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R/commander.R
In Rcmdr: R Commander
Defines functions
openGraphicsDevices
mergeCapabilities
popCommand
pushCommand
popOutput
pushOutput
messageTag
Message
pause
checkWarnings
doItAndPrint
justDoIt
logger
setupGUI
processMenus
processOperations
processModelCapabilities
processPlugins
platformIssues
setupFonts
createIcons
setupRcmdrOptions
manageRcmdrEnv
Commander
Documented in
Commander
doItAndPrint
justDoIt
logger
Message
popCommand
popOutput
# The R Commander and command logger
# last modified 2023-08-07 by John Fox
# contributions by Milan Bouchet-Valat, Richard Heiberger, Duncan Murdoch, Erich Neuwirth, Brian Ripley, Vilmantas Gegzna
Commander <- function(){
# set global options (to be restored on exit from Rcmdr GUI)
putRcmdr("quotes", options(useFancyQuotes=FALSE))
putRcmdr("max.print", options(max.print=2^30))
putRcmdr("scipen", getOption("scipen"))
manageRcmdrEnv()
DESCRIPTION <- readLines(file.path(find.package("Rcmdr"), "DESCRIPTION")[1])
setupRcmdrOptions(DESCRIPTION)
createIcons()
setupFonts()
platformIssues()
modelClasses <- scan(file.path(getRcmdr("etc"), "model-classes.txt"), what="", quiet=TRUE, comment.char="#") # default recognized models
Plugins <- processPlugins(modelClasses)
processModelCapabilities(Plugins)
processOperations(Plugins)
Menus <- processMenus(Plugins)
setupGUI(Menus)
openGraphicsDevices()
# optionally open Markdown editor
if (getRcmdr("open.markdown.editor") && getRcmdr("use.markdown")){
editMarkdown()
}
# keep start-up warnings out of Rcmdr log
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
library(Rcmdr, quietly=TRUE)
sink(type="message")
close(messages.connection)
}
manageRcmdrEnv <- function(){
RcmdrEnv.on.path <- getOption("Rcmdr")[["RcmdrEnv.on.path"]]
if (is.null(RcmdrEnv.on.path)) RcmdrEnv.on.path <- FALSE
if (RcmdrEnv.on.path){
RcmdrEnv <- function() {
pos <- match("RcmdrEnv", search())
if (is.na(pos)) { # Must create it
RcmdrAttach <- base::attach
RcmdrEnv <- list()
RcmdrAttach(RcmdrEnv, pos = length(search()) - 1)
rm(RcmdrEnv)
pos <- match("RcmdrEnv", search())
}
return(pos.to.env(pos))
}
# the following two lines to be commented-out for debugging:
assignInMyNamespace("RcmdrEnv", RcmdrEnv)
assignInMyNamespace(".RcmdrEnv", NULL)
}
}
setupRcmdrOptions <- function(DESCRIPTION){
current <- getOption("Rcmdr")
putRcmdr("messageNumber", 0)
if (exists(".RcmdrEnv") && is.environment(RcmdrEnv()) &&
exists("commanderWindow", RcmdrEnv()) &&
!is.null(get("commanderWindow", RcmdrEnv()))) {
return(invisible(NULL))
}
# check for auxiliary software
putRcmdr("capabilities", RcmdrCapabilities())
setOption("suppress.icon.images", FALSE)
# locate Rcmdr etc directory and directory for menus (usually the same)
etc <- setOption("etc", system.file("etc", package="Rcmdr"))
etcMenus <- setOption("etcMenus", etc)
putRcmdr("etcMenus", etcMenus)
# various initializations
messageTag(reset=TRUE)
putRcmdr("installed.packages", installed.packages())
RcmdrVersion <- trim.blanks(sub("^Version:", "",
grep("^Version:", DESCRIPTION, value=TRUE)))
putRcmdr("RcmdrVersion", RcmdrVersion)
RVersion <- paste(R.Version()[c("major", "minor")], collapse=".")
RVersionStatus <- R.Version()$status
putRcmdr("RVersion", RVersion)
putRcmdr("RVersionStatus", RVersionStatus)
putRcmdr("UserName", getUserName())
putRcmdr(".activeDataSet", NULL)
putRcmdr(".activeModel", NULL)
putRcmdr("nrow", NULL)
putRcmdr("ncol", NULL)
putRcmdr("logFileName", NULL)
putRcmdr("RmdFileName", "RcmdrMarkdown.Rmd")
putRcmdr("RnwFileName", "RcmdrKnitr.Rnw")
putRcmdr("outputFileName", NULL)
putRcmdr("saveFileName", NULL)
putRcmdr("modelNumber", 0)
putRcmdr("reset.model", FALSE)
putRcmdr("rgl", FALSE)
putRcmdr("rgl.command", FALSE)
putRcmdr("Identify3d", NULL)
putRcmdr("open.dialog.here", NULL)
putRcmdr("restoreTab", FALSE)
putRcmdr("cancelDialogReopen", FALSE)
putRcmdr("last.search", "")
putRcmdr("Markdown.editor.open", FALSE)
putRcmdr("knitr.editor.open", FALSE)
setOption("use.rgl", TRUE)
# set various options
options(scipen=setOption("scientific.notation", 5))
setOption("default.contrasts", c("contr.Treatment", "contr.poly"))
setOption("number.messages", TRUE)
setOption("log.commands", TRUE)
setOption("use.knitr", FALSE)
setOption("use.markdown", !getRcmdr("use.knitr"))
setOption("open.markdown.editor", FALSE)
setOption("rmarkdown.output", TRUE)
rmo.defaults <- list(
command.sections = TRUE, section.level=3, toc=TRUE, toc_float=TRUE, toc_depth=3,
number_sections=FALSE, translate.rmd.headers=TRUE
)
rmo.options <- applyDefaultValues(getRcmdr("rmarkdown.output"), rmo.defaults)
putRcmdr("command.sections", rmo.options$command.sections)
putRcmdr("section.level", paste(rep("#", rmo.options$section.level), collapse=""))
putRcmdr("translate.rmd.headers", rmo.options$translate.rmd.headers)
if ((!packageAvailable("markdown") && !packageAvailable("rmarkdown")) || (!packageAvailable("knitr")))
putRcmdr("use.markdown", FALSE)
if (!packageAvailable("knitr") || !getRcmdr("capabilities")$pdflatex) putRcmdr("use.knitr", FALSE)
setOption("rmd.output.format", "html")
putRcmdr("startNewCommandBlock", TRUE)
putRcmdr("startNewKnitrCommandBlock", TRUE)
putRcmdr("rmd.generated", FALSE)
putRcmdr("rnw.generated", FALSE)
setOption("RStudio", RStudioP())
setOption("console.output", getRcmdr("RStudio"))
setOption("retain.selections", TRUE)
setOption("open.graphics.devices", FALSE)
putRcmdr("dialog.values", list())
putRcmdr("dialog.values.noreset", list())
putRcmdr("savedTable", NULL)
putRcmdr("onApplyCalled", FALSE)
log.height <- as.character(setOption("log.height", if (!getRcmdr("log.commands")) 0 else 10))
log.width <- as.character(setOption("log.width", 80))
output.height <- as.character(setOption("output.height",
if (getRcmdr("console.output")) 0
else if ((as.numeric(log.height) != 0) || (!getRcmdr("log.commands"))) 2*as.numeric(log.height)
else 20))
messages.height <- as.character(setOption("messages.height", 4))
setOption("minimum.width", 1000)
setOption("minimum.height", 400)
putRcmdr("saveOptions", options(warn=1, contrasts=getRcmdr("default.contrasts"), width=as.numeric(log.width),
na.action="na.exclude", graphics.record=TRUE))
setOption("ask.to.exit", TRUE)
setOption("ask.on.exit", TRUE)
setOption("double.click", FALSE)
setOption("sort.names", TRUE)
setOption("grab.focus", TRUE)
setOption("attach.data.set", FALSE)
setOption("log.text.color", "black")
setOption("command.text.color", "darkred")
setOption("output.text.color", "darkblue")
setOption("error.text.color", "red")
setOption("warning.text.color", "darkgreen")
setOption("prefixes", c("Rcmdr> ", "Rcmdr+ ", "RcmdrMsg: ", "RcmdrMsg+ "))
setOption("multiple.select.mode", "extended")
setOption("suppress.X11.warnings",
interactive() && .Platform$GUI == "X11") # to address problem in X11 (Linux or Mac OS X)
setOption("showData.threshold", c(20000, 100))
setOption("editDataset.threshold", if (getRcmdr("capabilities")$tktable) 10000 else 0)
setOption("retain.messages", TRUE)
setOption("crisp.dialogs", TRUE)
setOption("length.output.stack", 10)
setOption("length.command.stack", 10)
setOption("quit.R.on.close", FALSE)
putRcmdr("outputStack", as.list(rep(NA, getRcmdr("length.output.stack"))))
putRcmdr("commandStack", as.list(rep(NA, getRcmdr("length.command.stack"))))
setOption("variable.list.height", 6)
setOption("variable.list.width", c(20, Inf))
setOption("valid.classes", c("factor", "ordered", "character", "logical",
"POSIXct", "POSIXlt", "Date", "chron", "yearmon", "yearqtr", "zoo",
"zooreg", "timeDate", "xts", "its", "ti", "jul", "timeSeries", "fts",
"Period", "hms", "difftime"))
setOption("discreteness.threshold", 0)
setOption("model.case.deletion", TRUE)
putRcmdr("open.showData.windows", list())
}
createIcons <- function(){
icon.images <- !getRcmdr("suppress.icon.images")
tkimage.create("photo", "::image::RlogoIcon", file = system.file("etc", "R-logo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::okIcon",
file = if (icon.images) system.file("etc", "ok.gif", package="Rcmdr") else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::cancelIcon", file = if (icon.images) system.file("etc", "cancel.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::helpIcon", file = if (icon.images) system.file("etc", "help.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::resetIcon", file = if (icon.images) system.file("etc", "reset.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::applyIcon", file = if (icon.images) system.file("etc", "apply.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::submitIcon", file = system.file("etc", "submit.gif", package="Rcmdr"))
tkimage.create("photo", "::image::editIcon", file = system.file("etc", "edit.gif", package="Rcmdr"))
tkimage.create("photo", "::image::viewIcon", file = system.file("etc", "view.gif", package="Rcmdr"))
tkimage.create("photo", "::image::dataIcon", file = system.file("etc", "data.gif", package="Rcmdr"))
tkimage.create("photo", "::image::modelIcon", file = system.file("etc", "model.gif", package="Rcmdr"))
tkimage.create("photo", "::image::removeIcon", file = system.file("etc", "remove.gif", package="Rcmdr"))
tkimage.create("photo", "::image::copyIcon", file = system.file("etc", "copy.gif", package="Rcmdr"))
tkimage.create("photo", "::image::cutIcon", file = system.file("etc", "cut.gif", package="Rcmdr"))
tkimage.create("photo", "::image::deleteIcon", file = system.file("etc", "delete.gif", package="Rcmdr"))
tkimage.create("photo", "::image::findIcon", file = system.file("etc", "find.gif", package="Rcmdr"))
tkimage.create("photo", "::image::pasteIcon", file = system.file("etc", "paste.gif", package="Rcmdr"))
tkimage.create("photo", "::image::redoIcon", file = system.file("etc", "redo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::undoIcon", file = system.file("etc", "undo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::saveEditsIcon", file = system.file("etc", "save-edits.gif", package="Rcmdr"))
tkimage.create("photo", "::image::infoIcon", file = system.file("etc", "info.gif", package="Rcmdr"))
tkimage.create("photo", "::image::warningIcon", file = system.file("etc", "warning.gif", package="Rcmdr"))
tkimage.create("photo", "::image::errorIcon", file = system.file("etc", "error.gif", package="Rcmdr"))
tkimage.create("photo", "::image::questionIcon", file = system.file("etc", "question.gif", package="Rcmdr"))
}
setupFonts <- function(){
current <- getOption("Rcmdr")
# set up Rcmdr default and text (log) fonts, Tk scaling factor
default.font.family.val <- tclvalue(.Tcl("font actual TkDefaultFont -family"))
default.font.family.val <- gsub("\\{", "", gsub("\\}", "", default.font.family.val))
default.font.family <- setOption("default.font.family", default.font.family.val)
if (!("RcmdrDefaultFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrDefaultFont", tclvalue(tkfont.actual("TkDefaultFont"))))
.Tcl("option add *font RcmdrDefaultFont")
}
.Tcl(paste("font configure RcmdrDefaultFont -family {", default.font.family, "}", sep=""))
if (!("RcmdrTitleFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrTitleFont", tclvalue(tkfont.actual("TkDefaultFont"))))
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, "}", sep=""))
if (!("RcmdrOutputMessagesFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrOutputMessagesFont", tclvalue(tkfont.actual("RcmdrTitleFont"))))
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, "}", sep=""))
.Tcl(paste("font configure RcmdrOutputMessagesFont -family {", default.font.family, "}", sep=""))
.Tcl(paste("font configure TkDefaultFont -family {", default.font.family, "}", sep=""))
log.font.family.val <- tclvalue(.Tcl("font actual TkFixedFont -family"))
log.font.family.val <- gsub("\\{", "", gsub("\\}", "", log.font.family.val))
log.font.family <- setOption("log.font.family", log.font.family.val)
if (!("RcmdrLogFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrLogFont", tclvalue(tkfont.actual("TkFixedFont"))))
}
.Tcl(paste("font configure RcmdrLogFont -family {", log.font.family, "}", sep=""))
.Tcl(paste("font configure TkFixedFont -family {", log.font.family, "}", sep=""))
putRcmdr("logFont", "RcmdrLogFont")
scale.factor <- current$scale.factor
if (!is.null(scale.factor)) .Tcl(paste("tk scaling ", scale.factor, sep=""))
# set various font sizes
if (WindowsP()){
default.font.size.val <- abs(as.numeric(.Tcl("font actual TkDefaultFont -size")))
if (is.na(default.font.size.val)) default.font.size.val <- 10
}
else default.font.size.val <- 10
default.font.size <- setOption("default.font.size", default.font.size.val)
tkfont.configure("RcmdrDefaultFont", size=default.font.size)
tkfont.configure("RcmdrTitleFont", size=default.font.size)
tkfont.configure("RcmdrOutputMessagesFont", size=default.font.size)
tkfont.configure("TkDefaultFont", size=default.font.size)
tkfont.configure("TkTextFont", size=default.font.size)
tkfont.configure("TkCaptionFont", size=default.font.size)
log.font.size <- setOption("log.font.size", 10)
tkfont.configure("RcmdrLogFont", size=log.font.size)
tkfont.configure("TkFixedFont", size=log.font.size)
.Tcl("ttk::style configure TButton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TLabel -font RcmdrDefaultFont")
.Tcl("ttk::style configure TCheckbutton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TRadiobutton -font RcmdrDefaultFont")
standard.title.color <- as.character(.Tcl("ttk::style lookup TLabelframe.Label -foreground"))
title.color <- setOption("title.color", standard.title.color)
if (tolower(title.color) == "black" || title.color == "#000000"){
tkfont.configure("RcmdrTitleFont", weight="bold")
}
else tkfont.configure("RcmdrTitleFont", weight="normal")
}
platformIssues <- function(){
current <- getOption("Rcmdr")
if (getRcmdr("suppress.X11.warnings")) {
putRcmdr("messages.connection", file(open = "w+"))
sink(getRcmdr("messages.connection"), type="message")
}
if (!(WindowsP())) {
putRcmdr("oldPager", options(pager=RcmdrPager))
}
putRcmdr("restore.help_type", getOption("help_type"))
if ((!WindowsP()) && getRcmdr("RVersion") == "4.2.0" && (getRcmdr("RVersionStatus") != "Patched")) {
setOption("help_type", "text")
} else {
setOption("help_type", "html")
}
options(help_type=getRcmdr("help_type"))
putRcmdr("restore.device", getOption("device"))
if (RStudioP()){
if (WindowsP()) options(device="windows")
else if (MacOSXP()) options(device="quartz")
else options(device="x11")
}
setOption("tkwait.dialog", FALSE)
if (getRcmdr("tkwait.dialog")) putRcmdr("editDataset.threshold", 0)
if (MacOSXP()){
# PATH <- system2("/usr/libexec/path_helper", "-s", stdout=TRUE)
# PATH <- sub("\"; export PATH;$", "", sub("^PATH=\\\"", "", PATH))
# Sys.setenv(PATH=PATH)
PATH <- Sys.getenv("PATH")
PATH <- unlist(strsplit(PATH, .Platform$path.sep, fixed=TRUE))
if (MacOSXP("15.0.0")){
if (length(grep("^/Library/TeX/texbin$", PATH)) == 0) {
PATH[length(PATH) + 1] <- "/Library/TeX/texbin"
Sys.setenv(PATH=paste(PATH, collapse=.Platform$path.sep))
}
}
else{
if (length(grep("^/usr/texbin$", PATH)) == 0) {
PATH[length(PATH) + 1] <- "/usr/texbin"
Sys.setenv(PATH=paste(PATH, collapse=.Platform$path.sep))
}
}
}
}
processPlugins <- function(modelClasses){
# source additional .R files, plug-ins preferred
etc <- getRcmdr("etc")
source.files <- list.files(etc, pattern="\\.[Rr]$")
for (file in source.files) {
source(file.path(etc, file))
cat(paste(gettextRcmdr("Sourced:"), file, "\n"))
}
# collect plug-ins to be used
Plugins <- options()$Rcmdr$plugins
allPlugins <- listPlugins(loaded=TRUE)
for (plugin in Plugins){
if (!require(plugin, character.only=TRUE)){
putRcmdr("commanderWindow", NULL)
stop(sprintf(gettextRcmdr("the plug-in package %s is missing"), plugin))
}
if (!is.element(plugin, allPlugins)){
putRcmdr("commanderWindow", NULL)
stop(sprintf(gettextRcmdr("the package %s is not an Rcmdr plug-in"), plugin))
}
}
for (plugin in Plugins){
description <- readLines(file.path(path.package(package=plugin)[1], "DESCRIPTION"))
addModels <- description[grep("Models:", description)]
addModels <- gsub(" ", "", sub("^Models:", "", addModels))
addModels <- unlist(strsplit(addModels, ","))
addRcmdrModels <- description[grep("RcmdrModels:", description)]
addRcmdrModels <- gsub(" ", "", sub("^RcmdrModels:", "", addRcmdrModels))
addRcmdrModels <- unlist(strsplit(addRcmdrModels, ","))
if (length(addModels) > 0) modelClasses <- c(modelClasses, addModels)
if (length(addRcmdrModels) > 0) modelClasses <- c(modelClasses, addRcmdrModels)
}
putRcmdr("modelClasses", modelClasses)
Plugins
}
processModelCapabilities <- function(Plugins){
modelCapabilities <- read.table(file.path(getRcmdr("etc"), "Rcmdr-model-capabilities.txt"), header=TRUE)
n.plugins <- length(Plugins)
if (n.plugins > 0){
modelCapabilitiesList <- vector(n.plugins + 1, mode="list")
modelCapabilitiesList[[1]] <- modelCapabilities
for (i in 1:n.plugins){
if (file.exists(file.path(path.package(package=Plugins[i])[1], "etc/model-capabilities.txt")))
modelCapabilitiesList[[i + 1]] <- read.table(file.path(path.package(package=Plugins[i])[1],
"etc/model-capabilities.txt"),
header=TRUE)
}
modelCapabilities <- mergeCapabilities(modelCapabilitiesList)
}
putRcmdr("modelCapabilities", modelCapabilities)
modelClasses <- getRcmdr("modelClasses")
modelCapabilitiesClasses <- rownames(modelCapabilities)
modelClasses <- union(modelClasses, modelCapabilitiesClasses)
putRcmdr("modelClasses", modelClasses)
}
processOperations <- function(Plugins){
Operations <- read.table(file.path(getRcmdr("etc"), "Rcmdr-operations.txt"),
header=TRUE, stringsAsFactors=FALSE)
for (plugin in Plugins){
operations.file <- file.path(path.package(package=plugin)[1], "etc", "operations.txt")
if (file.exists(operations.file)){
operations <- read.table(operations.file, header=TRUE, stringsAsFactors=FALSE)
if (any(conflicts <- rownames(operations) %in% rownames(Operations))){
message(sprintf("The following Markdown section titles in %s\n conflict with existing titles and were removed:\n ",
plugin), paste(rownames(operations)[conflicts], collapse=", "))
operations <- operations[!conflicts, ]
}
Operations <- rbind(Operations, operations)
}
}
putRcmdr("Operations", Operations)
}
processMenus <- function(Plugins){
current <- getOption("Rcmdr")
# build Rcmdr menus
Menus <- read.table(file.path(getRcmdr("etcMenus"), "Rcmdr-menus.txt"), colClasses = "character")
addMenus <- function(Menus){
removeMenus <- function(what){
children <- Menus[Menus[,3] == what, 2]
which <- what == Menus[,2] | what == Menus[,5]
Menus <<- Menus[!which,]
for (child in children) removeMenus(child)
}
nms <- c("type", "menuOrItem", "operationOrParent", "label",
"commandOrMenu", "activation", "install")
names(Menus) <- nms
for (plugin in Plugins) {
MenusToAdd <- read.table(file.path(path.package(package=plugin)[1], "etc/menus.txt"),
colClasses = "character")
names(MenusToAdd) <- nms
for (i in 1:nrow(MenusToAdd)){
line <- MenusToAdd[i,]
line[, "label"] <- gettext(line[,"label"], domain=paste("R=", plugin, sep=""))
if (line[1, "type"] == "remove"){
removeMenus(line[1, "menuOrItem"])
next
}
if (line[1, "type"] == "menu"){
where <- if (line[1, "operationOrParent"] == "topMenu") 0
else max(which((Menus[, "type"] == "menu") &
(Menus[, "menuOrItem"] == line[1, "operationOrParent"])))
}
else if (line[1, "type"] == "item"){
if ((line[1, "operationOrParent"] == "command") || (line[1, "operationOrParent"] == "separator")){
which <- which(((Menus[, "operationOrParent"] == "command") |
(Menus[, "operationOrParent"] == "separator")) &
(Menus[, "menuOrItem"] == line[1, "menuOrItem"]))
where <- if (length(which) == 0)
which((Menus[, "type"] == "menu")
& (Menus[, "menuOrItem"] == line[1, "menuOrItem"]))
else max(which)
if (line[1, "operationOrParent"] == "separator" && line[1, "commandOrMenu"] != "")
where <- max(which(line[1, "commandOrMenu"] == Menus[, "commandOrMenu"]))
}
else if (line[1, "operationOrParent"] == "cascade"){
where <- if (line[1, "menuOrItem"] != "topMenu")
max(which((Menus[, "operationOrParent"] == "cascade") &
(Menus[, "menuOrItem"] == line[1, "menuOrItem"]) | (Menus[, "commandOrMenu"] == line[1, "menuOrItem"])))
else {
max(which((Menus[, "operationOrParent"] == "cascade") &
(Menus[, "menuOrItem"] == "topMenu") &
(Menus[, "commandOrMenu"] != "toolsMenu") &
(Menus[, "commandOrMenu"] != "helpMenu")))
}
}
else stop(sprintf(gettextRcmdr('unrecognized operation, "%s", in plugin menu line %i'),
line[1, "operation"], i))
}
else stop(sprintf(gettextRcmdr('unrecognized type, "%s", in plugin menu line %i'),
line[1, "type"], i))
Menus <- insertRows(Menus, line, where)
}
}
Menus
}
Menus <- addMenus(Menus)
menuNames <- Menus[Menus[,1] == "menu",]
duplicateMenus <- duplicated(menuNames)
if (any(duplicateMenus)) stop(paste(gettextRcmdr("Duplicate menu names:"),
menuNames[duplicateMenus]))
setOption("suppress.menus", FALSE)
if (RExcelSupported()) # contributed by Erich Neuwirth
putRExcel(".rexcel.menu.dataframe", Menus)
Menus
}
setupGUI <- function(Menus){
current <- getOption("Rcmdr")
# standard edit actions
onCopy <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
selection <- strsplit(tclvalue(tktag.ranges(focused, "sel")), " ")[[1]]
if (is.na(selection[1])) return()
text <- tclvalue(tkget(focused, selection[1], selection[2]))
tkclipboard.clear()
tkclipboard.append(text)
}
onDelete <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
selection <- strsplit(tclvalue(tktag.ranges(focused, "sel")), " ")[[1]]
if (is.na(selection[1])) return()
tkdelete(focused, selection[1], selection[2])
}
onCut <- function(){
onCopy()
onDelete()
}
onPaste <- function(){
onDelete()
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
text <- tclvalue(.Tcl("selection get -selection CLIPBOARD"))
if (length(text) == 0) return()
tkinsert(focused, "insert", text)
}
onFind <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
initializeDialog(title=gettextRcmdr("Find"))
textFrame <- tkframe(top)
textVar <- tclVar(getRcmdr("last.search"))
textEntry <- ttkentry(textFrame, width="20", textvariable=textVar)
checkBoxes(frame="optionsFrame", boxes=c("regexpr", "case"), initialValues=c("0", "1"),
labels=gettextRcmdr(c("Regular-expression search", "Case sensitive")))
radioButtons(name="direction", buttons=c("foward", "backward"), labels=gettextRcmdr(c("Forward", "Backward")),
values=c("-forward", "-backward"), title=gettextRcmdr("Search Direction"))
onOK <- function(){
text <- tclvalue(textVar)
putRcmdr("last.search", text)
if (text == ""){
errorCondition(recall=onFind, message=gettextRcmdr("No search text specified."))
return()
}
type <- if (tclvalue(regexprVariable) == 1) "-regexp" else "-exact"
case <- tclvalue(caseVariable) == 1
direction <- tclvalue(directionVariable)
stop <- if (direction == "-forward") "end" else "1.0"
where.txt <- if (case) tksearch(focused, type, direction, "--", text, "insert", stop)
else tksearch(focused, type, direction, "-nocase", "--", text, "insert", stop)
where.txt <- tclvalue(where.txt)
if (where.txt == "") {
Message(message=gettextRcmdr("Text not found."),
type="note")
if (GrabFocus()) tkgrab.release(top)
tkdestroy(top)
tkfocus(CommanderWindow())
return()
}
if (GrabFocus()) tkgrab.release(top)
tkfocus(focused)
tkmark.set(focused, "insert", where.txt)
tksee(focused, where.txt)
tkdestroy(top)
}
.exit <- function(){
text <- tclvalue(textVar)
putRcmdr("last.search", text)
return("")
}
OKCancelHelp()
tkgrid(labelRcmdr(textFrame, text=gettextRcmdr("Search for:")), textEntry, sticky="w")
tkgrid(textFrame, sticky="w")
tkgrid(optionsFrame, sticky="w")
tkgrid(directionFrame, sticky="w")
tkgrid(buttonsFrame, sticky="w")
dialogSuffix(focus=textEntry)
}
onSelectAll <- function() {
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID)
&& (tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tktag.add(focused, "sel", "1.0", "end")
tkfocus(focused)
}
onClear <- function(){
onSelectAll()
onDelete()
}
onUndo <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tcl(focused, "edit", "undo")
}
onRedo <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tcl(focused, "edit", "redo")
}
.Tcl("ttk::style configure TNotebook.Tab -font RcmdrDefaultFont")
.Tcl(paste("ttk::style configure TNotebook.Tab -foreground", getRcmdr("title.color")))
all.themes <- tk2theme.list()
current.theme <- tk2theme()
all.themes <- union(all.themes, current.theme)
setOption("theme", current.theme)
theme <- (getRcmdr("theme"))
if (!(theme %in% all.themes)){
warning(gettextRcmdr("non-existent theme"), ', "', theme, '"\n ',
gettextRcmdr("theme set to"), ' "', current.theme, '"')
theme <- current.theme
}
putRcmdr("theme", theme)
tk2theme(theme)
# data-set edit
onEdit <- function(){
if (activeDataSet() == FALSE) {
tkfocus(CommanderWindow())
return()
}
dsnameValue <- ActiveDataSet()
size <- eval(parse(text=paste("prod(dim(", dsnameValue, "))", sep=""))) # prod(dim(save.dataset))
if (size < 1 || size > getRcmdr("editDataset.threshold")){
save.dataset <- get(dsnameValue, envir=.GlobalEnv)
command <- paste("fix(", dsnameValue, ")", sep="")
result <- justDoIt(command)
if (class(result)[1] != "try-error"){
if (nrow(get(dsnameValue)) == 0){
errorCondition(window=NULL, message=gettextRcmdr("empty data set."))
justDoIt(paste(dsnameValue, "<- save.dataset"))
return()
}
else{
logger(command, rmd=FALSE)
activeDataSet(dsnameValue)
}
}
else{
errorCondition(window=NULL, message=gettextRcmdr("data set edit error."))
return()
}
}
else {
command <- paste("editDataset(", dsnameValue, ")", sep="")
result <- justDoIt(command)
if (class(result)[1] != "try-error"){
logger(command, rmd=FALSE)
}
else{
errorCondition(window=NULL, message=gettextRcmdr("data set edit error."))
return()
}
}
tkwm.deiconify(CommanderWindow())
tkfocus(CommanderWindow())
}
# data-set view
onView <- function(){
# if (packageAvailable("relimp")) Library("relimp", rmd=FALSE)
if (activeDataSet() == FALSE) {
tkfocus(CommanderWindow())
return()
}
suppress <- if(getRcmdr("suppress.X11.warnings")) ", suppress.X11.warnings=FALSE" else ""
view.height <- max(getRcmdr("output.height") + getRcmdr("log.height"), 10)
dim <- dim(get(ActiveDataSet()))
nrows <- dim[1]
ncols <- dim[2]
threshold <- getRcmdr("showData.threshold")
command <- if (nrows <= threshold[1] && ncols <= threshold[2]){
posn <- commanderPosition() + c(as.numeric(tkwinfo("width", CommanderWindow())) + 10, 10)
paste("showData(as.data.frame(", ActiveDataSet(), "), title='", ActiveDataSet(), "', placement='+", posn[1], "+", posn[2],"', font=getRcmdr('logFont'), maxwidth=",
getRcmdr("log.width"), ", maxheight=", view.height, suppress, ")", sep="")
}
else paste("View(as.data.frame(", ActiveDataSet(), "))", sep="")
window <- justDoIt(command)
if (!is.null(window)){
open.showData.windows <- getRcmdr("open.showData.windows")
open.window <- open.showData.windows[[ActiveDataSet()]]
if (!is.null(open.window) && open.window$ID %in% as.character(tkwinfo("children", "."))) tkdestroy(open.window)
open.showData.windows[[ActiveDataSet()]] <- window
putRcmdr("open.showData.windows", open.showData.windows)
}
}
# submit command in script tab or compile .Rmd file in markdown tab or compile .Rnw file in knitr tab
onSubmit <- function(){
.log <- LogWindow()
.rmd <- RmdWindow()
.rnw <- RnwWindow()
if (as.character(tkselect(notebook)) == logFrame$ID) {
selection <- strsplit(tclvalue(tktag.ranges(.log, "sel")), " ")[[1]]
if (is.na(selection[1])) {
tktag.add(.log, "currentLine", "insert linestart", "insert lineend")
selection <- strsplit(tclvalue(tktag.ranges(.log,"currentLine")), " ")[[1]]
tktag.delete(.log, "currentLine")
if (is.na(selection[1])) {
Message(message=gettextRcmdr("Nothing is selected."),
type="error")
tkfocus(CommanderWindow())
return()
}
}
lines <- tclvalue(tkget(.log, selection[1], selection[2]))
lines <- strsplit(lines, "\n")[[1]]
.console.output <- getRcmdr("console.output")
.output <- OutputWindow()
iline <- 1
nlines <- length(lines)
while (iline <= nlines){
# while (nchar(lines[iline])==0) iline <- iline + 1
# if (iline > nlines) break
while (nchar(lines[iline])==0) iline <- iline + 1
current.line <- lines[iline]
if (.console.output) cat(paste("\n", getRcmdr("prefixes")[1], current.line,"\n", sep=""))
else{
tkinsert(.output, "end", paste("\n> ", current.line,"\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
}
jline <- iline + 1
while (jline <= nlines){
if (nchar(lines[jline])==0) lines[jline] <- " "
if (!inherits(try(parse(text=current.line),silent=TRUE), "try-error")) break
if (.console.output)cat(paste(getRcmdr("prefixes")[2], lines[jline],"\n", sep=""))
else{
tkinsert(.output, "end", paste("+ ", lines[jline],"\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
}
current.line <- if (nchar(lines[jline]) > 0) paste(current.line, lines[jline],sep="\n")
jline <- jline + 1
iline <- iline + 1
}
# protect against misprocessed comments
xlines <- strsplit(current.line, "\n")[[1]]
xlines <- trimws(sub("#.*$", "", xlines))
xlines <- xlines[nchar(xlines) > 0]
current.line <- paste(xlines, collapse="\n")
if (length(current.line) == 0 || nchar(current.line) == 0) current.line <- NULL
if (!(is.null(current.line) || is.na(current.line))) {
doItAndPrint(current.line, log=FALSE, rmd=TRUE)
}
iline <- iline + 1
tkyview.moveto(.output, 1)
tkfocus(.log)
}
if (length(as.character(tksearch(.log, "-regexp", "-forward", "--", "\\n\\n$", "1.0"))
) == 0){
tkinsert(.log, "end", "\n")
}
cursor.line.posn <- 1 + floor(as.numeric(tkindex(.log, "insert")))
tkmark.set(.log, "insert", paste(cursor.line.posn, ".0", sep=""))
tktag.remove(.log, "sel", "1.0", "end")
}
else if (as.character(tkselect(notebook)) == RmdFrame$ID) {
compileRmd()
}
else{
compileRnw()
}
}
# right-click context menus
contextMenuLog <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.log <- LogWindow()
tkfocus(.log)
contextMenu <- tkmenu(tkmenu(.log), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Submit"), command=onSubmit)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .log), tkwinfo("pointery", .log))
}
contextMenuRmd <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.rmd <- RmdWindow()
tkfocus(.rmd)
contextMenu <- tkmenu(tkmenu(.rmd), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Generate report"), command=onSubmit)
tkadd(contextMenu, "command", label=gettextRcmdr("Edit R Markdown document"), command=editMarkdown)
tkadd(contextMenu, "command", label=gettextRcmdr("Remove last Markdown command block"), command=removeLastRmdBlock)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
# tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind) # doesn't work FIXME
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .rmd), tkwinfo("pointery", .rmd))
}
contextMenuRnw <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.rnw <- RnwWindow()
tkfocus(.rnw)
contextMenu <- tkmenu(tkmenu(.rnw), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Generate PDF report"), command=onSubmit)
tkadd(contextMenu, "command", label=gettextRcmdr("Edit knitr document"), command=editKnitr)
tkadd(contextMenu, "command", label=gettextRcmdr("Remove last knitr command block"), command=removeLastRnwBlock)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
# tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind) # doesn't work FIXME
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .rnw), tkwinfo("pointery", .rnw))
}
contextMenuOutput <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.output <- OutputWindow()
tkfocus(.output)
contextMenu <- tkmenu(tkmenu(.output), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .output), tkwinfo("pointery", .output))
}
contextMenuMessages <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.messages <- MessagesWindow()
tkfocus(.messages)
contextMenu <- tkmenu(tkmenu(.messages), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .messages), tkwinfo("pointery", .messages))
}
# main Commander window
if (getRcmdr("crisp.dialogs")) tclServiceMode(on=FALSE)
putRcmdr("commanderWindow", tktoplevel(class="Rcommander"))
.commander <- CommanderWindow()
tkwm.minsize(.commander, getRcmdr("minimum.width"), getRcmdr("minimum.height"))
tcl("wm", "iconphoto", .commander, "-default", "::image::RlogoIcon")
placement <- setOption("placement", "", global=FALSE)
tkwm.geometry(.commander, placement)
tkwm.title(.commander, gettextRcmdr("R Commander"))
tkwm.protocol(.commander, "WM_DELETE_WINDOW",
if (getRcmdr("quit.R.on.close")) closeCommanderAndR else CloseCommander)
topMenu <- tkmenu(.commander)
tkconfigure(.commander, menu=topMenu)
position <- numeric(0)
# install menus
.Menus <- menus <- list()
menuItems <- 0
oldMenu <- ncol(Menus) == 6
if (!getRcmdr("suppress.menus")){
for (m in 1:nrow(Menus)){
install <- if (oldMenu) "" else Menus[m, 7]
if ((install != "") && (!eval(parse(text=install)))) next
if (Menus[m, 1] == "menu") {
position[Menus[m, 2]] <- 0
assign(Menus[m, 2], tkmenu(get(Menus[m, 3]), tearoff=FALSE))
menus[[Menus[m, 2]]] <- list(ID=get(Menus[m, 2])$ID, position=0)
}
else if (Menus[m, 1] == "item") {
position[Menus[m, 2]] <- position[Menus[m, 2]] + 1
if (Menus[m, 3] == "command"){
if (Menus[m, 6] == "")
tkadd(get(Menus[m, 2]), "command", label=gettextMenus(Menus[m, 4]),
command=get(Menus[m, 5]))
else {
tkadd(get(Menus[m, 2]), "command", label=gettextMenus(Menus[m, 4]),
command=get(Menus[m, 5]), state="disabled")
menuItems <- menuItems + 1
menus[[Menus[m, 2]]]$position <- position[Menus[m, 2]]
.Menus[[menuItems]] <- list(ID=menus[[Menus[m, 2]]]$ID, position=position[Menus[m, 2]],
activation=eval(parse(text=paste("function()", Menus[m, 6]))))
}
}
else if (Menus[m, 3] == "cascade")
tkadd(get(Menus[m, 2]), "cascade", label=gettextMenus(Menus[m, 4]),
menu=get(Menus[m, 5]))
else if (Menus[m, 3] == "separator")
tkadd(get(Menus[m, 2]), "separator")
else stop(paste(gettextRcmdr("menu definition error:"), Menus[m, ], collapse=" "),
domain=NA)
}
else stop(paste(gettextRcmdr("menu definition error:"), Menus[m, ], collapse=" "),
domain=NA)
}
}
putRcmdr("Menus", .Menus)
putRcmdr("autoRestart", FALSE)
activateMenus()
# toolbar
controlsFrame <- tkframe(CommanderWindow())
editButton <- buttonRcmdr(controlsFrame, text=gettextRcmdr("Edit data set"), command=onEdit,
image="::image::editIcon", compound="left")
viewButton <- buttonRcmdr(controlsFrame, text=gettextRcmdr("View data set"), command=onView,
image="::image::viewIcon", compound="left")
putRcmdr("dataSetName", tclVar(gettextRcmdr("<No active dataset>")))
putRcmdr("dataSetLabel", tkbutton(controlsFrame, textvariable=getRcmdr("dataSetName"), foreground="red",
relief="groove", command=selectActiveDataSet, image="::image::dataIcon", compound="left"))
# script and markdown tabs
notebook <- ttknotebook(CommanderWindow())
logFrame <- ttkframe(CommanderWindow())
putRcmdr("logWindow", tktext(logFrame, bg="white", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.log <- LogWindow()
logXscroll <- ttkscrollbar(logFrame, orient="horizontal",
command=function(...) tkxview(.log, ...))
logYscroll <- ttkscrollbar(logFrame,
command=function(...) tkyview(.log, ...))
tkconfigure(.log, xscrollcommand=function(...) tkset(logXscroll, ...))
tkconfigure(.log, yscrollcommand=function(...) tkset(logYscroll, ...))
RmdFrame <- ttkframe(CommanderWindow())
putRcmdr("RmdWindow", tktext(RmdFrame, bg="#FAFAFA", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.rmd <- RmdWindow()
rmd.template <- setOption("rmd.template",
system.file("etc", if (getRcmdr("capabilities")$pandoc) "Rcmdr-RMarkdown-Template.Rmd"
else "Rcmdr-Markdown-Template.Rmd", package="Rcmdr"))
template <- paste(readLines(rmd.template), collapse="\n")
# template customization and translation:
template <- sub("Your Name", getRcmdr("UserName"), template)
template <- sub("Replace with Main Title",
gettextRcmdr("Replace with Main Title"), template)
template <- sub("include this code chunk as-is to set options",
gettextRcmdr("include this code chunk as-is to set options"),
template)
template <- sub("You can edit this R Markdown document, for example to explain what you're\ndoing and to draw conclusions from your data analysis.",
gettextRcmdr("You can edit this R Markdown document, for example to explain what you're\ndoing and to draw conclusions from your data analysis."),
template)
template <- sub("Auto-generated section titles, typically preceded by ###, can also be edited.",
gettextRcmdr("Auto-generated section titles, typically preceded by ###, can also be edited."),
template)
template <- sub("It's generally not a good idea to edit the R code that the R Commander writes, \nbut you can freely edit between (not within) R \"code blocks.\" Each R code\nblock starts with ```{r} and ends with ```.",
gettextRcmdr("It's generally not a good idea to edit the R code that the R Commander writes, \nbut you can freely edit between (not within) R \"code blocks.\" Each R code\nblock starts with ```{r} and ends with ```."),
template, fixed = TRUE)
# if (getRcmdr("use.rgl")) template <- paste0(template,
# "\n\n```{r echo=FALSE}\n# include this code chunk as-is to enable 3D graphs\nlibrary(rgl)\noptions(rgl.useNULL = TRUE)\n```\n\n")
tkinsert(.rmd, "end", template)
putRcmdr("markdown.output", FALSE)
RmdXscroll <- ttkscrollbar(RmdFrame, orient="horizontal",
command=function(...) tkxview(.rmd, ...))
RmdYscroll <- ttkscrollbar(RmdFrame,
command=function(...) tkyview(.rmd, ...))
tkconfigure(.rmd, xscrollcommand=function(...) tkset(RmdXscroll, ...))
tkconfigure(.rmd, yscrollcommand=function(...) tkset(RmdYscroll, ...))
RnwFrame <- ttkframe(CommanderWindow())
putRcmdr("RnwWindow", tktext(RnwFrame, bg="#FAFAFA", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.rnw <- RnwWindow()
rnw.template <- setOption("rnw.template",
system.file("etc", "Rcmdr-knitr-Template.Rnw", package="Rcmdr"))
template <- paste(readLines(rnw.template), collapse="\n")
template <- sub("Your Name", getRcmdr("UserName"), template)
template <- sub("Replace with Main Title",
gettextRcmdr("Replace with Main Title"), template)
tkinsert(.rnw, "end", template)
putRcmdr("knitr.output", FALSE)
RnwXscroll <- ttkscrollbar(RnwFrame, orient="horizontal",
command=function(...) tkxview(.rnw, ...))
RnwYscroll <- ttkscrollbar(RnwFrame,
command=function(...) tkyview(.rnw, ...))
tkconfigure(.rnw, xscrollcommand=function(...) tkset(RnwXscroll, ...))
tkconfigure(.rnw, yscrollcommand=function(...) tkset(RnwYscroll, ...))
outputFrame <- tkframe(.commander)
submitButtonLabel <- tclVar(gettextRcmdr("Submit"))
submitButton <- if (getRcmdr("console.output"))
buttonRcmdr(CommanderWindow(), textvariable=submitButtonLabel, borderwidth="2", command=onSubmit,
image="::image::submitIcon", compound="left")
else buttonRcmdr(outputFrame, textvariable=submitButtonLabel, borderwidth="2", command=onSubmit,
image="::image::submitIcon", compound="left")
tkbind(CommanderWindow(), "<Button-1>", function() {
if (as.character(tkselect(notebook)) == logFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Submit")
if (as.character(tkselect(notebook)) == RmdFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Generate report")
if (as.character(tkselect(notebook)) == RnwFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Generate PDF report")
})
putRcmdr("outputWindow", tktext(outputFrame, bg="white", foreground=getRcmdr("output.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("output.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.output <- OutputWindow()
outputXscroll <- ttkscrollbar(outputFrame, orient="horizontal",
command=function(...) tkxview(.output, ...))
outputYscroll <- ttkscrollbar(outputFrame,
command=function(...) tkyview(.output, ...))
tkconfigure(.output, xscrollcommand=function(...) tkset(outputXscroll, ...))
tkconfigure(.output, yscrollcommand=function(...) tkset(outputYscroll, ...))
# messages window
messagesFrame <- tkframe(.commander)
putRcmdr("messagesWindow", tktext(messagesFrame, bg="lightgray",
font=getRcmdr("logFont"), height=getRcmdr("messages.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.messages <- MessagesWindow()
messagesXscroll <- ttkscrollbar(messagesFrame, orient="horizontal",
command=function(...) tkxview(.messages, ...))
messagesYscroll <- ttkscrollbar(messagesFrame,
command=function(...) tkyview(.messages, ...))
tkconfigure(.messages, xscrollcommand=function(...) tkset(messagesXscroll, ...))
tkconfigure(.messages, yscrollcommand=function(...) tkset(messagesYscroll, ...))
# configure toolbar, etc., install various windows and widgets
putRcmdr("modelName", tclVar(gettextRcmdr("<No active model>")))
putRcmdr("modelLabel", tkbutton(controlsFrame, textvariable=getRcmdr("modelName"), foreground="red",
relief="groove", command=selectActiveModel, image="::image::modelIcon", compound="left"))
show.edit.button <- options("Rcmdr")[[1]]$show.edit.button
show.edit.button <- if (is.null(show.edit.button)) TRUE else show.edit.button
if (!getRcmdr("suppress.menus")){
tkgrid(labelRcmdr(controlsFrame, image="::image::RlogoIcon", compound="left"),
labelRcmdr(controlsFrame, text=gettextRcmdr(" Data set:")), getRcmdr("dataSetLabel"),
if(show.edit.button) editButton, viewButton,
labelRcmdr(controlsFrame, text=gettextRcmdr("Model:")), getRcmdr("modelLabel"), sticky="w", pady=c(3, 3))
tkgrid(controlsFrame, sticky="w")
tkgrid.configure(getRcmdr("dataSetLabel"), padx=c(2, 5))
tkgrid.configure(getRcmdr("modelLabel"), padx=c(2, 10))
tkgrid.configure(editButton, padx=c(10, 1))
if (show.edit.button) tkgrid.configure(viewButton, padx=c(1, 15))
else tkgrid.configure(viewButton, padx=c(10, 15))
}
.log.commands <- getRcmdr("log.commands")
.console.output <- getRcmdr("console.output")
if (.log.commands) {
tkgrid(.log, logYscroll, sticky="news", columnspan=2)
tkgrid(logXscroll)
tkgrid(logFrame, sticky="news", padx=10, pady=0, columnspan=2)
tkgrid(.rmd, RmdYscroll, sticky="news", columnspan=2)
tkgrid(RmdXscroll)
tkgrid(.rnw, RnwYscroll, sticky="news", columnspan=2)
tkgrid(RnwXscroll)
if (getRcmdr("use.markdown")) tkgrid(RmdFrame, sticky="news", padx=10, pady=0, columnspan=2)
if (getRcmdr("use.knitr")) tkgrid(RnwFrame, sticky="news", padx=10, pady=0, columnspan=2)
}
tkadd(notebook, logFrame, text=gettextRcmdr("R Script"), padding=6)
if (getRcmdr("use.markdown")) tkadd(notebook, RmdFrame, text=gettextRcmdr("R Markdown"), padding=6)
if (getRcmdr("use.knitr")) tkadd(notebook, RnwFrame, text=gettextRcmdr("knitr Document"), padding=6)
# tkgrid(notebook, sticky="news")
if (.log.commands) {
tkgrid(notebook, sticky="news")
}
# if (.log.commands && .console.output) tkgrid(submitButton, sticky="w", pady=c(0, 6))
if (.log.commands && .console.output) tkgrid(submitButton, sticky="e", pady=c(0, 6), padx=c(0, 6))
tkgrid(labelRcmdr(outputFrame, text=gettextRcmdr("Output"), font="RcmdrOutputMessagesFont", foreground=getRcmdr("title.color")),
if (.log.commands && !.console.output) submitButton, sticky="sw", pady=c(6, 6))
tkgrid(.output, outputYscroll, sticky="news", columnspan=2)
tkgrid(outputXscroll, columnspan=1 + (.log.commands && !.console.output))
if (!.console.output) tkgrid(outputFrame, sticky="news", padx=10, pady=0, columnspan=2)
tkgrid(labelRcmdr(messagesFrame, text=gettextRcmdr("Messages"), font="RcmdrOutputMessagesFont", foreground=getRcmdr("title.color")),
sticky="w", pady=c(6, 6))
tkgrid(.messages, messagesYscroll, sticky="news", columnspan=2)
tkgrid(messagesXscroll)
if (!.console.output) tkgrid(messagesFrame, sticky="news", padx=10, pady=0, columnspan=2) ##rmh & J. Fox
tkgrid.configure(logYscroll, sticky="ns")
tkgrid.configure(logXscroll, sticky="ew")
tkgrid.configure(RmdYscroll, sticky="ns")
tkgrid.configure(RmdXscroll, sticky="ew")
tkgrid.configure(RnwYscroll, sticky="ns")
tkgrid.configure(RnwXscroll, sticky="ew")
tkgrid.configure(outputYscroll, sticky="ns")
tkgrid.configure(outputXscroll, sticky="ew")
tkgrid.configure(messagesYscroll, sticky="ns")
tkgrid.configure(messagesXscroll, sticky="ew")
.commander <- CommanderWindow()
tkgrid.rowconfigure(.commander, 0, weight=0)
tkgrid.rowconfigure(.commander, 1, weight=1)
# tkgrid.rowconfigure(.commander, 2, weight=1)
w <- if (.log.commands && !.console.output) 1 else 0
tkgrid.rowconfigure(.commander, 2, weight=w)
tkgrid.columnconfigure(.commander, 0, weight=1)
tkgrid.columnconfigure(.commander, 1, weight=0)
if (.log.commands){
tkgrid.rowconfigure(logFrame, 0, weight=1)
tkgrid.rowconfigure(logFrame, 1, weight=0)
tkgrid.columnconfigure(logFrame, 0, weight=1)
tkgrid.columnconfigure(logFrame, 1, weight=0)
if (getRcmdr("use.markdown")){
tkgrid.rowconfigure(RmdFrame, 0, weight=1)
tkgrid.rowconfigure(RmdFrame, 1, weight=0)
tkgrid.columnconfigure(RmdFrame, 0, weight=1)
tkgrid.columnconfigure(RmdFrame, 1, weight=0)
}
if (getRcmdr("use.knitr")){
tkgrid.rowconfigure(RnwFrame, 0, weight=1)
tkgrid.rowconfigure(RnwFrame, 1, weight=0)
tkgrid.columnconfigure(RnwFrame, 0, weight=1)
tkgrid.columnconfigure(RnwFrame, 1, weight=0)
}
}
if (!.console.output){
tkgrid.rowconfigure(outputFrame, 0, weight=0)
tkgrid.rowconfigure(outputFrame, 1, weight=1)
tkgrid.rowconfigure(outputFrame, 2, weight=0)
tkgrid.columnconfigure(outputFrame, 0, weight=1)
tkgrid.columnconfigure(outputFrame, 1, weight=0)
}
tkgrid.rowconfigure(messagesFrame, 0, weight=0)
tkgrid.rowconfigure(messagesFrame, 1, weight=0)
tkgrid.rowconfigure(messagesFrame, 2, weight=0)
tkgrid.columnconfigure(messagesFrame, 0, weight=1)
tkgrid.columnconfigure(messagesFrame, 1, weight=0)
.Tcl("update idletasks")
tkbind(.commander, "<Control-x>", onCut)
tkbind(.commander, "<Control-X>", onCut)
tkbind(.commander, "<Control-c>", onCopy)
tkbind(.commander, "<Control-C>", onCopy)
tkbind(.commander, "<Control-r>", onSubmit)
tkbind(.commander, "<Control-R>", onSubmit)
tkbind(.commander, "<Control-Tab>", onSubmit)
tkbind(.commander, "<Control-f>", onFind)
tkbind(.commander, "<Control-F>", onFind)
tkbind(.commander, "<F3>", onFind)
tkbind(.commander, "<Control-s>", saveLog)
tkbind(.commander, "<Control-S>", saveLog)
tkbind(.commander, "<Control-a>", onSelectAll)
tkbind(.commander, "<Control-A>", onSelectAll)
tkbind(.commander, "<Control-w>", onRedo)
tkbind(.commander, "<Control-W>", onRedo)
tkbind(.commander, "<Alt-BackSpace>", onUndo)
tkbind(.log, "<ButtonPress-3>", contextMenuLog)
tkbind(.rmd, "<ButtonPress-3>", contextMenuRmd)
tkbind(.rnw, "<ButtonPress-3>", contextMenuRnw)
tkbind(.output, "<ButtonPress-3>", contextMenuOutput)
tkbind(.messages, "<ButtonPress-3>", contextMenuMessages)
tkbind(.log, "<Control-ButtonPress-1>", contextMenuLog)
tkbind(.rmd, "<Control-ButtonPress-1>", contextMenuRmd)
tkbind(.rnw, "<Control-ButtonPress-1>", contextMenuRnw)
tkbind(.output, "<Control-ButtonPress-1>", contextMenuOutput)
tkbind(.messages, "<Control-ButtonPress-1>", contextMenuMessages)
tkbind(.rmd, "<Control-e>", editMarkdown)
tkbind(.rmd, "<Control-E>", editMarkdown)
tkbind(.rnw, "<Control-e>", editKnitr)
tkbind(.rnw, "<Control-E>", editKnitr)
if (MacOSXP()){
tkbind(.commander, "<Meta-x>", onCut)
tkbind(.commander, "<Meta-X>", onCut)
tkbind(.commander, "<Meta-c>", onCopy)
tkbind(.commander, "<Meta-C>", onCopy)
tkbind(.commander, "<Meta-v>", onPaste)
tkbind(.commander, "<Meta-V>", onPaste)
tkbind(.commander, "<Meta-r>", onSubmit)
tkbind(.commander, "<Meta-R>", onSubmit)
tkbind(.commander, "<Meta-Tab>", onSubmit)
tkbind(.commander, "<Meta-f>", onFind)
tkbind(.commander, "<Meta-F>", onFind)
tkbind(.commander, "<Meta-s>", saveLog)
tkbind(.commander, "<Meta-S>", saveLog)
tkbind(.commander, "<Meta-a>", onSelectAll)
tkbind(.commander, "<Meta-A>", onSelectAll)
tkbind(.commander, "<Meta-w>", onRedo)
tkbind(.commander, "<Meta-W>", onRedo)
tkbind(.commander, "<Meta-z>", onUndo)
tkbind(.commander, "<Meta-Z>", onUndo)
tkbind(.commander, "<Shift-Meta-z>", onRedo)
tkbind(.commander, "<Shift-Meta-Z>", onRedo)
tkbind(.log, "<Meta-ButtonPress-1>", contextMenuLog)
tkbind(.rmd, "<Meta-ButtonPress-1>", contextMenuRmd)
tkbind(.rnw, "<Meta-ButtonPress-1>", contextMenuRnw)
tkbind(.output, "<Meta-ButtonPress-1>", contextMenuOutput)
tkbind(.messages, "<Meta-ButtonPress-1>", contextMenuMessages)
tkbind(.rmd, "<Meta-e>", editMarkdown)
tkbind(.rmd, "<Meta-E>", editMarkdown)
tkbind(.rnw, "<Meta-e>", editKnitr)
tkbind(.rnw, "<Meta-E>", editKnitr)
}
tkwm.deiconify(.commander)
tkfocus(.commander)
if (getRcmdr("crisp.dialogs")) tclServiceMode(on=TRUE)
tkwait.commander <- options("Rcmdr")[[1]]$tkwait.commander # to address problem in Debian Linux
if ((!is.null(tkwait.commander)) && tkwait.commander) {
putRcmdr(".commander.done", tclVar("0"))
tkwait.variable(getRcmdr(".commander.done"))
}
Message(paste(gettextRcmdr("R Commander Version "), " ", getRcmdr("RcmdrVersion"), ": ", date(), sep=""))
Message(paste(gettextRcmdr("R Version"), getRcmdr("RVersion"), getRcmdr("RVersionStatus")))
Message(paste(gettextRcmdr("Hello "), getRcmdr("UserName"), sep=""))
if (.Platform$GUI == "Rgui" && ismdi()) Message(gettextRcmdr(
"The Windows version of the R Commander works best under\nRGui with the single-document interface (SDI); see ?Commander."),
type="warning")
if (RappP() && mavericksP() && appnap() == "on") Message(gettextRcmdr(
"The Mac OS X version of the R Commander works best under R.app\nwith app nap turned off. See ?Commander and the Tools menu."),
type="warning")
}
# put commands in script, markdown, and knitr tabs
logger <- function(command, rmd=TRUE){
pushCommand(command)
.log <- LogWindow()
.rmd <- RmdWindow()
.rnw <- RnwWindow()
.output <- OutputWindow()
.markdown.editor.open <- getRcmdr("Markdown.editor.open")
.markdown.editor <- MarkdownEditorWindow()
.knitr.editor.open <- getRcmdr("knitr.editor.open")
.knitr.editor <- knitrEditorWindow()
Rmd <- rmd && is.null(attr(command, "suppressRmd")) && (getRcmdr("use.markdown") || getRcmdr("use.knitr"))
command <- splitCmd(command)
if (getRcmdr("log.commands")) {
last2 <- tclvalue(tkget(.log, "end -2 chars", "end"))
if (last2 != "\n\n") tkinsert(.log, "end", "\n")
tkinsert(.log, "end", paste(command,"\n", sep=""))
tkyview.moveto(.log, 1)
if (Rmd){
if (getRcmdr("use.markdown")){
if (getRcmdr("startNewCommandBlock")){
beginRmdBlock()
tkinsert(.rmd, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rmd, 1)
putRcmdr("markdown.output", TRUE)
if (.markdown.editor.open){
tkinsert(.markdown.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.markdown.editor, 1)
}
endRmdBlock()
}
else{
tkinsert(.rmd, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rmd, 1)
putRcmdr("markdown.output", TRUE)
putRcmdr("rmd.generated", TRUE)
if (.markdown.editor.open){
tkinsert(.markdown.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.markdown.editor, 1)
}
}
if (getRcmdr("command.sections")){
command.name <- findCommandName(command)
if(!is.na(command.name)){
insertRmdSection(command.name)
}
}
}
if (getRcmdr("use.knitr")){
if (getRcmdr("startNewKnitrCommandBlock")){
beginRnwBlock()
tkinsert(.rnw, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rnw, 1)
putRcmdr("knitr.output", TRUE)
if (.knitr.editor.open){
tkinsert(.knitr.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.knitr.editor, 1)
}
endRnwBlock()
}
else{
tkinsert(.rnw, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rnw, 1)
putRcmdr("knitr.output", TRUE)
putRcmdr("rnw.generated", TRUE)
if (.knitr.editor.open){
tkinsert(.knitr.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.knitr.editor, 1)
}
}
}
}
}
lines <- strsplit(command, "\n")[[1]]
tkinsert(.output, "end", "\n")
if (getRcmdr("console.output")) {
for (line in seq(along.with=lines)) {
prompt <- ifelse (line==1, paste("\n", getRcmdr("prefixes")[1], sep=""), paste("\n", getRcmdr("prefixes")[2], sep=""))
cat(paste(prompt, lines[line]))
}
cat("\n")
}
else {
for (line in seq(along.with=lines)) {
prompt <- ifelse(line==1, "> ", "+ ")
tkinsert(.output, "end", paste(prompt, lines[line], "\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
tkyview.moveto(.output, 1)
}
}
command
}
justDoIt <- function(command) {
command <- enc2native(command)
Message()
if (!getRcmdr("suppress.X11.warnings")){
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
on.exit({
sink(type="message")
close(messages.connection)
})
}
else messages.connection <- getRcmdr("messages.connection")
capture.output(result <- try(eval(parse(text=command), envir=.GlobalEnv), silent=TRUE))
if (class(result)[1] == "try-error"){
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
tkfocus(CommanderWindow())
return(result)
}
checkWarnings(readLines(messages.connection))
if (getRcmdr("RStudio")) Sys.sleep(0)
result
}
# execute commands, save commands and output
doItAndPrint <- function(command, log=TRUE, rmd=log) {
command <- enc2native(command)
Message()
.console.output <- getRcmdr("console.output")
.output <- OutputWindow()
if (!.console.output) {
width <- (as.numeric(tkwinfo("width", .output)) - 2*as.numeric(tkcget(.output, borderwidth=NULL)) - 2)/
as.numeric(tkfont.measure(tkcget(.output, font=NULL), "0"))
eval(parse(text=paste("options(width=", floor(width), ")", sep="")))
}
if (!getRcmdr("suppress.X11.warnings")){
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
on.exit({
sink(type="message")
close(messages.connection)
})
}
else messages.connection <- getRcmdr("messages.connection")
output.connection <- file(open="w+")
sink(output.connection, type="output")
on.exit({
if (!.console.output) sink(type="output") # if .console.output, output connection already closed
close(output.connection)
}, add=TRUE)
if (log) logger(command, rmd=rmd)
else {
pushCommand(command)
if (rmd) {
if (getRcmdr("use.markdown")) enterMarkdown(command)
if (getRcmdr("use.knitr")) enterKnitr(command)
}
}
result <- try(parse(text=paste(command)), silent=TRUE)
if (class(result)[1] == "try-error"){
if (rmd) {
if (getRcmdr("use.markdown")) {
removeLastRmdBlock()
putRcmdr("startNewCommandBlock", TRUE)
}
if (getRcmdr("use.knitr")) {
removeLastRnwBlock()
putRcmdr("startNewKnitrCommandBlock", TRUE)
}
}
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
if (.console.output) sink(type="output")
tkfocus(CommanderWindow())
return(result)
} else {
exprs <- result
result <- NULL
}
for (i in seq_along(exprs)) {
ei <- exprs[i]
tcl("update")
result <- try(withVisible(eval(ei, envir=.GlobalEnv)), silent=TRUE)
if (class(result)[1] == "try-error"){
if (rmd) {
if (getRcmdr("use.markdown")) {
removeLastRmdBlock()
putRcmdr("startNewCommandBlock", TRUE)
}
if (getRcmdr("use.knitr")) {
removeLastRnwBlock()
putRcmdr("startNewKnitrCommandBlock", TRUE)
}
}
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
if (.console.output) sink(type="output")
tkfocus(CommanderWindow())
return(result)
}
result <- if (result$visible == FALSE) NULL else result$value
if (!is.null(result)) pushOutput(result)
if (isS4object(result)) show(result) else print(result)
.Output <- readLines(output.connection)
if (length(.Output) > 0 && .Output[length(.Output)] == "NULL")
.Output <- .Output[-length(.Output)] # suppress "NULL" line at end of output
if (length(.Output) != 0) { # is there output to print?
if (.console.output) {
out <- .Output
sink(type="output")
for (line in out) cat(paste(line, "\n", sep=""))
}
else{
for (line in .Output) tkinsert(.output, "end", paste(line, "\n", sep=""))
tkyview.moveto(.output, 1)
}
}
else if (.console.output) sink(type="output")
if (RExcelSupported()) # added by Erich Neuwirth
putRExcel(".rexcel.last.output",.Output)
# errors already intercepted, display any warnings
checkWarnings(readLines(messages.connection))
}
if (getRcmdr("RStudio")) Sys.sleep(0)
result
}
checkWarnings <- function(messages){
if (getRcmdr("suppress.X11.warnings")){
X11.warning <- grep("X11 protocol error|Warning in structure", messages)
if (length(X11.warning) > 0){
messages <- messages[-X11.warning]
}
if (length(messages) == 0) Message()
else if (length(messages) > 10) {
messages <- c(paste(length(messages), "warnings."),
gettextRcmdr("First and last 5 warnings:"),
head(messages,5), ". . .", tail(messages, 5))
Message(message=paste(messages, collapse="\n"), type="warning")
}
else {
if (length(grep("warning", messages, ignore.case=TRUE)) > 0)
Message(message=paste(messages, collapse="\n"), type="warning")
else Message(message=paste(messages, collapse="\n"), type="note")
}
}
else{
if (length(messages) == 0) Message()
else if (length(messages) > 10){
messages <- c(paste(length(messages), "warnings."),
gettextRcmdr("First and last 5 warnings:"),
head(messages, 5), ". . .", tail(messages, 5))
Message(message=paste(messages, collapse="\n"), type="warning")
}
else {
if (length(grep("warning", messages, ignore.case=TRUE)) > 0)
Message(message=paste(messages, collapse="\n"), type="warning")
else Message(message=paste(messages, collapse="\n"), type="note")
}
}
tkfocus(CommanderWindow())
}
pause <- function(seconds = 1){
if (seconds <= 0) stop("seconds must be positive")
start <- proc.time()[3]
while (as.numeric(elapsed <- (proc.time()[3] - start)) < seconds) {}
elapsed
}
Message <- function(message, type=c("note", "error", "warning")){
tcl("update")
.message <- MessagesWindow()
type <- match.arg(type)
if (type != "note") tkbell()
if (getRcmdr("retain.messages")) {
if (missing(message) && !is.null(getRcmdr("last.message"))) {
putRcmdr("last.message", NULL)
tkyview.moveto(.message, 1.0)
}
}
else if (type == "note"){
lastMessage <- tclvalue(tkget(MessagesWindow(), "end - 2 lines", "end"))
if (length(c(grep(gettextRcmdr("ERROR:"), lastMessage), grep(gettextRcmdr("WARNING:"), lastMessage))) == 0)
tkdelete(.message, "1.0", "end")
}
else tkdelete(.message, "1.0", "end")
col <- if (type == "error") getRcmdr("error.text.color")
else if (type == "warning") getRcmdr("warning.text.color")
else getRcmdr("output.text.color")
prefix <- switch(type, error=gettextRcmdr("ERROR"), warning=gettextRcmdr("WARNING"), note=gettextRcmdr("NOTE"))
if (missing(message)){
return()
}
putRcmdr("last.message", type)
message <- paste(prefix, ": ", message, sep="")
if (getRcmdr("retain.messages") && getRcmdr("number.messages")) {
messageNumber <- getRcmdr("messageNumber") + 1
putRcmdr("messageNumber", messageNumber)
message <- paste("[", messageNumber, "] ", message, sep="")
}
if (RExcelSupported()) # added by Erich Neuwirth
putRExcel(".rexcel.last.message",message)
lines <- strsplit(message, "\n")[[1]]
console.output <- getRcmdr("console.output")
if (!console.output){
width <- (as.numeric(tkwinfo("width", .message)) - 2*as.numeric(tkcget(.message, borderwidth=NULL)) - 2)/
as.numeric(tkfont.measure(tkcget(.message, font=NULL), "0"))
eval(parse(text=paste("options(width=", floor(width), ")", sep="")))
}
lines <- strwrap(lines)
if (console.output) {
if (sink.number() != 0) sink()
for (jline in seq(along.with=lines)) {
Header <- if (jline==1) getRcmdr("prefixes")[3] else getRcmdr("prefixes")[4]
cat(paste(Header, lines[jline], "\n", sep=""))
}
}
else
for (line in lines){
tagName <- messageTag()
tkinsert(.message, "end", paste(line, "\n", sep=""))
tktag.add(.message, tagName, "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.message, tagName, foreground=col)
tkyview.moveto(.message, 1.0)
}
}
messageTag <- function(reset=FALSE){
if (reset){
putRcmdr("tagNumber", 0)
return()
}
tagNumber <- getRcmdr("tagNumber") + 1
putRcmdr("tagNumber", tagNumber)
paste("message", tagNumber, sep="")
}
pushOutput <- function(element) {
stack <- getRcmdr("outputStack")
stack <- c(list(element), stack[-getRcmdr("length.output.stack")])
putRcmdr("outputStack", stack)
}
popOutput <- function(keep=FALSE){
stack <- getRcmdr("outputStack")
lastOutput <- stack[[1]]
if (!keep) putRcmdr("outputStack", c(stack[-1], NA))
lastOutput
}
pushCommand <- function(element) {
stack <- getRcmdr("commandStack")
stack <- c(list(element), stack[-getRcmdr("length.command.stack")])
putRcmdr("commandStack", stack)
}
popCommand <- function(keep=FALSE){
stack <- getRcmdr("commandStack")
lastCommand <- stack[[1]]
if (!keep) putRcmdr("commandStack", c(stack[-1], NA))
lastCommand
}
# handle model capabilities
mergeCapabilities <- function(allCapabilities){
allCapabilities <- allCapabilities[!sapply(allCapabilities, is.null)]
allrows <- unlist(lapply(allCapabilities, rownames))
if (length(allrows) > length(unique(allrows)))
stop(gettextRcmdr("redundant model class or classes in plug-in package model capabilities table"))
capabilities <- lapply(allCapabilities, names)
all <- unique(unlist(capabilities))
for (i in 1:length(allCapabilities)) allCapabilities[[i]][, setdiff(all, capabilities[[i]])] <- FALSE
do.call(rbind, allCapabilities)
}
# optionally open graphics device(s)
openGraphicsDevices <- function(){
if (!getRcmdr("open.graphics.devices")) return()
dev.new()
if (getRcmdr("use.rgl")) {
Library("rgl")
if (requireNamespace("rgl")) rgl::open3d()
}
}
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Defines functions openGraphicsDevices mergeCapabilities popCommand pushCommand popOutput pushOutput messageTag Message pause checkWarnings doItAndPrint justDoIt logger setupGUI processMenus processOperations processModelCapabilities processPlugins platformIssues setupFonts createIcons setupRcmdrOptions manageRcmdrEnv Commander
Documented in Commander doItAndPrint justDoIt logger Message popCommand popOutput
# The R Commander and command logger
# last modified 2023-08-07 by John Fox
# contributions by Milan Bouchet-Valat, Richard Heiberger, Duncan Murdoch, Erich Neuwirth, Brian Ripley, Vilmantas Gegzna
Commander <- function(){
# set global options (to be restored on exit from Rcmdr GUI)
putRcmdr("quotes", options(useFancyQuotes=FALSE))
putRcmdr("max.print", options(max.print=2^30))
putRcmdr("scipen", getOption("scipen"))
manageRcmdrEnv()
DESCRIPTION <- readLines(file.path(find.package("Rcmdr"), "DESCRIPTION")[1])
setupRcmdrOptions(DESCRIPTION)
createIcons()
setupFonts()
platformIssues()
modelClasses <- scan(file.path(getRcmdr("etc"), "model-classes.txt"), what="", quiet=TRUE, comment.char="#") # default recognized models
Plugins <- processPlugins(modelClasses)
processModelCapabilities(Plugins)
processOperations(Plugins)
Menus <- processMenus(Plugins)
setupGUI(Menus)
openGraphicsDevices()
# optionally open Markdown editor
if (getRcmdr("open.markdown.editor") && getRcmdr("use.markdown")){
editMarkdown()
}
# keep start-up warnings out of Rcmdr log
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
library(Rcmdr, quietly=TRUE)
sink(type="message")
close(messages.connection)
}
manageRcmdrEnv <- function(){
RcmdrEnv.on.path <- getOption("Rcmdr")[["RcmdrEnv.on.path"]]
if (is.null(RcmdrEnv.on.path)) RcmdrEnv.on.path <- FALSE
if (RcmdrEnv.on.path){
RcmdrEnv <- function() {
pos <- match("RcmdrEnv", search())
if (is.na(pos)) { # Must create it
RcmdrAttach <- base::attach
RcmdrEnv <- list()
RcmdrAttach(RcmdrEnv, pos = length(search()) - 1)
rm(RcmdrEnv)
pos <- match("RcmdrEnv", search())
}
return(pos.to.env(pos))
}
# the following two lines to be commented-out for debugging:
assignInMyNamespace("RcmdrEnv", RcmdrEnv)
assignInMyNamespace(".RcmdrEnv", NULL)
}
}
setupRcmdrOptions <- function(DESCRIPTION){
current <- getOption("Rcmdr")
putRcmdr("messageNumber", 0)
if (exists(".RcmdrEnv") && is.environment(RcmdrEnv()) &&
exists("commanderWindow", RcmdrEnv()) &&
!is.null(get("commanderWindow", RcmdrEnv()))) {
return(invisible(NULL))
}
# check for auxiliary software
putRcmdr("capabilities", RcmdrCapabilities())
setOption("suppress.icon.images", FALSE)
# locate Rcmdr etc directory and directory for menus (usually the same)
etc <- setOption("etc", system.file("etc", package="Rcmdr"))
etcMenus <- setOption("etcMenus", etc)
putRcmdr("etcMenus", etcMenus)
# various initializations
messageTag(reset=TRUE)
putRcmdr("installed.packages", installed.packages())
RcmdrVersion <- trim.blanks(sub("^Version:", "",
grep("^Version:", DESCRIPTION, value=TRUE)))
putRcmdr("RcmdrVersion", RcmdrVersion)
RVersion <- paste(R.Version()[c("major", "minor")], collapse=".")
RVersionStatus <- R.Version()$status
putRcmdr("RVersion", RVersion)
putRcmdr("RVersionStatus", RVersionStatus)
putRcmdr("UserName", getUserName())
putRcmdr(".activeDataSet", NULL)
putRcmdr(".activeModel", NULL)
putRcmdr("nrow", NULL)
putRcmdr("ncol", NULL)
putRcmdr("logFileName", NULL)
putRcmdr("RmdFileName", "RcmdrMarkdown.Rmd")
putRcmdr("RnwFileName", "RcmdrKnitr.Rnw")
putRcmdr("outputFileName", NULL)
putRcmdr("saveFileName", NULL)
putRcmdr("modelNumber", 0)
putRcmdr("reset.model", FALSE)
putRcmdr("rgl", FALSE)
putRcmdr("rgl.command", FALSE)
putRcmdr("Identify3d", NULL)
putRcmdr("open.dialog.here", NULL)
putRcmdr("restoreTab", FALSE)
putRcmdr("cancelDialogReopen", FALSE)
putRcmdr("last.search", "")
putRcmdr("Markdown.editor.open", FALSE)
putRcmdr("knitr.editor.open", FALSE)
setOption("use.rgl", TRUE)
# set various options
options(scipen=setOption("scientific.notation", 5))
setOption("default.contrasts", c("contr.Treatment", "contr.poly"))
setOption("number.messages", TRUE)
setOption("log.commands", TRUE)
setOption("use.knitr", FALSE)
setOption("use.markdown", !getRcmdr("use.knitr"))
setOption("open.markdown.editor", FALSE)
setOption("rmarkdown.output", TRUE)
rmo.defaults <- list(
command.sections = TRUE, section.level=3, toc=TRUE, toc_float=TRUE, toc_depth=3,
number_sections=FALSE, translate.rmd.headers=TRUE
)
rmo.options <- applyDefaultValues(getRcmdr("rmarkdown.output"), rmo.defaults)
putRcmdr("command.sections", rmo.options$command.sections)
putRcmdr("section.level", paste(rep("#", rmo.options$section.level), collapse=""))
putRcmdr("translate.rmd.headers", rmo.options$translate.rmd.headers)
if ((!packageAvailable("markdown") && !packageAvailable("rmarkdown")) || (!packageAvailable("knitr")))
putRcmdr("use.markdown", FALSE)
if (!packageAvailable("knitr") || !getRcmdr("capabilities")$pdflatex) putRcmdr("use.knitr", FALSE)
setOption("rmd.output.format", "html")
putRcmdr("startNewCommandBlock", TRUE)
putRcmdr("startNewKnitrCommandBlock", TRUE)
putRcmdr("rmd.generated", FALSE)
putRcmdr("rnw.generated", FALSE)
setOption("RStudio", RStudioP())
setOption("console.output", getRcmdr("RStudio"))
setOption("retain.selections", TRUE)
setOption("open.graphics.devices", FALSE)
putRcmdr("dialog.values", list())
putRcmdr("dialog.values.noreset", list())
putRcmdr("savedTable", NULL)
putRcmdr("onApplyCalled", FALSE)
log.height <- as.character(setOption("log.height", if (!getRcmdr("log.commands")) 0 else 10))
log.width <- as.character(setOption("log.width", 80))
output.height <- as.character(setOption("output.height",
if (getRcmdr("console.output")) 0
else if ((as.numeric(log.height) != 0) || (!getRcmdr("log.commands"))) 2*as.numeric(log.height)
else 20))
messages.height <- as.character(setOption("messages.height", 4))
setOption("minimum.width", 1000)
setOption("minimum.height", 400)
putRcmdr("saveOptions", options(warn=1, contrasts=getRcmdr("default.contrasts"), width=as.numeric(log.width),
na.action="na.exclude", graphics.record=TRUE))
setOption("ask.to.exit", TRUE)
setOption("ask.on.exit", TRUE)
setOption("double.click", FALSE)
setOption("sort.names", TRUE)
setOption("grab.focus", TRUE)
setOption("attach.data.set", FALSE)
setOption("log.text.color", "black")
setOption("command.text.color", "darkred")
setOption("output.text.color", "darkblue")
setOption("error.text.color", "red")
setOption("warning.text.color", "darkgreen")
setOption("prefixes", c("Rcmdr> ", "Rcmdr+ ", "RcmdrMsg: ", "RcmdrMsg+ "))
setOption("multiple.select.mode", "extended")
setOption("suppress.X11.warnings",
interactive() && .Platform$GUI == "X11") # to address problem in X11 (Linux or Mac OS X)
setOption("showData.threshold", c(20000, 100))
setOption("editDataset.threshold", if (getRcmdr("capabilities")$tktable) 10000 else 0)
setOption("retain.messages", TRUE)
setOption("crisp.dialogs", TRUE)
setOption("length.output.stack", 10)
setOption("length.command.stack", 10)
setOption("quit.R.on.close", FALSE)
putRcmdr("outputStack", as.list(rep(NA, getRcmdr("length.output.stack"))))
putRcmdr("commandStack", as.list(rep(NA, getRcmdr("length.command.stack"))))
setOption("variable.list.height", 6)
setOption("variable.list.width", c(20, Inf))
setOption("valid.classes", c("factor", "ordered", "character", "logical",
"POSIXct", "POSIXlt", "Date", "chron", "yearmon", "yearqtr", "zoo",
"zooreg", "timeDate", "xts", "its", "ti", "jul", "timeSeries", "fts",
"Period", "hms", "difftime"))
setOption("discreteness.threshold", 0)
setOption("model.case.deletion", TRUE)
putRcmdr("open.showData.windows", list())
}
createIcons <- function(){
icon.images <- !getRcmdr("suppress.icon.images")
tkimage.create("photo", "::image::RlogoIcon", file = system.file("etc", "R-logo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::okIcon",
file = if (icon.images) system.file("etc", "ok.gif", package="Rcmdr") else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::cancelIcon", file = if (icon.images) system.file("etc", "cancel.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::helpIcon", file = if (icon.images) system.file("etc", "help.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::resetIcon", file = if (icon.images) system.file("etc", "reset.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::applyIcon", file = if (icon.images) system.file("etc", "apply.gif", package="Rcmdr")
else system.file("etc", "blank.gif", package="Rcmdr"))
tkimage.create("photo", "::image::submitIcon", file = system.file("etc", "submit.gif", package="Rcmdr"))
tkimage.create("photo", "::image::editIcon", file = system.file("etc", "edit.gif", package="Rcmdr"))
tkimage.create("photo", "::image::viewIcon", file = system.file("etc", "view.gif", package="Rcmdr"))
tkimage.create("photo", "::image::dataIcon", file = system.file("etc", "data.gif", package="Rcmdr"))
tkimage.create("photo", "::image::modelIcon", file = system.file("etc", "model.gif", package="Rcmdr"))
tkimage.create("photo", "::image::removeIcon", file = system.file("etc", "remove.gif", package="Rcmdr"))
tkimage.create("photo", "::image::copyIcon", file = system.file("etc", "copy.gif", package="Rcmdr"))
tkimage.create("photo", "::image::cutIcon", file = system.file("etc", "cut.gif", package="Rcmdr"))
tkimage.create("photo", "::image::deleteIcon", file = system.file("etc", "delete.gif", package="Rcmdr"))
tkimage.create("photo", "::image::findIcon", file = system.file("etc", "find.gif", package="Rcmdr"))
tkimage.create("photo", "::image::pasteIcon", file = system.file("etc", "paste.gif", package="Rcmdr"))
tkimage.create("photo", "::image::redoIcon", file = system.file("etc", "redo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::undoIcon", file = system.file("etc", "undo.gif", package="Rcmdr"))
tkimage.create("photo", "::image::saveEditsIcon", file = system.file("etc", "save-edits.gif", package="Rcmdr"))
tkimage.create("photo", "::image::infoIcon", file = system.file("etc", "info.gif", package="Rcmdr"))
tkimage.create("photo", "::image::warningIcon", file = system.file("etc", "warning.gif", package="Rcmdr"))
tkimage.create("photo", "::image::errorIcon", file = system.file("etc", "error.gif", package="Rcmdr"))
tkimage.create("photo", "::image::questionIcon", file = system.file("etc", "question.gif", package="Rcmdr"))
}
setupFonts <- function(){
current <- getOption("Rcmdr")
# set up Rcmdr default and text (log) fonts, Tk scaling factor
default.font.family.val <- tclvalue(.Tcl("font actual TkDefaultFont -family"))
default.font.family.val <- gsub("\\{", "", gsub("\\}", "", default.font.family.val))
default.font.family <- setOption("default.font.family", default.font.family.val)
if (!("RcmdrDefaultFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrDefaultFont", tclvalue(tkfont.actual("TkDefaultFont"))))
.Tcl("option add *font RcmdrDefaultFont")
}
.Tcl(paste("font configure RcmdrDefaultFont -family {", default.font.family, "}", sep=""))
if (!("RcmdrTitleFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrTitleFont", tclvalue(tkfont.actual("TkDefaultFont"))))
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, "}", sep=""))
if (!("RcmdrOutputMessagesFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrOutputMessagesFont", tclvalue(tkfont.actual("RcmdrTitleFont"))))
}
.Tcl(paste("font configure RcmdrTitleFont -family {", default.font.family, "}", sep=""))
.Tcl(paste("font configure RcmdrOutputMessagesFont -family {", default.font.family, "}", sep=""))
.Tcl(paste("font configure TkDefaultFont -family {", default.font.family, "}", sep=""))
log.font.family.val <- tclvalue(.Tcl("font actual TkFixedFont -family"))
log.font.family.val <- gsub("\\{", "", gsub("\\}", "", log.font.family.val))
log.font.family <- setOption("log.font.family", log.font.family.val)
if (!("RcmdrLogFont" %in% as.character(.Tcl("font names")))){
.Tcl(paste("font create RcmdrLogFont", tclvalue(tkfont.actual("TkFixedFont"))))
}
.Tcl(paste("font configure RcmdrLogFont -family {", log.font.family, "}", sep=""))
.Tcl(paste("font configure TkFixedFont -family {", log.font.family, "}", sep=""))
putRcmdr("logFont", "RcmdrLogFont")
scale.factor <- current$scale.factor
if (!is.null(scale.factor)) .Tcl(paste("tk scaling ", scale.factor, sep=""))
# set various font sizes
if (WindowsP()){
default.font.size.val <- abs(as.numeric(.Tcl("font actual TkDefaultFont -size")))
if (is.na(default.font.size.val)) default.font.size.val <- 10
}
else default.font.size.val <- 10
default.font.size <- setOption("default.font.size", default.font.size.val)
tkfont.configure("RcmdrDefaultFont", size=default.font.size)
tkfont.configure("RcmdrTitleFont", size=default.font.size)
tkfont.configure("RcmdrOutputMessagesFont", size=default.font.size)
tkfont.configure("TkDefaultFont", size=default.font.size)
tkfont.configure("TkTextFont", size=default.font.size)
tkfont.configure("TkCaptionFont", size=default.font.size)
log.font.size <- setOption("log.font.size", 10)
tkfont.configure("RcmdrLogFont", size=log.font.size)
tkfont.configure("TkFixedFont", size=log.font.size)
.Tcl("ttk::style configure TButton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TLabel -font RcmdrDefaultFont")
.Tcl("ttk::style configure TCheckbutton -font RcmdrDefaultFont")
.Tcl("ttk::style configure TRadiobutton -font RcmdrDefaultFont")
standard.title.color <- as.character(.Tcl("ttk::style lookup TLabelframe.Label -foreground"))
title.color <- setOption("title.color", standard.title.color)
if (tolower(title.color) == "black" || title.color == "#000000"){
tkfont.configure("RcmdrTitleFont", weight="bold")
}
else tkfont.configure("RcmdrTitleFont", weight="normal")
}
platformIssues <- function(){
current <- getOption("Rcmdr")
if (getRcmdr("suppress.X11.warnings")) {
putRcmdr("messages.connection", file(open = "w+"))
sink(getRcmdr("messages.connection"), type="message")
}
if (!(WindowsP())) {
putRcmdr("oldPager", options(pager=RcmdrPager))
}
putRcmdr("restore.help_type", getOption("help_type"))
if ((!WindowsP()) && getRcmdr("RVersion") == "4.2.0" && (getRcmdr("RVersionStatus") != "Patched")) {
setOption("help_type", "text")
} else {
setOption("help_type", "html")
}
options(help_type=getRcmdr("help_type"))
putRcmdr("restore.device", getOption("device"))
if (RStudioP()){
if (WindowsP()) options(device="windows")
else if (MacOSXP()) options(device="quartz")
else options(device="x11")
}
setOption("tkwait.dialog", FALSE)
if (getRcmdr("tkwait.dialog")) putRcmdr("editDataset.threshold", 0)
if (MacOSXP()){
# PATH <- system2("/usr/libexec/path_helper", "-s", stdout=TRUE)
# PATH <- sub("\"; export PATH;$", "", sub("^PATH=\\\"", "", PATH))
# Sys.setenv(PATH=PATH)
PATH <- Sys.getenv("PATH")
PATH <- unlist(strsplit(PATH, .Platform$path.sep, fixed=TRUE))
if (MacOSXP("15.0.0")){
if (length(grep("^/Library/TeX/texbin$", PATH)) == 0) {
PATH[length(PATH) + 1] <- "/Library/TeX/texbin"
Sys.setenv(PATH=paste(PATH, collapse=.Platform$path.sep))
}
}
else{
if (length(grep("^/usr/texbin$", PATH)) == 0) {
PATH[length(PATH) + 1] <- "/usr/texbin"
Sys.setenv(PATH=paste(PATH, collapse=.Platform$path.sep))
}
}
}
}
processPlugins <- function(modelClasses){
# source additional .R files, plug-ins preferred
etc <- getRcmdr("etc")
source.files <- list.files(etc, pattern="\\.[Rr]$")
for (file in source.files) {
source(file.path(etc, file))
cat(paste(gettextRcmdr("Sourced:"), file, "\n"))
}
# collect plug-ins to be used
Plugins <- options()$Rcmdr$plugins
allPlugins <- listPlugins(loaded=TRUE)
for (plugin in Plugins){
if (!require(plugin, character.only=TRUE)){
putRcmdr("commanderWindow", NULL)
stop(sprintf(gettextRcmdr("the plug-in package %s is missing"), plugin))
}
if (!is.element(plugin, allPlugins)){
putRcmdr("commanderWindow", NULL)
stop(sprintf(gettextRcmdr("the package %s is not an Rcmdr plug-in"), plugin))
}
}
for (plugin in Plugins){
description <- readLines(file.path(path.package(package=plugin)[1], "DESCRIPTION"))
addModels <- description[grep("Models:", description)]
addModels <- gsub(" ", "", sub("^Models:", "", addModels))
addModels <- unlist(strsplit(addModels, ","))
addRcmdrModels <- description[grep("RcmdrModels:", description)]
addRcmdrModels <- gsub(" ", "", sub("^RcmdrModels:", "", addRcmdrModels))
addRcmdrModels <- unlist(strsplit(addRcmdrModels, ","))
if (length(addModels) > 0) modelClasses <- c(modelClasses, addModels)
if (length(addRcmdrModels) > 0) modelClasses <- c(modelClasses, addRcmdrModels)
}
putRcmdr("modelClasses", modelClasses)
Plugins
}
processModelCapabilities <- function(Plugins){
modelCapabilities <- read.table(file.path(getRcmdr("etc"), "Rcmdr-model-capabilities.txt"), header=TRUE)
n.plugins <- length(Plugins)
if (n.plugins > 0){
modelCapabilitiesList <- vector(n.plugins + 1, mode="list")
modelCapabilitiesList[[1]] <- modelCapabilities
for (i in 1:n.plugins){
if (file.exists(file.path(path.package(package=Plugins[i])[1], "etc/model-capabilities.txt")))
modelCapabilitiesList[[i + 1]] <- read.table(file.path(path.package(package=Plugins[i])[1],
"etc/model-capabilities.txt"),
header=TRUE)
}
modelCapabilities <- mergeCapabilities(modelCapabilitiesList)
}
putRcmdr("modelCapabilities", modelCapabilities)
modelClasses <- getRcmdr("modelClasses")
modelCapabilitiesClasses <- rownames(modelCapabilities)
modelClasses <- union(modelClasses, modelCapabilitiesClasses)
putRcmdr("modelClasses", modelClasses)
}
processOperations <- function(Plugins){
Operations <- read.table(file.path(getRcmdr("etc"), "Rcmdr-operations.txt"),
header=TRUE, stringsAsFactors=FALSE)
for (plugin in Plugins){
operations.file <- file.path(path.package(package=plugin)[1], "etc", "operations.txt")
if (file.exists(operations.file)){
operations <- read.table(operations.file, header=TRUE, stringsAsFactors=FALSE)
if (any(conflicts <- rownames(operations) %in% rownames(Operations))){
message(sprintf("The following Markdown section titles in %s\n conflict with existing titles and were removed:\n ",
plugin), paste(rownames(operations)[conflicts], collapse=", "))
operations <- operations[!conflicts, ]
}
Operations <- rbind(Operations, operations)
}
}
putRcmdr("Operations", Operations)
}
processMenus <- function(Plugins){
current <- getOption("Rcmdr")
# build Rcmdr menus
Menus <- read.table(file.path(getRcmdr("etcMenus"), "Rcmdr-menus.txt"), colClasses = "character")
addMenus <- function(Menus){
removeMenus <- function(what){
children <- Menus[Menus[,3] == what, 2]
which <- what == Menus[,2] | what == Menus[,5]
Menus <<- Menus[!which,]
for (child in children) removeMenus(child)
}
nms <- c("type", "menuOrItem", "operationOrParent", "label",
"commandOrMenu", "activation", "install")
names(Menus) <- nms
for (plugin in Plugins) {
MenusToAdd <- read.table(file.path(path.package(package=plugin)[1], "etc/menus.txt"),
colClasses = "character")
names(MenusToAdd) <- nms
for (i in 1:nrow(MenusToAdd)){
line <- MenusToAdd[i,]
line[, "label"] <- gettext(line[,"label"], domain=paste("R=", plugin, sep=""))
if (line[1, "type"] == "remove"){
removeMenus(line[1, "menuOrItem"])
next
}
if (line[1, "type"] == "menu"){
where <- if (line[1, "operationOrParent"] == "topMenu") 0
else max(which((Menus[, "type"] == "menu") &
(Menus[, "menuOrItem"] == line[1, "operationOrParent"])))
}
else if (line[1, "type"] == "item"){
if ((line[1, "operationOrParent"] == "command") || (line[1, "operationOrParent"] == "separator")){
which <- which(((Menus[, "operationOrParent"] == "command") |
(Menus[, "operationOrParent"] == "separator")) &
(Menus[, "menuOrItem"] == line[1, "menuOrItem"]))
where <- if (length(which) == 0)
which((Menus[, "type"] == "menu")
& (Menus[, "menuOrItem"] == line[1, "menuOrItem"]))
else max(which)
if (line[1, "operationOrParent"] == "separator" && line[1, "commandOrMenu"] != "")
where <- max(which(line[1, "commandOrMenu"] == Menus[, "commandOrMenu"]))
}
else if (line[1, "operationOrParent"] == "cascade"){
where <- if (line[1, "menuOrItem"] != "topMenu")
max(which((Menus[, "operationOrParent"] == "cascade") &
(Menus[, "menuOrItem"] == line[1, "menuOrItem"]) | (Menus[, "commandOrMenu"] == line[1, "menuOrItem"])))
else {
max(which((Menus[, "operationOrParent"] == "cascade") &
(Menus[, "menuOrItem"] == "topMenu") &
(Menus[, "commandOrMenu"] != "toolsMenu") &
(Menus[, "commandOrMenu"] != "helpMenu")))
}
}
else stop(sprintf(gettextRcmdr('unrecognized operation, "%s", in plugin menu line %i'),
line[1, "operation"], i))
}
else stop(sprintf(gettextRcmdr('unrecognized type, "%s", in plugin menu line %i'),
line[1, "type"], i))
Menus <- insertRows(Menus, line, where)
}
}
Menus
}
Menus <- addMenus(Menus)
menuNames <- Menus[Menus[,1] == "menu",]
duplicateMenus <- duplicated(menuNames)
if (any(duplicateMenus)) stop(paste(gettextRcmdr("Duplicate menu names:"),
menuNames[duplicateMenus]))
setOption("suppress.menus", FALSE)
if (RExcelSupported()) # contributed by Erich Neuwirth
putRExcel(".rexcel.menu.dataframe", Menus)
Menus
}
setupGUI <- function(Menus){
current <- getOption("Rcmdr")
# standard edit actions
onCopy <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
selection <- strsplit(tclvalue(tktag.ranges(focused, "sel")), " ")[[1]]
if (is.na(selection[1])) return()
text <- tclvalue(tkget(focused, selection[1], selection[2]))
tkclipboard.clear()
tkclipboard.append(text)
}
onDelete <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
selection <- strsplit(tclvalue(tktag.ranges(focused, "sel")), " ")[[1]]
if (is.na(selection[1])) return()
tkdelete(focused, selection[1], selection[2])
}
onCut <- function(){
onCopy()
onDelete()
}
onPaste <- function(){
onDelete()
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
text <- tclvalue(.Tcl("selection get -selection CLIPBOARD"))
if (length(text) == 0) return()
tkinsert(focused, "insert", text)
}
onFind <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
initializeDialog(title=gettextRcmdr("Find"))
textFrame <- tkframe(top)
textVar <- tclVar(getRcmdr("last.search"))
textEntry <- ttkentry(textFrame, width="20", textvariable=textVar)
checkBoxes(frame="optionsFrame", boxes=c("regexpr", "case"), initialValues=c("0", "1"),
labels=gettextRcmdr(c("Regular-expression search", "Case sensitive")))
radioButtons(name="direction", buttons=c("foward", "backward"), labels=gettextRcmdr(c("Forward", "Backward")),
values=c("-forward", "-backward"), title=gettextRcmdr("Search Direction"))
onOK <- function(){
text <- tclvalue(textVar)
putRcmdr("last.search", text)
if (text == ""){
errorCondition(recall=onFind, message=gettextRcmdr("No search text specified."))
return()
}
type <- if (tclvalue(regexprVariable) == 1) "-regexp" else "-exact"
case <- tclvalue(caseVariable) == 1
direction <- tclvalue(directionVariable)
stop <- if (direction == "-forward") "end" else "1.0"
where.txt <- if (case) tksearch(focused, type, direction, "--", text, "insert", stop)
else tksearch(focused, type, direction, "-nocase", "--", text, "insert", stop)
where.txt <- tclvalue(where.txt)
if (where.txt == "") {
Message(message=gettextRcmdr("Text not found."),
type="note")
if (GrabFocus()) tkgrab.release(top)
tkdestroy(top)
tkfocus(CommanderWindow())
return()
}
if (GrabFocus()) tkgrab.release(top)
tkfocus(focused)
tkmark.set(focused, "insert", where.txt)
tksee(focused, where.txt)
tkdestroy(top)
}
.exit <- function(){
text <- tclvalue(textVar)
putRcmdr("last.search", text)
return("")
}
OKCancelHelp()
tkgrid(labelRcmdr(textFrame, text=gettextRcmdr("Search for:")), textEntry, sticky="w")
tkgrid(textFrame, sticky="w")
tkgrid(optionsFrame, sticky="w")
tkgrid(directionFrame, sticky="w")
tkgrid(buttonsFrame, sticky="w")
dialogSuffix(focus=textEntry)
}
onSelectAll <- function() {
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID)
&& (tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tktag.add(focused, "sel", "1.0", "end")
tkfocus(focused)
}
onClear <- function(){
onSelectAll()
onDelete()
}
onUndo <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tcl(focused, "edit", "undo")
}
onRedo <- function(){
focused <- tkfocus()
if ((tclvalue(focused) != LogWindow()$ID) && (tclvalue(focused) != OutputWindow()$ID) &&
(tclvalue(focused) != MessagesWindow()$ID) && (tclvalue(focused) != RmdWindow()$ID) && (tclvalue(focused) != RnwWindow()$ID))
focused <- LogWindow()
tcl(focused, "edit", "redo")
}
.Tcl("ttk::style configure TNotebook.Tab -font RcmdrDefaultFont")
.Tcl(paste("ttk::style configure TNotebook.Tab -foreground", getRcmdr("title.color")))
all.themes <- tk2theme.list()
current.theme <- tk2theme()
all.themes <- union(all.themes, current.theme)
setOption("theme", current.theme)
theme <- (getRcmdr("theme"))
if (!(theme %in% all.themes)){
warning(gettextRcmdr("non-existent theme"), ', "', theme, '"\n ',
gettextRcmdr("theme set to"), ' "', current.theme, '"')
theme <- current.theme
}
putRcmdr("theme", theme)
tk2theme(theme)
# data-set edit
onEdit <- function(){
if (activeDataSet() == FALSE) {
tkfocus(CommanderWindow())
return()
}
dsnameValue <- ActiveDataSet()
size <- eval(parse(text=paste("prod(dim(", dsnameValue, "))", sep=""))) # prod(dim(save.dataset))
if (size < 1 || size > getRcmdr("editDataset.threshold")){
save.dataset <- get(dsnameValue, envir=.GlobalEnv)
command <- paste("fix(", dsnameValue, ")", sep="")
result <- justDoIt(command)
if (class(result)[1] != "try-error"){
if (nrow(get(dsnameValue)) == 0){
errorCondition(window=NULL, message=gettextRcmdr("empty data set."))
justDoIt(paste(dsnameValue, "<- save.dataset"))
return()
}
else{
logger(command, rmd=FALSE)
activeDataSet(dsnameValue)
}
}
else{
errorCondition(window=NULL, message=gettextRcmdr("data set edit error."))
return()
}
}
else {
command <- paste("editDataset(", dsnameValue, ")", sep="")
result <- justDoIt(command)
if (class(result)[1] != "try-error"){
logger(command, rmd=FALSE)
}
else{
errorCondition(window=NULL, message=gettextRcmdr("data set edit error."))
return()
}
}
tkwm.deiconify(CommanderWindow())
tkfocus(CommanderWindow())
}
# data-set view
onView <- function(){
# if (packageAvailable("relimp")) Library("relimp", rmd=FALSE)
if (activeDataSet() == FALSE) {
tkfocus(CommanderWindow())
return()
}
suppress <- if(getRcmdr("suppress.X11.warnings")) ", suppress.X11.warnings=FALSE" else ""
view.height <- max(getRcmdr("output.height") + getRcmdr("log.height"), 10)
dim <- dim(get(ActiveDataSet()))
nrows <- dim[1]
ncols <- dim[2]
threshold <- getRcmdr("showData.threshold")
command <- if (nrows <= threshold[1] && ncols <= threshold[2]){
posn <- commanderPosition() + c(as.numeric(tkwinfo("width", CommanderWindow())) + 10, 10)
paste("showData(as.data.frame(", ActiveDataSet(), "), title='", ActiveDataSet(), "', placement='+", posn[1], "+", posn[2],"', font=getRcmdr('logFont'), maxwidth=",
getRcmdr("log.width"), ", maxheight=", view.height, suppress, ")", sep="")
}
else paste("View(as.data.frame(", ActiveDataSet(), "))", sep="")
window <- justDoIt(command)
if (!is.null(window)){
open.showData.windows <- getRcmdr("open.showData.windows")
open.window <- open.showData.windows[[ActiveDataSet()]]
if (!is.null(open.window) && open.window$ID %in% as.character(tkwinfo("children", "."))) tkdestroy(open.window)
open.showData.windows[[ActiveDataSet()]] <- window
putRcmdr("open.showData.windows", open.showData.windows)
}
}
# submit command in script tab or compile .Rmd file in markdown tab or compile .Rnw file in knitr tab
onSubmit <- function(){
.log <- LogWindow()
.rmd <- RmdWindow()
.rnw <- RnwWindow()
if (as.character(tkselect(notebook)) == logFrame$ID) {
selection <- strsplit(tclvalue(tktag.ranges(.log, "sel")), " ")[[1]]
if (is.na(selection[1])) {
tktag.add(.log, "currentLine", "insert linestart", "insert lineend")
selection <- strsplit(tclvalue(tktag.ranges(.log,"currentLine")), " ")[[1]]
tktag.delete(.log, "currentLine")
if (is.na(selection[1])) {
Message(message=gettextRcmdr("Nothing is selected."),
type="error")
tkfocus(CommanderWindow())
return()
}
}
lines <- tclvalue(tkget(.log, selection[1], selection[2]))
lines <- strsplit(lines, "\n")[[1]]
.console.output <- getRcmdr("console.output")
.output <- OutputWindow()
iline <- 1
nlines <- length(lines)
while (iline <= nlines){
# while (nchar(lines[iline])==0) iline <- iline + 1
# if (iline > nlines) break
while (nchar(lines[iline])==0) iline <- iline + 1
current.line <- lines[iline]
if (.console.output) cat(paste("\n", getRcmdr("prefixes")[1], current.line,"\n", sep=""))
else{
tkinsert(.output, "end", paste("\n> ", current.line,"\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
}
jline <- iline + 1
while (jline <= nlines){
if (nchar(lines[jline])==0) lines[jline] <- " "
if (!inherits(try(parse(text=current.line),silent=TRUE), "try-error")) break
if (.console.output)cat(paste(getRcmdr("prefixes")[2], lines[jline],"\n", sep=""))
else{
tkinsert(.output, "end", paste("+ ", lines[jline],"\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
}
current.line <- if (nchar(lines[jline]) > 0) paste(current.line, lines[jline],sep="\n")
jline <- jline + 1
iline <- iline + 1
}
# protect against misprocessed comments
xlines <- strsplit(current.line, "\n")[[1]]
xlines <- trimws(sub("#.*$", "", xlines))
xlines <- xlines[nchar(xlines) > 0]
current.line <- paste(xlines, collapse="\n")
if (length(current.line) == 0 || nchar(current.line) == 0) current.line <- NULL
if (!(is.null(current.line) || is.na(current.line))) {
doItAndPrint(current.line, log=FALSE, rmd=TRUE)
}
iline <- iline + 1
tkyview.moveto(.output, 1)
tkfocus(.log)
}
if (length(as.character(tksearch(.log, "-regexp", "-forward", "--", "\\n\\n$", "1.0"))
) == 0){
tkinsert(.log, "end", "\n")
}
cursor.line.posn <- 1 + floor(as.numeric(tkindex(.log, "insert")))
tkmark.set(.log, "insert", paste(cursor.line.posn, ".0", sep=""))
tktag.remove(.log, "sel", "1.0", "end")
}
else if (as.character(tkselect(notebook)) == RmdFrame$ID) {
compileRmd()
}
else{
compileRnw()
}
}
# right-click context menus
contextMenuLog <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.log <- LogWindow()
tkfocus(.log)
contextMenu <- tkmenu(tkmenu(.log), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Submit"), command=onSubmit)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .log), tkwinfo("pointery", .log))
}
contextMenuRmd <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.rmd <- RmdWindow()
tkfocus(.rmd)
contextMenu <- tkmenu(tkmenu(.rmd), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Generate report"), command=onSubmit)
tkadd(contextMenu, "command", label=gettextRcmdr("Edit R Markdown document"), command=editMarkdown)
tkadd(contextMenu, "command", label=gettextRcmdr("Remove last Markdown command block"), command=removeLastRmdBlock)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
# tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind) # doesn't work FIXME
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .rmd), tkwinfo("pointery", .rmd))
}
contextMenuRnw <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.rnw <- RnwWindow()
tkfocus(.rnw)
contextMenu <- tkmenu(tkmenu(.rnw), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Generate PDF report"), command=onSubmit)
tkadd(contextMenu, "command", label=gettextRcmdr("Edit knitr document"), command=editKnitr)
tkadd(contextMenu, "command", label=gettextRcmdr("Remove last knitr command block"), command=removeLastRnwBlock)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
# tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind) # doesn't work FIXME
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .rnw), tkwinfo("pointery", .rnw))
}
contextMenuOutput <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.output <- OutputWindow()
tkfocus(.output)
contextMenu <- tkmenu(tkmenu(.output), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .output), tkwinfo("pointery", .output))
}
contextMenuMessages <- function(){
# focused <- tkfocus()
# on.exit(tkfocus(focused))
.messages <- MessagesWindow()
tkfocus(.messages)
contextMenu <- tkmenu(tkmenu(.messages), tearoff=FALSE)
tkadd(contextMenu, "command", label=gettextRcmdr("Cut"), command=onCut)
tkadd(contextMenu, "command", label=gettextRcmdr("Copy"), command=onCopy)
tkadd(contextMenu, "command", label=gettextRcmdr("Paste"), command=onPaste)
tkadd(contextMenu, "command", label=gettextRcmdr("Delete"), command=onDelete)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Find..."), command=onFind)
tkadd(contextMenu, "command", label=gettextRcmdr("Select all"), command=onSelectAll)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Undo"), command=onUndo)
tkadd(contextMenu, "command", label=gettextRcmdr("Redo"), command=onRedo)
tkadd(contextMenu, "separator")
tkadd(contextMenu, "command", label=gettextRcmdr("Clear window"), command=onClear)
tkpopup(contextMenu, tkwinfo("pointerx", .messages), tkwinfo("pointery", .messages))
}
# main Commander window
if (getRcmdr("crisp.dialogs")) tclServiceMode(on=FALSE)
putRcmdr("commanderWindow", tktoplevel(class="Rcommander"))
.commander <- CommanderWindow()
tkwm.minsize(.commander, getRcmdr("minimum.width"), getRcmdr("minimum.height"))
tcl("wm", "iconphoto", .commander, "-default", "::image::RlogoIcon")
placement <- setOption("placement", "", global=FALSE)
tkwm.geometry(.commander, placement)
tkwm.title(.commander, gettextRcmdr("R Commander"))
tkwm.protocol(.commander, "WM_DELETE_WINDOW",
if (getRcmdr("quit.R.on.close")) closeCommanderAndR else CloseCommander)
topMenu <- tkmenu(.commander)
tkconfigure(.commander, menu=topMenu)
position <- numeric(0)
# install menus
.Menus <- menus <- list()
menuItems <- 0
oldMenu <- ncol(Menus) == 6
if (!getRcmdr("suppress.menus")){
for (m in 1:nrow(Menus)){
install <- if (oldMenu) "" else Menus[m, 7]
if ((install != "") && (!eval(parse(text=install)))) next
if (Menus[m, 1] == "menu") {
position[Menus[m, 2]] <- 0
assign(Menus[m, 2], tkmenu(get(Menus[m, 3]), tearoff=FALSE))
menus[[Menus[m, 2]]] <- list(ID=get(Menus[m, 2])$ID, position=0)
}
else if (Menus[m, 1] == "item") {
position[Menus[m, 2]] <- position[Menus[m, 2]] + 1
if (Menus[m, 3] == "command"){
if (Menus[m, 6] == "")
tkadd(get(Menus[m, 2]), "command", label=gettextMenus(Menus[m, 4]),
command=get(Menus[m, 5]))
else {
tkadd(get(Menus[m, 2]), "command", label=gettextMenus(Menus[m, 4]),
command=get(Menus[m, 5]), state="disabled")
menuItems <- menuItems + 1
menus[[Menus[m, 2]]]$position <- position[Menus[m, 2]]
.Menus[[menuItems]] <- list(ID=menus[[Menus[m, 2]]]$ID, position=position[Menus[m, 2]],
activation=eval(parse(text=paste("function()", Menus[m, 6]))))
}
}
else if (Menus[m, 3] == "cascade")
tkadd(get(Menus[m, 2]), "cascade", label=gettextMenus(Menus[m, 4]),
menu=get(Menus[m, 5]))
else if (Menus[m, 3] == "separator")
tkadd(get(Menus[m, 2]), "separator")
else stop(paste(gettextRcmdr("menu definition error:"), Menus[m, ], collapse=" "),
domain=NA)
}
else stop(paste(gettextRcmdr("menu definition error:"), Menus[m, ], collapse=" "),
domain=NA)
}
}
putRcmdr("Menus", .Menus)
putRcmdr("autoRestart", FALSE)
activateMenus()
# toolbar
controlsFrame <- tkframe(CommanderWindow())
editButton <- buttonRcmdr(controlsFrame, text=gettextRcmdr("Edit data set"), command=onEdit,
image="::image::editIcon", compound="left")
viewButton <- buttonRcmdr(controlsFrame, text=gettextRcmdr("View data set"), command=onView,
image="::image::viewIcon", compound="left")
putRcmdr("dataSetName", tclVar(gettextRcmdr("<No active dataset>")))
putRcmdr("dataSetLabel", tkbutton(controlsFrame, textvariable=getRcmdr("dataSetName"), foreground="red",
relief="groove", command=selectActiveDataSet, image="::image::dataIcon", compound="left"))
# script and markdown tabs
notebook <- ttknotebook(CommanderWindow())
logFrame <- ttkframe(CommanderWindow())
putRcmdr("logWindow", tktext(logFrame, bg="white", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.log <- LogWindow()
logXscroll <- ttkscrollbar(logFrame, orient="horizontal",
command=function(...) tkxview(.log, ...))
logYscroll <- ttkscrollbar(logFrame,
command=function(...) tkyview(.log, ...))
tkconfigure(.log, xscrollcommand=function(...) tkset(logXscroll, ...))
tkconfigure(.log, yscrollcommand=function(...) tkset(logYscroll, ...))
RmdFrame <- ttkframe(CommanderWindow())
putRcmdr("RmdWindow", tktext(RmdFrame, bg="#FAFAFA", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.rmd <- RmdWindow()
rmd.template <- setOption("rmd.template",
system.file("etc", if (getRcmdr("capabilities")$pandoc) "Rcmdr-RMarkdown-Template.Rmd"
else "Rcmdr-Markdown-Template.Rmd", package="Rcmdr"))
template <- paste(readLines(rmd.template), collapse="\n")
# template customization and translation:
template <- sub("Your Name", getRcmdr("UserName"), template)
template <- sub("Replace with Main Title",
gettextRcmdr("Replace with Main Title"), template)
template <- sub("include this code chunk as-is to set options",
gettextRcmdr("include this code chunk as-is to set options"),
template)
template <- sub("You can edit this R Markdown document, for example to explain what you're\ndoing and to draw conclusions from your data analysis.",
gettextRcmdr("You can edit this R Markdown document, for example to explain what you're\ndoing and to draw conclusions from your data analysis."),
template)
template <- sub("Auto-generated section titles, typically preceded by ###, can also be edited.",
gettextRcmdr("Auto-generated section titles, typically preceded by ###, can also be edited."),
template)
template <- sub("It's generally not a good idea to edit the R code that the R Commander writes, \nbut you can freely edit between (not within) R \"code blocks.\" Each R code\nblock starts with ```{r} and ends with ```.",
gettextRcmdr("It's generally not a good idea to edit the R code that the R Commander writes, \nbut you can freely edit between (not within) R \"code blocks.\" Each R code\nblock starts with ```{r} and ends with ```."),
template, fixed = TRUE)
# if (getRcmdr("use.rgl")) template <- paste0(template,
# "\n\n```{r echo=FALSE}\n# include this code chunk as-is to enable 3D graphs\nlibrary(rgl)\noptions(rgl.useNULL = TRUE)\n```\n\n")
tkinsert(.rmd, "end", template)
putRcmdr("markdown.output", FALSE)
RmdXscroll <- ttkscrollbar(RmdFrame, orient="horizontal",
command=function(...) tkxview(.rmd, ...))
RmdYscroll <- ttkscrollbar(RmdFrame,
command=function(...) tkyview(.rmd, ...))
tkconfigure(.rmd, xscrollcommand=function(...) tkset(RmdXscroll, ...))
tkconfigure(.rmd, yscrollcommand=function(...) tkset(RmdYscroll, ...))
RnwFrame <- ttkframe(CommanderWindow())
putRcmdr("RnwWindow", tktext(RnwFrame, bg="#FAFAFA", foreground=getRcmdr("log.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("log.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.rnw <- RnwWindow()
rnw.template <- setOption("rnw.template",
system.file("etc", "Rcmdr-knitr-Template.Rnw", package="Rcmdr"))
template <- paste(readLines(rnw.template), collapse="\n")
template <- sub("Your Name", getRcmdr("UserName"), template)
template <- sub("Replace with Main Title",
gettextRcmdr("Replace with Main Title"), template)
tkinsert(.rnw, "end", template)
putRcmdr("knitr.output", FALSE)
RnwXscroll <- ttkscrollbar(RnwFrame, orient="horizontal",
command=function(...) tkxview(.rnw, ...))
RnwYscroll <- ttkscrollbar(RnwFrame,
command=function(...) tkyview(.rnw, ...))
tkconfigure(.rnw, xscrollcommand=function(...) tkset(RnwXscroll, ...))
tkconfigure(.rnw, yscrollcommand=function(...) tkset(RnwYscroll, ...))
outputFrame <- tkframe(.commander)
submitButtonLabel <- tclVar(gettextRcmdr("Submit"))
submitButton <- if (getRcmdr("console.output"))
buttonRcmdr(CommanderWindow(), textvariable=submitButtonLabel, borderwidth="2", command=onSubmit,
image="::image::submitIcon", compound="left")
else buttonRcmdr(outputFrame, textvariable=submitButtonLabel, borderwidth="2", command=onSubmit,
image="::image::submitIcon", compound="left")
tkbind(CommanderWindow(), "<Button-1>", function() {
if (as.character(tkselect(notebook)) == logFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Submit")
if (as.character(tkselect(notebook)) == RmdFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Generate report")
if (as.character(tkselect(notebook)) == RnwFrame$ID) tclvalue(submitButtonLabel) <- gettextRcmdr("Generate PDF report")
})
putRcmdr("outputWindow", tktext(outputFrame, bg="white", foreground=getRcmdr("output.text.color"),
font=getRcmdr("logFont"), height=getRcmdr("output.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.output <- OutputWindow()
outputXscroll <- ttkscrollbar(outputFrame, orient="horizontal",
command=function(...) tkxview(.output, ...))
outputYscroll <- ttkscrollbar(outputFrame,
command=function(...) tkyview(.output, ...))
tkconfigure(.output, xscrollcommand=function(...) tkset(outputXscroll, ...))
tkconfigure(.output, yscrollcommand=function(...) tkset(outputYscroll, ...))
# messages window
messagesFrame <- tkframe(.commander)
putRcmdr("messagesWindow", tktext(messagesFrame, bg="lightgray",
font=getRcmdr("logFont"), height=getRcmdr("messages.height"),
width=getRcmdr("log.width"), wrap="none", undo=TRUE))
.messages <- MessagesWindow()
messagesXscroll <- ttkscrollbar(messagesFrame, orient="horizontal",
command=function(...) tkxview(.messages, ...))
messagesYscroll <- ttkscrollbar(messagesFrame,
command=function(...) tkyview(.messages, ...))
tkconfigure(.messages, xscrollcommand=function(...) tkset(messagesXscroll, ...))
tkconfigure(.messages, yscrollcommand=function(...) tkset(messagesYscroll, ...))
# configure toolbar, etc., install various windows and widgets
putRcmdr("modelName", tclVar(gettextRcmdr("<No active model>")))
putRcmdr("modelLabel", tkbutton(controlsFrame, textvariable=getRcmdr("modelName"), foreground="red",
relief="groove", command=selectActiveModel, image="::image::modelIcon", compound="left"))
show.edit.button <- options("Rcmdr")[[1]]$show.edit.button
show.edit.button <- if (is.null(show.edit.button)) TRUE else show.edit.button
if (!getRcmdr("suppress.menus")){
tkgrid(labelRcmdr(controlsFrame, image="::image::RlogoIcon", compound="left"),
labelRcmdr(controlsFrame, text=gettextRcmdr(" Data set:")), getRcmdr("dataSetLabel"),
if(show.edit.button) editButton, viewButton,
labelRcmdr(controlsFrame, text=gettextRcmdr("Model:")), getRcmdr("modelLabel"), sticky="w", pady=c(3, 3))
tkgrid(controlsFrame, sticky="w")
tkgrid.configure(getRcmdr("dataSetLabel"), padx=c(2, 5))
tkgrid.configure(getRcmdr("modelLabel"), padx=c(2, 10))
tkgrid.configure(editButton, padx=c(10, 1))
if (show.edit.button) tkgrid.configure(viewButton, padx=c(1, 15))
else tkgrid.configure(viewButton, padx=c(10, 15))
}
.log.commands <- getRcmdr("log.commands")
.console.output <- getRcmdr("console.output")
if (.log.commands) {
tkgrid(.log, logYscroll, sticky="news", columnspan=2)
tkgrid(logXscroll)
tkgrid(logFrame, sticky="news", padx=10, pady=0, columnspan=2)
tkgrid(.rmd, RmdYscroll, sticky="news", columnspan=2)
tkgrid(RmdXscroll)
tkgrid(.rnw, RnwYscroll, sticky="news", columnspan=2)
tkgrid(RnwXscroll)
if (getRcmdr("use.markdown")) tkgrid(RmdFrame, sticky="news", padx=10, pady=0, columnspan=2)
if (getRcmdr("use.knitr")) tkgrid(RnwFrame, sticky="news", padx=10, pady=0, columnspan=2)
}
tkadd(notebook, logFrame, text=gettextRcmdr("R Script"), padding=6)
if (getRcmdr("use.markdown")) tkadd(notebook, RmdFrame, text=gettextRcmdr("R Markdown"), padding=6)
if (getRcmdr("use.knitr")) tkadd(notebook, RnwFrame, text=gettextRcmdr("knitr Document"), padding=6)
# tkgrid(notebook, sticky="news")
if (.log.commands) {
tkgrid(notebook, sticky="news")
}
# if (.log.commands && .console.output) tkgrid(submitButton, sticky="w", pady=c(0, 6))
if (.log.commands && .console.output) tkgrid(submitButton, sticky="e", pady=c(0, 6), padx=c(0, 6))
tkgrid(labelRcmdr(outputFrame, text=gettextRcmdr("Output"), font="RcmdrOutputMessagesFont", foreground=getRcmdr("title.color")),
if (.log.commands && !.console.output) submitButton, sticky="sw", pady=c(6, 6))
tkgrid(.output, outputYscroll, sticky="news", columnspan=2)
tkgrid(outputXscroll, columnspan=1 + (.log.commands && !.console.output))
if (!.console.output) tkgrid(outputFrame, sticky="news", padx=10, pady=0, columnspan=2)
tkgrid(labelRcmdr(messagesFrame, text=gettextRcmdr("Messages"), font="RcmdrOutputMessagesFont", foreground=getRcmdr("title.color")),
sticky="w", pady=c(6, 6))
tkgrid(.messages, messagesYscroll, sticky="news", columnspan=2)
tkgrid(messagesXscroll)
if (!.console.output) tkgrid(messagesFrame, sticky="news", padx=10, pady=0, columnspan=2) ##rmh & J. Fox
tkgrid.configure(logYscroll, sticky="ns")
tkgrid.configure(logXscroll, sticky="ew")
tkgrid.configure(RmdYscroll, sticky="ns")
tkgrid.configure(RmdXscroll, sticky="ew")
tkgrid.configure(RnwYscroll, sticky="ns")
tkgrid.configure(RnwXscroll, sticky="ew")
tkgrid.configure(outputYscroll, sticky="ns")
tkgrid.configure(outputXscroll, sticky="ew")
tkgrid.configure(messagesYscroll, sticky="ns")
tkgrid.configure(messagesXscroll, sticky="ew")
.commander <- CommanderWindow()
tkgrid.rowconfigure(.commander, 0, weight=0)
tkgrid.rowconfigure(.commander, 1, weight=1)
# tkgrid.rowconfigure(.commander, 2, weight=1)
w <- if (.log.commands && !.console.output) 1 else 0
tkgrid.rowconfigure(.commander, 2, weight=w)
tkgrid.columnconfigure(.commander, 0, weight=1)
tkgrid.columnconfigure(.commander, 1, weight=0)
if (.log.commands){
tkgrid.rowconfigure(logFrame, 0, weight=1)
tkgrid.rowconfigure(logFrame, 1, weight=0)
tkgrid.columnconfigure(logFrame, 0, weight=1)
tkgrid.columnconfigure(logFrame, 1, weight=0)
if (getRcmdr("use.markdown")){
tkgrid.rowconfigure(RmdFrame, 0, weight=1)
tkgrid.rowconfigure(RmdFrame, 1, weight=0)
tkgrid.columnconfigure(RmdFrame, 0, weight=1)
tkgrid.columnconfigure(RmdFrame, 1, weight=0)
}
if (getRcmdr("use.knitr")){
tkgrid.rowconfigure(RnwFrame, 0, weight=1)
tkgrid.rowconfigure(RnwFrame, 1, weight=0)
tkgrid.columnconfigure(RnwFrame, 0, weight=1)
tkgrid.columnconfigure(RnwFrame, 1, weight=0)
}
}
if (!.console.output){
tkgrid.rowconfigure(outputFrame, 0, weight=0)
tkgrid.rowconfigure(outputFrame, 1, weight=1)
tkgrid.rowconfigure(outputFrame, 2, weight=0)
tkgrid.columnconfigure(outputFrame, 0, weight=1)
tkgrid.columnconfigure(outputFrame, 1, weight=0)
}
tkgrid.rowconfigure(messagesFrame, 0, weight=0)
tkgrid.rowconfigure(messagesFrame, 1, weight=0)
tkgrid.rowconfigure(messagesFrame, 2, weight=0)
tkgrid.columnconfigure(messagesFrame, 0, weight=1)
tkgrid.columnconfigure(messagesFrame, 1, weight=0)
.Tcl("update idletasks")
tkbind(.commander, "<Control-x>", onCut)
tkbind(.commander, "<Control-X>", onCut)
tkbind(.commander, "<Control-c>", onCopy)
tkbind(.commander, "<Control-C>", onCopy)
tkbind(.commander, "<Control-r>", onSubmit)
tkbind(.commander, "<Control-R>", onSubmit)
tkbind(.commander, "<Control-Tab>", onSubmit)
tkbind(.commander, "<Control-f>", onFind)
tkbind(.commander, "<Control-F>", onFind)
tkbind(.commander, "<F3>", onFind)
tkbind(.commander, "<Control-s>", saveLog)
tkbind(.commander, "<Control-S>", saveLog)
tkbind(.commander, "<Control-a>", onSelectAll)
tkbind(.commander, "<Control-A>", onSelectAll)
tkbind(.commander, "<Control-w>", onRedo)
tkbind(.commander, "<Control-W>", onRedo)
tkbind(.commander, "<Alt-BackSpace>", onUndo)
tkbind(.log, "<ButtonPress-3>", contextMenuLog)
tkbind(.rmd, "<ButtonPress-3>", contextMenuRmd)
tkbind(.rnw, "<ButtonPress-3>", contextMenuRnw)
tkbind(.output, "<ButtonPress-3>", contextMenuOutput)
tkbind(.messages, "<ButtonPress-3>", contextMenuMessages)
tkbind(.log, "<Control-ButtonPress-1>", contextMenuLog)
tkbind(.rmd, "<Control-ButtonPress-1>", contextMenuRmd)
tkbind(.rnw, "<Control-ButtonPress-1>", contextMenuRnw)
tkbind(.output, "<Control-ButtonPress-1>", contextMenuOutput)
tkbind(.messages, "<Control-ButtonPress-1>", contextMenuMessages)
tkbind(.rmd, "<Control-e>", editMarkdown)
tkbind(.rmd, "<Control-E>", editMarkdown)
tkbind(.rnw, "<Control-e>", editKnitr)
tkbind(.rnw, "<Control-E>", editKnitr)
if (MacOSXP()){
tkbind(.commander, "<Meta-x>", onCut)
tkbind(.commander, "<Meta-X>", onCut)
tkbind(.commander, "<Meta-c>", onCopy)
tkbind(.commander, "<Meta-C>", onCopy)
tkbind(.commander, "<Meta-v>", onPaste)
tkbind(.commander, "<Meta-V>", onPaste)
tkbind(.commander, "<Meta-r>", onSubmit)
tkbind(.commander, "<Meta-R>", onSubmit)
tkbind(.commander, "<Meta-Tab>", onSubmit)
tkbind(.commander, "<Meta-f>", onFind)
tkbind(.commander, "<Meta-F>", onFind)
tkbind(.commander, "<Meta-s>", saveLog)
tkbind(.commander, "<Meta-S>", saveLog)
tkbind(.commander, "<Meta-a>", onSelectAll)
tkbind(.commander, "<Meta-A>", onSelectAll)
tkbind(.commander, "<Meta-w>", onRedo)
tkbind(.commander, "<Meta-W>", onRedo)
tkbind(.commander, "<Meta-z>", onUndo)
tkbind(.commander, "<Meta-Z>", onUndo)
tkbind(.commander, "<Shift-Meta-z>", onRedo)
tkbind(.commander, "<Shift-Meta-Z>", onRedo)
tkbind(.log, "<Meta-ButtonPress-1>", contextMenuLog)
tkbind(.rmd, "<Meta-ButtonPress-1>", contextMenuRmd)
tkbind(.rnw, "<Meta-ButtonPress-1>", contextMenuRnw)
tkbind(.output, "<Meta-ButtonPress-1>", contextMenuOutput)
tkbind(.messages, "<Meta-ButtonPress-1>", contextMenuMessages)
tkbind(.rmd, "<Meta-e>", editMarkdown)
tkbind(.rmd, "<Meta-E>", editMarkdown)
tkbind(.rnw, "<Meta-e>", editKnitr)
tkbind(.rnw, "<Meta-E>", editKnitr)
}
tkwm.deiconify(.commander)
tkfocus(.commander)
if (getRcmdr("crisp.dialogs")) tclServiceMode(on=TRUE)
tkwait.commander <- options("Rcmdr")[[1]]$tkwait.commander # to address problem in Debian Linux
if ((!is.null(tkwait.commander)) && tkwait.commander) {
putRcmdr(".commander.done", tclVar("0"))
tkwait.variable(getRcmdr(".commander.done"))
}
Message(paste(gettextRcmdr("R Commander Version "), " ", getRcmdr("RcmdrVersion"), ": ", date(), sep=""))
Message(paste(gettextRcmdr("R Version"), getRcmdr("RVersion"), getRcmdr("RVersionStatus")))
Message(paste(gettextRcmdr("Hello "), getRcmdr("UserName"), sep=""))
if (.Platform$GUI == "Rgui" && ismdi()) Message(gettextRcmdr(
"The Windows version of the R Commander works best under\nRGui with the single-document interface (SDI); see ?Commander."),
type="warning")
if (RappP() && mavericksP() && appnap() == "on") Message(gettextRcmdr(
"The Mac OS X version of the R Commander works best under R.app\nwith app nap turned off. See ?Commander and the Tools menu."),
type="warning")
}
# put commands in script, markdown, and knitr tabs
logger <- function(command, rmd=TRUE){
pushCommand(command)
.log <- LogWindow()
.rmd <- RmdWindow()
.rnw <- RnwWindow()
.output <- OutputWindow()
.markdown.editor.open <- getRcmdr("Markdown.editor.open")
.markdown.editor <- MarkdownEditorWindow()
.knitr.editor.open <- getRcmdr("knitr.editor.open")
.knitr.editor <- knitrEditorWindow()
Rmd <- rmd && is.null(attr(command, "suppressRmd")) && (getRcmdr("use.markdown") || getRcmdr("use.knitr"))
command <- splitCmd(command)
if (getRcmdr("log.commands")) {
last2 <- tclvalue(tkget(.log, "end -2 chars", "end"))
if (last2 != "\n\n") tkinsert(.log, "end", "\n")
tkinsert(.log, "end", paste(command,"\n", sep=""))
tkyview.moveto(.log, 1)
if (Rmd){
if (getRcmdr("use.markdown")){
if (getRcmdr("startNewCommandBlock")){
beginRmdBlock()
tkinsert(.rmd, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rmd, 1)
putRcmdr("markdown.output", TRUE)
if (.markdown.editor.open){
tkinsert(.markdown.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.markdown.editor, 1)
}
endRmdBlock()
}
else{
tkinsert(.rmd, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rmd, 1)
putRcmdr("markdown.output", TRUE)
putRcmdr("rmd.generated", TRUE)
if (.markdown.editor.open){
tkinsert(.markdown.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.markdown.editor, 1)
}
}
if (getRcmdr("command.sections")){
command.name <- findCommandName(command)
if(!is.na(command.name)){
insertRmdSection(command.name)
}
}
}
if (getRcmdr("use.knitr")){
if (getRcmdr("startNewKnitrCommandBlock")){
beginRnwBlock()
tkinsert(.rnw, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rnw, 1)
putRcmdr("knitr.output", TRUE)
if (.knitr.editor.open){
tkinsert(.knitr.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.knitr.editor, 1)
}
endRnwBlock()
}
else{
tkinsert(.rnw, "end", paste(command, "\n", sep=""))
tkyview.moveto(.rnw, 1)
putRcmdr("knitr.output", TRUE)
putRcmdr("rnw.generated", TRUE)
if (.knitr.editor.open){
tkinsert(.knitr.editor, "end", paste(command, "\n", sep=""))
tkyview.moveto(.knitr.editor, 1)
}
}
}
}
}
lines <- strsplit(command, "\n")[[1]]
tkinsert(.output, "end", "\n")
if (getRcmdr("console.output")) {
for (line in seq(along.with=lines)) {
prompt <- ifelse (line==1, paste("\n", getRcmdr("prefixes")[1], sep=""), paste("\n", getRcmdr("prefixes")[2], sep=""))
cat(paste(prompt, lines[line]))
}
cat("\n")
}
else {
for (line in seq(along.with=lines)) {
prompt <- ifelse(line==1, "> ", "+ ")
tkinsert(.output, "end", paste(prompt, lines[line], "\n", sep=""))
tktag.add(.output, "currentLine", "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.output, "currentLine", foreground=getRcmdr("command.text.color"))
tkyview.moveto(.output, 1)
}
}
command
}
justDoIt <- function(command) {
command <- enc2native(command)
Message()
if (!getRcmdr("suppress.X11.warnings")){
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
on.exit({
sink(type="message")
close(messages.connection)
})
}
else messages.connection <- getRcmdr("messages.connection")
capture.output(result <- try(eval(parse(text=command), envir=.GlobalEnv), silent=TRUE))
if (class(result)[1] == "try-error"){
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
tkfocus(CommanderWindow())
return(result)
}
checkWarnings(readLines(messages.connection))
if (getRcmdr("RStudio")) Sys.sleep(0)
result
}
# execute commands, save commands and output
doItAndPrint <- function(command, log=TRUE, rmd=log) {
command <- enc2native(command)
Message()
.console.output <- getRcmdr("console.output")
.output <- OutputWindow()
if (!.console.output) {
width <- (as.numeric(tkwinfo("width", .output)) - 2*as.numeric(tkcget(.output, borderwidth=NULL)) - 2)/
as.numeric(tkfont.measure(tkcget(.output, font=NULL), "0"))
eval(parse(text=paste("options(width=", floor(width), ")", sep="")))
}
if (!getRcmdr("suppress.X11.warnings")){
messages.connection <- file(open="w+")
sink(messages.connection, type="message")
on.exit({
sink(type="message")
close(messages.connection)
})
}
else messages.connection <- getRcmdr("messages.connection")
output.connection <- file(open="w+")
sink(output.connection, type="output")
on.exit({
if (!.console.output) sink(type="output") # if .console.output, output connection already closed
close(output.connection)
}, add=TRUE)
if (log) logger(command, rmd=rmd)
else {
pushCommand(command)
if (rmd) {
if (getRcmdr("use.markdown")) enterMarkdown(command)
if (getRcmdr("use.knitr")) enterKnitr(command)
}
}
result <- try(parse(text=paste(command)), silent=TRUE)
if (class(result)[1] == "try-error"){
if (rmd) {
if (getRcmdr("use.markdown")) {
removeLastRmdBlock()
putRcmdr("startNewCommandBlock", TRUE)
}
if (getRcmdr("use.knitr")) {
removeLastRnwBlock()
putRcmdr("startNewKnitrCommandBlock", TRUE)
}
}
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
if (.console.output) sink(type="output")
tkfocus(CommanderWindow())
return(result)
} else {
exprs <- result
result <- NULL
}
for (i in seq_along(exprs)) {
ei <- exprs[i]
tcl("update")
result <- try(withVisible(eval(ei, envir=.GlobalEnv)), silent=TRUE)
if (class(result)[1] == "try-error"){
if (rmd) {
if (getRcmdr("use.markdown")) {
removeLastRmdBlock()
putRcmdr("startNewCommandBlock", TRUE)
}
if (getRcmdr("use.knitr")) {
removeLastRnwBlock()
putRcmdr("startNewKnitrCommandBlock", TRUE)
}
}
Message(message=paste(strsplit(result, ":")[[1]][2]), type="error")
if (.console.output) sink(type="output")
tkfocus(CommanderWindow())
return(result)
}
result <- if (result$visible == FALSE) NULL else result$value
if (!is.null(result)) pushOutput(result)
if (isS4object(result)) show(result) else print(result)
.Output <- readLines(output.connection)
if (length(.Output) > 0 && .Output[length(.Output)] == "NULL")
.Output <- .Output[-length(.Output)] # suppress "NULL" line at end of output
if (length(.Output) != 0) { # is there output to print?
if (.console.output) {
out <- .Output
sink(type="output")
for (line in out) cat(paste(line, "\n", sep=""))
}
else{
for (line in .Output) tkinsert(.output, "end", paste(line, "\n", sep=""))
tkyview.moveto(.output, 1)
}
}
else if (.console.output) sink(type="output")
if (RExcelSupported()) # added by Erich Neuwirth
putRExcel(".rexcel.last.output",.Output)
# errors already intercepted, display any warnings
checkWarnings(readLines(messages.connection))
}
if (getRcmdr("RStudio")) Sys.sleep(0)
result
}
checkWarnings <- function(messages){
if (getRcmdr("suppress.X11.warnings")){
X11.warning <- grep("X11 protocol error|Warning in structure", messages)
if (length(X11.warning) > 0){
messages <- messages[-X11.warning]
}
if (length(messages) == 0) Message()
else if (length(messages) > 10) {
messages <- c(paste(length(messages), "warnings."),
gettextRcmdr("First and last 5 warnings:"),
head(messages,5), ". . .", tail(messages, 5))
Message(message=paste(messages, collapse="\n"), type="warning")
}
else {
if (length(grep("warning", messages, ignore.case=TRUE)) > 0)
Message(message=paste(messages, collapse="\n"), type="warning")
else Message(message=paste(messages, collapse="\n"), type="note")
}
}
else{
if (length(messages) == 0) Message()
else if (length(messages) > 10){
messages <- c(paste(length(messages), "warnings."),
gettextRcmdr("First and last 5 warnings:"),
head(messages, 5), ". . .", tail(messages, 5))
Message(message=paste(messages, collapse="\n"), type="warning")
}
else {
if (length(grep("warning", messages, ignore.case=TRUE)) > 0)
Message(message=paste(messages, collapse="\n"), type="warning")
else Message(message=paste(messages, collapse="\n"), type="note")
}
}
tkfocus(CommanderWindow())
}
pause <- function(seconds = 1){
if (seconds <= 0) stop("seconds must be positive")
start <- proc.time()[3]
while (as.numeric(elapsed <- (proc.time()[3] - start)) < seconds) {}
elapsed
}
Message <- function(message, type=c("note", "error", "warning")){
tcl("update")
.message <- MessagesWindow()
type <- match.arg(type)
if (type != "note") tkbell()
if (getRcmdr("retain.messages")) {
if (missing(message) && !is.null(getRcmdr("last.message"))) {
putRcmdr("last.message", NULL)
tkyview.moveto(.message, 1.0)
}
}
else if (type == "note"){
lastMessage <- tclvalue(tkget(MessagesWindow(), "end - 2 lines", "end"))
if (length(c(grep(gettextRcmdr("ERROR:"), lastMessage), grep(gettextRcmdr("WARNING:"), lastMessage))) == 0)
tkdelete(.message, "1.0", "end")
}
else tkdelete(.message, "1.0", "end")
col <- if (type == "error") getRcmdr("error.text.color")
else if (type == "warning") getRcmdr("warning.text.color")
else getRcmdr("output.text.color")
prefix <- switch(type, error=gettextRcmdr("ERROR"), warning=gettextRcmdr("WARNING"), note=gettextRcmdr("NOTE"))
if (missing(message)){
return()
}
putRcmdr("last.message", type)
message <- paste(prefix, ": ", message, sep="")
if (getRcmdr("retain.messages") && getRcmdr("number.messages")) {
messageNumber <- getRcmdr("messageNumber") + 1
putRcmdr("messageNumber", messageNumber)
message <- paste("[", messageNumber, "] ", message, sep="")
}
if (RExcelSupported()) # added by Erich Neuwirth
putRExcel(".rexcel.last.message",message)
lines <- strsplit(message, "\n")[[1]]
console.output <- getRcmdr("console.output")
if (!console.output){
width <- (as.numeric(tkwinfo("width", .message)) - 2*as.numeric(tkcget(.message, borderwidth=NULL)) - 2)/
as.numeric(tkfont.measure(tkcget(.message, font=NULL), "0"))
eval(parse(text=paste("options(width=", floor(width), ")", sep="")))
}
lines <- strwrap(lines)
if (console.output) {
if (sink.number() != 0) sink()
for (jline in seq(along.with=lines)) {
Header <- if (jline==1) getRcmdr("prefixes")[3] else getRcmdr("prefixes")[4]
cat(paste(Header, lines[jline], "\n", sep=""))
}
}
else
for (line in lines){
tagName <- messageTag()
tkinsert(.message, "end", paste(line, "\n", sep=""))
tktag.add(.message, tagName, "end - 2 lines linestart", "end - 2 lines lineend")
tktag.configure(.message, tagName, foreground=col)
tkyview.moveto(.message, 1.0)
}
}
messageTag <- function(reset=FALSE){
if (reset){
putRcmdr("tagNumber", 0)
return()
}
tagNumber <- getRcmdr("tagNumber") + 1
putRcmdr("tagNumber", tagNumber)
paste("message", tagNumber, sep="")
}
pushOutput <- function(element) {
stack <- getRcmdr("outputStack")
stack <- c(list(element), stack[-getRcmdr("length.output.stack")])
putRcmdr("outputStack", stack)
}
popOutput <- function(keep=FALSE){
stack <- getRcmdr("outputStack")
lastOutput <- stack[[1]]
if (!keep) putRcmdr("outputStack", c(stack[-1], NA))
lastOutput
}
pushCommand <- function(element) {
stack <- getRcmdr("commandStack")
stack <- c(list(element), stack[-getRcmdr("length.command.stack")])
putRcmdr("commandStack", stack)
}
popCommand <- function(keep=FALSE){
stack <- getRcmdr("commandStack")
lastCommand <- stack[[1]]
if (!keep) putRcmdr("commandStack", c(stack[-1], NA))
lastCommand
}
# handle model capabilities
mergeCapabilities <- function(allCapabilities){
allCapabilities <- allCapabilities[!sapply(allCapabilities, is.null)]
allrows <- unlist(lapply(allCapabilities, rownames))
if (length(allrows) > length(unique(allrows)))
stop(gettextRcmdr("redundant model class or classes in plug-in package model capabilities table"))
capabilities <- lapply(allCapabilities, names)
all <- unique(unlist(capabilities))
for (i in 1:length(allCapabilities)) allCapabilities[[i]][, setdiff(all, capabilities[[i]])] <- FALSE
do.call(rbind, allCapabilities)
}
# optionally open graphics device(s)
openGraphicsDevices <- function(){
if (!getRcmdr("open.graphics.devices")) return()
dev.new()
if (getRcmdr("use.rgl")) {
Library("rgl")
if (requireNamespace("rgl")) rgl::open3d()
}
}
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