Add explicit namespace to non-base functions

Author: wch

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

@@ -71,16 +71,16 @@ 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)){
     on.exit(unlink(fileDir, recursive = TRUE), add = TRUE)
   }
 
   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