Add explicit namespace to non-base functions

NEWS

@@ -24,6 +24,9 @@ shiny 0.12.1.9xxx
 * Added two alias functions of `updateTabsetPanel()` to update the selected tab:
   `updateNavbarPage()` and `updateNavlistPanel()`. (#881)
 
+* All non-base functions are now explicitly namespaced, to pass checks in
+  R-devel.
+
 shiny 0.12.1
 --------------------------------------------------------------------------------
 

R/app.R

@@ -91,7 +91,7 @@ shinyApp <- function(ui=NULL, server=NULL, onStart=NULL, options=list(),
 #'   file and either ui.R or www/index.html)
 #' @export
 shinyAppDir <- function(appDir, options=list()) {
-  if (!file_test('-d', appDir)) {
+  if (!utils::file_test('-d', appDir)) {
     stop("No Shiny application exists at the path \"", appDir, "\"")
   }
 

R/graph.R

@@ -37,7 +37,7 @@ writeReactLog <- function(file=stdout()) {
 #'
 #' @export
 showReactLog <- function() {
-  browseURL(renderReactLog())
+  utils::browseURL(renderReactLog())
 }
 
 renderReactLog <- function() {
@@ -91,7 +91,7 @@ renderReactLog <- function() {
   .graphAppend(list(
     action = 'valueChange',
     id = label,
-    value = paste(capture.output(str(value)), collapse='\n')
+    value = paste(utils::capture.output(utils::str(value)), collapse='\n')
   ))
 }
 

R/imageutils.R

@@ -33,12 +33,12 @@ plotPNG <- function(func, filename=tempfile(fileext='.png'),
   # Otherwise, if the Cairo package is installed, use CairoPNG().
   # Finally, if neither quartz nor Cairo, use png().
   if (capabilities("aqua")) {
-    pngfun <- png
+    pngfun <- grDevices::png
   } else if ((getOption('shiny.usecairo') %OR% TRUE) &&
              nchar(system.file(package = "Cairo"))) {
     pngfun <- Cairo::CairoPNG
   } else {
-    pngfun <- png
+    pngfun <- grDevices::png
   }
 
   pngfun(filename=filename, width=width, height=height, res=res, ...)
@@ -49,10 +49,10 @@ plotPNG <- function(func, filename=tempfile(fileext='.png'),
   # by plot.new() with the default (large) margin. However, this does not
   # guarantee user's code in func() will not trigger the error -- they may have
   # to set par(mar = smaller_value) before they draw base graphics.
-  op <- par(mar = rep(0, 4))
-  tryCatch(plot.new(), finally = par(op))
-  dv <- dev.cur()
-  tryCatch(shinyCallingHandlers(func()), finally = dev.off(dv))
+  op <- graphics::par(mar = rep(0, 4))
+  tryCatch(graphics::plot.new(), finally = graphics::par(op))
+  dv <- grDevices::dev.cur()
+  tryCatch(shinyCallingHandlers(func()), finally = grDevices::dev.off(dv))
 
   filename
 }

R/progress.R

@@ -87,7 +87,7 @@ Progress <- R6Class(
         stop("'session' is not a ShinySession object.")
 
       private$session <- session
-      private$id <- paste(as.character(as.raw(runif(8, min=0, max=255))), collapse='')
+      private$id <- paste(as.character(as.raw(stats::runif(8, min=0, max=255))), collapse='')
       private$min <- min
       private$max <- max
       private$value <- NULL

R/reactives.R

@@ -307,10 +307,10 @@ reactiveValuesToList <- function(x, all.names=FALSE) {
 # x[['impl']].
 #' @export
 str.reactivevalues <- function(object, indent.str = " ", ...) {
-  str(unclass(object), indent.str = indent.str, ...)
+  utils::str(unclass(object), indent.str = indent.str, ...)
   # Need to manually print out the class field,
   cat(indent.str, '- attr(*, "class")=', sep = "")
-  str(class(object))
+  utils::str(class(object))
 }
 
 # Observable ----------------------------------------------------------------

R/render-plot.R

@@ -93,9 +93,9 @@ renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
 
         # Special case for ggplot objects - need to capture coordmap
         if (inherits(result$value, "ggplot")) {
-          capture.output(coordmap <<- getGgplotCoordmap(result$value, pixelratio))
+          utils::capture.output(coordmap <<- getGgplotCoordmap(result$value, pixelratio))
         } else {
-          capture.output(print(result$value))
+          utils::capture.output(print(result$value))
         }
       }
 
@@ -237,12 +237,12 @@ renderPlot <- function(expr, width='auto', height='auto', res=72, ...,
 # Requires width and height of output image, in pixels.
 # Must be called before the graphics device is closed.
 getPrevPlotCoordmap <- function(width, height) {
-  usrCoords <- par('usr')
+  usrCoords <- graphics::par('usr')
   usrBounds <- usrCoords
-  if (par('xlog')) {
+  if (graphics::par('xlog')) {
     usrBounds[c(1,2)] <- 10 ^ usrBounds[c(1,2)]
   }
-  if (par('ylog')) {
+  if (graphics::par('ylog')) {
     usrBounds[c(3,4)] <- 10 ^ usrBounds[c(3,4)]
   }
 
@@ -257,14 +257,14 @@ getPrevPlotCoordmap <- function(width, height) {
     ),
     # The bounds of the plot area, in DOM pixels
     range = list(
-      left = grconvertX(usrBounds[1], 'user', 'nfc') * width,
-      right = grconvertX(usrBounds[2], 'user', 'nfc') * width,
-      bottom = (1-grconvertY(usrBounds[3], 'user', 'nfc')) * height - 1,
-      top = (1-grconvertY(usrBounds[4], 'user', 'nfc')) * height - 1
+      left = graphics::grconvertX(usrBounds[1], 'user', 'nfc') * width,
+      right = graphics::grconvertX(usrBounds[2], 'user', 'nfc') * width,
+      bottom = (1-graphics::grconvertY(usrBounds[3], 'user', 'nfc')) * height - 1,
+      top = (1-graphics::grconvertY(usrBounds[4], 'user', 'nfc')) * height - 1
     ),
     log = list(
-      x = if (par('xlog')) 10 else NULL,
-      y = if (par('ylog')) 10 else NULL
+      x = if (graphics::par('xlog')) 10 else NULL,
+      y = if (graphics::par('ylog')) 10 else NULL
     ),
     # We can't extract the original variable names from a base graphic.
     # `mapping` is an empty _named_ list, so that it is converted to an object
@@ -304,7 +304,7 @@ getGgplotCoordmap <- function(p, pixelratio) {
   which_method <- function(generic, x) {
     classes <- class(x)
     method_names <- paste(generic, classes, sep = ".")
-    idx <- which(method_names %in% methods(generic))
+    idx <- which(method_names %in% utils::methods(generic))
 
     if (length(idx) == 0)
       return(NULL)
@@ -539,7 +539,7 @@ getGgplotCoordmap <- function(p, pixelratio) {
     # the image has double size. In the latter case we don't have to scale the
     # numbers down.
     pix_ratio <- 1
-    if (!grepl("^quartz", names(dev.cur()))) {
+    if (!grepl("^quartz", names(grDevices::dev.cur()))) {
       pix_ratio <- pixelratio
     }
 

R/run-url.R

@@ -71,8 +71,8 @@ runUrl <- function(url, filetype = NULL, subdir = NULL, destdir = NULL, ...) {
     untar2(filePath, exdir = fileDir)
 
   } else if (fileext == ".zip") {
-    first <- as.character(unzip(filePath, list=TRUE)$Name)[1]
-    unzip(filePath, exdir = fileDir)
+    first <- as.character(utils::unzip(filePath, list=TRUE)$Name)[1]
+    utils::unzip(filePath, exdir = fileDir)
   }
 
   if(is.null(destdir)){
@@ -80,7 +80,7 @@ runUrl <- function(url, filetype = NULL, subdir = NULL, destdir = NULL, ...) {
   }
 
   appdir <- file.path(fileDir, first)
-  if (!file_test('-d', appdir)) appdir <- dirname(appdir)
+  if (!utils::file_test('-d', appdir)) appdir <- dirname(appdir)
 
   if (!is.null(subdir)) appdir <- file.path(appdir, subdir)
   runApp(appdir, ...)

R/server.R

@@ -547,7 +547,7 @@ runApp <- function(appDir=getwd(),
     # SHINY_SERVER_VERSION, those will return "" which is considered less than
     # any valid version.
     ver <- Sys.getenv('SHINY_SERVER_VERSION')
-    if (compareVersion(ver, .shinyServerMinVersion) < 0) {
+    if (utils::compareVersion(ver, .shinyServerMinVersion) < 0) {
       warning('Shiny Server v', .shinyServerMinVersion,
               ' or later is required; please upgrade!')
     }

R/shiny.R

@@ -499,7 +499,7 @@ ShinySession <- R6Class(
             private$invalidatedOutputErrors$set(
               name,
               list(message = cond$message,
-                   call = capture.output(print(cond$call)),
+                   call = utils::capture.output(print(cond$call)),
                    type = if (length(type)) type))
           }
           else

R/shinyui.R

@@ -39,7 +39,7 @@ renderPage <- function(ui, connection, showcase=0) {
     list(
       htmlDependency("json2", "2014.02.04", c(href="shared"), script = "json2-min.js"),
       htmlDependency("jquery", "1.11.0", c(href="shared"), script = "jquery.min.js"),
-      htmlDependency("shiny", packageVersion("shiny"), c(href="shared"),
+      htmlDependency("shiny", utils::packageVersion("shiny"), c(href="shared"),
         script = if (getOption("shiny.minified", TRUE)) "shiny.min.js" else "shiny.js",
         stylesheet = "shiny.css")
     ),

R/shinywrappers.R

@@ -185,7 +185,7 @@ renderTable <- function(expr, ..., env=parent.frame(), quoted=FALSE, func=NULL)
       return("")
 
     return(paste(
-      capture.output(
+      utils::capture.output(
         print(xtable(data, ...),
               type='html',
               html.table.attributes=paste('class="',
@@ -238,7 +238,7 @@ renderPrint <- function(expr, env = parent.frame(), quoted = FALSE, func = NULL,
   markRenderFunction(verbatimTextOutput, function() {
     op <- options(width = width)
     on.exit(options(op), add = TRUE)
-    paste(capture.output(func()), collapse = "\n")
+    paste(utils::capture.output(func()), collapse = "\n")
   })
 }
 
@@ -278,7 +278,7 @@ renderText <- function(expr, env=parent.frame(), quoted=FALSE, func=NULL) {
 
   markRenderFunction(textOutput, function() {
     value <- func()
-    return(paste(capture.output(cat(value)), collapse="\n"))
+    return(paste(utils::capture.output(cat(value)), collapse="\n"))
   })
 }
 
@@ -460,7 +460,7 @@ renderDataTable <- function(expr, options = NULL, searchDelay = 500,
     colnames <- colnames(data)
     # if escape is column names, turn names to numeric indices
     if (is.character(escape)) {
-      escape <- setNames(seq_len(ncol(data)), colnames)[escape]
+      escape <- stats::setNames(seq_len(ncol(data)), colnames)[escape]
       if (any(is.na(escape)))
         stop("Some column names in the 'escape' argument not found in data")
     }
@@ -481,8 +481,10 @@ renderDataTable <- function(expr, options = NULL, searchDelay = 500,
 # a data frame containing the DataTables 1.9 and 1.10 names
 DT10Names <- function() {
   rbind(
-    read.table(system.file('www/shared/datatables/upgrade1.10.txt', package = 'shiny'),
-               stringsAsFactors = FALSE),
+    utils::read.table(
+      system.file('www/shared/datatables/upgrade1.10.txt', package = 'shiny'),
+      stringsAsFactors = FALSE
+    ),
     c('aoColumns', 'Removed')  # looks like an omission on the upgrade guide
   )
 }
@@ -500,7 +502,7 @@ checkDT9 <- function(options) {
     'and DataTables 1.10.x uses different parameter names with 1.9.x. ',
     'Please follow the upgrade guide https://datatables.net/upgrade/1.10-convert',
     ' to change your DataTables parameter names:\n\n',
-    paste(formatUL(nms[i]), collapse = '\n'), '\n', sep = ''
+    paste(utils::formatUL(nms[i]), collapse = '\n'), '\n', sep = ''
   )
   j <- gsub('[.].*', '', DT10[, 1]) %in% nms
   # I cannot help you upgrade automatically in these cases, so I have to stop
@@ -509,7 +511,7 @@ checkDT9 <- function(options) {
   nms10 <- DT10[match(nms[i], DT10[, 1]), 2]
   if (any(nms10 == 'Removed')) stop(
     "These parameters have been removed in DataTables 1.10.x:\n\n",
-    paste(formatUL(nms[i][nms10 == 'Removed']), collapse = '\n'),
+    paste(utils::formatUL(nms[i][nms10 == 'Removed']), collapse = '\n'),
     "\n\n", msg
   )
   names(options)[i] <- nms10

R/tar.R

@@ -46,7 +46,7 @@ untar2 <- function(tarfile, files = NULL, list = FALSE, exdir = ".")
     mydir.create <- function(path, ...) {
         ## for Windows' sake
         path <- sub("[\\/]$", "", path)
-        if(file_test("-d", path)) return()
+        if(utils::file_test("-d", path)) return()
         if(!dir.create(path, showWarnings = TRUE, recursive = TRUE, ...))
            stop(gettextf("failed to create directory %s", sQuote(path)),
                 domain = NA)

R/update-input.R

@@ -517,7 +517,7 @@ selectizeJSON <- function(data, req) {
     idx <- idx | apply(matches, 1, cjn)
   }
   # only return the first n rows (n = maximum options in configuration)
-  idx <- head(if (length(key)) which(idx) else seq_along(idx), mop)
+  idx <- utils::head(if (length(key)) which(idx) else seq_along(idx), mop)
   data <- data[idx, ]
 
   res <- toJSON(columnToRowData(data))

R/utils.R

@@ -25,7 +25,7 @@ NULL
 #' rnormB(5)  # [1] -0.7946034  0.2568374 -0.6567597  1.2451387 -0.8375699
 #'
 #' @export
-repeatable <- function(rngfunc, seed = runif(1, 0, .Machine$integer.max)) {
+repeatable <- function(rngfunc, seed = stats::runif(1, 0, .Machine$integer.max)) {
   force(seed)
 
   function(...) {
@@ -95,7 +95,7 @@ reinitializeSeed <- if (getRversion() >= '3.0.0') {
 
 # Version of runif that runs with private seed
 p_runif <- function(...) {
-  withPrivateSeed(runif(...))
+  withPrivateSeed(stats::runif(...))
 }
 
 # Version of sample that runs with private seed
@@ -258,7 +258,7 @@ download <- function(url, ...) {
 
       # Needed for https
       mySI2(TRUE)
-      download.file(url, ...)
+      utils::download.file(url, ...)
 
     } else {
       # If non-Windows, check for curl/wget/lynx, then call download.file with
@@ -282,11 +282,11 @@ download <- function(url, ...) {
         stop("no download method found")
       }
 
-      download.file(url, method = method, ...)
+      utils::download.file(url, method = method, ...)
     }
 
   } else {
-    download.file(url, ...)
+    utils::download.file(url, ...)
   }
 }
 
@@ -474,7 +474,7 @@ parseQueryString <- function(str, nested = FALSE) {
   keys   <- URLdecode(keys)
   values <- URLdecode(values)
 
-  res <- setNames(as.list(values), keys)
+  res <- stats::setNames(as.list(values), keys)
   if (!nested) return(res)
 
   # Make a nested list from a query of the form ?a[1][1]=x11&a[1][2]=x12&...
@@ -892,7 +892,7 @@ validate <- function(..., errorClass = character(0)) {
       stop("Unexpected validation result: ", as.character(x))
   })
 
-  results <- na.omit(results)
+  results <- stats::na.omit(results)
   if (length(results) == 0)
     return(invisible())
 
@@ -936,11 +936,11 @@ isTruthy <- function(x) {
     return(FALSE)
   if (all(is.na(x)))
     return(FALSE)
-  if (is.character(x) && !any(nzchar(na.omit(x))))
+  if (is.character(x) && !any(nzchar(stats::na.omit(x))))
     return(FALSE)
   if (inherits(x, 'shinyActionButtonValue') && x == 0)
     return(FALSE)
-  if (is.logical(x) && !any(na.omit(x)))
+  if (is.logical(x) && !any(stats::na.omit(x)))
     return(FALSE)
 
   return(TRUE)

man/repeatable.Rd

@@ -4,7 +4,7 @@
 \alias{repeatable}
 \title{Make a random number generator repeatable}
 \usage{
-repeatable(rngfunc, seed = runif(1, 0, .Machine$integer.max))
+repeatable(rngfunc, seed = stats::runif(1, 0, .Machine$integer.max))
 }
 \arguments{
 \item{rngfunc}{The function that is affected by the R session's seed.}