This incurs a substantial performance penalty and should not be used in
-#'   production.}
-#' \item{shiny.sanitize.errors (defaults to `FALSE`)}{If `TRUE`, then normal errors (i.e.
-#'   errors not wrapped in `safeError`) won't show up in the app; a simple
-#'   generic error message is printed instead (the error and strack trace printed
-#'   to the console remain unchanged). If you want to sanitize errors in general, but you DO want a
-#'   particular error `e` to get displayed to the user, then set this option
-#'   to `TRUE` and use `stop(safeError(e))` for errors you want the
-#'   user to see.}
-#' \item{shiny.stacktraceoffset (defaults to `TRUE`)}{If `TRUE`, then Shiny's printed stack
-#'   traces will display srcrefs one line above their usual location. This is
-#'   an arguably more intuitive arrangement for casual R users, as the name
-#'   of a function appears next to the srcref where it is defined, rather than
-#'   where it is currently being called from.}
-#' \item{shiny.suppressMissingContextError (defaults to `FALSE`)}{Normally, invoking a reactive
-#'   outside of a reactive context (or [isolate()]) results in
-#'   an error. If this is `TRUE`, don't error in these cases. This
-#'   should only be used for debugging or demonstrations of reactivity at the
-#'   console.}
-#' \item{shiny.testmode (defaults to `FALSE`)}{If `TRUE`, then various features for testing Shiny
-#'   applications are enabled.}
-#' \item{shiny.trace (defaults to `FALSE`)}{Print messages sent between the R server and the web
-#'   browser client to the R console. This is useful for debugging. Possible
-#'   values are `"send"` (only print messages sent to the client),
-#'   `"recv"` (only print messages received by the server), `TRUE`
-#'   (print all messages), or `FALSE` (default; don't print any of these
-#'   messages).}
-#' \item{shiny.usecairo (defaults to `TRUE`)}{This is used to disable graphical rendering by the
-#'   Cairo package, if it is installed. See [plotPNG()] for more
-#'   information.}
-#' }
-#' @param ... Options to set, with the form `name = value`.
-#' @aliases shiny-options
 #' @examples
 #' \dontrun{
 #' shinyOptions(myOption = 10)

R/shiny.R

@@ -8,11 +8,11 @@ NULL
 #' prebuilt widgets make it possible to build beautiful, responsive, and
 #' powerful applications with minimal effort.
 #'
-#' The Shiny tutorial at <http://shiny.rstudio.com/tutorial/> explains
+#' The Shiny tutorial at \url{http://shiny.rstudio.com/tutorial/} explains
 #' the framework in depth, walks you through building a simple application, and
 #' includes extensive annotated examples.
 #'
-#' @seealso [shiny-options] for documentation about global options.
+#' @seealso \link{shiny-options} for documentation about global options.
 #'
 #' @name shiny-package
 #' @aliases shiny
@@ -28,6 +28,91 @@ NULL
 #' @import methods
 NULL
 
+
+#' Global options for Shiny
+#'
+#' There are a number of global options that affect Shiny's behavior. These can
+#' be set with (for example) \code{options(shiny.trace=TRUE)}.
+#'
+#' \describe{
+#'   \item{shiny.launch.browser}{A boolean which controls the default behavior
+#'     when an app is run. See \code{\link{runApp}} for more information.}
+#'   \item{shiny.port}{A port number that Shiny will listen on. See
+#'     \code{\link{runApp}} for more information.}
+#'   \item{shiny.trace}{Print messages sent between the R server and the web
+#'     browser client to the R console. This is useful for debugging. Possible
+#'     values are \code{"send"} (only print messages sent to the client),
+#'     \code{"recv"} (only print messages received by the server), \code{TRUE}
+#'     (print all messages), or \code{FALSE} (default; don't print any of these
+#'     messages).}
+#'   \item{shiny.autoreload}{If \code{TRUE} when a Shiny app is launched, the
+#'     app directory will be continually monitored for changes to files that
+#'     have the extensions: r, htm, html, js, css, png, jpg, jpeg, gif. If any
+#'     changes are detected, all connected Shiny sessions are reloaded. This
+#'     allows for fast feedback loops when tweaking Shiny UI.
+#'
+#'     Since monitoring for changes is expensive (we simply poll for last
+#'     modified times), 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:
+#'     \code{options(shiny.autoreload.pattern = glob2rx("ui.R"))}
+#'
+#'     The default polling interval is 500 milliseconds. You can change this
+#'     by setting e.g. \code{options(shiny.autoreload.interval = 2000)} (every
+#'     two seconds).}
+#'   \item{shiny.reactlog}{If \code{TRUE}, enable logging of reactive events,
+#'     which can be viewed later with the \code{\link{reactlogShow}} function.
+#'     This incurs a substantial performance penalty and should not be used in
+#'     production.}
+#'   \item{shiny.usecairo}{This is used to disable graphical rendering by the
+#'     Cairo package, if it is installed. See \code{\link{plotPNG}} for more
+#'     information.}
+#'   \item{shiny.maxRequestSize}{This is a number which specifies the maximum
+#'     web request size, which serves as a size limit for file uploads. If
+#'     unset, the maximum request size defaults to 5MB.}
+#'   \item{shiny.suppressMissingContextError}{Normally, invoking a reactive
+#'     outside of a reactive context (or \code{\link{isolate}()}) results in
+#'     an error. If this is \code{TRUE}, don't error in these cases. This
+#'     should only be used for debugging or demonstrations of reactivity at the
+#'     console.}
+#'   \item{shiny.host}{The IP address that Shiny should listen on. See
+#'     \code{\link{runApp}} for more information.}
+#'   \item{shiny.json.digits}{The number of digits to use when converting
+#'     numbers to JSON format to send to the client web browser.}
+#'   \item{shiny.minified}{If this is \code{TRUE} or unset (the default), then
+#'     Shiny will use minified JavaScript (\code{shiny.min.js}). If
+#'     \code{FALSE}, then Shiny will use the un-minified JavaScript
+#'     (\code{shiny.js}); this can be useful during development.}
+#'   \item{shiny.error}{This can be a function which is called when an error
+#'     occurs. For example, \code{options(shiny.error=recover)} will result a
+#'     the debugger prompt when an error occurs.}
+#'   \item{shiny.table.class}{CSS class names to use for tables.}
+#'   \item{shiny.deprecation.messages}{This controls whether messages for
+#'     deprecated functions in Shiny will be printed. See
+#'     \code{\link{shinyDeprecated}} for more information.}
+#'   \item{shiny.fullstacktrace}{Controls whether "pretty" or full stack traces
+#'     are dumped to the console when errors occur during Shiny app execution.
+#'     The default is \code{FALSE} (pretty stack traces).}
+#'   \item{shiny.stacktraceoffset}{If \code{TRUE}, then Shiny's printed stack
+#'     traces will display srcrefs one line above their usual location. This is
+#'     an arguably more intuitive arrangement for casual R users, as the name
+#'     of a function appears next to the srcref where it is defined, rather than
+#'     where it is currently being called from.}
+#'   \item{shiny.sanitize.errors}{If \code{TRUE}, then normal errors (i.e.
+#'     errors not wrapped in \code{safeError}) won't show up in the app; a simple
+#'     generic error message is printed instead (the error and strack trace printed
+#'     to the console remain unchanged). The default is \code{FALSE} (unsanitized
+#'     errors).If you want to sanitize errors in general, but you DO want a
+#'     particular error \code{e} to get displayed to the user, then set this option
+#'     to \code{TRUE} and use \code{stop(safeError(e))} for errors you want the
+#'     user to see.}
+#'   \item{shiny.testmode}{If \code{TRUE}, then enable features for testing Shiny
+#'     applications. If \code{FALSE} (the default), do not enable those features.
+#'   }
+#' }
+#' @name shiny-options
+NULL
 createUniqueId <- function(bytes, prefix = "", suffix = "") {
   withPrivateSeed({
     paste(
@@ -94,78 +179,78 @@ workerId <- local({
 
 #' Session object
 #'
-#' Shiny server functions can optionally include `session` as a parameter
-#' (e.g. `function(input, output, session)`). The session object is an
+#' Shiny server functions can optionally include \code{session} as a parameter
+#' (e.g. \code{function(input, output, session)}). The session object is an
 #' environment that can be used to access information and functionality
 #' relating to the session. The following list describes the items available
-#' in the environment; they can be accessed using the `$` operator (for
-#' example, `session$clientData$url_search`).
+#' in the environment; they can be accessed using the \code{$} operator (for
+#' example, \code{session$clientData$url_search}).
 #'
 #' @return
 #' \item{allowReconnect(value)}{
-#'   If `value` is `TRUE` and run in a hosting environment (Shiny
+#'   If \code{value} is \code{TRUE} and run in a hosting environment (Shiny
 #'   Server or Connect) with reconnections enabled,  then when the session ends
 #'   due to the network connection closing, the client will attempt to
 #'   reconnect to the server. If a reconnection is successful, the browser will
 #'   send all the current input values to the new session on the server, and
 #'   the server will recalculate any outputs and send them back to the client.
-#'   If `value` is `FALSE`, reconnections will be disabled (this is
-#'   the default state). If `"force"`, then the client browser will always
-#'   attempt to reconnect. The only reason to use `"force"` is for testing
+#'   If \code{value} is \code{FALSE}, reconnections will be disabled (this is
+#'   the default state). If \code{"force"}, then the client browser will always
+#'   attempt to reconnect. The only reason to use \code{"force"} is for testing
 #'   on a local connection (without Shiny Server or Connect).
 #' }
 #' \item{clientData}{
-#'   A [reactiveValues()] object that contains information about the client.
+#'   A \code{\link{reactiveValues}} object that contains information about the client.
 #'   \itemize{
-#'     \item{`allowDataUriScheme` is a logical value that indicates whether
-#'       the browser is able to handle URIs that use the `data:` scheme.
+#'     \item{\code{allowDataUriScheme} is a logical value that indicates whether
+#'       the browser is able to handle URIs that use the \code{data:} scheme.
 #'     }
-#'     \item{`pixelratio` reports the "device pixel ratio" from the web browser,
+#'     \item{\code{pixelratio} reports the "device pixel ratio" from the web browser,
 #'       or 1 if none is reported. The value is 2 for Apple Retina displays.
 #'     }
-#'     \item{`singletons` - for internal use}
-#'     \item{`url_protocol`, `url_hostname`, `url_port`,
-#'       `url_pathname`, `url_search`, `url_hash_initial`
-#'       and `url_hash` can be used to get the components of the URL
+#'     \item{\code{singletons} - for internal use}
+#'     \item{\code{url_protocol}, \code{url_hostname}, \code{url_port},
+#'       \code{url_pathname}, \code{url_search}, \code{url_hash_initial}
+#'       and \code{url_hash} can be used to get the components of the URL
 #'       that was requested by the browser to load the Shiny app page.
 #'       These values are from the browser's perspective, so neither HTTP
 #'       proxies nor Shiny Server will affect these values. The
-#'       `url_search` value may be used with [parseQueryString()]
+#'       \code{url_search} value may be used with \code{\link{parseQueryString}}
 #'       to access query string parameters.
 #'     }
 #'   }
-#'   `clientData` also contains information about each output.
+#'   \code{clientData} also contains information about each output.
 #'   \code{output_\var{outputId}_width} and \code{output_\var{outputId}_height}
-#'   give the dimensions (using `offsetWidth` and `offsetHeight`) of
+#'   give the dimensions (using \code{offsetWidth} and \code{offsetHeight}) of
 #'   the DOM element that is bound to \code{\var{outputId}}, and
 #'   \code{output_\var{outputId}_hidden} is a logical that indicates whether
-#'   the element is hidden. These values may be `NULL` if the output is
+#'   the element is hidden. These values may be \code{NULL} if the output is
 #'   not bound.
 #' }
 #' \item{input}{
-#'   The session's `input` object (the same as is passed into the Shiny
+#'   The session's \code{input} object (the same as is passed into the Shiny
 #'   server function as an argument).
 #' }
-#' \item{isClosed()}{A function that returns `TRUE` if the client has
+#' \item{isClosed()}{A function that returns \code{TRUE} if the client has
 #'   disconnected.
 #' }
 #' \item{ns(id)}{
-#'   Server-side version of [`ns <- NS(id)`][NS]. If bare IDs need to be
-#'   explicitly namespaced for the current module, `session$ns("name")`
+#'   Server-side version of \code{ns <- \link{NS}(id)}. If bare IDs need to be
+#'   explicitly namespaced for the current module, \code{session$ns("name")}
 #'   will return the fully-qualified ID.
 #' }
 #' \item{onEnded(callback)}{
-#'   Synonym for `onSessionEnded`.
+#'   Synonym for \code{onSessionEnded}.
 #' }
 #' \item{onFlush(func, once=TRUE)}{
-#'   Registers a function to be called before the next time (if `once=TRUE`)
-#'   or every time (if `once=FALSE`) Shiny flushes the reactive system.
+#'   Registers a function to be called before the next time (if \code{once=TRUE})
+#'   or every time (if \code{once=FALSE}) Shiny flushes the reactive system.
 #'   Returns a function that can be called with no arguments to cancel the
 #'   registration.
 #' }
 #' \item{onFlushed(func, once=TRUE)}{
-#'   Registers a function to be called after the next time (if `once=TRUE`)
-#'   or every time (if `once=FALSE`) Shiny flushes the reactive system.
+#'   Registers a function to be called after the next time (if \code{once=TRUE})
+#'   or every time (if \code{once=FALSE}) Shiny flushes the reactive system.
 #'   Returns a function that can be called with no arguments to cancel the
 #'   registration.
 #' }
@@ -175,7 +260,7 @@ workerId <- local({
 #'   registration.
 #' }
 #' \item{output}{
-#'   The session's `output` object (the same as is passed into the Shiny
+#'   The session's \code{output} object (the same as is passed into the Shiny
 #'   server function as an argument).
 #' }
 #' \item{reactlog}{
@@ -183,13 +268,13 @@ workerId <- local({
 #' }
 #' \item{registerDataObj(name, data, filterFunc)}{
 #'   Publishes any R object as a URL endpoint that is unique to this session.
-#'   `name` must be a single element character vector; it will be used
-#'   to form part of the URL. `filterFunc` must be a function that takes
-#'   two arguments: `data` (the value that was passed into
-#'   `registerDataObj`) and `req` (an environment that implements
-#'   the Rook specification for HTTP requests). `filterFunc` will be
+#'   \code{name} must be a single element character vector; it will be used
+#'   to form part of the URL. \code{filterFunc} must be a function that takes
+#'   two arguments: \code{data} (the value that was passed into
+#'   \code{registerDataObj}) and \code{req} (an environment that implements
+#'   the Rook specification for HTTP requests). \code{filterFunc} will be
 #'   called with these values whenever an HTTP request is made to the URL
-#'   endpoint. The return value of `filterFunc` should be a Rook-style
+#'   endpoint. The return value of \code{filterFunc} should be a Rook-style
 #'   response.
 #' }
 #' \item{reload()}{
@@ -206,35 +291,35 @@ workerId <- local({
 #'   session-specific data they want.
 #' }
 #' \item{resetBrush(brushId)}{
-#'   Resets/clears the brush with the given `brushId`, if it exists on
-#'   any `imageOutput` or `plotOutput` in the app.
+#'   Resets/clears the brush with the given \code{brushId}, if it exists on
+#'   any \code{imageOutput} or \code{plotOutput} in the app.
 #' }
 #' \item{sendCustomMessage(type, message)}{
-#'   Sends a custom message to the web page. `type` must be a
+#'   Sends a custom message to the web page. \code{type} must be a
 #'   single-element character vector giving the type of message, while
-#'   `message` can be any jsonlite-encodable value. Custom messages
+#'   \code{message} can be any jsonlite-encodable value. Custom messages
 #'   have no meaning to Shiny itself; they are used soley to convey information
 #'   to custom JavaScript logic in the browser. You can do this by adding
 #'   JavaScript code to the browser that calls
 #'   \code{Shiny.addCustomMessageHandler(type, function(message){...})}
 #'   as the page loads; the function you provide to
-#'   `addCustomMessageHandler` will be invoked each time
-#'   `sendCustomMessage` is called on the server.
+#'   \code{addCustomMessageHandler} will be invoked each time
+#'   \code{sendCustomMessage} is called on the server.
 #' }
 #' \item{sendBinaryMessage(type, message)}{
-#'   Similar to `sendCustomMessage`, but the message must be a raw vector
+#'   Similar to \code{sendCustomMessage}, but the message must be a raw vector
 #'   and the registration method on the client is
 #'   \code{Shiny.addBinaryMessageHandler(type, function(message){...})}. The
 #'   message argument on the client will be a
-#'   [DataView](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/DataView).
+#'   \href{https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/DataView}{DataView}.
 #' }
 #' \item{sendInputMessage(inputId, message)}{
 #'   Sends a message to an input on the session's client web page; if the input
 #'   is present and bound on the page at the time the message is received, then
-#'   the input binding object's `receiveMessage(el, message)` method will
-#'   be called. `sendInputMessage` should generally not be called directly
+#'   the input binding object's \code{receiveMessage(el, message)} method will
+#'   be called. \code{sendInputMessage} should generally not be called directly
 #'   from Shiny apps, but through friendlier wrapper functions like
-#'   [updateTextInput()].
+#'   \code{\link{updateTextInput}}.
 #' }
 #' \item{setBookmarkExclude(names)}{
 #'   Set input names to be excluded from bookmarking.
@@ -266,10 +351,10 @@ workerId <- local({
 #' \item{getTestSnapshotUrl(input=TRUE, output=TRUE, export=TRUE,
 #'   format="json")}{
 #'   Returns a URL for the test snapshots. Only has an effect when the
-#'   `shiny.testmode` option is set to TRUE. For the input, output, and
+#'   \code{shiny.testmode} option is set to TRUE. For the input, output, and
 #'   export arguments, TRUE means to return all of these values. It is also
 #'   possible to specify by name which values to return by providing a
-#'   character vector, as in `input=c("x", "y")`. The format can be
+#'   character vector, as in \code{input=c("x", "y")}. The format can be
 #'   "rds" or "json".
 #' }
 #'
@@ -278,26 +363,26 @@ NULL
 
 #' Namespaced IDs for inputs/outputs
 #'
-#' The `NS` function creates namespaced IDs out of bare IDs, by joining
-#' them using `ns.sep` as the delimiter. It is intended for use in Shiny
-#' modules. See <http://shiny.rstudio.com/articles/modules.html>.
+#' The \code{NS} function creates namespaced IDs out of bare IDs, by joining
+#' them using \code{ns.sep} as the delimiter. It is intended for use in Shiny
+#' modules. See \url{http://shiny.rstudio.com/articles/modules.html}.
 #'
 #' Shiny applications use IDs to identify inputs and outputs. These IDs must be
 #' unique within an application, as accidentally using the same input/output ID
 #' more than once will result in unexpected behavior. The traditional solution
-#' for preventing name collisions is *namespaces*; a namespace is to an ID
-#' as a directory is to a file. Use the `NS` function to turn a bare ID
-#' into a namespaced one, by combining them with `ns.sep` in between.
+#' for preventing name collisions is \emph{namespaces}; a namespace is to an ID
+#' as a directory is to a file. Use the \code{NS} function to turn a bare ID
+#' into a namespaced one, by combining them with \code{ns.sep} in between.
 #'
 #' @param namespace The character vector to use for the namespace. This can have
 #'   any length, though a single element is most common. Length 0 will cause the
-#'   `id` to be returned without a namespace, and length 2 will be
+#'   \code{id} to be returned without a namespace, and length 2 will be
 #'   interpreted as multiple namespaces, in increasing order of specificity
 #'   (i.e. starting with the top-level namespace).
 #' @param id The id string to be namespaced (optional).
-#' @return If `id` is missing, returns a function that expects an id string
+#' @return If \code{id} is missing, returns a function that expects an id string
 #'   as its only argument and returns that id with the namespace prepended.
-#' @seealso <http://shiny.rstudio.com/articles/modules.html>
+#' @seealso \url{http://shiny.rstudio.com/articles/modules.html}
 #' @export
 NS <- function(namespace, id = NULL) {
   if (length(namespace) == 0)
@@ -554,7 +639,7 @@ ShinySession <- R6Class(
           # that the resulting object is represented as an object in JSON
           # instead of an array, and so that the RDS data structure is of a
           # consistent type.
-          values <- lapply(values, asNamed)
+          values <- lapply(values, asNamedVector)
 
           if (length(values) == 0) {
             return(httpResponse(400, "text/plain",
@@ -723,12 +808,6 @@ ShinySession <- R6Class(
     requestFlush = function() {
       appsNeedingFlush$set(self$token, self)
     },
-    .scheduleTask = function(millis, callback) {
-      scheduleTask(millis, callback)
-    },
-    .now = function(){
-      getTimeMs()
-    },
     rootScope = function() {
       self
     },
@@ -962,9 +1041,7 @@ ShinySession <- R6Class(
         output$suspend()
       }
       # ..stacktraceon matches with the top-level ..stacktraceoff..
-      withReactiveDomain(self, {
-        private$closedCallbacks$invoke(onError = printError, ..stacktraceon = TRUE)
-      })
+      private$closedCallbacks$invoke(onError = printError, ..stacktraceon = TRUE)
     },
     isClosed = function() {
       return(self$closed)
@@ -1010,9 +1087,6 @@ ShinySession <- R6Class(
         # will be attached to the observer after it's created.
         outputAttrs <- attr(func, "outputAttrs", TRUE)
 
-        # Save this for getOutput purposes
-        outputAttrs$renderFunc <- func
-
         funcFormals <- formals(func)
         # ..stacktraceon matches with the top-level ..stacktraceoff.., because
         # the observer we set up below has ..stacktraceon=FALSE
@@ -1120,9 +1194,6 @@ ShinySession <- R6Class(
         stop(paste("Unexpected", class(func), "output for", name))
       }
     },
-    getOutput = function(name) {
-      attr(private$.outputs[[name]], "renderFunc", exact = TRUE)
-    },
     flushOutput = function() {
       if (private$busyCount > 0)
         return()
@@ -1299,9 +1370,6 @@ ShinySession <- R6Class(
 
     getCurrentOutputInfo = function() {
       name <- private$currentOutputName
-      if (is.null(name)) {
-        return(NULL)
-      }
 
       tmp_info <- private$outputInfo[[name]] %OR% list(name = name)
 
@@ -1555,14 +1623,8 @@ ShinySession <- R6Class(
     reactlog = function(logEntry) {
       # Use sendCustomMessage instead of sendMessage, because the handler in
       # shiny-showcase.js only has access to public API of the Shiny object.
-      if (private$showcase) {
-        srcref <- logEntry$srcref
-        srcfile <- logEntry$srcfile
-        if (!is.null(srcref) && !is.null(srcfile)) {
-          # only send needed information, not all of reactlog info.
-          self$sendCustomMessage("showcase-src", list(srcref = srcref, srcfile = srcfile))
-        }
-      }
+      if (private$showcase)
+        self$sendCustomMessage("reactlog", logEntry)
     },
     reload = function() {
       private$sendMessage(reload = TRUE)
@@ -2031,13 +2093,7 @@ ShinySession <- R6Class(
 
 #' @export
 `$.shinyoutput` <- function(x, name) {
-  name <- .subset2(x, 'ns')(name)
-
-  if (getOption("shiny.allowoutputreads", FALSE)) {
-    .subset2(x, 'impl')$getOutput(name)
-  } else {
-    stop("Reading from shinyoutput object is not allowed.")
-  }
+  stop("Reading objects from shinyoutput object not allowed.")
 }
 
 #' @export
@@ -2057,9 +2113,9 @@ ShinySession <- R6Class(
 #'
 #' These are the available options for an output object:
 #' \itemize{
-#'   \item suspendWhenHidden. When `TRUE` (the default), the output object
+#'   \item suspendWhenHidden. When \code{TRUE} (the default), the output object
 #'     will be suspended (not execute) when it is hidden on the web page. When
-#'     `FALSE`, the output object will not suspend when hidden, and if it
+#'     \code{FALSE}, the output object will not suspend when hidden, and if it
 #'     was already hidden and suspended, then it will resume immediately.
 #'   \item priority. The priority level of the output object. Queued outputs
 #'     with higher priority values will execute before those with lower values.
@@ -2080,7 +2136,7 @@ ShinySession <- R6Class(
 #' outputOptions(output, "myplot")
 #' }
 #'
-#' @param x A shinyoutput object (typically `output`).
+#' @param x A shinyoutput object (typically \code{output}).
 #' @param name The name of an output observer in the shinyoutput object.
 #' @param ... Options to set for the output observer.
 #' @export
@@ -2101,10 +2157,6 @@ outputOptions <- function(x, name, ...) {
 
 #' Get information about the output that is currently being executed.
 #'
-#' @return A list with information about the current output, including the
-#'   `name` of the output. If no output is currently being executed, this will
-#'   return `NULL`.
-#'
 #' @param session The current Shiny session.
 #'
 #' @export
@@ -2115,9 +2167,9 @@ getCurrentOutputInfo <- function(session = getDefaultReactiveDomain()) {
 #' Add callbacks for Shiny session events
 #'
 #' These functions are for registering callbacks on Shiny session events.
-#' `onFlush` registers a function that will be called before Shiny flushes
-#' the reactive system. `onFlushed` registers a function that will be
-#' called after Shiny flushes the reactive system. `onSessionEnded`
+#' \code{onFlush} registers a function that will be called before Shiny flushes
+#' the reactive system. \code{onFlushed} registers a function that will be
+#' called after Shiny flushes the reactive system. \code{onSessionEnded}
 #' registers a function to be called after the client has disconnected.
 #'
 #' These functions should be called within the application's server function.
@@ -2127,8 +2179,8 @@ getCurrentOutputInfo <- function(session = getDefaultReactiveDomain()) {
 #'
 #' @param fun A callback function.
 #' @param once Should the function be run once, and then cleared, or should it
-#'   re-run each time the event occurs. (Only for `onFlush` and
-#'   `onFlushed`.)
+#'   re-run each time the event occurs. (Only for \code{onFlush} and
+#'   \code{onFlushed}.)
 #' @param session A shiny session object.
 #'
 #' @export
@@ -2144,7 +2196,7 @@ onFlushed <- function(fun, once = TRUE, session = getDefaultReactiveDomain()) {
 
 #' @rdname onFlush
 #'
-#' @seealso [onStop()] for registering callbacks that will be
+#' @seealso \code{\link{onStop}()} for registering callbacks that will be
 #'   invoked when the application exits, or when a session ends.
 #' @export
 onSessionEnded <- function(fun, session = getDefaultReactiveDomain()) {
@@ -2167,25 +2219,26 @@ flushPendingSessions <- function() {
   })
 }
 
-.globals$onStopCallbacks <- Callbacks$new()
+# Initialized in .onLoad
+.globals$onStopCallbacks <- NULL
 
 #' Run code after an application or session ends
 #'
 #' This function registers callback functions that are invoked when the
-#' application exits (when [runApp()] exits), or after each user
+#' application exits (when \code{\link{runApp}} exits), or after each user
 #' session ends (when a client disconnects).
 #'
 #' @param fun A function that will be called after the app has finished running.
-#' @param session A scope for when the callback will run. If `onStop` is
+#' @param session A scope for when the callback will run. If \code{onStop} is
 #'   called from within the server function, this will default to the current
 #'   session, and the callback will be invoked when the current session ends. If
-#'   `onStop` is called outside a server function, then the callback will
-#'   be invoked with the application exits. If `NULL`, it is the same as
-#'   calling `onStop` outside of the server function, and the callback will
+#'   \code{onStop} is called outside a server function, then the callback will
+#'   be invoked with the application exits. If \code{NULL}, it is the same as
+#'   calling \code{onStop} outside of the server function, and the callback will
 #'   be invoked when the application exits.
 #'
 #'
-#' @seealso [onSessionEnded()] for the same functionality, but at
+#' @seealso \code{\link{onSessionEnded}()} for the same functionality, but at
 #'   the session level only.
 #'
 #' @return A function which, if invoked, will cancel the callback.
@@ -2296,56 +2349,3 @@ ShinyServerTimingRecorder <- R6Class("ShinyServerTimingRecorder",
 )
 
 missingOutput <- function(...) req(FALSE)
-
-#' Insert inline Markdown
-#'
-#' This function accepts
-#' [Markdown](https://en.wikipedia.org/wiki/Markdown)-syntax text and returns
-#' HTML that may be included in Shiny UIs.
-#'
-#' Leading whitespace is trimmed from Markdown text with [glue::trim()].
-#' Whitespace trimming ensures Markdown is processed correctly even when the
-#' call to `markdown()` is indented within surrounding R code.
-#'
-#' By default, [Github extensions][commonmark::extensions] are enabled, but this
-#' can be disabled by passing `extensions = FALSE`.
-#'
-#' Markdown rendering is performed by [commonmark::markdown_html()]. Additional
-#' arguments to `markdown()` are passed as arguments to `markdown_html()`
-#'
-#' @param mds A character vector of Markdown source to convert to HTML. If the
-#'   vector has more than one element, a single-element character vector of
-#'   concatenated HTML is returned.
-#' @param extensions Enable Github syntax extensions; defaults to `TRUE`.
-#' @param .noWS Character vector used to omit some of the whitespace that would
-#'   normally be written around generated HTML. Valid options include `before`,
-#'   `after`, and `outside` (equivalent to `before` and `end`).
-#' @param ... Additional arguments to pass to [commonmark::markdown_html()].
-#'   These arguments are _[dynamic][rlang::dyn-dots]_.
-#'
-#' @return a character vector marked as HTML.
-#' @export
-#' @examples
-#' ui <- fluidPage(
-#'   markdown("
-#'     # Markdown Example
-#'
-#'     This is a markdown paragraph, and will be contained within a `<p>` tag
-#'     in the UI.
-#'
-#'     The following is an unordered list, which will be represented in the UI as
-#'     a `<ul>` with `<li>` children:
-#'
-#'     * a bullet
-#'     * another
-#'
-#'     [Links](https://developer.mozilla.org/en-US/docs/Web/HTML/Element/a) work;
-#'     so does *emphasis*.
-#'
-#'     To see more of what's possible, check out [commonmark.org/help](https://commonmark.org/help).
-#'     ")
-#' )
-markdown <- function(mds, extensions = TRUE, .noWS = NULL, ...) {
-  html <- rlang::exec(commonmark::markdown_html, glue::trim(mds), extensions = extensions, ...)
-  htmltools::HTML(html, .noWS = .noWS)
-}

R/shinyui.R

@@ -4,9 +4,9 @@ NULL
 #' Load the MathJax library and typeset math expressions
 #'
 #' This function adds MathJax to the page and typeset the math expressions (if
-#' found) in the content `...`. It only needs to be called once in an app
-#' unless the content is rendered *after* the page is loaded, e.g. via
-#' [renderUI()], in which case we have to call it explicitly every
+#' found) in the content \code{...}. It only needs to be called once in an app
+#' unless the content is rendered \emph{after} the page is loaded, e.g. via
+#' \code{\link{renderUI}}, in which case we have to call it explicitly every
 #' time we write math expressions to the output.
 #' @param ... any HTML elements to apply MathJax to
 #' @export
@@ -42,28 +42,9 @@ renderPage <- function(ui, connection, showcase=0, testMode=FALSE) {
     )
   }
 
-  jquery <- function() {
-    version <- getOption("shiny.jquery.version", 3)
-    if (version == 3) {
-      return(htmlDependency(
-        "jquery", "3.4.1",
-        c(href = "shared"),
-        script = "jquery.min.js"
-      ))
-    }
-    if (version == 1) {
-      return(htmlDependency(
-        "jquery", "1.12.4",
-        c(href = "shared/legacy"),
-        script = "jquery.min.js"
-      ))
-    }
-    stop("Unsupported version of jQuery: ", version)
-  }
-
   shiny_deps <- list(
     htmlDependency("json2", "2014.02.04", c(href="shared"), script = "json2-min.js"),
-    jquery(),
+    htmlDependency("jquery", "1.12.4", 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")
@@ -90,7 +71,6 @@ renderPage <- function(ui, connection, showcase=0, testMode=FALSE) {
 #'
 #' @param ui A user interace definition
 #' @return The user interface definition, without modifications or side effects.
-#' @keywords internal
 #' @export
 shinyUI <- function(ui) {
   .globals$ui <- list(ui)

R/shinywrappers.R

@@ -2,7 +2,7 @@ utils::globalVariables('func')
 
 #' Mark a function as a render function
 #'
-#' Should be called by implementers of `renderXXX` functions in order to
+#' Should be called by implementers of \code{renderXXX} functions in order to
 #' mark their return values as Shiny render functions, and to provide a hint to
 #' Shiny regarding what UI function is most commonly used with this type of
 #' render function. This can be used in R Markdown documents to create complete
@@ -12,13 +12,13 @@ utils::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 `uiFunc`. Render
-#'   functions should include `outputArgs = list()` in their own parameter
-#'   list, and pass through the value to `markRenderFunction`, to allow
+#' @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 `renderFunc` function, with annotations.
+#' @return The \code{renderFunc} function, with annotations.
 #' @export
 markRenderFunction <- function(uiFunc, renderFunc, outputArgs = list()) {
   # a mutable object that keeps track of whether `useRenderFunction` has been
@@ -52,32 +52,27 @@ markRenderFunction <- function(uiFunc, renderFunc, outputArgs = list()) {
             hasExecuted = hasExecuted)
 }
 
-#' @export
-print.shiny.render.function <- function(x, ...) {
-  cat_line("<shiny.render.function>")
-}
-
 #' Implement render functions
 #'
 #' @param func A function without parameters, that returns user data. If the
 #'   returned value is a promise, then the render function will proceed in async
 #'   mode.
-#' @param transform A function that takes four arguments: `value`,
-#'   `session`, `name`, and `...` (for future-proofing). This
-#'   function will be invoked each time a value is returned from `func`,
+#' @param transform A function that takes four arguments: \code{value},
+#'   \code{session}, \code{name}, and \code{...} (for future-proofing). This
+#'   function will be invoked each time a value is returned from \code{func},
 #'   and is responsible for changing the value into a JSON-ready value to be
 #'   JSON-encoded and sent to the browser.
 #' @param outputFunc The UI function that is used (or most commonly used) with
 #'   this render function. This can be used in R Markdown documents to create
 #'   complete output widgets out of just the render function.
-#' @param outputArgs A list of arguments to pass to the `outputFunc`.
-#'   Render functions should include `outputArgs = list()` in their own
+#' @param outputArgs A list of arguments to pass to the \code{outputFunc}.
+#'   Render functions should include \code{outputArgs = list()} in their own
 #'   parameter list, and pass through the value as this argument, 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 An annotated render function, ready to be assigned to an
-#'   `output` slot.
+#'   \code{output} slot.
 #'
 #' @export
 createRenderFunction <- function(
@@ -170,37 +165,37 @@ markOutputAttrs <- function(renderFunc, snapshotExclude = NULL,
 
 #' Image file output
 #'
-#' Renders a reactive image that is suitable for assigning to an `output`
+#' Renders a reactive image that is suitable for assigning to an \code{output}
 #' slot.
 #'
-#' The expression `expr` must return a list containing the attributes for
-#' the `img` object on the client web page. For the image to display,
-#' properly, the list must have at least one entry, `src`, which is the
-#' path to the image file. It may also useful to have a `contentType`
+#' The expression \code{expr} must return a list containing the attributes for
+#' the \code{img} object on the client web page. For the image to display,
+#' properly, the list must have at least one entry, \code{src}, which is the
+#' path to the image file. It may also useful to have a \code{contentType}
 #' entry specifying the MIME type of the image. If one is not provided,
-#' `renderImage` will try to autodetect the type, based on the file
+#' \code{renderImage} will try to autodetect the type, based on the file
 #' extension.
 #'
-#' Other elements such as `width`, `height`, `class`, and
-#' `alt`, can also be added to the list, and they will be used as
-#' attributes in the `img` object.
+#' Other elements such as \code{width}, \code{height}, \code{class}, and
+#' \code{alt}, can also be added to the list, and they will be used as
+#' attributes in the \code{img} object.
 #'
-#' The corresponding HTML output tag should be `div` or `img` and have
-#' the CSS class name `shiny-image-output`.
+#' The corresponding HTML output tag should be \code{div} or \code{img} and have
+#' the CSS class name \code{shiny-image-output}.
 #'
 #' @seealso For more details on how the images are generated, and how to control
-#'   the output, see [plotPNG()].
+#'   the output, see \code{\link{plotPNG}}.
 #'
 #' @param expr An expression that returns a list.
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)? This
+#' @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 deleteFile Should the file in `func()$src` be deleted after
+#' @param deleteFile Should the file in \code{func()$src} be deleted after
 #'   it is sent to the client browser? Generally speaking, if the image is a
-#'   temp file generated within `func`, then this should be `TRUE`;
-#'   if the image is not a temp file, this should be `FALSE`.
+#'   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 [imageOutput()] when `renderImage` is used in an
+#'   call to \code{\link{imageOutput}} when \code{renderImage} is used in an
 #'   interactive R Markdown document.
 #' @export
 #'
@@ -300,30 +295,30 @@ renderImage <- function(expr, env=parent.frame(), quoted=FALSE,
 #'
 #' Makes a reactive version of the given function that captures any printed
 #' output, and also captures its printable result (unless
-#' [base::invisible()]), into a string. The resulting function is suitable
-#' for assigning to an  `output` slot.
+#' \code{\link[base]{invisible}}), into a string. The resulting function is suitable
+#' for assigning to an  \code{output} slot.
 #'
-#' The corresponding HTML output tag can be anything (though `pre` is
+#' The corresponding HTML output tag can be anything (though \code{pre} is
 #' recommended if you need a monospace font and whitespace preserved) and should
-#' have the CSS class name `shiny-text-output`.
+#' have the CSS class name \code{shiny-text-output}.
 #'
-#' The result of executing `func` will be printed inside a
-#' [utils::capture.output()] call.
+#' The result of executing \code{func} will be printed inside a
+#' \code{\link[utils]{capture.output}} call.
 #'
 #' Note that unlike most other Shiny output functions, if the given function
-#' returns `NULL` then `NULL` will actually be visible in the output.
-#' To display nothing, make your function return [base::invisible()].
+#' returns \code{NULL} then \code{NULL} will actually be visible in the output.
+#' To display nothing, make your function return \code{\link[base]{invisible}()}.
 #'
 #' @param expr An expression that may print output and/or return a printable R
 #'   object.
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)? This
+#' @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 width The value for `[options][base::options]('width')`.
+#' @param width The value for \code{\link[base]{options}('width')}.
 #' @param outputArgs A list of arguments to be passed through to the implicit
-#'   call to [verbatimTextOutput()] when `renderPrint` is used
+#'   call to \code{\link{verbatimTextOutput}} when \code{renderPrint} is used
 #'   in an interactive R Markdown document.
-#' @seealso [renderText()] for displaying the value returned from a
+#' @seealso \code{\link{renderText}} for displaying the value returned from a
 #'   function, instead of the printed output.
 #'
 #' @example res/text-example.R
@@ -403,40 +398,38 @@ createRenderPrintPromiseDomain <- function(width) {
 #' Text Output
 #'
 #' Makes a reactive version of the given function that also uses
-#' [base::cat()] to turn its result into a single-element character
+#' \code{\link[base]{cat}} to turn its result into a single-element character
 #' vector.
 #'
-#' The corresponding HTML output tag can be anything (though `pre` is
+#' The corresponding HTML output tag can be anything (though \code{pre} is
 #' recommended if you need a monospace font and whitespace preserved) and should
-#' have the CSS class name `shiny-text-output`.
+#' have the CSS class name \code{shiny-text-output}.
 #'
-#' The result of executing `func` will passed to `cat`, inside a
-#' [utils::capture.output()] call.
+#' The result of executing \code{func} will passed to \code{cat}, inside a
+#' \code{\link[utils]{capture.output}} call.
 #'
 #' @param expr An expression that returns an R object that can be used as an
-#'   argument to `cat`.
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)? This
+#'   argument to \code{cat}.
+#' @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 [textOutput()] when `renderText` is used in an
+#'   call to \code{\link{textOutput}} when \code{renderText} is used in an
 #'   interactive R Markdown document.
-#' @param sep A separator passed to `cat` to be appended after each
-#'   element.
 #'
-#' @seealso [renderPrint()] for capturing the print output of a
+#' @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,
-                       outputArgs=list(), sep=" ") {
+                       outputArgs=list()) {
   installExprFunction(expr, "func", env, quoted)
 
   createRenderFunction(
     func,
     function(value, session, name, ...) {
-      paste(utils::capture.output(cat(value, sep=sep)), collapse="\n")
+      paste(utils::capture.output(cat(value)), collapse="\n")
     },
     textOutput, outputArgs
   )
@@ -446,19 +439,19 @@ renderText <- function(expr, env=parent.frame(), quoted=FALSE,
 #'
 #' Renders reactive HTML using the Shiny UI library.
 #'
-#' The corresponding HTML output tag should be `div` and have the CSS class
-#' name `shiny-html-output` (or use [uiOutput()]).
+#' The corresponding HTML output tag should be \code{div} and have the CSS class
+#' name \code{shiny-html-output} (or use \code{\link{uiOutput}}).
 #'
-#' @param expr An expression that returns a Shiny tag object, [HTML()],
+#' @param expr An expression that returns a Shiny tag object, \code{\link{HTML}},
 #'   or a list of such objects.
-#' @param env The environment in which to evaluate `expr`.
-#' @param quoted Is `expr` a quoted expression (with `quote()`)? This
+#' @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 [uiOutput()] when `renderUI` is used in an
+#'   call to \code{\link{uiOutput}} when \code{renderUI} is used in an
 #'   interactive R Markdown document.
 #'
-#' @seealso [uiOutput()]
+#' @seealso \code{\link{uiOutput}}
 #' @export
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -501,25 +494,25 @@ renderUI <- function(expr, env=parent.frame(), quoted=FALSE,
 #' file downloads (for example, downloading the currently visible data as a CSV
 #' file). Both filename and contents can be calculated dynamically at the time
 #' the user initiates the download. Assign the return value to a slot on
-#' `output` in your server function, and in the UI use
-#' [downloadButton()] or [downloadLink()] to make the
+#' \code{output} in your server function, and in the UI use
+#' \code{\link{downloadButton}} or \code{\link{downloadLink}} to make the
 #' download available.
 #'
 #' @param filename A string of the filename, including extension, that the
 #'   user's web browser should default to when downloading the file; or a
 #'   function that returns such a string. (Reactive values and functions may be
 #'   used from this function.)
-#' @param content A function that takes a single argument `file` that is a
+#' @param content A function that takes a single argument \code{file} that is a
 #'   file path (string) of a nonexistent temp file, and writes the content to
 #'   that file path. (Reactive values and functions may be used from this
 #'   function.)
 #' @param contentType A string of the download's
-#'   [content type](http://en.wikipedia.org/wiki/Internet_media_type), for
-#'   example `"text/csv"` or `"image/png"`. If `NULL` or
-#'   `NA`, the content type will be guessed based on the filename
-#'   extension, or `application/octet-stream` if the extension is unknown.
+#'   \href{http://en.wikipedia.org/wiki/Internet_media_type}{content type}, for
+#'   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 [downloadButton()] when `downloadHandler` is used
+#'   call to \code{\link{downloadButton}} when \code{downloadHandler} is used
 #'   in an interactive R Markdown document.
 #'
 #' @examples
@@ -563,12 +556,12 @@ downloadHandler <- function(filename, content, contentType=NA, outputArgs=list()
 #' searching, filtering, and sorting can be done on the R side using Shiny as
 #' the server infrastructure.
 #'
-#' For the `options` argument, the character elements that have the class
-#' `"AsIs"` (usually returned from [base::I()]) will be evaluated in
+#' For the \code{options} argument, the character elements that have the class
+#' \code{"AsIs"} (usually returned from \code{\link[base]{I}()}) will be evaluated in
 #' JavaScript. This is useful when the type of the option value is not supported
 #' in JSON, e.g., a JavaScript function, which can be obtained by evaluating a
 #' character string. Note this only applies to the root-level elements of the
-#' options list, and the `I()` notation does not work for lower-level
+#' options list, and the \code{I()} notation does not work for lower-level
 #' elements in the list.
 #' @param expr An expression that returns a data frame or a matrix.
 #' @param options A list of initialization options to be passed to DataTables,
@@ -577,25 +570,25 @@ downloadHandler <- function(filename, content, contentType=NA, outputArgs=list()
 #'   frequent search requests).
 #' @param callback A JavaScript function to be applied to the DataTable object.
 #'   This is useful for DataTables plug-ins, which often require the DataTable
-#'   instance to be available (<http://datatables.net/extensions/>).
-#' @param escape Whether to escape HTML entities in the table: `TRUE` means
-#'   to escape the whole table, and `FALSE` means not to escape it.
+#'   instance to be available (\url{http://datatables.net/extensions/}).
+#' @param escape Whether to escape HTML entities in the table: \code{TRUE} means
+#'   to escape the whole table, and \code{FALSE} means not to escape it.
 #'   Alternatively, you can specify numeric column indices or column names to
-#'   indicate which columns to escape, e.g. `1:5` (the first 5 columns),
-#'   `c(1, 3, 4)`, or `c(-1, -3)` (all columns except the first and
-#'   third), or `c('Species', 'Sepal.Length')`.
+#'   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 [dataTableOutput()] when `renderDataTable` is used
+#'   call to \code{\link{dataTableOutput}} when \code{renderDataTable} is used
 #'   in an interactive R Markdown document.
 #'
-#' @references <http://datatables.net>
+#' @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
-#'   separate package \pkg{DT} (<https://github.com/rstudio/DT>) that allows
+#'   separate package \pkg{DT} (\url{https://github.com/rstudio/DT}) that allows
 #'   you to create both server-side and client-side DataTables, and supports
-#'   additional DataTables features. Consider using `DT::renderDataTable()`
-#'   and `DT::dataTableOutput()` (see
-#'   <http://rstudio.github.io/DT/shiny.html> for more information).
+#'   additional DataTables features. Consider using \code{DT::renderDataTable()}
+#'   and \code{DT::dataTableOutput()} (see
+#'   \url{http://rstudio.github.io/DT/shiny.html} for more information).
 #' @export
 #' @inheritParams renderPlot
 #' @examples
@@ -714,19 +707,13 @@ checkDT9 <- function(options) {
 
 # Deprecated functions ------------------------------------------------------
 
-#' Deprecated reactive functions
-#' @name deprecatedReactives
-#' @keywords internal
-NULL
-
 #' Plot output (deprecated)
 #'
-#' `reactivePlot` has been replaced by [renderPlot()].
+#' See \code{\link{renderPlot}}.
 #' @param func A function.
 #' @param width Width.
 #' @param height Height.
 #' @param ... Other arguments to pass on.
-#' @rdname deprecatedReactives
 #' @export
 reactivePlot <- function(func, width='auto', height='auto', ...) {
   shinyDeprecated(new="renderPlot")
@@ -735,8 +722,9 @@ reactivePlot <- function(func, width='auto', height='auto', ...) {
 
 #' Table output (deprecated)
 #'
-#' `reactiveTable` has been replaced by [renderTable()].
-#' @rdname deprecatedReactives
+#' See \code{\link{renderTable}}.
+#' @param func A function.
+#' @param ... Other arguments to pass on.
 #' @export
 reactiveTable <- function(func, ...) {
   shinyDeprecated(new="renderTable")
@@ -745,8 +733,8 @@ reactiveTable <- function(func, ...) {
 
 #' Print output (deprecated)
 #'
-#' `reactivePrint` has been replaced by [renderPrint()].
-#' @rdname deprecatedReactives
+#' See \code{\link{renderPrint}}.
+#' @param func A function.
 #' @export
 reactivePrint <- function(func) {
   shinyDeprecated(new="renderPrint")
@@ -755,8 +743,8 @@ reactivePrint <- function(func) {
 
 #' UI output (deprecated)
 #'
-#' `reactiveUI` has been replaced by [renderUI()].
-#' @rdname deprecatedReactives
+#' See \code{\link{renderUI}}.
+#' @param func A function.
 #' @export
 reactiveUI <- function(func) {
   shinyDeprecated(new="renderUI")
@@ -765,8 +753,8 @@ reactiveUI <- function(func) {
 
 #' Text output (deprecated)
 #'
-#' `reactiveText` has been replaced by [renderText()].
-#' @rdname deprecatedReactives
+#' See \code{\link{renderText}}.
+#' @param func A function.
 #' @export
 reactiveText <- function(func) {
   shinyDeprecated(new="renderText")

R/showcase.R

@@ -104,18 +104,20 @@ navTabsDropdown <- function(files) {
 
 tabContentHelper <- function(files, path, language) {
   lapply(files, function(file) {
-      tags$div(class=paste("tab-pane",
+    with(tags,
+      div(class=paste("tab-pane",
                       if (tolower(file) %in% c("app.r", "server.r")) " active"
                       else "",
                       sep=""),
           id=paste(gsub(".", "_", file, fixed=TRUE),
                    "_code", sep=""),
-          tags$pre(class="shiny-code",
+          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))))
+    )
   })
 }
 

R/test-export.R

@@ -4,10 +4,10 @@
 #' event occurs. These events are triggered by accessing a snapshot URL.
 #'
 #' This function only has an effect if the app is launched in test mode. This is
-#' done by calling `runApp()` with `test.mode=TRUE`, or by setting the
-#' global option `shiny.testmode` to `TRUE`.
+#' done by calling \code{runApp()} with \code{test.mode=TRUE}, or by setting the
+#' global option \code{shiny.testmode} to \code{TRUE}.
 #'
-#' @param quoted_ Are the expression quoted? Default is `FALSE`.
+#' @param quoted_ Are the expression quoted? Default is \code{FALSE}.
 #' @param env_ The environment in which the expression should be evaluated.
 #' @param session_ A Shiny session object.
 #' @param ... Named arguments that are quoted or unquoted expressions that will

R/test-server.R

@@ -1,145 +0,0 @@
-#' @noRd
-isModuleServer <- function(x) {
-  is.function(x) && names(formals(x))[1] == "id"
-}
-
-#' Reactive testing for Shiny server functions and modules
-#'
-#' A way to test the reactive interactions in Shiny applications. Reactive
-#' interactions are defined in the server function of applications and in
-#' modules.
-#' @param app The path to an application or module to test. In addition to
-#'   paths, applications may be represented by any object suitable for coercion
-#'   to an `appObj` by `as.shiny.appobj`. Application server functions must
-#'   include a `session` argument in order to be tested. If `app` is `NULL` or
-#'   not supplied, the nearest enclosing directory that is a Shiny app, starting
-#'   with the current directory, is used.
-#' @param expr Test code containing expectations. The test expression will run
-#'   in the server function environment, meaning that the parameters of the
-#'   server function (e.g. `input`, `output`, and `session`) will be available
-#'   along with any other values created inside of the server function.
-#' @param args Additional arguments to pass to the module function.
-#'   If `app` is a module, and no `id` argument is provided, one will be
-#'   generated and supplied automatically.
-#' @return The result of evaluating `expr`.
-#' @include mock-session.R
-#' @rdname testServer
-#' @examples
-#' server <- function(id, multiplier = 2, prefix = "I am ") {
-#'   moduleServer(id, function(input, output, session) {
-#'     myreactive <- reactive({
-#'       input$x * multiplier
-#'     })
-#'     output$txt <- renderText({
-#'       paste0(prefix, myreactive())
-#'     })
-#'   })
-#' }
-#'
-#' testServer(server, args = list(multiplier = 2), {
-#'   session$setInputs(x = 1)
-#'   # You're also free to use third-party
-#'   # testing packages like testthat:
-#'   #   expect_equal(myreactive(), 2)
-#'   stopifnot(myreactive() == 2)
-#'   stopifnot(output$txt == "I am 2")
-#'
-#'   session$setInputs(x = 2)
-#'   stopifnot(myreactive() == 4)
-#'   stopifnot(output$txt == "I am 4")
-#'   # Any additional arguments, below, are passed along to the module.
-#' })
-#' @export
-testServer <- function(app = NULL, expr, args = list()) {
-
-  require(shiny)
-
-  quosure <- rlang::enquo(expr)
-  session <- getDefaultReactiveDomain()
-
-  if (inherits(session, "MockShinySession"))
-    stop("Test expressions may not call testServer()")
-  if (inherits(session, "session_proxy")
-      && inherits(get("parent", envir = session), "MockShinySession"))
-    stop("Modules may not call testServer()")
-
-  session <- MockShinySession$new()
-  on.exit(if (!session$isClosed()) session$close())
-
-  if (isModuleServer(app)) {
-    if (!("id" %in% names(args)))
-      args[["id"]] <- session$genId()
-    # app is presumed to be a module, and modules may take additional arguments,
-    # so splice in any args.
-    isolate(
-      withReactiveDomain(
-        session,
-        withr::with_options(list(`shiny.allowoutputreads` = TRUE), {
-          rlang::exec(app, !!!args)
-        })
-      )
-    )
-
-    # If app is a module, then we must use both the module function's immediate
-    # environment and also its enclosing environment to construct the mask.
-    parent_clone <- rlang::env_clone(parent.env(session$env))
-    clone <- rlang::env_clone(session$env, parent_clone)
-    mask <- rlang::new_data_mask(clone, parent_clone)
-
-    isolate(
-      withReactiveDomain(
-        session,
-        withr::with_options(list(`shiny.allowoutputreads` = TRUE), {
-          rlang::eval_tidy(quosure, mask, rlang::caller_env())
-        })
-      )
-    )
-  } else {
-    if (is.null(app)) {
-      app <- findEnclosingApp(".")
-    }
-
-    appobj <- as.shiny.appobj(app)
-    if (!is.null(appobj$onStart))
-      appobj$onStart()
-    # Ensure appobj$onStop() is called, and the current directory is restored,
-    # regardless of whether invoking the server function is successful.
-    tryCatch({
-      server <- appobj$serverFuncSource()
-      if (! "session" %in% names(formals(server)))
-        stop("Tested application server functions must declare input, output, and session arguments.")
-      body(server) <- rlang::expr({
-        session$setEnv(base::environment())
-        !!!body(server)
-      })
-      if (length(args))
-        stop("Arguments were provided to a server function.")
-      isolate(
-        withReactiveDomain(
-          session,
-          withr::with_options(list(`shiny.allowoutputreads` = TRUE), {
-            server(input = session$input, output = session$output, session = session)
-          })
-        )
-      )
-    }, finally = {
-      if (!is.null(appobj$onStop))
-        appobj$onStop()
-    })
-
-    # If app is a server, we use only the server function's immediate
-    # environment to construct the mask.
-    mask <- rlang::new_data_mask(rlang::env_clone(session$env))
-
-    isolate(
-      withReactiveDomain(
-        session,
-        withr::with_options(list(`shiny.allowoutputreads` = TRUE), {
-          rlang::eval_tidy(quosure, mask, rlang::caller_env())
-        })
-      )
-    )
-  }
-
-  invisible()
-}

R/test.R

@@ -1,264 +0,0 @@
-#' Creates and returns run result data frame.
-#'
-#' @param file Name of the test runner file, a character vector of length 1.
-#' @param pass Whether or not the test passed, a logical vector of length 1.
-#' @param result Value (wrapped in a list) obtained by evaluating `file`.
-#'   This can also by any errors signaled when evaluating the `file`.
-#'
-#' @return A 1-row data frame representing a single test run. `result` and
-#'   is a "list column", or a column that contains list elements.
-#' @noRd
-result_row <- function(file, pass, result) {
-  stopifnot(is.list(result))
-  df <- data.frame(
-    file = file,
-    pass = pass,
-    result = I(result),
-    stringsAsFactors = FALSE
-  )
-  class(df) <- c("shiny_runtests", class(df))
-  df
-}
-
-#' Check to see if the given directory contains at least one script, and that
-#' all scripts in the directory are shinytest scripts.
-#' Scans for the magic string of `app <- ShinyDriver$new(` as an indicator that
-#' this is a shinytest.
-#' @noRd
-is_legacy_shinytest_dir <- function(path){
-  is_shinytest_script <- function(file) {
-    if (!file.exists(file)) {
-      return(FALSE)
-    }
-
-    text <- readLines(file, warn = FALSE)
-    any(
-      grepl("app\\s*<-\\s*ShinyDriver\\$new\\(", text, perl=TRUE)
-    )
-  }
-
-  files <- dir(path, full.names = TRUE)
-  files <- files[!file.info(files)$isdir]
-  if (length(files) == 0) {
-    return(FALSE)
-  }
-  all(vapply(files, is_shinytest_script, logical(1)))
-}
-
-#' Runs the tests associated with this Shiny app
-#'
-#' Sources the `.R` files in the top-level of `tests/` much like `R CMD check`.
-#' These files are typically simple runners for tests nested in other
-#' directories under `tests/`.
-#'
-#' @param appDir The base directory for the application.
-#' @param filter If not `NULL`, only tests with file names matching this regular
-#'   expression will be executed. Matching is performed on the file name
-#'   including the extension.
-#' @param assert Logical value which determines if an error should be thrown if any error is captured.
-#' @param envir Parent testing environment in which to base the individual testing environments.
-#'
-#' @return A data frame classed with the supplemental class `"shiny_runtests"`.
-#'   The data frame has the following columns:
-#'
-#' | **Name** | **Type** | **Meaning** |
-#' | :-- | :-- | :-- |
-#' | `file` | `character(1)` | File name of the runner script in `tests/` that was sourced. |
-#' | `pass` | `logical(1)` | Whether or not the runner script signaled an error when sourced. |
-#' | `result` | any or `NA` | The return value of the runner |
-#'
-#' @details Historically, [shinytest](https://rstudio.github.io/shinytest/)
-#'   recommended placing tests at the top-level of the `tests/` directory.
-#'   This older folder structure is not supported by runTests.
-#'   Please see [shinyAppTemplate()] for more details.
-#' @export
-runTests <- function(
-  appDir = ".",
-  filter = NULL,
-  assert = TRUE,
-  envir = globalenv()
-) {
-  # similar to runApp()
-  # Allows shiny's functions to be available in the UI, server, and test code
-  require(shiny)
-
-  testsDir <- file.path(appDir, "tests")
-  if (!dirExists(testsDir)) {
-    stop("No tests directory found: ", testsDir)
-  }
-  runners <- list.files(testsDir, pattern="\\.r$", ignore.case = TRUE)
-
-  if (length(runners) == 0) {
-    message("No test runners found in ", testsDir)
-    return(result_row(character(0), logical(0), list()))
-  }
-
-  if (!is.null(filter)) {
-    runners <- runners[grepl(filter, runners)]
-  }
-  if (length(runners) == 0) {
-    stop("No test runners matched the given filter: '", filter, "'")
-  }
-
-  # See the @details section of the runTests() docs above for why this branch exists.
-  if (is_legacy_shinytest_dir(testsDir)) {
-    stop(
-      "It appears that the .R files in ", testsDir, " are all shinytests.",
-      " This is not supported by `shiny::runTests()`.",
-      "\nPlease see `?shiny::migrateLegacyShinytest` to migrate your shinytest file structure to the new format.",
-      "\nSee `?shiny::shinyAppTemplate` for an example of the new testing file structure."
-    )
-  }
-
-  renv <- new.env(parent = envir)
-
-  # Otherwise source all the runners -- each in their own environment.
-  ret <- do.call(rbind, lapply(runners, function(r) {
-    pass <- FALSE
-    result <-
-      tryCatch({
-        env <- new.env(parent = renv)
-        withr::with_dir(testsDir, {
-          ret <- sourceUTF8(r, envir = env)
-        })
-        pass <- TRUE
-        ret
-      }, error = function(err) {
-        message("Error in ", r, "\n", err)
-        err
-      })
-    result_row(file.path(testsDir, r), pass, list(result))
-  }))
-
-  if (isTRUE(assert)) {
-    if (!all(ret$pass)) {
-      stop("Shiny App Test Failures detected in\n", paste0("* ", runtest_pretty_file(ret$file[!ret$pass]), collapse = "\n"), call. = FALSE)
-    }
-  }
-
-  ret
-}
-
-
-runtest_pretty_file <- function(f) {
-  test_folder <- dirname(f)
-  app_folder <- dirname(test_folder)
-  file.path(
-    basename(app_folder),
-    basename(test_folder),
-    basename(f)
-  )
-}
-
-
-print.shiny_runtests <- function(x, ..., reporter = "summary") {
-
-  cat("Shiny App Test Results\n")
-
-
-  if (any(x$pass)) {
-    # TODO in future... use clisymbols::symbol$tick and crayon green
-    cat("* Success\n")
-    mapply(
-      x$file,
-      x$pass,
-      x$result,
-      FUN = function(file, pass, result) {
-        if (!pass) return()
-        # print(result)
-        cat("  - ", runtest_pretty_file(file), "\n", sep = "")
-      }
-    )
-  }
-  if (any(!x$pass)) {
-    # TODO in future... use clisymbols::symbol$cross and crayon red
-    cat("* Failure\n")
-    mapply(
-      x$file,
-      x$pass,
-      x$result,
-      FUN = function(file, pass, result) {
-        if (pass) return()
-        cat("  - ", runtest_pretty_file(file), "\n", sep = "")
-      }
-    )
-  }
-
-  invisible(x)
-}
-
-
-#' Migrate legacy \pkg{shinytest} files to new test directory structure
-#'
-#' This function migrates the old-style directory structure used by
-#' \pkg{shinytest} to (versions 1.3.1 and below) new test directory structure
-#' used in Shiny 1.5.0 and above.
-#'
-#' In Shiny 1.5.0, the [runTests()] function was added, and it will run test
-#' scripts tests/ subdirectory of the application. The directory structure will
-#' look something like this:
-#'
-#' ```
-#' appdir/
-#'  |- R
-#'  |- tests
-#'      |- shinytest.R
-#'      |- shinytest
-#'      |   `- mytest.R
-#'      |- testthat.R
-#'      `- testthat
-#'          `- test-script.R
-#' ```
-#'
-#' This allows for tests using the \pkg{shinytest} package as well as other
-#' testing tools, such as the [testServer()] function, which can be used for
-#' testing module and server logic, and for unit tests of functions in an R/
-#' subdirectory.
-#'
-#'
-#' With the \pkg{shinytest} package, in versions 1.3.0 and below, the tests/
-#' subdirectory of the application was used specifically for \pkg{shinytest},
-#' and could not be used for other types of tests. So the directory structure
-#' would look like this:
-#'
-#' ```
-#' appdir/
-#'  `- tests
-#'      `- mytest.R
-#' ```
-#'
-#' In \pkg{shinytest} 1.4.0 and above, it defaults to the new directory
-#' structure.
-#'
-#' @param appdir A directory containing a Shiny application.
-#' @param prompt If \code{TRUE}, ask for confirmation when moving files.
-#'
-#' @export
-migrateLegacyShinytest <- function(appdir, prompt = interactive()) {
-  appdir <- findEnclosingApp(appdir)
-
-  test_dir <- file.path(appdir, "tests")
-  shinytest_dir <- file.path(test_dir, "shinytest")
-
-  if (!is_legacy_shinytest_dir(test_dir)) {
-    stop("The .R files in ", test_dir,
-         " must all be test scripts for the shinytest package.")
-  }
-
-  if (prompt) {
-    res <- readline(
-      paste0(
-        "Creating ", shinytest_dir, " and moving files from\n", test_dir,
-        " into it.\nAre you sure you want to do this? [y/n]\n"
-      )
-    )
-    if (!identical(tolower(res), "y")) {
-      return(invisible())
-    }
-  }
-
-  files <- dir(test_dir)
-  dir.create(shinytest_dir, showWarnings = FALSE)
-  file.rename(file.path(test_dir, files), file.path(shinytest_dir, files))
-  invisible()
-}

R/timer.R

@@ -1,5 +1,6 @@
-# Return the current time, in milliseconds from epoch.
-getTimeMs <- function() {
+# Return the current time, in milliseconds from epoch, with
+# unspecified time zone.
+now <- function() {
   as.numeric(Sys.time()) * 1000
 }
 
@@ -11,11 +12,9 @@ TimerCallbacks <- R6Class(
     .nextId = 0L,
     .funcs = 'Map',
     .times = data.frame(),
-    .now = 'Function',
 
-    initialize = function(nowFn = getTimeMs) {
+    initialize = function() {
       .funcs <<- Map$new()
-      .now <<- nowFn
     },
     clear = function() {
       .nextId <<- 0L
@@ -31,7 +30,7 @@ TimerCallbacks <- R6Class(
       id <- .nextId
       .nextId <<- .nextId + 1L
 
-      t <- .now()
+      t <- now()
 
       # TODO: Horribly inefficient, use a heap instead
       .times <<- rbind(.times, data.frame(time=t+millis,
@@ -57,17 +56,17 @@ TimerCallbacks <- R6Class(
     timeToNextEvent = function() {
       if (dim(.times)[1] == 0)
         return(Inf)
-      return(.times[1, 'time'] - .now())
+      return(.times[1, 'time'] - now())
     },
     takeElapsed = function() {
-      t <- .now()
-      elapsed <- .times$time <= .now()
+      t <- now()
+      elapsed <- .times$time < now()
       result <- .times[elapsed,]
       .times <<- .times[!elapsed,]
 
       # TODO: Examine scheduled column to check if any funny business
       #       has occurred with the system clock (e.g. if scheduled
-      #       is later than .now())
+      #       is later than now())
 
       return(result)
     },
@@ -87,31 +86,8 @@ TimerCallbacks <- R6Class(
   )
 )
 
-MockableTimerCallbacks <- R6Class(
-  'MockableTimerCallbacks',
-  inherit = TimerCallbacks,
-  portable = FALSE,
-  class = FALSE,
-  public = list(
-    # Empty constructor defaults to the getNow implementation
-    initialize = function() {
-      super$initialize(self$mockNow)
-    },
-    mockNow = function() {
-      return(private$time)
-    },
-    elapse = function(millis) {
-      private$time <- private$time + millis
-    },
-    getElapsed = function() {
-      private$time
-    }
-  ), private = list(
-    time = 0L
-  )
-)
-
-timerCallbacks <- TimerCallbacks$new()
+# Initialized in onLoad() because TimerCallbacks uses Map.
+timerCallbacks <- NULL
 
 scheduleTask <- function(millis, callback) {
   cancelled <- FALSE
@@ -121,27 +97,3 @@ scheduleTask <- function(millis, callback) {
     invisible(timerCallbacks$unschedule(id))
   }
 }
-
-#' Get a scheduler function for scheduling tasks. Give priority to the
-#' session scheduler, but if it doesn't exist, use the global one.
-#' @noRd
-defineScheduler <- function(session){
-  if (!is.null(session) && !is.null(session$.scheduleTask)){
-    return(session$.scheduleTask)
-  }
-  scheduleTask
-}
-
-
-#' Get the current time using the current reactive domain. This will try to use
-#' the session's .now() method, but if that's not available, it will just return
-#' the real time (from getTimeMs()). The purpose of this function is to allow
-#' MockableTimerCallbacks to work.
-#' @noRd
-getDomainTimeMs <- function(session){
-  if (!is.null(session) && !is.null(session$.now)){
-    return(session$.now())
-  } else {
-    getTimeMs()
-  }
-}

R/update-input.R

@@ -4,7 +4,7 @@
 #' @param value The value to set for the input object.
 #' @param placeholder The placeholder to set for the input object.
 #'
-#' @seealso [textInput()]
+#' @seealso \code{\link{textInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -45,7 +45,7 @@ updateTextInput <- function(session, inputId, label = NULL, value = NULL, placeh
 #' @template update-input
 #' @inheritParams updateTextInput
 #'
-#' @seealso [textAreaInput()]
+#' @seealso \code{\link{textAreaInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -84,7 +84,7 @@ updateTextAreaInput <- updateTextInput
 #' @template update-input
 #' @param value The value to set for the input object.
 #'
-#' @seealso [checkboxInput()]
+#' @seealso \code{\link{checkboxInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -117,24 +117,22 @@ updateCheckboxInput <- function(session, inputId, label = NULL, value = NULL) {
 #'
 #' @template update-input
 #' @param icon The icon to set for the input object. To remove the
-#' current icon, use `icon=character(0)`.
+#' current icon, use \code{icon=character(0)}.
 #'
-#' @seealso [actionButton()]
+#' @seealso \code{\link{actionButton}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
 #' if (interactive()) {
 #'
 #' ui <- fluidPage(
-#'   actionButton("update", "Update other buttons and link"),
+#'   actionButton("update", "Update other buttons"),
 #'   br(),
 #'   actionButton("goButton", "Go"),
 #'   br(),
 #'   actionButton("goButton2", "Go 2", icon = icon("area-chart")),
 #'   br(),
-#'   actionButton("goButton3", "Go 3"),
-#'   br(),
-#'   actionLink("goLink", "Go Link")
+#'   actionButton("goButton3", "Go 3")
 #' )
 #'
 #' server <- function(input, output, session) {
@@ -155,39 +153,30 @@ updateCheckboxInput <- function(session, inputId, label = NULL, value = NULL) {
 #'     # unchaged and changes its label
 #'     updateActionButton(session, "goButton3",
 #'       label = "New label 3")
-#'
-#'     # Updates goLink's label and icon
-#'     updateActionButton(session, "goLink",
-#'       label = "New link label",
-#'       icon = icon("link"))
 #'   })
 #' }
 #'
 #' shinyApp(ui, server)
 #' }
-#' @rdname updateActionButton
 #' @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)
 }
-#' @rdname updateActionButton
-#' @export
-updateActionLink <- updateActionButton
 
 
 #' 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
-#'   `yyyy-mm-dd` format. Supply `NA` to clear the date.
+#'   \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
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #'
-#' @seealso [dateInput()]
+#' @seealso \code{\link{dateInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -229,15 +218,15 @@ updateDateInput <- function(session, inputId, label = NULL, value = NULL,
 #'
 #' @template update-input
 #' @param start The start date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format. Supplying `NA` clears the start date.
+#'   \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
-#'   `yyyy-mm-dd` format. Supplying `NA` clears the end date.
+#'   \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
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #' @param max The maximum allowed date. Either a Date object, or a string in
-#'   `yyyy-mm-dd` format.
+#'   \code{yyyy-mm-dd} format.
 #'
-#' @seealso [dateRangeInput()]
+#' @seealso \code{\link{dateRangeInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -286,14 +275,14 @@ updateDateRangeInput <- function(session, inputId, label = NULL,
 
 #' Change the selected tab on the client
 #'
-#' @param session The `session` object passed to function given to
-#'   `shinyServer`.
-#' @param inputId The id of the `tabsetPanel`, `navlistPanel`,
-#' or `navbarPage` object.
+#' @param session The \code{session} object passed to function given to
+#'   \code{shinyServer}.
+#' @param inputId The id of the \code{tabsetPanel}, \code{navlistPanel},
+#' or \code{navbarPage} object.
 #' @param selected The name of the tab to make active.
 #'
-#' @seealso [tabsetPanel()], [navlistPanel()],
-#' [navbarPage()]
+#' @seealso \code{\link{tabsetPanel}}, \code{\link{navlistPanel}},
+#' \code{\link{navbarPage}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -344,7 +333,7 @@ updateNavlistPanel <- updateTabsetPanel
 #' @param max Maximum value.
 #' @param step Step size.
 #'
-#' @seealso [numericInput()]
+#' @seealso \code{\link{numericInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -396,7 +385,7 @@ updateNumericInput <- function(session, inputId, label = NULL, value = NULL,
 #' @param timeFormat Date and POSIXt formatting.
 #' @param timezone The timezone offset for POSIXt objects.
 #'
-#' @seealso [sliderInput()]
+#' @seealso \code{\link{sliderInput}}
 #'
 #' @examples
 #' ## Only run this example in interactive R sessions
@@ -484,7 +473,7 @@ updateInputOptions <- function(session, inputId, label = NULL, choices = NULL,
 #' @template update-input
 #' @inheritParams checkboxGroupInput
 #'
-#' @seealso [checkboxGroupInput()]
+#' @seealso \code{\link{checkboxGroupInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -531,7 +520,7 @@ updateCheckboxGroupInput <- function(session, inputId, label = NULL,
 #' @template update-input
 #' @inheritParams radioButtons
 #'
-#' @seealso [radioButtons()]
+#' @seealso \code{\link{radioButtons}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -579,7 +568,7 @@ updateRadioButtons <- function(session, inputId, label = NULL, choices = NULL,
 #' @template update-input
 #' @inheritParams selectInput
 #'
-#' @seealso [selectInput()] [varSelectInput()]
+#' @seealso \code{\link{selectInput}} \code{\link{varSelectInput}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -624,9 +613,9 @@ updateSelectInput <- function(session, inputId, label = NULL, choices = NULL,
 
 #' @rdname updateSelectInput
 #' @inheritParams selectizeInput
-#' @param server whether to store `choices` on the server side, and load
+#' @param server whether to store \code{choices} on the server side, and load
 #'   the select options dynamically on searching, instead of writing all
-#'   `choices` into the page at once (i.e., only use the client-side
+#'   \code{choices} into the page at once (i.e., only use the client-side
 #'   version of \pkg{selectize.js})
 #' @export
 updateSelectizeInput <- function(session, inputId, label = NULL, choices = NULL,

R/utils.R

@@ -14,7 +14,7 @@ NULL
 #'
 #' @note When called, the returned function attempts to preserve the R session's
 #'   current seed by snapshotting and restoring
-#'   [base::.Random.seed()].
+#'   \code{\link[base]{.Random.seed}}.
 #'
 #' @examples
 #' rnormA <- repeatable(rnorm)
@@ -173,12 +173,12 @@ anyUnnamed <- function(x) {
 }
 
 
-# Given a vector/list, returns a named vector/list (the labels will be blank).
-asNamed <- function(x) {
-  if (is.null(names(x))) {
-    names(x) <- character(length(x))
-  }
+# Given a vector/list, returns a named vector (the labels will be blank).
+asNamedVector <- function(x) {
+  if (!is.null(names(x)))
+    return(x)
 
+  names(x) <- rep.int("", length(x))
   x
 }
 
@@ -316,15 +316,6 @@ resolve <- function(dir, relpath) {
   return(abs.path)
 }
 
-# Given a string, make sure it has a trailing slash.
-ensure_trailing_slash <- function(path) {
-  if (!grepl("/$", path)) {
-    path <- paste0(path, "/")
-  }
-  path
-}
-
-
 isWindows <- function() .Platform$OS.type == 'windows'
 
 # This is a wrapper for download.file and has the same interface.
@@ -477,12 +468,12 @@ exprToFunction <- function(expr, env=parent.frame(), quoted=FALSE) {
 #' Installs an expression in the given environment as a function, and registers
 #' debug hooks so that breakpoints may be set in the function.
 #'
-#' This function can replace `exprToFunction` as follows: we may use
-#' `func <- exprToFunction(expr)` if we do not want the debug hooks, or
-#' `installExprFunction(expr, "func")` if we do. Both approaches create a
-#' function named `func` in the current environment.
+#' This function can replace \code{exprToFunction} as follows: we may use
+#' \code{func <- exprToFunction(expr)} if we do not want the debug hooks, or
+#' \code{installExprFunction(expr, "func")} if we do. Both approaches create a
+#' function named \code{func} in the current environment.
 #'
-#' @seealso Wraps [exprToFunction()]; see that method's documentation
+#' @seealso Wraps \code{\link{exprToFunction}}; see that method's documentation
 #'   for more documentation and examples.
 #'
 #' @param expr A quoted or unquoted expression
@@ -494,7 +485,7 @@ exprToFunction <- function(expr, env=parent.frame(), quoted=FALSE) {
 #' @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
-#'   [stacktrace()].
+#'   \code{\link{stacktrace}}.
 #' @export
 installExprFunction <- function(expr, name, eval.env = parent.frame(2),
                                 quoted = FALSE,
@@ -525,7 +516,6 @@ installExprFunction <- function(expr, name, eval.env = parent.frame(2),
 #'
 #' Returns a named list of key-value pairs.
 #'
-#' @noMd
 #' @param str The query string. It can have a leading \code{"?"} or not.
 #' @param nested Whether to parse the query string of as a nested list when it
 #'   contains pairs of square brackets \code{[]}. For example, the query
@@ -623,7 +613,7 @@ shinyCallingHandlers <- function(expr) {
 
 #' Print message for deprecated functions in Shiny
 #'
-#' To disable these messages, use `options(shiny.deprecation.messages=FALSE)`.
+#' To disable these messages, use \code{options(shiny.deprecation.messages=FALSE)}.
 #'
 #' @param new Name of replacement function.
 #' @param msg Message to print. If used, this will override the default message.
@@ -809,14 +799,7 @@ dataTablesJSON <- function(data, req) {
 
   fdata <- unname(as.matrix(fdata))
   if (is.character(fdata) && q$escape != 'false') {
-    if (q$escape == 'true') {
-      # fdata must be a matrix at this point, and we need to preserve
-      # dimensions. Note that it could be a 1xn matrix.
-      dims <- dim(fdata)
-      fdata <- htmlEscape(fdata)
-      dim(fdata) <- dims
-
-    } else {
+    if (q$escape == 'true') fdata <- htmlEscape(fdata) else {
       k <- as.integer(strsplit(q$escape, ',')[[1]])
       # use seq_len() in case escape = negative indices, e.g. c(-1, -5)
       for (j in seq_len(ncol(fdata))[k]) fdata[, j] <- htmlEscape(fdata[, j])
@@ -966,28 +949,28 @@ columnToRowData <- function(data) {
 #'
 #' 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 `e` and call `stop(safeError(e))`, then Shiny will
-#' ignore the value of `getOption("shiny.sanitize.errors")` and always
+#' 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 `safeError`.
+#' returned by \code{safeError}.
 #'
 #' @return An "error" object
 #'
-#' @details An error generated by `safeError` has priority over all
+#' @details An error generated by \code{safeError} has priority over all
 #' other Shiny errors. This can be dangerous. For example, if you have set
-#' `options(shiny.sanitize.errors = TRUE)`, then by default all error
+#' \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 `safeError`: whatever you pass
-#' through `error` will be displayed to the user. So, this should only
+#' 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, `safeError` can make
+#' 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 [shiny-options()]
+#' @seealso \code{\link{shiny-options}}
 #'
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -1101,58 +1084,58 @@ reactiveStop <- function(message = "", class = NULL) {
 
 #' Validate input values and other conditions
 #'
-#' For an output rendering function (e.g. [renderPlot()]), you may
+#' For an output rendering function (e.g. \code{\link{renderPlot}()}), you may
 #' need to check that certain input values are available and valid before you
-#' can render the output. `validate` gives you a convenient mechanism for
+#' can render the output. \code{validate} gives you a convenient mechanism for
 #' doing so.
 #'
-#' The `validate` function takes any number of (unnamed) arguments, each of
+#' The \code{validate} function takes any number of (unnamed) arguments, each of
 #' which represents a condition to test. If any of the conditions represent
 #' failure, then a special type of error is signaled which stops execution. If
 #' this error is not handled by application-specific code, it is displayed to
 #' the user by Shiny.
 #'
-#' An easy way to provide arguments to `validate` is to use the `need`
+#' An easy way to provide arguments to \code{validate} is to use the \code{need}
 #' function, which takes an expression and a string; if the expression is
 #' considered a failure, then the string will be used as the error message. The
-#' `need` function considers its expression to be a failure if it is any of
+#' \code{need} function considers its expression to be a failure if it is any of
 #' the following:
 #'
 #' \itemize{
-#'   \item{`FALSE`}
-#'   \item{`NULL`}
-#'   \item{`""`}
+#'   \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 `FALSE` or missing values}
-#'   \item{An object of class `"try-error"`}
-#'   \item{A value that represents an unclicked [actionButton()]}
+#'   \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}}}
 #' }
 #'
 #' If any of these values happen to be valid, you can explicitly turn them to
-#' logical values. For example, if you allow `NA` but not `NULL`, you
-#' can use the condition `!is.null(input$foo)`, because `!is.null(NA)
-#' == TRUE`.
+#' logical values. For example, if you allow \code{NA} but not \code{NULL}, you
+#' can use the condition \code{!is.null(input$foo)}, because \code{!is.null(NA)
+#' == TRUE}.
 #'
-#' If you need validation logic that differs significantly from `need`, you
+#' If you need validation logic that differs significantly from \code{need}, you
 #' can create other validation test functions. A passing test should return
-#' `NULL`. A failing test should return an error message as a
+#' \code{NULL}. A failing test should return an error message as a
 #' single-element character vector, or if the failure should happen silently,
-#' `FALSE`.
+#' \code{FALSE}.
 #'
 #' Because validation failure is signaled as an error, you can use
-#' `validate` in reactive expressions, and validation failures will
+#' \code{validate} in reactive expressions, and validation failures will
 #' automatically propagate to outputs that use the reactive expression. In
-#' other words, if reactive expression `a` needs `input$x`, and two
-#' outputs use `a` (and thus depend indirectly on `input$x`), it's
-#' not necessary for the outputs to validate `input$x` explicitly, as long
-#' as `a` does validate it.
+#' other words, if reactive expression \code{a} needs \code{input$x}, and two
+#' outputs use \code{a} (and thus depend indirectly on \code{input$x}), it's
+#' not necessary for the outputs to validate \code{input$x} explicitly, as long
+#' as \code{a} does validate it.
 #'
-#' @param ... A list of tests. Each test should equal `NULL` for success,
-#'   `FALSE` for silent failure, or a string for failure with an error
+#' @param ... A list of tests. Each test should equal \code{NULL} for success,
+#'   \code{FALSE} for silent failure, or a string for failure with an error
 #'   message.
 #' @param errorClass A CSS class to apply. The actual CSS string will have
-#'   `shiny-output-error-` prepended to this value.
+#'   \code{shiny-output-error-} prepended to this value.
 #' @export
 #' @examples
 #' ## Only run examples in interactive R sessions
@@ -1204,10 +1187,10 @@ validate <- function(..., errorClass = character(0)) {
 #' @param expr An expression to test. The condition will pass if the expression
 #'   meets the conditions spelled out in Details.
 #' @param message A message to convey to the user if the validation condition is
-#'   not met. If no message is provided, one will be created using `label`.
-#'   To fail with no message, use `FALSE` for the message.
+#'   not met. If no message is provided, one will be created using \code{label}.
+#'   To fail with no message, use \code{FALSE} for the message.
 #' @param label A human-readable name for the field that may be missing. This
-#'   parameter is not needed if `message` is provided, but must be provided
+#'   parameter is not needed if \code{message} is provided, but must be provided
 #'   otherwise.
 #' @export
 #' @rdname validate
@@ -1228,7 +1211,7 @@ need <- function(expr, message = paste(label, "must be provided"), label) {
 #' operation is stopped by raising a "silent" exception (not logged by Shiny,
 #' nor displayed in the Shiny app's UI).
 #'
-#' The `req` function was designed to be used in one of two ways. The first
+#' 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:
 #'
@@ -1238,9 +1221,9 @@ need <- function(expr, message = paste(label, "must be provided"), label) {
 #'   # Code that uses input$a, input$b, and/or rv$state...
 #' })}
 #'
-#' In this example, if `r()` is called and any of `input$a`,
-#' `input$b`, and `rv$state` are `NULL`, `FALSE`, `""`,
-#' etc., then the `req` call will trigger an error that propagates all the
+#' In this example, if \code{r()} is called and any of \code{input$a},
+#' \code{input$b}, and \code{rv$state} are \code{NULL}, \code{FALSE}, \code{""},
+#' etc., then the \code{req} call will trigger an error that propagates all the
 #' way up to whatever render block or observer is executing.
 #'
 #' The second is to use it to wrap an expression that must be truthy:
@@ -1253,70 +1236,70 @@ need <- function(expr, message = paste(label, "must be provided"), label) {
 #'   }
 #' })}
 #'
-#' In this example, `req(input$plotType)` first checks that
-#' `input$plotType` is truthy, and if so, returns it. This is a convenient
+#' In this example, \code{req(input$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.
 #'
-#' **Truthy and falsy values**
+#' \strong{Truthy and falsy values}
 #'
 #' The terms "truthy" and "falsy" generally indicate whether a value, when
-#' coerced to a [base::logical()], is `TRUE` or `FALSE`. We use
+#' coerced to a \code{\link[base]{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 `textInput` that has not been filled out by the user has
-#' a value of `""`, so that is considered a falsy value.
+#' 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, `req` considers a value truthy *unless* it is one
+#' To be precise, \code{req} considers a value truthy \emph{unless} it is one
 #' of:
 #'
 #' \itemize{
-#'   \item{`FALSE`}
-#'   \item{`NULL`}
-#'   \item{`""`}
+#'   \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 `FALSE` or missing values}
-#'   \item{An object of class `"try-error"`}
-#'   \item{A value that represents an unclicked [actionButton()]}
+#'   \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 `0` is considered truthy, even though
-#' `as.logical(0)` is `FALSE`.
+#' 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 `FALSE` is falsy, you can simply provide
-#' the results of your own checks to `req`:
+#' always work around them. Since \code{FALSE} is falsy, you can simply provide
+#' the results of your own checks to \code{req}:
 #'
-#' `req(input$a != 0)`
+#' \code{req(input$a != 0)}
 #'
-#' **Using `req(FALSE)`**
+#' \strong{Using \code{req(FALSE)}}
 #'
-#' You can use `req(FALSE)` (i.e. no condition) if you've already performed
+#' You can use \code{req(FALSE)} (i.e. no condition) if you've already performed
 #' all the checks you needed to by that point and just want to stop the reactive
 #' chain now. There is no advantange to this, except perhaps ease of readibility
 #' if you have a complicated condition to check for (or perhaps if you'd like to
-#' divide your condition into nested `if` statements).
+#' divide your condition into nested \code{if} statements).
 #'
-#' **Using `cancelOutput = TRUE`**
+#' \strong{Using \code{cancelOutput = TRUE}}
 #'
-#' When `req(..., cancelOutput = TRUE)` is used, the "silent" exception is
+#' When \code{req(..., cancelOutput = TRUE)} is used, the "silent" exception is
 #' also raised, but it is treated slightly differently if one or more outputs are
 #' currently being evaluated. In those cases, the reactive chain does not proceed
 #' or update, but the output(s) are left is whatever state they happen to be in
 #' (whatever was their last valid state).
 #'
 #' Note that this is always going to be the case if
-#' this is used inside an output context (e.g. `output$txt <- ...`). It may
+#' this is used inside an output context (e.g. \code{output$txt <- ...}). It may
 #' or may not be the case if it is used inside a non-output context (e.g.
-#' [reactive()], [observe()] or [observeEvent()])
-#' --- depending on whether or not there is an `output$...` that is triggered
+#' \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 `TRUE` and an output is being evaluated, stop
+#' @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
@@ -1455,7 +1438,7 @@ stopWithCondition <- function(class, message) {
 #' This function returns the information about the current Shiny Server, such as
 #' its version, and whether it is the open source edition or professional
 #' edition. If the app is not served through the Shiny Server, this function
-#' just returns `list(shinyServer = FALSE)`.
+#' just returns \code{list(shinyServer = FALSE)}.
 #'
 #' This function will only return meaningful data when using Shiny Server
 #' version 1.2.2 or later.
@@ -1816,60 +1799,3 @@ constantTimeEquals <- function(raw1, raw2) {
 
   sum(as.integer(xor(raw1, raw2))) == 0
 }
-
-cat_line <- function(...) {
-  cat(paste(..., "\n", collapse = ""))
-}
-
-select_menu <- function(choices, title = NULL, msg = "Enter one or more numbers (with spaces), or an empty line to exit: \n")
-{
-  if (!is.null(title)) {
-    cat(title, "\n", sep = "")
-  }
-  nc <- length(choices)
-  op <- paste0(format(seq_len(nc)), ": ", choices)
-  fop <- format(op)
-  cat("", fop, "", sep = "\n")
-  repeat {
-    answer <- readline(msg)
-    answer <- strsplit(answer, "[ ,]+")[[1]]
-    if (all(answer %in% seq_along(choices))) {
-      return(choices[as.integer(answer)])
-    }
-  }
-}
-
-#' @noRd
-isAppDir <- function(path) {
-
-  if (file.exists(file.path.ci(path, "app.R")))
-    return(TRUE)
-
-  if (file.exists(file.path.ci(path, "server.R"))
-      && file.exists(file.path.ci(path, "ui.R")))
-    return(TRUE)
-
-  FALSE
-}
-
-# Borrowed from rprojroot which borrowed from devtools
-#' @noRd
-is_root <- function(path) {
-  identical(
-    normalizePath(path, winslash = "/"),
-    normalizePath(dirname(path), winslash = "/")
-  )
-}
-
-#' @noRd
-findEnclosingApp <- function(path = ".") {
-  orig_path <- path
-  path <- normalizePath(path, winslash = "/", mustWork = TRUE)
-  repeat {
-    if (isAppDir(path))
-      return(path)
-    if (is_root(path))
-      stop("Shiny app not found at ", orig_path, " or in any parent directory.")
-    path <- dirname(path)
-  }
-}

README.md

@@ -61,7 +61,7 @@ The Javascript code in Shiny is minified using tools that run on Node.js. See th
 
 ## Guidelines for contributing
 
-We welcome contributions to the **shiny** package. Please see our [CONTRIBUTING.md](https://github.com/rstudio/shiny/blob/master/.github/CONTRIBUTING.md) file for detailed guidelines of how to contribute.
+We welcome contributions to the **shiny** package. Please see our [CONTRIBUTING.md](CONTRIBUTING.md) file for detailed guidelines of how to contribute.
 
 ## License
 

appveyor.yml

@@ -11,12 +11,7 @@ install:
   ps: Bootstrap
 
 cache:
-  # Bust library cache every time the description file changes
-  #   as appveyor cache can not be busted manually
-  # This helps get around errors such as "can't update curl because it's already loaded"
-  #  when trying to update the existing cache
-  # PR: https://github.com/rstudio/shiny/pull/2722
-  - C:\RLibrary -> DESCRIPTION
+  - C:\RLibrary
 
 # Adapt as necessary starting from here
 

inst/app_template/R/my-module.R

@@ -1,27 +0,0 @@
-mymoduleUI <- function(id, label = "Counter") {
-  # Al uses of Shiny input/output IDs in the UI must be namespaced,
-  # as in ns("x").
-  ns <- NS(id)
-  tagList(
-    actionButton(ns("button"), label = label),
-    verbatimTextOutput(ns("out"))
-  )
-}
-
-mymoduleServer <- function(id) {
-  # moduleServer() wraps a function to create the server component of a
-  # module.
-  moduleServer(
-    id,
-    function(input, output, session) {
-      count <- reactiveVal(0)
-      observeEvent(input$button, {
-        count(count() + 1)
-      })
-      output$out <- renderText({
-        count()
-      })
-      count
-    }
-  )
-}

inst/app_template/R/sort.R

@@ -1,5 +0,0 @@
-# Given a numeric vector, convert to strings, sort, and convert back to
-# numeric.
-lexical_sort <- function(x) {
-  as.numeric(sort(as.character(x)))
-}

inst/app_template/app.R

@@ -1,52 +0,0 @@
-ui <- fluidPage(
-{{
-# These blocks of code are processed with htmlTemplate()
-if (isTRUE(module)) {
-'  # ======== Modules ========
-  # mymoduleUI is defined in R/my-module.R
-  mymoduleUI("mymodule1", "Click counter #1"),
-  mymoduleUI("mymodule2", "Click counter #2"),
-  # =========================
-'
-}
-}}
-  wellPanel(
-    sliderInput("size", "Data size", min = 5, max = 20, value = 10),
-{{
-if (isTRUE(rdir)) {
-  '    div("Lexically sorted sequence:"),'
-} else {
-  '    div("Sorted sequence:"),'
-}
-}}
-    verbatimTextOutput("sequence")
-  )
-)
-
-server <- function(input, output, session) {
-{{
-if (isTRUE(module)) {
-'  # ======== Modules ========
-  # mymoduleServer is defined in R/my-module.R
-  mymoduleServer("mymodule1")
-  mymoduleServer("mymodule2")
-  # =========================
-'
-}
-}}
-  data <- reactive({
-{{
-if (isTRUE(rdir)) {
-'    # lexical_sort from R/sort.R
-    lexical_sort(seq_len(input$size))'
-} else {
-'    sort(seq_len(input$size))'
-}
-}}
-  })
-  output$sequence <- renderText({
-    paste(data(), collapse = " ")
-  })
-}
-
-shinyApp(ui, server)

inst/app_template/tests/shinytest.R

@@ -1,3 +0,0 @@
-library(shinytest)
-shinytest::testApp("../")
-

inst/app_template/tests/shinytest/mytest.R

@@ -1,12 +0,0 @@
-app <- ShinyDriver$new("../../")
-app$snapshotInit("mytest")
-
-app$snapshot()
-{{
-if (isTRUE(module)) {
-'
-app$setInputs(`mymodule1-button` = "click")
-app$setInputs(`mymodule1-button` = "click")
-app$snapshot()'
-}
-}}

inst/app_template/tests/testthat.R

@@ -1,9 +0,0 @@
-library(testthat)
-
-test_dir(
-  "./testthat",
-  # Run in the app's environment containing all support methods.
-  env = shiny::loadSupport(),
-  # Display the regular progress output and throw an error if any test error is found
-  reporter = c("progress", "fail")
-)

inst/app_template/tests/testthat/test-mymodule.R

@@ -1,18 +0,0 @@
-context("mymoduleServer")
-
-# See ?testServer for more information
-testServer(mymoduleServer, {
-  # Set initial value of a button
-  session$setInputs(button = 0)
-
-  # Check the value of the reactiveVal `count()`
-  expect_equal(count(), 1)
-  # Check the value of the renderText()
-  expect_equal(output$out, "1")
-
-  # Simulate a click
-  session$setInputs(button = 1)
-
-  expect_equal(count(), 2)
-  expect_equal(output$out, "2")
-})

inst/app_template/tests/testthat/test-server.R

@@ -1,20 +0,0 @@
-context("app")
-
-testServer(expr = {
-  # Set the `size` slider and check the output
-  session$setInputs(size = 6)
-  expect_equal(output$sequence, "1 2 3 4 5 6")
-{{
-if (isTRUE(rdir)) {
-'
-  session$setInputs(size = 12)
-  expect_equal(output$sequence, "1 10 11 12 2 3 4 5 6 7 8 9")
-'
-} else {
-'
-  session$setInputs(size = 12)
-  expect_equal(output$sequence, "1 2 3 4 5 6 7 8 9 10 11 12")
-'
-}
-}}
-})

inst/app_template/tests/testthat/test-sort.R

@@ -1,7 +0,0 @@
-# Test the lexical_sort function from R/utils.R
-context("sort")
-
-test_that("Lexical sorting works", {
-  expect_equal(lexical_sort(c(1, 2, 3)), c(1, 2, 3))
-  expect_equal(lexical_sort(c(1, 2, 3, 13, 11, 21)), c(1, 11, 13, 2, 21, 3))
-})

inst/staticdocs/index.r

@@ -0,0 +1,243 @@
+sd_section("UI Layout",
+  "Functions for laying out the user interface for your application.",
+  c(
+    "absolutePanel",
+    "bootstrapPage",
+    "column",
+    "conditionalPanel",
+    "fillPage",
+    "fillRow",
+    "fixedPage",
+    "fluidPage",
+    "headerPanel",
+    "helpText",
+    "icon",
+    "mainPanel",
+    "navbarPage",
+    "navlistPanel",
+    "pageWithSidebar",
+    "sidebarLayout",
+    "sidebarPanel",
+    "tabPanel",
+    "tabsetPanel",
+    "titlePanel",
+    "inputPanel",
+    "flowLayout",
+    "splitLayout",
+    "verticalLayout",
+    "wellPanel",
+    "withMathJax"
+  )
+)
+sd_section("UI Inputs",
+  "Functions for creating user interface elements that prompt the user for input values or interaction.",
+  c(
+    "actionButton",
+    "checkboxGroupInput",
+    "checkboxInput",
+    "dateInput",
+    "dateRangeInput",
+    "fileInput",
+    "numericInput",
+    "radioButtons",
+    "selectInput",
+    "varSelectInput",
+    "sliderInput",
+    "submitButton",
+    "textInput",
+    "textAreaInput",
+    "passwordInput",
+    "modalButton",
+    "updateActionButton",
+    "updateCheckboxGroupInput",
+    "updateCheckboxInput",
+    "updateDateInput",
+    "updateDateRangeInput",
+    "updateNumericInput",
+    "updateRadioButtons",
+    "updateSelectInput",
+    "updateSliderInput",
+    "updateTabsetPanel",
+    "insertTab",
+    "showTab",
+    "updateTextInput",
+    "updateTextAreaInput",
+    "updateQueryString",
+    "getQueryString"
+  )
+)
+sd_section("UI Outputs",
+  "Functions for creating user interface elements that, in conjunction with rendering functions, display different kinds of output from your application.",
+  c(
+    "htmlOutput",
+    "plotOutput",
+    "outputOptions",
+    "tableOutput",
+    "textOutput",
+    "verbatimTextOutput",
+    "downloadButton",
+    "Progress",
+    "withProgress",
+    "modalDialog",
+    "urlModal",
+    "showModal",
+    "showNotification"
+  )
+)
+sd_section("Interface builder functions",
+  "A sub-library for writing HTML using R functions. These functions form the foundation on which the higher level user interface functions are built, and can also be used in your Shiny UI to provide custom HTML, CSS, and JavaScript.",
+  c(
+    "builder",
+    "HTML",
+    "include",
+    "singleton",
+    "tag",
+    "validateCssUnit",
+    "withTags",
+    "htmlTemplate",
+    "bootstrapLib",
+    "suppressDependencies",
+    "insertUI",
+    "removeUI"
+  )
+)
+sd_section("Rendering functions",
+  "Functions that you use in your application's server side code, assigning them to outputs that appear in your user interface.",
+  c(
+    "renderPlot",
+    "renderCachedPlot",
+    "renderText",
+    "renderPrint",
+    "renderDataTable",
+    "renderImage",
+    "renderTable",
+    "renderUI",
+    "downloadHandler",
+    "reactivePlot",
+    "reactivePrint",
+    "reactiveTable",
+    "reactiveText",
+    "reactiveUI",
+    "createRenderFunction"
+  )
+)
+sd_section("Reactive programming",
+  "A sub-library that provides reactive programming facilities for R.",
+  c(
+    "reactive",
+    "observe",
+    "observeEvent",
+    "reactiveVal",
+    "reactiveValues",
+    "reactiveValuesToList",
+    "is.reactivevalues",
+    "isolate",
+    "invalidateLater",
+    "debounce",
+    "reactlog",
+    "makeReactiveBinding",
+    "reactiveFileReader",
+    "reactivePoll",
+    "reactiveTimer",
+    "domains",
+    "freezeReactiveValue"
+  )
+)
+sd_section("Boilerplate",
+  "Functions that are required boilerplate in ui.R and server.R.",
+  c(
+    "shinyUI",
+    "shinyServer"
+  )
+)
+sd_section("Running",
+  "Functions that are used to run or stop Shiny applications.",
+  c(
+    "runApp",
+    "runGadget",
+    "runExample",
+    "runGadget",
+    "runUrl",
+    "stopApp",
+    "viewer",
+    "isRunning"
+  )
+)
+sd_section("Bookmarking state",
+  "Functions that are used for bookmarking and restoring state.",
+  c(
+    "bookmarkButton",
+    "enableBookmarking",
+    "setBookmarkExclude",
+    "showBookmarkUrlModal",
+    "onBookmark"
+  )
+)
+sd_section("Extending Shiny",
+  "Functions that are intended to be called by third-party packages that extend Shiny.",
+  c(
+    "createWebDependency",
+    "addResourcePath",
+    "registerInputHandler",
+    "removeInputHandler",
+    "markRenderFunction"
+  )
+)
+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",
+    "getCurrentOutputInfo",
+    "plotPNG",
+    "sizeGrowthRatio",
+    "exportTestValues",
+    "setSerializer",
+    "snapshotExclude",
+    "snapshotPreprocessInput",
+    "snapshotPreprocessOutput",
+    "markOutputAttrs",
+    "repeatable",
+    "shinyDeprecated",
+    "serverInfo",
+    "shiny-options",
+    "onStop",
+    "diskCache",
+    "memoryCache",
+    "key_missing"
+  )
+)
+sd_section("Plot interaction",
+  "Functions related to interactive plots",
+  c(
+    "brushedPoints",
+    "brushOpts",
+    "clickOpts",
+    "dblclickOpts",
+    "hoverOpts",
+    "nearPoints"
+  )
+)
+sd_section("Modules",
+  "Functions for modularizing Shiny apps",
+  c(
+    "NS",
+    "callModule"
+  )
+)
+sd_section("Embedding",
+  "Functions that are intended for third-party packages that embed Shiny applications.",
+  c(
+    "shinyApp",
+    "maskReactiveContext"
+  )
+)

inst/template/error.html

@@ -1,13 +0,0 @@
-<html>
-
-<head>
-  <title>An error has occurred</title>
-</head>
-
-<body>
-
-<h1>An error has occurred!</h1>
-<p>{{message}}</p>
-
-</body>
-</html>

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

@@ -1,6 +1,6 @@
 /*!
- * Bootstrap v3.4.1 (https://getbootstrap.com/)
- * Copyright 2011-2019 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,
@@ -9,9 +9,9 @@
 .btn-info,
 .btn-warning,
 .btn-danger {
-  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.2);
-  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.15), 0 1px 1px rgba(0, 0, 0, 0.075);
-  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.15), 0 1px 1px rgba(0, 0, 0, 0.075);
+  text-shadow: 0 -1px 0 rgba(0, 0, 0, .2);
+  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
+          box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 1px rgba(0, 0, 0, .075);
 }
 .btn-default:active,
 .btn-primary:active,
@@ -25,8 +25,8 @@
 .btn-info.active,
 .btn-warning.active,
 .btn-danger.active {
-  -webkit-box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
-  box-shadow: inset 0 3px 5px rgba(0, 0, 0, 0.125);
+  -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,
@@ -47,7 +47,7 @@ fieldset[disabled] .btn-info,
 fieldset[disabled] .btn-warning,
 fieldset[disabled] .btn-danger {
   -webkit-box-shadow: none;
-  box-shadow: none;
+          box-shadow: none;
 }
 .btn-default .badge,
 .btn-primary .badge,
@@ -62,15 +62,15 @@ fieldset[disabled] .btn-danger {
   background-image: none;
 }
 .btn-default {
+  text-shadow: 0 1px 0 #fff;
   background-image: -webkit-linear-gradient(top, #fff 0%, #e0e0e0 100%);
-  background-image: -o-linear-gradient(top, #fff 0%, #e0e0e0 100%);
+  background-image:      -o-linear-gradient(top, #fff 0%, #e0e0e0 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#e0e0e0));
-  background-image: linear-gradient(to bottom, #fff 0%, #e0e0e0 100%);
+  background-image:         linear-gradient(to bottom, #fff 0%, #e0e0e0 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe0e0e0', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
   border-color: #dbdbdb;
-  text-shadow: 0 1px 0 #fff;
   border-color: #ccc;
 }
 .btn-default:hover,
@@ -106,9 +106,9 @@ fieldset[disabled] .btn-default.active {
 }
 .btn-primary {
   background-image: -webkit-linear-gradient(top, #337ab7 0%, #265a88 100%);
-  background-image: -o-linear-gradient(top, #337ab7 0%, #265a88 100%);
+  background-image:      -o-linear-gradient(top, #337ab7 0%, #265a88 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#265a88));
-  background-image: linear-gradient(to bottom, #337ab7 0%, #265a88 100%);
+  background-image:         linear-gradient(to bottom, #337ab7 0%, #265a88 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff265a88', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
@@ -147,9 +147,9 @@ fieldset[disabled] .btn-primary.active {
 }
 .btn-success {
   background-image: -webkit-linear-gradient(top, #5cb85c 0%, #419641 100%);
-  background-image: -o-linear-gradient(top, #5cb85c 0%, #419641 100%);
+  background-image:      -o-linear-gradient(top, #5cb85c 0%, #419641 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#419641));
-  background-image: linear-gradient(to bottom, #5cb85c 0%, #419641 100%);
+  background-image:         linear-gradient(to bottom, #5cb85c 0%, #419641 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff419641', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
@@ -188,9 +188,9 @@ fieldset[disabled] .btn-success.active {
 }
 .btn-info {
   background-image: -webkit-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
-  background-image: -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
+  background-image:      -o-linear-gradient(top, #5bc0de 0%, #2aabd2 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#2aabd2));
-  background-image: linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%);
+  background-image:         linear-gradient(to bottom, #5bc0de 0%, #2aabd2 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff2aabd2', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
@@ -229,9 +229,9 @@ fieldset[disabled] .btn-info.active {
 }
 .btn-warning {
   background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
-  background-image: -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
+  background-image:      -o-linear-gradient(top, #f0ad4e 0%, #eb9316 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#eb9316));
-  background-image: linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%);
+  background-image:         linear-gradient(to bottom, #f0ad4e 0%, #eb9316 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffeb9316', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
@@ -270,9 +270,9 @@ fieldset[disabled] .btn-warning.active {
 }
 .btn-danger {
   background-image: -webkit-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
-  background-image: -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
+  background-image:      -o-linear-gradient(top, #d9534f 0%, #c12e2a 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c12e2a));
-  background-image: linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%);
+  background-image:         linear-gradient(to bottom, #d9534f 0%, #c12e2a 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc12e2a', GradientType=0);
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
   background-repeat: repeat-x;
@@ -311,81 +311,81 @@ fieldset[disabled] .btn-danger.active {
 }
 .thumbnail,
 .img-thumbnail {
-  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.075);
-  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.075);
+  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+          box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
 }
 .dropdown-menu > li > a:hover,
 .dropdown-menu > li > a:focus {
+  background-color: #e8e8e8;
   background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
-  background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+  background-image:      -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8));
-  background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+  background-image:         linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
   background-repeat: repeat-x;
-  background-color: #e8e8e8;
 }
 .dropdown-menu > .active > a,
 .dropdown-menu > .active > a:hover,
 .dropdown-menu > .active > a:focus {
+  background-color: #2e6da4;
   background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
-  background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
+  background-image:      -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4));
-  background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
+  background-image:         linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);
   background-repeat: repeat-x;
-  background-color: #2e6da4;
 }
 .navbar-default {
-  background-image: -webkit-linear-gradient(top, #ffffff 0%, #f8f8f8 100%);
-  background-image: -o-linear-gradient(top, #ffffff 0%, #f8f8f8 100%);
-  background-image: -webkit-gradient(linear, left top, left bottom, from(#ffffff), to(#f8f8f8));
-  background-image: linear-gradient(to bottom, #ffffff 0%, #f8f8f8 100%);
+  background-image: -webkit-linear-gradient(top, #fff 0%, #f8f8f8 100%);
+  background-image:      -o-linear-gradient(top, #fff 0%, #f8f8f8 100%);
+  background-image: -webkit-gradient(linear, left top, left bottom, from(#fff), to(#f8f8f8));
+  background-image:         linear-gradient(to bottom, #fff 0%, #f8f8f8 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#fff8f8f8', GradientType=0);
-  background-repeat: repeat-x;
   filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
+  background-repeat: repeat-x;
   border-radius: 4px;
-  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.15), 0 1px 5px rgba(0, 0, 0, 0.075);
-  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.15), 0 1px 5px rgba(0, 0, 0, 0.075);
+  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
+          box-shadow: inset 0 1px 0 rgba(255, 255, 255, .15), 0 1px 5px rgba(0, 0, 0, .075);
 }
 .navbar-default .navbar-nav > .open > a,
 .navbar-default .navbar-nav > .active > a {
   background-image: -webkit-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%);
-  background-image: -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%);
+  background-image:      -o-linear-gradient(top, #dbdbdb 0%, #e2e2e2 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#dbdbdb), to(#e2e2e2));
-  background-image: linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%);
+  background-image:         linear-gradient(to bottom, #dbdbdb 0%, #e2e2e2 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdbdbdb', endColorstr='#ffe2e2e2', GradientType=0);
   background-repeat: repeat-x;
-  -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, 0.075);
-  box-shadow: inset 0 3px 9px rgba(0, 0, 0, 0.075);
+  -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
+          box-shadow: inset 0 3px 9px rgba(0, 0, 0, .075);
 }
 .navbar-brand,
 .navbar-nav > li > a {
-  text-shadow: 0 1px 0 rgba(255, 255, 255, 0.25);
+  text-shadow: 0 1px 0 rgba(255, 255, 255, .25);
 }
 .navbar-inverse {
   background-image: -webkit-linear-gradient(top, #3c3c3c 0%, #222 100%);
-  background-image: -o-linear-gradient(top, #3c3c3c 0%, #222 100%);
+  background-image:      -o-linear-gradient(top, #3c3c3c 0%, #222 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#3c3c3c), to(#222));
-  background-image: linear-gradient(to bottom, #3c3c3c 0%, #222 100%);
+  background-image:         linear-gradient(to bottom, #3c3c3c 0%, #222 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff3c3c3c', endColorstr='#ff222222', GradientType=0);
-  background-repeat: repeat-x;
   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 {
   background-image: -webkit-linear-gradient(top, #080808 0%, #0f0f0f 100%);
-  background-image: -o-linear-gradient(top, #080808 0%, #0f0f0f 100%);
+  background-image:      -o-linear-gradient(top, #080808 0%, #0f0f0f 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#080808), to(#0f0f0f));
-  background-image: linear-gradient(to bottom, #080808 0%, #0f0f0f 100%);
+  background-image:         linear-gradient(to bottom, #080808 0%, #0f0f0f 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff080808', endColorstr='#ff0f0f0f', GradientType=0);
   background-repeat: repeat-x;
-  -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, 0.25);
-  box-shadow: inset 0 3px 9px rgba(0, 0, 0, 0.25);
+  -webkit-box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
+          box-shadow: inset 0 3px 9px rgba(0, 0, 0, .25);
 }
 .navbar-inverse .navbar-brand,
 .navbar-inverse .navbar-nav > li > a {
-  text-shadow: 0 -1px 0 rgba(0, 0, 0, 0.25);
+  text-shadow: 0 -1px 0 rgba(0, 0, 0, .25);
 }
 .navbar-static-top,
 .navbar-fixed-top,
@@ -398,120 +398,120 @@ fieldset[disabled] .btn-danger.active {
   .navbar .navbar-nav .open .dropdown-menu > .active > a:focus {
     color: #fff;
     background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
-    background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
+    background-image:      -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
     background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4));
-    background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
+    background-image:         linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
     filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);
     background-repeat: repeat-x;
   }
 }
 .alert {
-  text-shadow: 0 1px 0 rgba(255, 255, 255, 0.2);
-  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.25), 0 1px 2px rgba(0, 0, 0, 0.05);
-  box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.25), 0 1px 2px rgba(0, 0, 0, 0.05);
+  text-shadow: 0 1px 0 rgba(255, 255, 255, .2);
+  -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
+          box-shadow: inset 0 1px 0 rgba(255, 255, 255, .25), 0 1px 2px rgba(0, 0, 0, .05);
 }
 .alert-success {
   background-image: -webkit-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
-  background-image: -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
+  background-image:      -o-linear-gradient(top, #dff0d8 0%, #c8e5bc 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#c8e5bc));
-  background-image: linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%);
+  background-image:         linear-gradient(to bottom, #dff0d8 0%, #c8e5bc 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffc8e5bc', GradientType=0);
   background-repeat: repeat-x;
   border-color: #b2dba1;
 }
 .alert-info {
   background-image: -webkit-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
-  background-image: -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
+  background-image:      -o-linear-gradient(top, #d9edf7 0%, #b9def0 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#b9def0));
-  background-image: linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%);
+  background-image:         linear-gradient(to bottom, #d9edf7 0%, #b9def0 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffb9def0', GradientType=0);
   background-repeat: repeat-x;
   border-color: #9acfea;
 }
 .alert-warning {
   background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
-  background-image: -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
+  background-image:      -o-linear-gradient(top, #fcf8e3 0%, #f8efc0 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#f8efc0));
-  background-image: linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%);
+  background-image:         linear-gradient(to bottom, #fcf8e3 0%, #f8efc0 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fff8efc0', GradientType=0);
   background-repeat: repeat-x;
   border-color: #f5e79e;
 }
 .alert-danger {
   background-image: -webkit-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
-  background-image: -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
+  background-image:      -o-linear-gradient(top, #f2dede 0%, #e7c3c3 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#e7c3c3));
-  background-image: linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%);
+  background-image:         linear-gradient(to bottom, #f2dede 0%, #e7c3c3 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffe7c3c3', GradientType=0);
   background-repeat: repeat-x;
   border-color: #dca7a7;
 }
 .progress {
   background-image: -webkit-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
-  background-image: -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
+  background-image:      -o-linear-gradient(top, #ebebeb 0%, #f5f5f5 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#ebebeb), to(#f5f5f5));
-  background-image: linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%);
+  background-image:         linear-gradient(to bottom, #ebebeb 0%, #f5f5f5 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffebebeb', endColorstr='#fff5f5f5', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar {
   background-image: -webkit-linear-gradient(top, #337ab7 0%, #286090 100%);
-  background-image: -o-linear-gradient(top, #337ab7 0%, #286090 100%);
+  background-image:      -o-linear-gradient(top, #337ab7 0%, #286090 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#286090));
-  background-image: linear-gradient(to bottom, #337ab7 0%, #286090 100%);
+  background-image:         linear-gradient(to bottom, #337ab7 0%, #286090 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff286090', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar-success {
   background-image: -webkit-linear-gradient(top, #5cb85c 0%, #449d44 100%);
-  background-image: -o-linear-gradient(top, #5cb85c 0%, #449d44 100%);
+  background-image:      -o-linear-gradient(top, #5cb85c 0%, #449d44 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#5cb85c), to(#449d44));
-  background-image: linear-gradient(to bottom, #5cb85c 0%, #449d44 100%);
+  background-image:         linear-gradient(to bottom, #5cb85c 0%, #449d44 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5cb85c', endColorstr='#ff449d44', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar-info {
   background-image: -webkit-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
-  background-image: -o-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
+  background-image:      -o-linear-gradient(top, #5bc0de 0%, #31b0d5 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#5bc0de), to(#31b0d5));
-  background-image: linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%);
+  background-image:         linear-gradient(to bottom, #5bc0de 0%, #31b0d5 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff5bc0de', endColorstr='#ff31b0d5', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar-warning {
   background-image: -webkit-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
-  background-image: -o-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
+  background-image:      -o-linear-gradient(top, #f0ad4e 0%, #ec971f 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f0ad4e), to(#ec971f));
-  background-image: linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%);
+  background-image:         linear-gradient(to bottom, #f0ad4e 0%, #ec971f 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff0ad4e', endColorstr='#ffec971f', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar-danger {
   background-image: -webkit-linear-gradient(top, #d9534f 0%, #c9302c 100%);
-  background-image: -o-linear-gradient(top, #d9534f 0%, #c9302c 100%);
+  background-image:      -o-linear-gradient(top, #d9534f 0%, #c9302c 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#d9534f), to(#c9302c));
-  background-image: linear-gradient(to bottom, #d9534f 0%, #c9302c 100%);
+  background-image:         linear-gradient(to bottom, #d9534f 0%, #c9302c 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9534f', endColorstr='#ffc9302c', GradientType=0);
   background-repeat: repeat-x;
 }
 .progress-bar-striped {
-  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
-  background-image: -o-linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
-  background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);
+  background-image: -webkit-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+  background-image:      -o-linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
+  background-image:         linear-gradient(45deg, rgba(255, 255, 255, .15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, .15) 50%, rgba(255, 255, 255, .15) 75%, transparent 75%, transparent);
 }
 .list-group {
   border-radius: 4px;
-  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.075);
-  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.075);
+  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
+          box-shadow: 0 1px 2px rgba(0, 0, 0, .075);
 }
 .list-group-item.active,
 .list-group-item.active:hover,
 .list-group-item.active:focus {
   text-shadow: 0 -1px 0 #286090;
   background-image: -webkit-linear-gradient(top, #337ab7 0%, #2b669a 100%);
-  background-image: -o-linear-gradient(top, #337ab7 0%, #2b669a 100%);
+  background-image:      -o-linear-gradient(top, #337ab7 0%, #2b669a 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2b669a));
-  background-image: linear-gradient(to bottom, #337ab7 0%, #2b669a 100%);
+  background-image:         linear-gradient(to bottom, #337ab7 0%, #2b669a 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2b669a', GradientType=0);
   background-repeat: repeat-x;
   border-color: #2b669a;
@@ -522,66 +522,66 @@ fieldset[disabled] .btn-danger.active {
   text-shadow: none;
 }
 .panel {
-  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05);
-  box-shadow: 0 1px 2px rgba(0, 0, 0, 0.05);
+  -webkit-box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
+          box-shadow: 0 1px 2px rgba(0, 0, 0, .05);
 }
 .panel-default > .panel-heading {
   background-image: -webkit-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
-  background-image: -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
+  background-image:      -o-linear-gradient(top, #f5f5f5 0%, #e8e8e8 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f5f5f5), to(#e8e8e8));
-  background-image: linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
+  background-image:         linear-gradient(to bottom, #f5f5f5 0%, #e8e8e8 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff5f5f5', endColorstr='#ffe8e8e8', GradientType=0);
   background-repeat: repeat-x;
 }
 .panel-primary > .panel-heading {
   background-image: -webkit-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
-  background-image: -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
+  background-image:      -o-linear-gradient(top, #337ab7 0%, #2e6da4 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#337ab7), to(#2e6da4));
-  background-image: linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
+  background-image:         linear-gradient(to bottom, #337ab7 0%, #2e6da4 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ff337ab7', endColorstr='#ff2e6da4', GradientType=0);
   background-repeat: repeat-x;
 }
 .panel-success > .panel-heading {
   background-image: -webkit-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
-  background-image: -o-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
+  background-image:      -o-linear-gradient(top, #dff0d8 0%, #d0e9c6 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#dff0d8), to(#d0e9c6));
-  background-image: linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%);
+  background-image:         linear-gradient(to bottom, #dff0d8 0%, #d0e9c6 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffdff0d8', endColorstr='#ffd0e9c6', GradientType=0);
   background-repeat: repeat-x;
 }
 .panel-info > .panel-heading {
   background-image: -webkit-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
-  background-image: -o-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
+  background-image:      -o-linear-gradient(top, #d9edf7 0%, #c4e3f3 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#d9edf7), to(#c4e3f3));
-  background-image: linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%);
+  background-image:         linear-gradient(to bottom, #d9edf7 0%, #c4e3f3 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffd9edf7', endColorstr='#ffc4e3f3', GradientType=0);
   background-repeat: repeat-x;
 }
 .panel-warning > .panel-heading {
   background-image: -webkit-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
-  background-image: -o-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
+  background-image:      -o-linear-gradient(top, #fcf8e3 0%, #faf2cc 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#fcf8e3), to(#faf2cc));
-  background-image: linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%);
+  background-image:         linear-gradient(to bottom, #fcf8e3 0%, #faf2cc 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fffcf8e3', endColorstr='#fffaf2cc', GradientType=0);
   background-repeat: repeat-x;
 }
 .panel-danger > .panel-heading {
   background-image: -webkit-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
-  background-image: -o-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
+  background-image:      -o-linear-gradient(top, #f2dede 0%, #ebcccc 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#f2dede), to(#ebcccc));
-  background-image: linear-gradient(to bottom, #f2dede 0%, #ebcccc 100%);
+  background-image:         linear-gradient(to bottom, #f2dede 0%, #ebcccc 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#fff2dede', endColorstr='#ffebcccc', GradientType=0);
   background-repeat: repeat-x;
 }
 .well {
   background-image: -webkit-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
-  background-image: -o-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
+  background-image:      -o-linear-gradient(top, #e8e8e8 0%, #f5f5f5 100%);
   background-image: -webkit-gradient(linear, left top, left bottom, from(#e8e8e8), to(#f5f5f5));
-  background-image: linear-gradient(to bottom, #e8e8e8 0%, #f5f5f5 100%);
+  background-image:         linear-gradient(to bottom, #e8e8e8 0%, #f5f5f5 100%);
   filter: progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffe8e8e8', endColorstr='#fff5f5f5', GradientType=0);
   background-repeat: repeat-x;
   border-color: #dcdcdc;
-  -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, 0.05), 0 1px 0 rgba(255, 255, 255, 0.1);
-  box-shadow: inset 0 1px 3px rgba(0, 0, 0, 0.05), 0 1px 0 rgba(255, 255, 255, 0.1);
+  -webkit-box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
+          box-shadow: inset 0 1px 3px rgba(0, 0, 0, .05), 0 1px 0 rgba(255, 255, 255, .1);
 }
-/*# sourceMappingURL=bootstrap-theme.css.map */
+/*# sourceMappingURL=bootstrap-theme.css.map */

inst/www/shared/bootstrap/js/bootstrap.js

@@ -1,6 +1,6 @@
 /*!
- * Bootstrap v3.4.1 (https://getbootstrap.com/)
- * Copyright 2011-2019 Twitter, Inc.
+ * Bootstrap v3.3.7 (http://getbootstrap.com)
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under the MIT license
  */
 
@@ -17,10 +17,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: transition.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#transitions
+ * Bootstrap: transition.js v3.3.7
+ * http://getbootstrap.com/javascript/#transitions
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -28,7 +28,7 @@ if (typeof jQuery === 'undefined') {
 +function ($) {
   'use strict';
 
-  // CSS TRANSITION SUPPORT (Shoutout: https://modernizr.com/)
+  // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/)
   // ============================================================
 
   function transitionEnd() {
@@ -50,7 +50,7 @@ if (typeof jQuery === 'undefined') {
     return false // explicit for ie8 (  ._.)
   }
 
-  // https://blog.alexmaccaw.com/css-transitions
+  // http://blog.alexmaccaw.com/css-transitions
   $.fn.emulateTransitionEnd = function (duration) {
     var called = false
     var $el = this
@@ -77,10 +77,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: alert.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#alerts
+ * Bootstrap: alert.js v3.3.7
+ * http://getbootstrap.com/javascript/#alerts
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -96,7 +96,7 @@ if (typeof jQuery === 'undefined') {
     $(el).on('click', dismiss, this.close)
   }
 
-  Alert.VERSION = '3.4.1'
+  Alert.VERSION = '3.3.7'
 
   Alert.TRANSITION_DURATION = 150
 
@@ -109,8 +109,7 @@ if (typeof jQuery === 'undefined') {
       selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
     }
 
-    selector    = selector === '#' ? [] : selector
-    var $parent = $(document).find(selector)
+    var $parent = $(selector === '#' ? [] : selector)
 
     if (e) e.preventDefault()
 
@@ -173,10 +172,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: button.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#buttons
+ * Bootstrap: button.js v3.3.7
+ * http://getbootstrap.com/javascript/#buttons
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -193,7 +192,7 @@ if (typeof jQuery === 'undefined') {
     this.isLoading = false
   }
 
-  Button.VERSION  = '3.4.1'
+  Button.VERSION  = '3.3.7'
 
   Button.DEFAULTS = {
     loadingText: 'loading...'
@@ -299,10 +298,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: carousel.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#carousel
+ * Bootstrap: carousel.js v3.3.7
+ * http://getbootstrap.com/javascript/#carousel
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -330,7 +329,7 @@ if (typeof jQuery === 'undefined') {
       .on('mouseleave.bs.carousel', $.proxy(this.cycle, this))
   }
 
-  Carousel.VERSION  = '3.4.1'
+  Carousel.VERSION  = '3.3.7'
 
   Carousel.TRANSITION_DURATION = 600
 
@@ -444,9 +443,7 @@ if (typeof jQuery === 'undefined') {
     var slidEvent = $.Event('slid.bs.carousel', { relatedTarget: relatedTarget, direction: direction }) // yes, "slid"
     if ($.support.transition && this.$element.hasClass('slide')) {
       $next.addClass(type)
-      if (typeof $next === 'object' && $next.length) {
-        $next[0].offsetWidth // force reflow
-      }
+      $next[0].offsetWidth // force reflow
       $active.addClass(direction)
       $next.addClass(direction)
       $active
@@ -508,17 +505,10 @@ if (typeof jQuery === 'undefined') {
   // =================
 
   var clickHandler = function (e) {
+    var href
     var $this   = $(this)
-    var href    = $this.attr('href')
-    if (href) {
-      href = href.replace(/.*(?=#[^\s]+$)/, '') // strip for ie7
-    }
-
-    var target  = $this.attr('data-target') || href
-    var $target = $(document).find(target)
-
+    var $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) // strip for ie7
     if (!$target.hasClass('carousel')) return
-
     var options = $.extend({}, $target.data(), $this.data())
     var slideIndex = $this.attr('data-slide-to')
     if (slideIndex) options.interval = false
@@ -546,10 +536,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: collapse.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#collapse
+ * Bootstrap: collapse.js v3.3.7
+ * http://getbootstrap.com/javascript/#collapse
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -577,7 +567,7 @@ if (typeof jQuery === 'undefined') {
     if (this.options.toggle) this.toggle()
   }
 
-  Collapse.VERSION  = '3.4.1'
+  Collapse.VERSION  = '3.3.7'
 
   Collapse.TRANSITION_DURATION = 350
 
@@ -684,7 +674,7 @@ if (typeof jQuery === 'undefined') {
   }
 
   Collapse.prototype.getParent = function () {
-    return $(document).find(this.options.parent)
+    return $(this.options.parent)
       .find('[data-toggle="collapse"][data-parent="' + this.options.parent + '"]')
       .each($.proxy(function (i, element) {
         var $element = $(element)
@@ -707,7 +697,7 @@ if (typeof jQuery === 'undefined') {
     var target = $trigger.attr('data-target')
       || (href = $trigger.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') // strip for ie7
 
-    return $(document).find(target)
+    return $(target)
   }
 
 
@@ -759,10 +749,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: dropdown.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#dropdowns
+ * Bootstrap: dropdown.js v3.3.7
+ * http://getbootstrap.com/javascript/#dropdowns
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -779,7 +769,7 @@ if (typeof jQuery === 'undefined') {
     $(element).on('click.bs.dropdown', this.toggle)
   }
 
-  Dropdown.VERSION = '3.4.1'
+  Dropdown.VERSION = '3.3.7'
 
   function getParent($this) {
     var selector = $this.attr('data-target')
@@ -789,7 +779,7 @@ if (typeof jQuery === 'undefined') {
       selector = selector && /#[A-Za-z]/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') // strip for ie7
     }
 
-    var $parent = selector !== '#' ? $(document).find(selector) : null
+    var $parent = selector && $(selector)
 
     return $parent && $parent.length ? $parent : $this.parent()
   }
@@ -925,10 +915,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: modal.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#modals
+ * Bootstrap: modal.js v3.3.7
+ * http://getbootstrap.com/javascript/#modals
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -940,16 +930,15 @@ if (typeof jQuery === 'undefined') {
   // ======================
 
   var Modal = function (element, options) {
-    this.options = options
-    this.$body = $(document.body)
-    this.$element = $(element)
-    this.$dialog = this.$element.find('.modal-dialog')
-    this.$backdrop = null
-    this.isShown = null
-    this.originalBodyPad = null
-    this.scrollbarWidth = 0
+    this.options             = options
+    this.$body               = $(document.body)
+    this.$element            = $(element)
+    this.$dialog             = this.$element.find('.modal-dialog')
+    this.$backdrop           = null
+    this.isShown             = null
+    this.originalBodyPad     = null
+    this.scrollbarWidth      = 0
     this.ignoreBackdropClick = false
-    this.fixedContent = '.navbar-fixed-top, .navbar-fixed-bottom'
 
     if (this.options.remote) {
       this.$element
@@ -960,7 +949,7 @@ if (typeof jQuery === 'undefined') {
     }
   }
 
-  Modal.VERSION = '3.4.1'
+  Modal.VERSION  = '3.3.7'
 
   Modal.TRANSITION_DURATION = 300
   Modal.BACKDROP_TRANSITION_DURATION = 150
@@ -977,7 +966,7 @@ if (typeof jQuery === 'undefined') {
 
   Modal.prototype.show = function (_relatedTarget) {
     var that = this
-    var e = $.Event('show.bs.modal', { relatedTarget: _relatedTarget })
+    var e    = $.Event('show.bs.modal', { relatedTarget: _relatedTarget })
 
     this.$element.trigger(e)
 
@@ -1068,8 +1057,8 @@ if (typeof jQuery === 'undefined') {
       .off('focusin.bs.modal') // guard against infinite focus loop
       .on('focusin.bs.modal', $.proxy(function (e) {
         if (document !== e.target &&
-          this.$element[0] !== e.target &&
-          !this.$element.has(e.target).length) {
+            this.$element[0] !== e.target &&
+            !this.$element.has(e.target).length) {
           this.$element.trigger('focus')
         }
       }, this))
@@ -1171,7 +1160,7 @@ if (typeof jQuery === 'undefined') {
     var modalIsOverflowing = this.$element[0].scrollHeight > document.documentElement.clientHeight
 
     this.$element.css({
-      paddingLeft: !this.bodyIsOverflowing && modalIsOverflowing ? this.scrollbarWidth : '',
+      paddingLeft:  !this.bodyIsOverflowing && modalIsOverflowing ? this.scrollbarWidth : '',
       paddingRight: this.bodyIsOverflowing && !modalIsOverflowing ? this.scrollbarWidth : ''
     })
   }
@@ -1196,26 +1185,11 @@ if (typeof jQuery === 'undefined') {
   Modal.prototype.setScrollbar = function () {
     var bodyPad = parseInt((this.$body.css('padding-right') || 0), 10)
     this.originalBodyPad = document.body.style.paddingRight || ''
-    var scrollbarWidth = this.scrollbarWidth
-    if (this.bodyIsOverflowing) {
-      this.$body.css('padding-right', bodyPad + scrollbarWidth)
-      $(this.fixedContent).each(function (index, element) {
-        var actualPadding = element.style.paddingRight
-        var calculatedPadding = $(element).css('padding-right')
-        $(element)
-          .data('padding-right', actualPadding)
-          .css('padding-right', parseFloat(calculatedPadding) + scrollbarWidth + 'px')
-      })
-    }
+    if (this.bodyIsOverflowing) this.$body.css('padding-right', bodyPad + this.scrollbarWidth)
   }
 
   Modal.prototype.resetScrollbar = function () {
     this.$body.css('padding-right', this.originalBodyPad)
-    $(this.fixedContent).each(function (index, element) {
-      var padding = $(element).data('padding-right')
-      $(element).removeData('padding-right')
-      element.style.paddingRight = padding ? padding : ''
-    })
   }
 
   Modal.prototype.measureScrollbar = function () { // thx walsh
@@ -1233,8 +1207,8 @@ if (typeof jQuery === 'undefined') {
 
   function Plugin(option, _relatedTarget) {
     return this.each(function () {
-      var $this = $(this)
-      var data = $this.data('bs.modal')
+      var $this   = $(this)
+      var data    = $this.data('bs.modal')
       var options = $.extend({}, Modal.DEFAULTS, $this.data(), typeof option == 'object' && option)
 
       if (!data) $this.data('bs.modal', (data = new Modal(this, options)))
@@ -1245,7 +1219,7 @@ if (typeof jQuery === 'undefined') {
 
   var old = $.fn.modal
 
-  $.fn.modal = Plugin
+  $.fn.modal             = Plugin
   $.fn.modal.Constructor = Modal
 
 
@@ -1262,13 +1236,10 @@ if (typeof jQuery === 'undefined') {
   // ==============
 
   $(document).on('click.bs.modal.data-api', '[data-toggle="modal"]', function (e) {
-    var $this = $(this)
-    var href = $this.attr('href')
-    var target = $this.attr('data-target') ||
-      (href && href.replace(/.*(?=#[^\s]+$)/, '')) // strip for ie7
-
-    var $target = $(document).find(target)
-    var option = $target.data('bs.modal') ? 'toggle' : $.extend({ remote: !/#/.test(href) && href }, $target.data(), $this.data())
+    var $this   = $(this)
+    var href    = $this.attr('href')
+    var $target = $($this.attr('data-target') || (href && href.replace(/.*(?=#[^\s]+$)/, ''))) // strip for ie7
+    var option  = $target.data('bs.modal') ? 'toggle' : $.extend({ remote: !/#/.test(href) && href }, $target.data(), $this.data())
 
     if ($this.is('a')) e.preventDefault()
 
@@ -1284,148 +1255,18 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: tooltip.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#tooltip
+ * Bootstrap: tooltip.js v3.3.7
+ * http://getbootstrap.com/javascript/#tooltip
  * Inspired by the original jQuery.tipsy by Jason Frame
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
+
 +function ($) {
   'use strict';
 
-  var DISALLOWED_ATTRIBUTES = ['sanitize', 'whiteList', 'sanitizeFn']
-
-  var uriAttrs = [
-    'background',
-    'cite',
-    'href',
-    'itemtype',
-    'longdesc',
-    'poster',
-    'src',
-    'xlink:href'
-  ]
-
-  var ARIA_ATTRIBUTE_PATTERN = /^aria-[\w-]*$/i
-
-  var DefaultWhitelist = {
-    // Global attributes allowed on any supplied element below.
-    '*': ['class', 'dir', 'id', 'lang', 'role', ARIA_ATTRIBUTE_PATTERN],
-    a: ['target', 'href', 'title', 'rel'],
-    area: [],
-    b: [],
-    br: [],
-    col: [],
-    code: [],
-    div: [],
-    em: [],
-    hr: [],
-    h1: [],
-    h2: [],
-    h3: [],
-    h4: [],
-    h5: [],
-    h6: [],
-    i: [],
-    img: ['src', 'alt', 'title', 'width', 'height'],
-    li: [],
-    ol: [],
-    p: [],
-    pre: [],
-    s: [],
-    small: [],
-    span: [],
-    sub: [],
-    sup: [],
-    strong: [],
-    u: [],
-    ul: []
-  }
-
-  /**
-   * A pattern that recognizes a commonly useful subset of URLs that are safe.
-   *
-   * Shoutout to Angular 7 https://github.com/angular/angular/blob/7.2.4/packages/core/src/sanitization/url_sanitizer.ts
-   */
-  var SAFE_URL_PATTERN = /^(?:(?:https?|mailto|ftp|tel|file):|[^&:/?#]*(?:[/?#]|$))/gi
-
-  /**
-   * A pattern that matches safe data URLs. Only matches image, video and audio types.
-   *
-   * Shoutout to Angular 7 https://github.com/angular/angular/blob/7.2.4/packages/core/src/sanitization/url_sanitizer.ts
-   */
-  var DATA_URL_PATTERN = /^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[a-z0-9+/]+=*$/i
-
-  function allowedAttribute(attr, allowedAttributeList) {
-    var attrName = attr.nodeName.toLowerCase()
-
-    if ($.inArray(attrName, allowedAttributeList) !== -1) {
-      if ($.inArray(attrName, uriAttrs) !== -1) {
-        return Boolean(attr.nodeValue.match(SAFE_URL_PATTERN) || attr.nodeValue.match(DATA_URL_PATTERN))
-      }
-
-      return true
-    }
-
-    var regExp = $(allowedAttributeList).filter(function (index, value) {
-      return value instanceof RegExp
-    })
-
-    // Check if a regular expression validates the attribute.
-    for (var i = 0, l = regExp.length; i < l; i++) {
-      if (attrName.match(regExp[i])) {
-        return true
-      }
-    }
-
-    return false
-  }
-
-  function sanitizeHtml(unsafeHtml, whiteList, sanitizeFn) {
-    if (unsafeHtml.length === 0) {
-      return unsafeHtml
-    }
-
-    if (sanitizeFn && typeof sanitizeFn === 'function') {
-      return sanitizeFn(unsafeHtml)
-    }
-
-    // IE 8 and below don't support createHTMLDocument
-    if (!document.implementation || !document.implementation.createHTMLDocument) {
-      return unsafeHtml
-    }
-
-    var createdDocument = document.implementation.createHTMLDocument('sanitization')
-    createdDocument.body.innerHTML = unsafeHtml
-
-    var whitelistKeys = $.map(whiteList, function (el, i) { return i })
-    var elements = $(createdDocument.body).find('*')
-
-    for (var i = 0, len = elements.length; i < len; i++) {
-      var el = elements[i]
-      var elName = el.nodeName.toLowerCase()
-
-      if ($.inArray(elName, whitelistKeys) === -1) {
-        el.parentNode.removeChild(el)
-
-        continue
-      }
-
-      var attributeList = $.map(el.attributes, function (el) { return el })
-      var whitelistedAttributes = [].concat(whiteList['*'] || [], whiteList[elName] || [])
-
-      for (var j = 0, len2 = attributeList.length; j < len2; j++) {
-        if (!allowedAttribute(attributeList[j], whitelistedAttributes)) {
-          el.removeAttribute(attributeList[j].nodeName)
-        }
-      }
-    }
-
-    return createdDocument.body.innerHTML
-  }
-
   // TOOLTIP PUBLIC CLASS DEFINITION
   // ===============================
 
@@ -1441,7 +1282,7 @@ if (typeof jQuery === 'undefined') {
     this.init('tooltip', element, options)
   }
 
-  Tooltip.VERSION  = '3.4.1'
+  Tooltip.VERSION  = '3.3.7'
 
   Tooltip.TRANSITION_DURATION = 150
 
@@ -1458,10 +1299,7 @@ if (typeof jQuery === 'undefined') {
     viewport: {
       selector: 'body',
       padding: 0
-    },
-    sanitize : true,
-    sanitizeFn : null,
-    whiteList : DefaultWhitelist
+    }
   }
 
   Tooltip.prototype.init = function (type, element, options) {
@@ -1469,7 +1307,7 @@ if (typeof jQuery === 'undefined') {
     this.type      = type
     this.$element  = $(element)
     this.options   = this.getOptions(options)
-    this.$viewport = this.options.viewport && $(document).find($.isFunction(this.options.viewport) ? this.options.viewport.call(this, this.$element) : (this.options.viewport.selector || this.options.viewport))
+    this.$viewport = this.options.viewport && $($.isFunction(this.options.viewport) ? this.options.viewport.call(this, this.$element) : (this.options.viewport.selector || this.options.viewport))
     this.inState   = { click: false, hover: false, focus: false }
 
     if (this.$element[0] instanceof document.constructor && !this.options.selector) {
@@ -1502,15 +1340,7 @@ if (typeof jQuery === 'undefined') {
   }
 
   Tooltip.prototype.getOptions = function (options) {
-    var dataAttributes = this.$element.data()
-
-    for (var dataAttr in dataAttributes) {
-      if (dataAttributes.hasOwnProperty(dataAttr) && $.inArray(dataAttr, DISALLOWED_ATTRIBUTES) !== -1) {
-        delete dataAttributes[dataAttr]
-      }
-    }
-
-    options = $.extend({}, this.getDefaults(), dataAttributes, options)
+    options = $.extend({}, this.getDefaults(), this.$element.data(), options)
 
     if (options.delay && typeof options.delay == 'number') {
       options.delay = {
@@ -1519,10 +1349,6 @@ if (typeof jQuery === 'undefined') {
       }
     }
 
-    if (options.sanitize) {
-      options.template = sanitizeHtml(options.template, options.whiteList, options.sanitizeFn)
-    }
-
     return options
   }
 
@@ -1634,7 +1460,7 @@ if (typeof jQuery === 'undefined') {
         .addClass(placement)
         .data('bs.' + this.type, this)
 
-      this.options.container ? $tip.appendTo($(document).find(this.options.container)) : $tip.insertAfter(this.$element)
+      this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element)
       this.$element.trigger('inserted.bs.' + this.type)
 
       var pos          = this.getPosition()
@@ -1736,16 +1562,7 @@ if (typeof jQuery === 'undefined') {
     var $tip  = this.tip()
     var title = this.getTitle()
 
-    if (this.options.html) {
-      if (this.options.sanitize) {
-        title = sanitizeHtml(title, this.options.whiteList, this.options.sanitizeFn)
-      }
-
-      $tip.find('.tooltip-inner').html(title)
-    } else {
-      $tip.find('.tooltip-inner').text(title)
-    }
-
+    $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title)
     $tip.removeClass('fade in top bottom left right')
   }
 
@@ -1926,9 +1743,6 @@ if (typeof jQuery === 'undefined') {
     })
   }
 
-  Tooltip.prototype.sanitizeHtml = function (unsafeHtml) {
-    return sanitizeHtml(unsafeHtml, this.options.whiteList, this.options.sanitizeFn)
-  }
 
   // TOOLTIP PLUGIN DEFINITION
   // =========================
@@ -1962,10 +1776,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: popover.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#popovers
+ * Bootstrap: popover.js v3.3.7
+ * http://getbootstrap.com/javascript/#popovers
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -1982,7 +1796,7 @@ if (typeof jQuery === 'undefined') {
 
   if (!$.fn.tooltip) throw new Error('Popover requires tooltip.js')
 
-  Popover.VERSION  = '3.4.1'
+  Popover.VERSION  = '3.3.7'
 
   Popover.DEFAULTS = $.extend({}, $.fn.tooltip.Constructor.DEFAULTS, {
     placement: 'right',
@@ -2008,25 +1822,10 @@ if (typeof jQuery === 'undefined') {
     var title   = this.getTitle()
     var content = this.getContent()
 
-    if (this.options.html) {
-      var typeContent = typeof content
-
-      if (this.options.sanitize) {
-        title = this.sanitizeHtml(title)
-
-        if (typeContent === 'string') {
-          content = this.sanitizeHtml(content)
-        }
-      }
-
-      $tip.find('.popover-title').html(title)
-      $tip.find('.popover-content').children().detach().end()[
-        typeContent === 'string' ? 'html' : 'append'
-      ](content)
-    } else {
-      $tip.find('.popover-title').text(title)
-      $tip.find('.popover-content').children().detach().end().text(content)
-    }
+    $tip.find('.popover-title')[this.options.html ? 'html' : 'text'](title)
+    $tip.find('.popover-content').children().detach().end()[ // we use append for html objects to maintain js events
+      this.options.html ? (typeof content == 'string' ? 'html' : 'append') : 'text'
+    ](content)
 
     $tip.removeClass('fade top bottom left right in')
 
@@ -2045,8 +1844,8 @@ if (typeof jQuery === 'undefined') {
 
     return $e.attr('data-content')
       || (typeof o.content == 'function' ?
-        o.content.call($e[0]) :
-        o.content)
+            o.content.call($e[0]) :
+            o.content)
   }
 
   Popover.prototype.arrow = function () {
@@ -2086,10 +1885,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: scrollspy.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#scrollspy
+ * Bootstrap: scrollspy.js v3.3.7
+ * http://getbootstrap.com/javascript/#scrollspy
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -2115,7 +1914,7 @@ if (typeof jQuery === 'undefined') {
     this.process()
   }
 
-  ScrollSpy.VERSION  = '3.4.1'
+  ScrollSpy.VERSION  = '3.3.7'
 
   ScrollSpy.DEFAULTS = {
     offset: 10
@@ -2259,10 +2058,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: tab.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#tabs
+ * Bootstrap: tab.js v3.3.7
+ * http://getbootstrap.com/javascript/#tabs
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -2279,7 +2078,7 @@ if (typeof jQuery === 'undefined') {
     // jscs:enable requireDollarBeforejQueryAssignment
   }
 
-  Tab.VERSION = '3.4.1'
+  Tab.VERSION = '3.3.7'
 
   Tab.TRANSITION_DURATION = 150
 
@@ -2308,7 +2107,7 @@ if (typeof jQuery === 'undefined') {
 
     if (showEvent.isDefaultPrevented() || hideEvent.isDefaultPrevented()) return
 
-    var $target = $(document).find(selector)
+    var $target = $(selector)
 
     this.activate($this.closest('li'), $ul)
     this.activate($target, $target.parent(), function () {
@@ -2333,15 +2132,15 @@ if (typeof jQuery === 'undefined') {
       $active
         .removeClass('active')
         .find('> .dropdown-menu > .active')
-        .removeClass('active')
+          .removeClass('active')
         .end()
         .find('[data-toggle="tab"]')
-        .attr('aria-expanded', false)
+          .attr('aria-expanded', false)
 
       element
         .addClass('active')
         .find('[data-toggle="tab"]')
-        .attr('aria-expanded', true)
+          .attr('aria-expanded', true)
 
       if (transition) {
         element[0].offsetWidth // reflow for transition
@@ -2353,10 +2152,10 @@ if (typeof jQuery === 'undefined') {
       if (element.parent('.dropdown-menu').length) {
         element
           .closest('li.dropdown')
-          .addClass('active')
+            .addClass('active')
           .end()
           .find('[data-toggle="tab"]')
-          .attr('aria-expanded', true)
+            .attr('aria-expanded', true)
       }
 
       callback && callback()
@@ -2415,10 +2214,10 @@ if (typeof jQuery === 'undefined') {
 }(jQuery);
 
 /* ========================================================================
- * Bootstrap: affix.js v3.4.1
- * https://getbootstrap.com/docs/3.4/javascript/#affix
+ * Bootstrap: affix.js v3.3.7
+ * http://getbootstrap.com/javascript/#affix
  * ========================================================================
- * Copyright 2011-2019 Twitter, Inc.
+ * Copyright 2011-2016 Twitter, Inc.
  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
  * ======================================================================== */
 
@@ -2432,9 +2231,7 @@ if (typeof jQuery === 'undefined') {
   var Affix = function (element, options) {
     this.options = $.extend({}, Affix.DEFAULTS, options)
 
-    var target = this.options.target === Affix.DEFAULTS.target ? $(this.options.target) : $(document).find(this.options.target)
-
-    this.$target = target
+    this.$target = $(this.options.target)
       .on('scroll.bs.affix.data-api', $.proxy(this.checkPosition, this))
       .on('click.bs.affix.data-api',  $.proxy(this.checkPositionWithEventLoop, this))
 
@@ -2446,7 +2243,7 @@ if (typeof jQuery === 'undefined') {
     this.checkPosition()
   }
 
-  Affix.VERSION  = '3.4.1'
+  Affix.VERSION  = '3.3.7'
 
   Affix.RESET    = 'affix affix-top affix-bottom'
 

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

@@ -29,8 +29,8 @@ $.extend( true, DataTable.defaults, {
 /* Default class modification */
 $.extend( DataTable.ext.classes, {
 	sWrapper:      "dataTables_wrapper form-inline dt-bootstrap",
-	sFilterInput:  "form-control form-control-sm input-sm",
-	sLengthSelect: "form-control form-control-sm input-sm"
+	sFilterInput:  "form-control input-sm",
+	sLengthSelect: "form-control input-sm"
 } );