[education/rkward] rkward/rbackend/rpackages/rkward: more fixes to satisfy R CMD check
m.eik michalke
null at kde.org
Wed Sep 13 21:46:51 BST 2023
Git commit 30098a62993896464ad9dc3fcc9646cc40173f76 by m.eik michalke.
Committed on 13/09/2023 at 22:46.
Pushed by meikm into branch 'master'.
more fixes to satisfy R CMD check
- mostly put examples in \dontrun{} as a plain R session outside of RKWard isn't able to proberly run most RKWard specific functions
in this state, the R package rkward survives R CMD check without errors for the first time :)
M +15 -15 rkward/rbackend/rpackages/rkward/R/public_graphics.R
M +3 -2 rkward/rbackend/rpackages/rkward/R/rk.KDE_GUI-functions.R
M +2 -3 rkward/rbackend/rpackages/rkward/R/rk.demo.R
M +16 -16 rkward/rbackend/rpackages/rkward/R/rk.edit-functions.R
M +3 -4 rkward/rbackend/rpackages/rkward/R/rk.filename-functions.R
M +4 -5 rkward/rbackend/rpackages/rkward/R/rk.output.R
M +23 -29 rkward/rbackend/rpackages/rkward/R/rk.plugin-functions.R
M +7 -6 rkward/rbackend/rpackages/rkward/R/rk.print-functions.R
M +2 -4 rkward/rbackend/rpackages/rkward/R/rk.replace.function.R
M +2 -2 rkward/rbackend/rpackages/rkward/R/rk.sessionInfo.R
M +4 -4 rkward/rbackend/rpackages/rkward/R/rk.sync-functions.R
M +5 -8 rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
M +2 -3 rkward/rbackend/rpackages/rkward/man/RK.Output.Rd
D +0 -41 rkward/rbackend/rpackages/rkward/man/public.Rd
M +4 -6 rkward/rbackend/rpackages/rkward/man/rk.assign.preview.data.Rd
M +3 -3 rkward/rbackend/rpackages/rkward/man/rk.call.plugin.Rd
M +5 -3 rkward/rbackend/rpackages/rkward/man/rk.capture.output.Rd
M +2 -2 rkward/rbackend/rpackages/rkward/man/rk.demo.Rd
M +8 -5 rkward/rbackend/rpackages/rkward/man/rk.edit.Rd
M +2 -3 rkward/rbackend/rpackages/rkward/man/rk.embed.device.Rd
M +2 -3 rkward/rbackend/rpackages/rkward/man/rk.get.tempfile.name.Rd
M +2 -1 rkward/rbackend/rpackages/rkward/man/rk.graph.on.Rd
M +2 -3 rkward/rbackend/rpackages/rkward/man/rk.list.plugins.Rd
M +2 -5 rkward/rbackend/rpackages/rkward/man/rk.load.pluginmaps.Rd
M +2 -3 rkward/rbackend/rpackages/rkward/man/rk.printer.device.Rd
M +2 -5 rkward/rbackend/rpackages/rkward/man/rk.record.plot.Rd
M +2 -4 rkward/rbackend/rpackages/rkward/man/rk.replace.function.Rd
M +2 -1 rkward/rbackend/rpackages/rkward/man/rk.results.Rd
M +2 -1 rkward/rbackend/rpackages/rkward/man/rk.sessionInfo.Rd
M +2 -0 rkward/rbackend/rpackages/rkward/man/rk.show.messages.Rd
M +2 -2 rkward/rbackend/rpackages/rkward/man/rk.sync.Rd
M +2 -4 rkward/rbackend/rpackages/rkward/man/rk.with.window.hints.Rd
M +0 -1 rkward/rbackend/rpackages/rkward/man/rk.workplace.Rd
https://invent.kde.org/education/rkward/-/commit/30098a62993896464ad9dc3fcc9646cc40173f76
diff --git a/rkward/rbackend/rpackages/rkward/R/public_graphics.R b/rkward/rbackend/rpackages/rkward/R/public_graphics.R
index cf2130adf..2eb5788cf 100644
--- a/rkward/rbackend/rpackages/rkward/R/public_graphics.R
+++ b/rkward/rbackend/rpackages/rkward/R/public_graphics.R
@@ -24,8 +24,15 @@
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#'
#' @seealso \code{\link{rk.results}}, \code{\link{rk.print}}, \code{\link{rk.get.output.html.file}}, \code{\link[grDevices:dev.off]{dev.off}}, \code{\link[grDevices:svg]{svg}}, \code{\link[grDevices:png]{png}}, \code{\link[grDevices:jpeg]{jpeg}}
+#' @keywords devices
+#'
+#' @importFrom grDevices dev.cur png jpeg
+#' @export
+#' @aliases rk.graph.on rk.graph.off
+#' @rdname rk.graph.on
#'
#' @examples
+#' \dontrun{
#' ## Plot directly to the output (html) file, by-passing screen device:
#' rk.graph.on ("JPG", 480, 480, 75)
#' plot (rnorm (100))
@@ -39,13 +46,7 @@
#' ## WRONG USAGE: not run:
#' #plot (rnorm (100))
#' #dev.print (device = rk.graph.on)
-#'
-#' @keywords devices
-#'
-#' @importFrom grDevices dev.cur png jpeg
-#' @export
-#' @aliases rk.graph.on rk.graph.off
-#' @rdname rk.graph.on
+#' }
"rk.graph.on" <- function (device.type=getOption ("rk.graphics.type"), width=getOption ("rk.graphics.width"), height=getOption ("rk.graphics.height"), quality, ...)
{
make.url <- function (filename) {
@@ -162,14 +163,14 @@
#' window already "owned" by RKWard (importantly, \code{RK()} device windows) may lead to unexpected results, including crashes.
#'
#' @seealso \link{RK}
+#' @importFrom grDevices dev.cur
+#' @export
+#'
#' @examples
-#'
-#' ## Not run:
+#' \dontrun{
#' rk.embed.device (grDevices::X11(title="X11 device window"))
#' plot (rnorm (10))
-#'
-#' @importFrom grDevices dev.cur
-#' @export
+#' }
"rk.embed.device" <- function (expr) {
oldd <- dev.cur ()
.rk.do.call ("startOpenX11", as.character (oldd));
@@ -275,11 +276,10 @@
#' @export
#' @importFrom grDevices dev.cur postscript
#' @examples
-#'
-#' ## Not run:
+#' \dontrun{
#' plot (rnorm (10))
#' dev.print (rk.printer.device)
-#'
+#' }
# Produces a temporary postscript file and opens a print dialog for it
# Parameters are passed to postscript(), but typically this is simply used as
# dev.print(rk.print.preview)
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.KDE_GUI-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.KDE_GUI-functions.R
index f734e625e..af173b0b0 100755
--- a/rkward/rbackend/rpackages/rkward/R/rk.KDE_GUI-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.KDE_GUI-functions.R
@@ -79,7 +79,9 @@
#' \code{\link[base:file.choose]{file.choose}}
#' @keywords utilities
#' @rdname rk.show.messages
+#' @export
#' @examples
+#' \dontrun{
#' ## Message boxes
#' if (rk.show.question ("Question:\nDo you want to know about RKWard?",
#' button.yes = "Yes, I do!", button.no = "No, I don't care!", button.cancel = "")) {
@@ -93,8 +95,7 @@
#' multiple = TRUE, title = "vowels")
#' .rk.backups$select.list (LETTERS, preselect = c("A", "E", "I", "O", "U"),
#' multiple = TRUE, title = "vowels")
-
-#' @export
+#' }
"rk.show.message" <- function (message, caption = gettext("Information"), wait=TRUE) {
.Call ("rk.dialog", caption, message, "ok", "", "", "ok", isTRUE (wait), PACKAGE="(embedding)")
invisible (TRUE)
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.demo.R b/rkward/rbackend/rpackages/rkward/R/rk.demo.R
index d3b3a813a..bca94bafa 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.demo.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.demo.R
@@ -20,10 +20,9 @@
#' @rdname rk.demo
#' @export
#' @examples
-#'
-#' ## Not run
+#' \dontrun{
#' rk.demo("graphics")
-
+#' }
"rk.demo" <- function (topic, package, lib.loc=NULL) {
# for the time being, translate NULL into missingness and throw a warning
if(!missing(package)){
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.edit-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.edit-functions.R
index 3e183f998..cff0e1b5e 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.edit-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.edit-functions.R
@@ -17,19 +17,8 @@
#' by default, when run inside an RKWard session. (via \code{getOption("editor")},
#' and \code{getOption("browser")}.
#'
-#' @aliases rk.edit rk.edit.files rk.show.files rk.show.html
#' @param x an object to edit.
-#' @param name name of the environment to use (optional).
-#' @param file character vector, filenames to show or edit.
-#' @param title character vector, of the same length as \code{file}; This can
-#' be used to give descriptive titles to each file, which will be displayed
-#' to the user.
-#' @param wtitle character vector, of length 1. This will be used as the window
-#' title.
-#' @param prompt logical of length 1. If TRUE (the default) a prompt is dialog
-#' is shown along with the files to show / edit.
-#' @param delete a logical (not NA), when \code{TRUE} the shown file(s) are
-#' deleted after closing.
+#' @aliases rk.edit rk.edit.files rk.show.files rk.show.html
#' @return All functions described on this page return \code{NULL},
#' unconditionally.
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
@@ -37,18 +26,24 @@
#' \code{\link{file.show}}, \code{\link{browseURL}}
#' @keywords utilities IO
#' @rdname rk.edit
+#' @export
#' @examples
-#'
-#' ## Not run
+#' \dontrun{
#' x <- data.frame (a=c(1:3), b=c(2:4))
#' rk.edit(x)
-
-#' @export
+#' }
"rk.edit" <- function (x) {
object <- deparse (substitute (x))
.rk.do.call ("edit", object)
}
+#' @param name name of the environment to use (optional).
+#' @param file character vector, filenames to show or edit.
+#' @param title character vector, of the same length as \code{file}; This can
+#' be used to give descriptive titles to each file, which will be displayed
+#' to the user.
+#' @param prompt logical of length 1. If TRUE (the default) a prompt is dialog
+#' is shown along with the files to show / edit.
#' @export
#' @rdname rk.edit
"rk.edit.files" <- function (name, file="", title, prompt = TRUE) {
@@ -74,6 +69,10 @@
invisible (.Call ("rk.edit.files", as.character (file), as.character (title), as.character (name), isTRUE (prompt), PACKAGE="(embedding)"))
}
+#' @param header character, header to show.
+#' @param delete.file a logical (not NA), when \code{TRUE} the shown file(s) are
+#' deleted after closing.
+#' @param delete logical, for compatibility with earlier versions of R.
#' @export
#' @rdname rk.edit
"rk.show.files" <- function (file = file, header = file, title, delete.file=FALSE, prompt = TRUE,
@@ -91,6 +90,7 @@
invisible (.Call ("rk.show.files", as.character (file), as.character (header), as.character (title), delete, isTRUE (prompt), PACKAGE="(embedding)"))
}
+#' @param url a URL to show.
#' @export
#' @rdname rk.edit
"rk.show.html" <- function (url) {
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.filename-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.filename-functions.R
index ef3d69f4c..39cc0821d 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.filename-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.filename-functions.R
@@ -66,8 +66,9 @@
#' \link{rk.print}
#' @keywords utilities IO
#' @rdname rk.get.tempfile.name
+#' @export
#' @examples
-#'
+#' \dontrun{
#' testfile.name <- rk.get.tempfile.name(prefix="test", extension=".txt")
#' testfile <- file(testfile.name)
#' cat("This is a test\n", file=testfile)
@@ -76,14 +77,12 @@
#'
#' outfile <- rk.get.output.html.file()
#'
-#' ## Not run
#' rk.set.output.html.file("~/.rkward/another_file.html")
#' rk.header("Output on a different output file")
#' rk.show.html(rk.get.output.html.file())
#' rk.flush.output()
#' rk.set.output.html.file(outfile)
-#'
-#' @export
+#' }
"rk.get.tempfile.name" <- function (prefix="image", extension=".jpg", directory=dirname (rk.get.output.html.file ())) {
x <- .rk.do.simple.call ("unused.filename", c (prefix, extension, directory))
ret <- x[2]
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.output.R b/rkward/rbackend/rpackages/rkward/R/rk.output.R
index 5634f3118..0ca2fd2b3 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.output.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.output.R
@@ -46,19 +46,18 @@
#'
#' @returns NULL
#' @field id An internal identifier. NULL for a closed output. This should be treated as read-only, but you can use this to test whether two output handles are the same.
+#' @import methods
+#' @exportClass RK.Output
#'
#' @examples
-#'
-#' ## Not run
+#' \dontrun{
#' x <- rk.output(create=TRUE)
#' x$activate()
#' rk.print("Hello World!")
#' x$view()
#' x$save() # Will prompt for filename
#' x$close()
-#'
-#' @import methods
-#' @exportClass RK.Output
+#' }
RK.Output <- setRefClass(Class="RK.Output", fields=list(id="character"),
methods=list(
# The implementation of most of these is not terribly complex, but we need an implementation in the frontend, anyway, so we use that.
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.plugin-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.plugin-functions.R
index e2a723908..420bbd7d1 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.plugin-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.plugin-functions.R
@@ -43,22 +43,23 @@
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#' @seealso \code{\link{rk.results}}, \url{rkward://page/rkward_output}
#' @keywords utilities
+#' @export
+#' @rdname rk.call.plugin
+#'
#' @examples
-#'
+#'
#' ## "t_test_two_vars" plugin:
#' ## see the output: Windows->Show Output
+#' \dontrun{
#' local({
#' x1 <- rnorm (100)
#' x2 <- rnorm (100, 2)
-#'
-#' rk.call.plugin ("rkward::t_test_two_vars",
+#' rk.call.plugin ("rkward::t_test_two_vars",
#' confint.state="1", conflevel.real="0.95", hypothesis.string="greater", paired.state="0", varequal.state="0",
#' x.available="x1", y.available="x2",
#' submit.mode="submit")
#' })
-#'
-#' @export
-#' @rdname rk.call.plugin
+#' }
"rk.call.plugin" <- function (plugin, ..., submit.mode = c ("manual", "auto", "submit")) {
# prepare arguments
settings <- list (...)
@@ -100,17 +101,14 @@
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#' @seealso \code{\link{rk.call.plugin}}, \code{\link[rkwarddev:rk.plugin.skeleton]{rk.plugin.skeleton}}
#' @keywords utilities
+#' @rdname rk.load.pluginmaps
+#' @export
#'
#' @examples
-#'
-#' ## NOT RUN
-#'
+#' \dontrun{
#' ## reload all active pluginmaps
#' rk.load.pluginmaps()
-#'
-#' ## END NOT RUN
-#' @export
-#' @rdname rk.load.pluginmaps
+#' }
"rk.load.pluginmaps" <- function (pluginmap.files, force.add = TRUE, force.reload = TRUE) {
# for the time being, translate NULL into missingness and throw a warning
if(!missing(pluginmap.files)){
@@ -153,21 +151,19 @@
#'
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#' @keywords utilities
-#'
#' @seealso \code{\link{rk.call.plugin}} for invoking a plugin, programatically
+#' @rdname rk.list.plugins
+#' @aliases rk.list.plugins rk.set.plugin.status
+#' @export
#'
#' @examples
+#' \dontrun{
#' ## list all current plugins
#' rk.list.plugins ()
#'
-#' ## NOT RUN
#' ## hide t.test plugin
#' rk.set.plugin.status ("rkward::t_test", visible=FALSE)
-#' ## END NOT RUN
-#'
-#' @export
-#' @rdname rk.list.plugins
-#' @aliases rk.list.plugins rk.set.plugin.status
+#' }
"rk.list.plugins" <- function () {
plugs <- .rk.do.plain.call("listPlugins")
columns = c ("ID", "Context", "Menupath", "Label")
@@ -195,8 +191,8 @@ assign(".rk.preview.data", list (), envir=.rk.variables)
#' This gets called by the <preview>-box of the plugin, automtically, when the plugin dialog is closed.
#' You do not generally have to call it manually. See the notes for running custom clearnup code, below.
#'
-#' @param id (character). Id associated with the data. Usually this will be the 'id' value of the <preview>-box.
-#' @param value. The value to assign. If this is a list, and contains a function named "on.delete", this function
+#' @param id character, ID associated with the data. Usually this will be the 'id' value of the <preview>-box.
+#' @param value the value to assign. If this is a list, and contains a function named "on.delete", this function
#' will be run by rk.discard.preview.data (with the \code{id} as argument. This is useful for running custom clearnup
#' code, such as removing temporary files, etc.
#'
@@ -209,11 +205,13 @@ assign(".rk.preview.data", list (), envir=.rk.variables)
#'
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#' @keywords utilities
+#' @rdname rk.assign.preview.data
+#' @aliases rk.get.preview.data .rk.discard.preview.data
+#' @export
#'
#' @examples
#' ## To be generated in the preview() code section of a plugin
-#'
-#' ## NOT RUN
+#' \dontrun{
#' pdata <- rk.get.preview.data("SOMEID")
#' if (is.null (pdata)) {
#' outfile <- rk.get.tempfile.name(prefix="preview", extension=".txt", directory=rk.tempdir ())
@@ -226,11 +224,7 @@ assign(".rk.preview.data", list (), envir=.rk.variables)
#' cat ("This is a test", pdata$filename)
#' rk.edit.files(file=pdata$filename)
#' })
-#' ## END NOT RUN
-#'
-#' @export
-#' @rdname rk.assign.preview.data
-#' @aliases rk.get.preview.data .rk.discard.preview.data
+#' }
"rk.assign.preview.data" <- function (id, value=list ()) {
pdata <- .rk.variables$.rk.preview.data
pdata[[id]] <- value
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.print-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.print-functions.R
index c0b8f079f..577876a71 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.print-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.print-functions.R
@@ -59,8 +59,10 @@
#' \url{rkward://page/rkward_output}
#' @keywords utilities
#' @rdname rk.results
+#' @importFrom grDevices dev.cur
+#' @export
#' @examples
-#'
+#' \dontrun{
#' # code is only run when the R2HTML package can be loaded
#' if(require("R2HTML", quietly = TRUE)){
#'
@@ -93,8 +95,7 @@
#' 'confidence interval of difference'=result$conf.int ))
#' })
#' } else {}
-#' @importFrom grDevices dev.cur
-#' @export
+#' }
"rk.print" <- function(x,...) {
if (inherits (x, "htmlwidget")) {
requireNamespace ("htmlwidgets", quietly = TRUE)
@@ -280,7 +281,9 @@
#'
#' And arbitrary number of ouptut captures can be started and stopped, and these will form a push/pop stack.
#'
-#' @param suppress.messages message are not sent on, neither to surrounding captures, nor as regular output.
+#' @param capture.messages logical, whether messages should be captured.
+#' @param capture.output logical, whether output should be captured.
+#' @param suppress.messages logical, if \code{FALSE} message are not sent on, neither to surrounding captures, nor as regular output.
#' @param suppress.output like \code{suppress.messages}, but for output.
#' @param allow.nesting if false, output / message is not sent to surrounding captures, but is sent to regular output (unless suppressed)
#'
@@ -288,8 +291,6 @@
#'
#' \code{rk.end.capture.output} Stops capturing output, and returns the recorded output in a string.
#'
-#' @param LANG language code to use. "C" for no translation, i.e. generally English
-#'
#' @export
#' @rdname rk.capture.output
"rk.capture.output" <- function (capture.messages = TRUE, capture.output = TRUE, suppress.messages = FALSE, suppress.output = FALSE, allow.nesting = TRUE) {
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.replace.function.R b/rkward/rbackend/rpackages/rkward/R/rk.replace.function.R
index 0c5529110..2fc50a239 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.replace.function.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.replace.function.R
@@ -33,15 +33,13 @@
#' @export
#' @rdname rk.replace.function
#' @examples
-#'
-#' ## Not run
+#' \dontrun{
#' rk.replace.function ("history", as.environment ("package:utils"),
#' function () {
#' cat ("This is what you typed:\n")
#' eval (body (.rk.backups$history))
#' })
-#' ## End not run
-#'
+#' }
# Tries to replace a function inside its environemnt/namespace.
# Function formals are copied from the original.
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.sessionInfo.R b/rkward/rbackend/rpackages/rkward/R/rk.sessionInfo.R
index c65a3bb14..8a03f0871 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.sessionInfo.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.sessionInfo.R
@@ -20,9 +20,9 @@
#' @export
#' @rdname rk.sessionInfo
#' @examples
-#'
+#' \dontrun{
#' rk.sessionInfo()
-
+#' }
"rk.sessionInfo" <- function () {
cat (.rk.do.plain.call ("getSessionInfo"), sep="\n")
cat ("R runtime session info:\n")
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.sync-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.sync-functions.R
index 0e5d37c2b..1ddaac751 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.sync-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.sync-functions.R
@@ -25,12 +25,12 @@
#' @seealso \url{rkward://page/rkward_workspace_browser}
#' @keywords utilities misc
#' @rdname rk.sync
-#' @examples
-#'
-#' rk.sync (rkward::rk.record.plot)
-#'
# should this really be public?
#' @export
+#' @examples
+#' \dontrun{
+#' rk.sync (rkward::rk.record.plot)
+#' }
"rk.sync" <- function (x) {
object <- deparse (substitute (x))
.rk.do.call("sync", list(NULL, NULL, object))
diff --git a/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R b/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
index 9524875a3..50b9e6860 100644
--- a/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
+++ b/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
@@ -31,14 +31,13 @@
#' @seealso \url{rkward://page/rkward_for_r_users}, \link{rk.get.workspace.url}
#' @keywords utilities
#' @rdname rk.workplace
+#' @importFrom utils URLdecode
+#' @export
#' @examples
#' \dontrun{
#' rk.save.workplace ()
#' rk.restore.workplace ()
#' }
-#'
-#' @importFrom utils URLdecode
-#' @export
"rk.save.workplace" <- function (file, description) {
# for the time being, translate NULL into missingness and throw a warning
if(!missing(file)){
@@ -120,16 +119,14 @@
#' @author Thomas Friedrichsmeier \email{rkward-devel@@kde.org}
#' @keywords utilities
#' @rdname rk.with.window.hints
+#' @export
#' @examples
-#'
-#' ## Not run
+#' \dontrun{
#' .rk.with.window.hints ({
#' RK ()
#' plot (1, 1)
#' }, "attached")
-#' ## End not run
-#'
-#' @export
+#' }
".rk.with.window.hints" <- function (expr, placement="", name="", style="") {
.rk.do.plain.call ("set.window.placement.hint", as.character (c (placement, name, style)), FALSE)
on.exit (.rk.do.plain.call ("set.window.placement.hint", c ("", "", ""), FALSE))
diff --git a/rkward/rbackend/rpackages/rkward/man/RK.Output.Rd b/rkward/rbackend/rpackages/rkward/man/RK.Output.Rd
index 389fc833c..62bb4eec2 100644
--- a/rkward/rbackend/rpackages/rkward/man/RK.Output.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/RK.Output.Rd
@@ -90,13 +90,12 @@ Do not write anything to the target filename, directly! This is purely for infor
}}
\examples{
-
-## Not run
+\dontrun{
x <- rk.output(create=TRUE)
x$activate()
rk.print("Hello World!")
x$view()
x$save() # Will prompt for filename
x$close()
-
+}
}
diff --git a/rkward/rbackend/rpackages/rkward/man/public.Rd b/rkward/rbackend/rpackages/rkward/man/public.Rd
deleted file mode 100644
index 6a5f08b2a..000000000
--- a/rkward/rbackend/rpackages/rkward/man/public.Rd
+++ /dev/null
@@ -1,41 +0,0 @@
-\name{test}
-\alias{test}
-%- Also NEED an '\alias' for EACH other topic documented here.
-\title{ ~~function to do ... ~~ }
-\description{
- ~~ A concise (1-5 lines) description of what the function does. ~~
-}
-\usage{
-test(x)
-}
-%- maybe also 'usage' for other objects documented here.
-\arguments{
- \item{x}{ ~~Describe \code{x} here~~ }
-}
-\details{
- ~~ If necessary, more details than the __description__ above ~~
-}
-\value{
- ~Describe the value returned
- If it is a LIST, use
- \item{comp1 }{Description of 'comp1'}
- \item{comp2 }{Description of 'comp2'}
- ...
-}
-\references{ ~put references to the literature/web site here ~ }
-\author{ ~~who you are~~ }
-\note{ ~~further notes~~ }
-
-%- ~Make other sections like Warning with \section{Warning }{....} ~
-
-%- \seealso{ ~~objects to See Also as \code{\link{~~fun~~}}, ~~~ }
-\examples{
-##---- Should be DIRECTLY executable !! ----
-##-- ==> Define data, use random,
-##-- or do help(data=index) for the standard data sets.
-
-## The function is currently defined as
-function (x) { x }
-}
-\keyword{ ~kwd1 }% at least one, from doc/KEYWORDS
-\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.assign.preview.data.Rd b/rkward/rbackend/rpackages/rkward/man/rk.assign.preview.data.Rd
index 03529f8ac..e09b2c135 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.assign.preview.data.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.assign.preview.data.Rd
@@ -14,9 +14,9 @@ rk.get.preview.data(id)
rk.discard.preview.data(id)
}
\arguments{
-\item{id}{(character). Id associated with the data. Usually this will be the 'id' value of the <preview>-box.}
+\item{id}{character, ID associated with the data. Usually this will be the 'id' value of the <preview>-box.}
-\item{value.}{The value to assign. If this is a list, and contains a function named "on.delete", this function
+\item{value}{the value to assign. If this is a list, and contains a function named "on.delete", this function
will be run by rk.discard.preview.data (with the \code{id} as argument. This is useful for running custom clearnup
code, such as removing temporary files, etc.}
}
@@ -38,8 +38,7 @@ code, such as removing temporary files, etc.}
}
\examples{
## To be generated in the preview() code section of a plugin
-
-## NOT RUN
+\dontrun{
pdata <- rk.get.preview.data("SOMEID")
if (is.null (pdata)) {
outfile <- rk.get.tempfile.name(prefix="preview", extension=".txt", directory=rk.tempdir ())
@@ -52,8 +51,7 @@ try ({
cat ("This is a test", pdata$filename)
rk.edit.files(file=pdata$filename)
})
-## END NOT RUN
-
+}
}
\author{
Thomas Friedrichsmeier \email{rkward-devel at kde.org}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.call.plugin.Rd b/rkward/rbackend/rpackages/rkward/man/rk.call.plugin.Rd
index 4e4411555..601ab03f0 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.call.plugin.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.call.plugin.Rd
@@ -53,16 +53,16 @@ not available to the plugin.
## "t_test_two_vars" plugin:
## see the output: Windows->Show Output
+\dontrun{
local({
x1 <- rnorm (100)
x2 <- rnorm (100, 2)
-
-rk.call.plugin ("rkward::t_test_two_vars",
+rk.call.plugin ("rkward::t_test_two_vars",
confint.state="1", conflevel.real="0.95", hypothesis.string="greater", paired.state="0", varequal.state="0",
x.available="x1", y.available="x2",
submit.mode="submit")
})
-
+}
}
\seealso{
\code{\link{rk.results}}, \url{rkward://page/rkward_output}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.capture.output.Rd b/rkward/rbackend/rpackages/rkward/man/rk.capture.output.Rd
index 73d0a3518..0c8a74b8e 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.capture.output.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.capture.output.Rd
@@ -16,7 +16,11 @@ rk.capture.output(
rk.end.capture.output(highlight = FALSE)
}
\arguments{
-\item{suppress.messages}{message are not sent on, neither to surrounding captures, nor as regular output.}
+\item{capture.messages}{logical, whether messages should be captured.}
+
+\item{capture.output}{logical, whether output should be captured.}
+
+\item{suppress.messages}{logical, if \code{FALSE} message are not sent on, neither to surrounding captures, nor as regular output.}
\item{suppress.output}{like \code{suppress.messages}, but for output.}
@@ -25,8 +29,6 @@ rk.end.capture.output(highlight = FALSE)
\code{rk.capture.output} Starts capturing output.
\code{rk.end.capture.output} Stops capturing output, and returns the recorded output in a string.}
-
-\item{LANG}{language code to use. "C" for no translation, i.e. generally English}
}
\description{
This feature records and / or redirects output similar to the \code{\link{sink}} and \code{\link{capture.output}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.demo.Rd b/rkward/rbackend/rpackages/rkward/man/rk.demo.Rd
index c540ea64c..0154fa7e0 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.demo.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.demo.Rd
@@ -23,10 +23,10 @@ script for editing, instead of sourcing it. Contrary to \code{\link{demo}},
the specification of a topic is mandatory.
}
\examples{
-
-## Not run
+\dontrun{
rk.demo("graphics")
}
+}
\seealso{
\code{\link{rk.edit.files}}, \code{\link{rk.show.files}},
\code{\link{demo}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.edit.Rd b/rkward/rbackend/rpackages/rkward/man/rk.edit.Rd
index e59e66aea..392c02454 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.edit.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.edit.Rd
@@ -36,11 +36,14 @@ to the user.}
\item{prompt}{logical of length 1. If TRUE (the default) a prompt is dialog
is shown along with the files to show / edit.}
-\item{delete}{a logical (not NA), when \code{TRUE} the shown file(s) are
+\item{header}{character, header to show.}
+
+\item{delete.file}{a logical (not NA), when \code{TRUE} the shown file(s) are
deleted after closing.}
-\item{wtitle}{character vector, of length 1. This will be used as the window
-title.}
+\item{delete}{logical, for compatibility with earlier versions of R.}
+
+\item{url}{a URL to show.}
}
\value{
All functions described on this page return \code{NULL},
@@ -62,11 +65,11 @@ by default, when run inside an RKWard session. (via \code{getOption("editor")},
and \code{getOption("browser")}.
}
\examples{
-
-## Not run
+\dontrun{
x <- data.frame (a=c(1:3), b=c(2:4))
rk.edit(x)
}
+}
\seealso{
\code{\link{edit}}, \code{\link{file.edit}},
\code{\link{file.show}}, \code{\link{browseURL}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.embed.device.Rd b/rkward/rbackend/rpackages/rkward/man/rk.embed.device.Rd
index c023e49b6..4293e9c5d 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.embed.device.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.embed.device.Rd
@@ -23,11 +23,10 @@ Theoretically, \code{expr} can be any valid R expression. However typically this
window already "owned" by RKWard (importantly, \code{RK()} device windows) may lead to unexpected results, including crashes.
}
\examples{
-
-## Not run:
+\dontrun{
rk.embed.device (grDevices::X11(title="X11 device window"))
plot (rnorm (10))
-
+}
}
\seealso{
\link{RK}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.get.tempfile.name.Rd b/rkward/rbackend/rpackages/rkward/man/rk.get.tempfile.name.Rd
index 8fe937e37..6b0d33b89 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.get.tempfile.name.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.get.tempfile.name.Rd
@@ -110,7 +110,7 @@ via the RKWard GUI.
\link{R.home}.
}
\examples{
-
+\dontrun{
testfile.name <- rk.get.tempfile.name(prefix="test", extension=".txt")
testfile <- file(testfile.name)
cat("This is a test\n", file=testfile)
@@ -119,13 +119,12 @@ unlink(testfile.name)
outfile <- rk.get.output.html.file()
-## Not run
rk.set.output.html.file("~/.rkward/another_file.html")
rk.header("Output on a different output file")
rk.show.html(rk.get.output.html.file())
rk.flush.output()
rk.set.output.html.file(outfile)
-
+}
}
\seealso{
\url{rkward://page/rkward_output}, \link{tempfile}, \link{file},
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.graph.on.Rd b/rkward/rbackend/rpackages/rkward/man/rk.graph.on.Rd
index b965ef9b6..252fe7816 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.graph.on.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.graph.on.Rd
@@ -36,6 +36,7 @@ The default is to use the quality configured in Settings -> Configure RKWard ->
The default settings for \code{device.type}, \code{width}, \code{height}, and \code{quality} can be modified from Settings -> Configure RKWard -> Output.
}
\examples{
+\dontrun{
## Plot directly to the output (html) file, by-passing screen device:
rk.graph.on ("JPG", 480, 480, 75)
plot (rnorm (100))
@@ -49,7 +50,7 @@ rk.graph.off ()
## WRONG USAGE: not run:
#plot (rnorm (100))
#dev.print (device = rk.graph.on)
-
+}
}
\seealso{
\code{\link{rk.results}}, \code{\link{rk.print}}, \code{\link{rk.get.output.html.file}}, \code{\link[grDevices:dev.off]{dev.off}}, \code{\link[grDevices:svg]{svg}}, \code{\link[grDevices:png]{png}}, \code{\link[grDevices:jpeg]{jpeg}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.list.plugins.Rd b/rkward/rbackend/rpackages/rkward/man/rk.list.plugins.Rd
index 877c32bb0..e05130df0 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.list.plugins.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.list.plugins.Rd
@@ -41,14 +41,13 @@ registered plugins (in loaded pluginmaps).
only visibility can be controlled.
}
\examples{
+\dontrun{
## list all current plugins
rk.list.plugins ()
-## NOT RUN
## hide t.test plugin
rk.set.plugin.status ("rkward::t_test", visible=FALSE)
-## END NOT RUN
-
+}
}
\seealso{
\code{\link{rk.call.plugin}} for invoking a plugin, programatically
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.load.pluginmaps.Rd b/rkward/rbackend/rpackages/rkward/man/rk.load.pluginmaps.Rd
index d50da04da..261309193 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.load.pluginmaps.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.load.pluginmaps.Rd
@@ -28,13 +28,10 @@ priority setting. In scripted usage, this should generally be set to FALSE.}
(Re-)load the given pluginmap files into the RKWard GUI
}
\examples{
-
-## NOT RUN
-
+\dontrun{
## reload all active pluginmaps
rk.load.pluginmaps()
-
-## END NOT RUN
+}
}
\seealso{
\code{\link{rk.call.plugin}}, \code{\link[rkwarddev:rk.plugin.skeleton]{rk.plugin.skeleton}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.printer.device.Rd b/rkward/rbackend/rpackages/rkward/man/rk.printer.device.Rd
index 7128999ed..abf137146 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.printer.device.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.printer.device.Rd
@@ -22,11 +22,10 @@ Typically this device is used with \code{\link{dev.print}}, as shown in the
example, below.
}
\examples{
-
-## Not run:
+\dontrun{
plot (rnorm (10))
dev.print (rk.printer.device)
-
+}
}
\seealso{
\code{\link{postscript}}, \code{\link{dev.print}},
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.record.plot.Rd b/rkward/rbackend/rpackages/rkward/man/rk.record.plot.Rd
index 96b03bd97..58b87423e 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.record.plot.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.record.plot.Rd
@@ -97,9 +97,7 @@ rk.duplicate.device(devId = dev.cur())
}
\examples{
-## Example for this?
-require (rkward)
-
+\dontrun{
.L. <- getOption ("rk.graphics.hist.max.length")
local ({
@@ -116,10 +114,9 @@ local ({
rk.first.plot ()
for (i in 1:(rk.record.plot$sP.length-1)) rk.next.plot ()
-## Not run
rk.clear.plot.history ()
options ("rk.graphics.hist.max.length" = .L.)
-
+}
}
\keyword{device}
\keyword{dynamic}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.replace.function.Rd b/rkward/rbackend/rpackages/rkward/man/rk.replace.function.Rd
index 73244d79c..dbf1fb181 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.replace.function.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.replace.function.Rd
@@ -44,15 +44,13 @@ functions in arbitrary ways. You better know what you are doing.
\bold{WARNING}: Does not work well on generics!
}
\examples{
-
-## Not run
+\dontrun{
rk.replace.function ("history", as.environment ("package:utils"),
function () {
cat ("This is what you typed:\n")
eval (body (.rk.backups$history))
})
-## End not run
-
+}
}
\seealso{
\code{\link{assignInNamespace}}, \code{\link{debug}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.results.Rd b/rkward/rbackend/rpackages/rkward/man/rk.results.Rd
index 47b19a262..9b86fe748 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.results.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.results.Rd
@@ -82,7 +82,7 @@ a \code{htest}. This is similar to \code{stats:::print.htext} and makes
sense only when \code{x$alternatives} exists.
}
\examples{
-
+\dontrun{
# code is only run when the R2HTML package can be loaded
if(require("R2HTML", quietly = TRUE)){
@@ -116,6 +116,7 @@ if(require("R2HTML", quietly = TRUE)){
})
} else {}
}
+}
\seealso{
\code{\link[R2HTML:HTML]{HTML}}, \code{\link{rk.get.output.html.file}},
\code{\link{rk.get.description}}, \code{\link{rk.call.plugin}},
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.sessionInfo.Rd b/rkward/rbackend/rpackages/rkward/man/rk.sessionInfo.Rd
index 28f3711fa..a273f10bf 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.sessionInfo.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.sessionInfo.Rd
@@ -20,9 +20,10 @@ Typically, when reporting a bug, you should use \code{Help->Report Bug...}
from the menu. Internally, this will call \code{rk.sessionInfo()}.
}
\examples{
-
+\dontrun{
rk.sessionInfo()
}
+}
\seealso{
\code{\link{sessionInfo}}
}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.show.messages.Rd b/rkward/rbackend/rpackages/rkward/man/rk.show.messages.Rd
index 596dd9e66..c9f25c4f8 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.show.messages.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.show.messages.Rd
@@ -138,6 +138,7 @@ they expect. In those cases, the name of the target directory must be entered in
input field of the dialog manually.
}
\examples{
+\dontrun{
## Message boxes
if (rk.show.question ("Question:\nDo you want to know about RKWard?",
button.yes = "Yes, I do!", button.no = "No, I don't care!", button.cancel = "")) {
@@ -152,6 +153,7 @@ rk.select.list (LETTERS, preselect = c("A", "E", "I", "O", "U"),
.rk.backups$select.list (LETTERS, preselect = c("A", "E", "I", "O", "U"),
multiple = TRUE, title = "vowels")
}
+}
\seealso{
\code{\link{system}}, \code{\link{select.list}},
\code{\link[base:file.choose]{file.choose}}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.sync.Rd b/rkward/rbackend/rpackages/rkward/man/rk.sync.Rd
index 50ecfc8c4..102ab04ef 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.sync.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.sync.Rd
@@ -32,9 +32,9 @@ of objects. rk.sync() can be used, here, to inspect the objects inside
environments (see examples).
}
\examples{
-
+\dontrun{
rk.sync (rkward::rk.record.plot)
-
+}
}
\seealso{
\url{rkward://page/rkward_workspace_browser}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.with.window.hints.Rd b/rkward/rbackend/rpackages/rkward/man/rk.with.window.hints.Rd
index d8b78413f..0bc5d2b88 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.with.window.hints.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.with.window.hints.Rd
@@ -36,14 +36,12 @@ NOTE: This function is still somewhat experimental, and it is not guaranteed tha
it will remain in place, with compatible parameters.
}
\examples{
-
-## Not run
+\dontrun{
.rk.with.window.hints ({
RK ()
plot (1, 1)
}, "attached")
-## End not run
-
+}
}
\author{
Thomas Friedrichsmeier \email{rkward-devel at kde.org}
diff --git a/rkward/rbackend/rpackages/rkward/man/rk.workplace.Rd b/rkward/rbackend/rpackages/rkward/man/rk.workplace.Rd
index acadd41f7..9458fecec 100644
--- a/rkward/rbackend/rpackages/rkward/man/rk.workplace.Rd
+++ b/rkward/rbackend/rpackages/rkward/man/rk.workplace.Rd
@@ -44,7 +44,6 @@ device windows will not be restored (but WILL be closed by
rk.save.workplace ()
rk.restore.workplace ()
}
-
}
\seealso{
\url{rkward://page/rkward_for_r_users}, \link{rk.get.workspace.url}
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