R for Macintosh FAQ/DOC

Version for R 1.3.1

Changes specific to this version:

Added the "Config" menu

Fixed a bug in the lapack module. Complex functions are now available.

Added MPW makefiles to build standard libraries and modules

Added experimental script to build R via Apple's MRC compiler

Now R needs a new shared library "f2cLib" that will increase portability for all fortran based packages

Added support for apple events. R begins to be a scriptable application. Very limited support by now but will increase soon. Some demo scripts have been added.

link.html.help() function has been added by picking windows code.

* NEWS
* THE NEW GUI
* EXTERNAL EDITOR INTERACTION
* MEMORY
* SPECIFING OPTIONS: the .Renviron file
* R HELPERS
* SYSTEM REQUIREMENTS
* FIXED BUGS
* KNOWN BUGS
* SHORT FAQ

NEWS
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
 
 

THE NEW GUI
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
	About R		Opens the R information dialog
File
	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 Apple Menu under OSX
Edit
	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
	Clear
	Select All	A
	Goto line		Active only for editable windows. It moves thecursor  to a certain line
Tools
	Show Workspace		It is equivalent to  "ls()"
	Clear Workspace		It is equivalent to "rm(list=ls())"
	Load Workspace		Loads the ".RData" file; equivalentto     load(".RData")
	Save Workspace		Save the workspace to ".RData"; equivalentto "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()"
Windows
	R Console		This menu contains by default only the "R Console" item and it is dynamically    changed by appending/removingthe names      of any new/closed window
Config
	Allow Interrupt		It is equivalent to set the option "Interrupt=TRUE" in the .Renvironment config file but this can be changed at runtime.
	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.
Help
	R Help	?	It is equivalent to "help.start()"
	Help On Topic		Opens a dialog where the user canspecify an item he or she wants to see.     Equivalentto "help(topic)" or "?topic"
	Search Help On		Opens a dialog where the user can  specifyan argument to have help on. It     is equivalent to"help.search("topic")"
	Run An Example		Opens a dialog where the user can specifyan item of which he or she wants to run      anexample of. It is equivalent to "example(topic)".

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.
 

EXTERNAL EDITOR INTERACTION
From release 7.4.1 of the famous Alpha editor, there is a (tcl) mode called S+/R.
When you open a file in Apha 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 the .Renviron file accordingly (see below). In particular, the option “OnOpenSource” is set by default to "FALSE". You should set it to "TRUE". You can change this when R is still running by simply editing the .Renviron file. Use "Open File For Editing" from the "File" menu and select the file ".Renviron". Find the keyword "OnOpenSource" and set it to "TRUE" (i.e. OnOpneSource=TRUE). The latest version of Alpha can be found at http://www.alpha.olm.net

MEMORY
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 memeory you need. Under MacOS X, there is no need to reserve memory for R. R will used as much memory as it needs.

SPECIFING OPTIONS: the .Renviron file
In this file you can specify some of the options. This is not standard for general MacOS/X applications because it currently repleaces the Preferences one should expect. But, as we have not yet decided which and what number of preferences items the user can specify, for the time being this is the only flexible way to take care of user options.
The environment file is used by R application both to simulate the enviroment on a standard Unix or Windows system and both to set user options.
You can always use "Sys.getenv()" to see which options are enabled/set.
In this file you can specify font names for the R Console and for the graphic device as well as their sizes. 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.

Here are the options you can specify:

Lenght of the history size:
---------------------------

# The history size
# Default: RHISTSIZE=512
RHISTSIZE=512

R behaviour when R application receive a "break" event:
-------------------------------------------------------

# R can handle user breaks to
# interrupt lengthy calculations
# or output. As this code is not
# yet optimized, by default R
# does not accept user breaks.
# If the "Interrupt" switch
# is set to TRUE then R intercept
# user breaks. With this swtich on
# R is a bit slower than with the
# switch off
# Default: Interrupt=FALSE
 
This can be changed at runtime also via the Config menu.

R behaviour when R application receive an "open" event:
-------------------------------------------------------

# Wheter to show or source a file
# You should set this to TRUE if you
# want Alpha  be your external editor
# Default: OnOpenSource=FALSE
OnOpenSource=FALSE

This means that when you drag a file on top of the R icon or you submit something from an external editor, R application simply open it (FALSE) or sources it (TRUE). If the file is a worspace image file, then R loads that workspace. This can be changed at runtime also via the Config menu.
 

Tab size of text windows:
-------------------------

# The Tab size to use in text windows
# range [1,20]
# Default: TabSize=5
TabSize=5

Setting the text size of text and R Console windows:
----------------------------------------------------

# TextSize to be used in text windows
# range [8,14]
# Default: TextSize=12
TextSize=12

Macintosh device resolution:
----------------------------

# ScreenRes
# Useful values is only 72. Possibile other values
# are 144, 300, 600 but you should not use them unless
# you know exactly what you are doing ! So, please,
# don't change this parameter.
# Default: ScreenRes=72
ScreenRes=72

Name of the font for the R Console or text windows:
---------------------------------------------------

# FontName: this is the font used in text windows.
# There are several possibilities for this.
# You can specify any font you like but you should
# prefere a monospaced font. If the Monaco will be used instead.
# Font names are not case sensitive i.e.
# FontName=monaco and FontName=MoNacO are the same.
# If your font name includes spaces you should provide them
# without using quotes, i.e.
# FontName=Times New Roman
# Default: FontName=monaco
FontName=monaco

Name of the font for the Macintosh graphic device:
--------------------------------------------------

# GraphFontName: this font is used for graphic windows.
# There are several possibilities for this.
# If the font is not usable by R application, then
# the font Helvetica will be used instead.
# Font names are not case sensitive i.e.
# FontName=monaco and FontName=MoNacO are the same.
# If your font name includes spaces you should provide them
# without including quotes, i.e.
# FontName=Times New Roman
# Default: GraphFontName=helvetica
GraphFontName=helvetica
 
 

R HELPERS
* 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
 http://www.alpha.olm.net
* You also need MacZip to use the unzip feature of R. MacZip home page is
 http://ww.sitec.net/maczip
 
 

SYSTEM REQUIREMENTS

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 1.2.5 is the current non developer release. Normally it is included in System 9.1 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 no longer need the WasteLib library.

FIXED BUGS
This version has several bugs fixed. Mostly GUI incongruencies and problems have been resolved and few R internal numerical bugs. You have signalled a bug but this has not yet been fixed, please "don't give up" but send us again your feedback (stefano.iacus@unimi.it)
 

• There was an annoying bug concerning the edit menus that on some  (almost random) situations was disabled by R so no cut&paste was  then possible.
• Edit object on non existent R obejct produced a grabbled edit  window.
• Herhey fonts where not displayed correctly or at all unless the  user clicked on the graphic window rotated fonts where cutted on top
• Numerical problems with gamma function and polyroot. Now R pass  the tests
• Windows menus produced in some situations some strange
• The graphic device has been completely rewritten now it is  faster and resizing of windows is handled correctly.
• Copying to the clipboard images will non longer produce graphic  titles/texts printed twice.

KNOWN BUGS
 

•  In some situations R stops execution giving an error like this:

• On MacOS X  copying to the clipboard an image or saving it in a file  produces a picture without text in it. This problem is (probably) due to the fact that the fonts we use are saved as polygons/vectors and not  as images.
• From version 1.2.2, at startup time you can run scripts by selecting  input and output file and options (this is usefule when you want to run tests/checks). Both under MacOS and MacOS X you cannot choose a file  that is outside the directory where the R application is. This problem is not due to the R application but to a bug in Sioux Interface provided  by the compiler. This problem will be fixed with the next release of the compiler.
• For some reason MacZip does not intercat too much with R under MacOS X.  Moreover MacZip has not yet been “carbonized” so when R calls it to  uncompress items it also starts up Classic Environment. We suggest to  uncompress the help and examples files directly by using Stuffit Expander  that is part of the utilities provided with System X.
• This version of R and Adobe ATM are incompatible. We are looking at the problem. The solution is that you should switch ATM off before running R. (Thanks to R. Gill for feedback on this bug)
• Internet functionality is not available yet. We are working on this.
• Mathematical expressions are not yet well spaced moreover, mathemathic symbols are not rotated.