[rkward-cvs] SF.net SVN: rkward:[4191] trunk/rkward/rkward/rbackend/rpackages/rkward/R
m-eik at users.sourceforge.net
m-eik at users.sourceforge.net
Mon Mar 19 15:35:48 UTC 2012
Revision: 4191
http://rkward.svn.sourceforge.net/rkward/?rev=4191&view=rev
Author: m-eik
Date: 2012-03-19 15:35:48 +0000 (Mon, 19 Mar 2012)
Log Message:
-----------
added "#' @export" to all functions
Modified Paths:
--------------
trunk/rkward/rkward/rbackend/rpackages/rkward/R/base_overrides.R
trunk/rkward/rkward/rbackend/rpackages/rkward/R/internal.R
trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.label-functions.R
trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
Modified: trunk/rkward/rkward/rbackend/rpackages/rkward/R/base_overrides.R
===================================================================
--- trunk/rkward/rkward/rbackend/rpackages/rkward/R/base_overrides.R 2012-03-18 22:11:14 UTC (rev 4190)
+++ trunk/rkward/rkward/rbackend/rpackages/rkward/R/base_overrides.R 2012-03-19 15:35:48 UTC (rev 4191)
@@ -70,4 +70,3 @@
invisible (ret)
}
formals (setwd) <- formals (base::setwd)
-
Modified: trunk/rkward/rkward/rbackend/rpackages/rkward/R/internal.R
===================================================================
--- trunk/rkward/rkward/rbackend/rpackages/rkward/R/internal.R 2012-03-18 22:11:14 UTC (rev 4190)
+++ trunk/rkward/rkward/rbackend/rpackages/rkward/R/internal.R 2012-03-19 15:35:48 UTC (rev 4191)
@@ -1,9 +1,11 @@
# check the context in which this package is loaded
+#' @export
.onAttach <- function(...) {
.rk.inside.rkward.session(warn = TRUE)
}
# this function shall test if the rkward package was loaded in a running RKWard session
+#' @export
.rk.inside.rkward.session <- function(warn = FALSE){
inside.rkward <- is.loaded("rk.do.generic.request")
if(isTRUE(warn) & !isTRUE(inside.rkward)){
@@ -13,15 +15,18 @@
return(inside.rkward)
}
+#' @export
".rk.get.meta" <- function (x) {
y <- attr (x, ".rk.meta");
c (names (y), as.character (y))
}
+#' @export
".rk.set.meta" <- function (x, m) {
eval (substitute (attr (x, ".rk.meta") <<- m))
}
+#' @export
".rk.set.invalid.field" <- function (x, row, value) {
l <- attr (x, ".rk.invalid.fields");
if (is.null (l)) l <- list ();
@@ -30,6 +35,7 @@
eval (substitute (attr (x, ".rk.invalid.fields") <<- l))
}
+#' @export
".rk.data.frame.insert.row" <- function (x, index=0) {
if ((index == 0) || (index > dim (x)[1])) { # insert row at end
eval (substitute (x[dim(x)[1]+1,] <<- c (NA)))
@@ -43,6 +49,7 @@
}
# TODO: is there a nice way to get rid of a row without removing the meta-data?
+#' @export
".rk.data.frame.delete.row" <- function (x, index) {
attriblist <- list ()
for (i in 1:dim (x)[2]) {
@@ -57,6 +64,7 @@
}
# function below is only needed to ensure a nice ordering of the columns. Simply adding a new column would be much easier than this.
+#' @export
".rk.data.frame.insert.column" <- function (x, label, index=0) {
column <- rep (as.numeric (NA), times=dim (x)[1])
if ((index == 0) || (index > dim (x)[2])) { # insert column at end
@@ -71,6 +79,7 @@
}
}
+#' @export
".rk.do.error" <- function () {
# comment in R sources says, it may not be good to query options during error handling. But what can we do, if R_ShowErrorMessages is not longer exported?
if (getOption ("show.error.messages")) {
@@ -78,18 +87,22 @@
}
}
+#' @export
".rk.set.reply" <- function (x) .rk.variables$.rk.rkreply <- x
+#' @export
".rk.do.call" <- function (x, args=NULL) {
.rk.set.reply (NULL)
.Call ("rk.do.command", c (x, args));
return (.rk.variables$.rk.rkreply)
}
+#' @export
".rk.do.plain.call" <- function (x, args=NULL, synchronous=TRUE) {
.Call ("rk.do.generic.request", c (x, args), isTRUE (synchronous))
}
+#' @export
".rk.find.package.pluginmaps" <- function (package, all.maps=FALSE) {
if(isTRUE(all.maps)){
# look for all pluginmaps in the rkward folder
@@ -107,6 +120,7 @@
# Gather status information on installed and available packages.
# Return value is used in class RKRPackageInstallationStatus of the frontend
+#' @export
".rk.get.package.intallation.state" <- function () {
# fetch all status information
available <- .rk.cached.available.packages ()
@@ -133,6 +147,7 @@
# package information formats may - according to the help - be subject to change. Hence this function to cope with "missing" values
# also it concatenates everything to a single vector, so we can easily get the whole structure with a single call
+#' @export
".rk.get.installed.packages" <- function () {
x <- as.data.frame(installed.packages(fields="Title"))
# does a package enhance RKWard, i.e. provide plugins?
@@ -149,6 +164,7 @@
}
# This function works like available.packages (with no arguments), but does simple caching of the result, and of course uses a cache if available. Cache is only used, if it is less than 1 hour old, and options("repos") is unchanged.
+#' @export
".rk.cached.available.packages" <- function () {
x <- NULL
if (exists ("available.packages.cache", envir=.rk.variables) && (!is.null (.rk.variables$available.packages.cache))) {
@@ -173,8 +189,10 @@
#}
# these functions can be used to track assignments to R objects. The main interfaces are .rk.watch.symbol (k) and .rk.unwatch.symbol (k). This works by copying the symbol to a backup environment, removing it, and replacing it by an active binding to the backup location
+#' @export
".rk.watched.symbols" <- new.env ()
+#' @export
".rk.make.watch.f" <- function (k) {
# we need to make sure, the functions we use are *not* looked up as symbols in .GlobalEnv.
# else, for instance, if the user names a symbol "missing", and we try to resolve it in the
@@ -200,6 +218,7 @@
}
}
+#' @export
".rk.watch.symbol" <- function (k) {
f <- .rk.make.watch.f (k)
.Call ("rk.copy.no.eval", k, globalenv(), .rk.watched.symbols);
@@ -212,6 +231,7 @@
}
# not needed by rkward but provided for completeness
+#' @export
".rk.unwatch.symbol" <- function (k) {
rm (list=k, envir=globalenv ())
@@ -222,6 +242,7 @@
invisible (TRUE)
}
+#' @export
".rk.watch.globalenv" <- function () {
newlist <- ls (globalenv (), all.names=TRUE)
oldlist <- ls (.rk.watched.symbols, all.names=TRUE)
@@ -238,6 +259,7 @@
}
}
+#' @export
".rk.get.vector.data" <- function (x) {
ret <- list ();
ret$data <- as.vector (unclass (x));
@@ -251,6 +273,7 @@
# Change storage type of x to mode newmode.
# Most attributes will be kept, but the data is erased!
+#' @export
".rk.set.vector.mode" <- function (x, fun, envir=parent.frame ()) {
old_attr <- attributes (x)
old_attr$class <- NULL
@@ -268,18 +291,22 @@
eval (substitute (x <- y), envir=envir)
}
+#' @export
".rk.get.structure" <- function (x, name, envlevel=0, namespacename=NULL) {
.Call ("rk.get.structure", x, as.character (name), as.integer (envlevel), namespacename)
}
+#' @export
".rk.try.get.namespace" <- function (name) {
tryCatch (asNamespace (name), error = function(e) NULL)
}
+#' @export
".rk.get.structure.global" <- function (name, envlevel=0, namespacename=NULL) {
.Call ("rk.get.structure.global", as.character (name), as.integer (envlevel), namespacename)
}
+#' @export
".rk.get.slots" <- function (x) {
slotnames <- methods::slotNames (class (x))
ret <- lapply (slotnames, function (slotname) slot (x, slotname))
@@ -287,6 +314,7 @@
ret
}
+#' @export
".rk.get.environment.children" <- function (x, envlevel=0, namespacename=NULL) {
ret <- list ()
@@ -311,14 +339,17 @@
}
# hidden, as this is not portable to different output formats
+#' @export
".rk.cat.output" <- function (x) {
cat (x, file = rk.get.output.html.file(), append = TRUE)
}
+#' @export
".rk.rerun.plugin.link" <- function (plugin, settings, label) {
.rk.cat.output (paste ("<a href=\"rkward://runplugin/", plugin, "/", URLencode (settings), "\">", label, "</a>", sep=""))
}
+#' @export
".rk.make.hr" <- function () {
.rk.cat.output ("<hr>\n");
}
@@ -331,10 +362,12 @@
assign(".rk.rkreply", NULL, envir=.rk.variables)
assign("available.packages.cache", NULL, envir=.rk.variables)
+#' @export
".rk.backups" <- new.env ()
# where masking is not enough, we need to assign in the original environment / namespace. This can only be done after package loading,
# so we have a separate function for that.
+#' @export
".rk.fix.assignments" <- function () {
## History manipulation function (overloads for functions by the same name in package utils)
rk.replace.function ("loadhistory", as.environment ("package:utils"),
Modified: trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.label-functions.R
===================================================================
--- trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.label-functions.R 2012-03-18 22:11:14 UTC (rev 4190)
+++ trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.label-functions.R 2012-03-19 15:35:48 UTC (rev 4191)
@@ -31,7 +31,7 @@
#' the label" while the others return a character vector.
#' @author Thomas Friedrichsmeier \email{rkward-devel@@lists.sourceforge.net}
#' @keywords utilities
-#' @rdname rk.get.label
+#' @rdname rk.label
#' @examples
#'
#' x <- data.frame(a=c(1:3), b=c(2:4))
@@ -55,6 +55,7 @@
}
# set rkward label
+#' @rdname rk.label
#' @export
"rk.set.label" <- function (x, label, envir=parent.frame()) {
if (is.call (x) || is.name (x)) {
@@ -67,6 +68,7 @@
}
# get a short name for the given object
+#' @rdname rk.label
#' @export
"rk.get.short.name" <- function (x) {
if (is.call (x) || is.name (x)) {
@@ -90,6 +92,7 @@
}
# get descriptive strings for each of the arguments in ...
+#' @rdname rk.label
#' @export
"rk.get.description" <- function (..., paste.sep=NULL, is.substitute=FALSE) {
args <- list(...)
@@ -125,6 +128,7 @@
}
# Drop-in replacement for list(). Returns a list of the given arguments, but with names set according to rk.get.description
+#' @rdname rk.label
#' @export
"rk.list" <- function (...) {
ret <- list (...)
@@ -133,6 +137,7 @@
}
# this is basically copied from R-base table (). Returns the arguments passed to ... as a character vector
+#' @rdname rk.label
#' @export
"rk.list.names" <- function(..., deparse.level=2) {
l <- as.list(substitute(list(...)))[-1]
Modified: trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R
===================================================================
--- trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R 2012-03-18 22:11:14 UTC (rev 4190)
+++ trunk/rkward/rkward/rbackend/rpackages/rkward/R/rk.workspace-functions.R 2012-03-19 15:35:48 UTC (rev 4191)
@@ -47,6 +47,7 @@
writeLines (lines, file)
}
+#' @rdname rk.workplace
#' @export
"rk.restore.workplace" <- function (file=NULL, close.windows=TRUE) {
if (is.null (file)) {
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