R for Macintosh FAQ/DOC

Version for R 1.6.0

S. M. Iacus

Changes and bug fixing specific to this version:


This is the ReadMe file of R for Macintosh Application.

We discuss here the following topics:

* SPECIFYING OPTIONS: the Preferences pane
* SHORT FAQ (in the MAC-FAQ)

There are several enanchements in this release. Most of them concern the user interface of R application but one of the most important novelty is that now
R runs both on MacOS and MacOS X using Carbon technology. This means that when you run R from MacOS X it run natively under the new System without calling the Classic Compatibility Module. The use of R under MacOS X takes lots of advantages starting from the new Aqua look.

As this version is based on the new Carbon technology some new bugs can appear that we were'nt able to found before releasing R officially.

Any feedback is then welcome at stefano.iacus@unimi.it

Several menus are now present from this release. The structure of the menus is as follows with a brief description.
Menu Item Shortcut Brief description
Apple (or Application Menu under MacOS X)
About R Opens the R information dialog. Reports release informations.
Preferences (under OS X only, see the Config menu for pre X Systems) Opens the R Preferences pane
New Edit Window N Opens an empty editable window. You can usethis as an internal editor for R. If the current active window isa graphic device window than a new macintosh() device will be opened.
Edit Object E Is the equivalent of "edit(object)"
Source File O Opens a file and sources it. This is equivalent to "source(file)"
Open File For Editing Opens a file in an editable window.Useful when you want to modify an existing script and test it.
File Show F Open a file in a non editable window. This isthe equivalent of R command "show.file(file)"
Load Workspace File L If you want to load a wspace image otherthan ".RData"
Save Workspace As If you want to save an image file other the ".RData"
Page Setup Calls the printer driver page setup
Print P Print the text window (R Console etc) or the imagein the graphic device window. The image is rescaled to the page dimension of your printer.
Save S Save the window. This could be the content ofthe R Console i.e. your current R session any text window or the graphic device window.
Save As... Save the window. This could be the content ofthe R Console i.e. your current R session any text window or the graphicdevice window. This menu acts as a standard "Save As" menu so you have to specify each time the filename.
Close W Closes the current window. If it is the R Console window than it is interpreted as quitting R.
Quit Q This menu item is on the Application Menu under MacOS X
Undo Z
Cut X
Copy C If you use it on a graphic device window theimage is copied to the clipboard (see also knownbugs)
Paste V
Copy & Paste You copy some text and the resultis pasted into the R Console window. You use thiswhen you select a piece of R code of text windowand then you want to R to execute it. This is quite useful when you want to test part of your script of the examples of an help window
Select All A
Goto line Active only for editable windows. It moves thecursor to a certain line
Show Workspace It is equivalent to "ls()"
Clear Workspace It is equivalent to "rm(list=ls())"
Browse Workspace It is equivalent to "browseEnv(html=FALSE)"
Load Workspace Loads the ".RData" file; equivalent to load(".RData")
Save Workspace Save the workspace to ".RData"; equivalent to "save.image()"
Load History It is equivalent to "loadhistory()"
Save History It is equivalent to "savehistory()"
Show History It is equivalent to "history()"
Change Working Directory D Allows the user to change the workingdirectory by using a standard dialog
Show Working Directory It is equivalent to "getwd()"
Reset Working Directory It is equivalent to "setwd(R.home())"
Show Libraries It is equivalent to "library()"
Show DataSets It is equivalent to "data()"
R Console This menu contains by default only the "R Console" item and it is dynamically changed by appending/removing the names of any new/closed window
Allow Interrupt It is equivalent to set the option "Interrupt=TRUE" in the .Renvironment config file but this can be changed at runtime. This menu is syncronized with the option you select in the Preference pane.
On Open Source It is equivalent to set the option "OnOpenSource=TRUE" in the .Renvironment config file but this can be changed at runtime. Useful to work with external editor such as Alpha. This menu is syncronized with the option you select in the Preference pane.
Preferences (under Mac OS only) Opens the R Preferences pane
R Help ? It is equivalent to "help.start()"
Help On Topic Opens a dialog where the user can specify an item he or she wants to see. equivalent to "help(topic)" or "?topic"
Search Help On Opens a dialog where the user can specify an argument to have help on. It is equivalent to"help.search("topic")"
Run An Example Opens a dialog where the user can specify an item of which he or she wants to run anexample of. It is equivalent to "example(topic)".
Link Packages Help After installing a new package you need to link help files database.

About R windows.
Normally R opens windows to let 80 character/columns to be displayed. The size of the windows is calculated on the basis of the size of the font used.
For non fixed fonts the algorithm can fail so the window can result a bit larger or smaller then needed.
R windows are opened in cascade for each class (edit windows, file show windows and graphic windows). This functionality does not work on MacOS X yet.

From release 1.3.1 R has partial support for AppleScripts. This means two things: you can run applescripts from inside R using the command applescript() (see the corresponing help) or you can ask R to run commands from and applescript. The directory "scripts" in the main R folder contains two examples of applescripts. What follows is an example of applescript that interacts with R.

set CommandLine to "R.Version()"
tell application "R"
   with timeout of 90000 seconds
    cmd CommandLine
    cmd "Sys.getenv()"
   end timeout
  end tell
end try

Where cmd is the applescript command in the R dictionary that is used to tell R to execute an R command in the R Console. The syntax is cmd <command string>, where command string have to be in quotes. Actually, the output of the command is not sent back to the application that is calling R but to the R Console.

From release 7.4.1 of the famous Alpha editor, there is a (tcl) mode called S+/R.
When you open a file in Alpha with the extension ".s" or ".r" this new mode will be installed and you will in the Alpha menu bar the "S+/R" menu. Of this menu you can use "Process File" or "Process Selection" to interact with R. By default Alpha sends an `open' command to R and by default R opens a file in a non editable window (equivalent to the `File Show' menu). If you want R to source a file you should modify activate the option "OnOpenSource" that is set by default to "FALSE". You can change this at runtime running via the Config/OnOpenSource menu or accessing the Preferences pane. The latest version of Alpha can be found at ftp://ftp.ucsd.edu/pub/alpha/

Under MacOS you should reserve a fixed amount of memory to each application. As R is just an application, you need to set this to a bigger amount of memory if for some reason R went out of memory. To do this, go to the Finder and select the R aplication icon. Then with CMD+I key obtain the Information for R. Select "Memory" and the fix the amount of memory you need. Under MacOS X, there is no need to reserve memory to R. R will use as much memory as it needs.

SPECIFYING OPTIONS: the Preferences pane
The Preferences pane allow you to configure a bit R GUI and behaviour. You can set the tab size in your edit windows, the font type and size of text windows and R Console as well as the colors of the text in R Console. You can also specify a particular font for the graphic device and the resolution of the graphic device. Finally you can specify if R should accept User breaks (CMD+. or Esc). If this option is enabled R is a bit slower. You can instruct R on what to do when a file is opened: source it or simply show in the internal viewer.

Take care that under MacOS R creates a file in the Preferences folder of you System Folder. If you switch to MacOS X than, this folder is no longer the default Preferences folder so you have either to move th "R preferences" file to "~user/Library/Preferences/" directory or reset the preferences. If you have different logins under OS X, remember that each user should set its own preferences.

In this file you can specify some of options or environment variables. This is not standard for general MacOS/X applications but has been implemented for compatibility reasons. If you don't need to set environment variables you can ignore what is in this file.
The environment file is used by R application both to simulate the enviroment on a standard Unix or Windows system.
You can always use "Sys.getenv()" to see which variables are set to some values.
The .Renviron file looks like this: an option is a "Rkey" with its "keyvalue" that you can specify in new separate line as follows RKey=keyvalue. Consider that RKey=keyvalue and RKey = keyvalue are different, that means that blanks/spaces are significant. "RKey" and "keyvalue" are case sensitive. A symbol "#" at the beginning of a line means that this is a commented out line.
You can find more details on that in the .Renviron file itself.

The user has now the ability to create a menu with several menuitems, up to 99, where to keep preferred R commands.
With the commands add.menu.cmd("label","R_command") the user adds a menuitem named "label" to the User menu. When the command is selected from the menu, R executes the command "Rcommand" associated to it. The User menu is created dynamically, so that user will never see it if he does not add any item to it.
Several functions to manipulate the user menu are previewed:

get.menu.cmd("label")returns the R Command associated to menu item "label" and the corresponding menu number
get.num.cmd(menunum)returns the R Command associated to menu item number "menunum" and the corresponding menu label
del.menu.cmd("label")removes the menu item "label" from the User menu
del.num.cmd(menunum)removes the menu item numbered "menunum" from the User menu
del.usr.cmd("label")removes the whole User's menu
add.menu.cmd("label","RCommand")adds a menu item to the User's menu, if any, with associated the R command "RCommand"

* If you want to use an external editor we suggest you to use Alpha version 7.4.1 or newer that contains a S+/R mode. Alpha home page is located at http://www.kelehers.org/alpha/.


To run the R application you need at least 42MB of free memory for the application itself you work under MacOS but there is no limitations under MacOS X as virtual memory is always on.
You need the latest version of the CarbonLib library from Apple. At the time of this release, version 1.4 is the current non developer release. Normally it is included in System 9.2 and X.
Now R needs the f2cLib shared library to run. This library is distributed with R but in case you miss it you can found it here.
The minimum System version release is 8.6 (+ CarbonLib library).
You need the WasteLib library. This library is distributed with R binaries.
You need the zlibLib library. This library is distributed with R binaries.