macintosh

R for Macintosh DOC/FAQR for Macintosh FAQ/DOCVersion for R 1.6.0S. M. IacusChanges and bug fixing specific to this version:new scripts to build packages: makeAdd, makeRcmd, makeBioall the makefiles have been moved to src/macintosh/makefilesfolderimplemented the Quartz device (when running under OSX only)brand new worskspace browser, see Tools menuadded and/or fixed internally mkdir and rmdir. Nowunlink(), dir.create() etc work correctlyhtml help handled via applescript. More stable andalmost browser independentimproved applescript supportimplemented browseURLimplemented tempdir and tempfile according to Unix/WindowsbehaviourDate arithmetic fails (PR#1819). This bug have been partiallyfixed. Arithmetic is fine now but there is still a problem with the TZ (Time Zone) settings.fixed a bug in Locator of Macintosh device. Now it is possibleto interrupt it.From this version WasteLib 2.1x is requiredrmac-FAQ.htmlThis is the ReadMe file of R for Macintosh Application.We discuss here the following topics:* NEWS* THE GUI* APPLE SCRIPT SUPPORT* EXTERNAL EDITOR INTERACTION* MEMORY* SPECIFYING OPTIONS: the Preferences pane* SPECIFYING ENVIRONMENT VARIABLES: the .Renviron file* THE USER MENU* R HELPERS* SYSTEM REQUIREMENTS* KNOWN BUGS* SHORT FAQ (in the MAC-FAQ)* REMERCIEMENTESNEWSThere are several enanchements in this release. Most of them concernthe user interface of R application but one of the most important noveltyis that nowR runs both on MacOS and MacOS X using Carbon technology. This meansthat when you run R from MacOS X it run natively under the new System withoutcalling the Classic Compatibility Module. The use of R under MacOS X takeslots of advantages starting from the new Aqua look.As this version is based on the new Carbon technology some new bugscan appear that we were'nt able to found before releasing R officially.Any feedback is then welcome at stefano.iacus@unimi.itTHE NEW GUISeveral menus are now present from this release. The structure of themenus is as follows with a brief description.Menu ItemShortcutBrief descriptionApple (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 paneFileNew 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 newmacintosh() device will be opened.Edit ObjectE Is the equivalent of "edit(object)"Source FileOOpens a file and sources it. This is equivalent to "source(file)"Open File For EditingOpens a file in an editable window.Useful when you want to modify an existing script and test it.File Show FOpen a file in a non editable window. This isthe equivalent ofR command "show.file(file)"Load Workspace FileL If you want to load a wspace image otherthan ".RData"Save Workspace AsIf you want to save an image file other the ".RData"Page SetupCalls the printer driver page setupPrint PPrint the text window (R Console etc) or the imagein the graphic devicewindow. The image is rescaled to the page dimension of yourprinter.SaveSSave the window. This could be the content ofthe R Console i.e. yourcurrent 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. yourcurrent R session any text window or the graphicdevice window. This menuacts as a standard "Save As" menu so you have to specify each time thefilename.Close W Closes the current window. If it is the R Consolewindow than it is interpreted as quitting R.QuitQThis menu item is on the Application Menu under MacOS XEditUndoZCutXCopyC If you use it on a graphic device window theimage is copied to the clipboard (see also knownbugs)Paste VCopy & PasteYou copy some text and the resultis pasted into the R Consolewindow. You use thiswhen you select a piece of R code of text windowand then you want to R to execute it. This isquite useful when you want to test part of your scriptof the examples of an help windowClearSelect AllAGoto lineActive only for editable windows. It moves thecursor toa certain lineToolsShow WorkspaceIt is equivalent to "ls()"Clear WorkspaceIt is equivalent to "rm(list=ls())"Browse WorkspaceIt is equivalent to "browseEnv(html=FALSE)"Load WorkspaceLoads the ".RData" file; equivalent to load(".RData")Save WorkspaceSave the workspace to ".RData"; equivalent to "save.image()"Load HistoryIt is equivalent to "loadhistory()"Save History It is equivalent to "savehistory()"Show History It is equivalent to "history()"Change Working DirectoryD Allows the user to change the workingdirectory by using a standarddialogShow Working DirectoryIt 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()"WindowsR ConsoleThis menu contains by default only the "R Console" itemand it is dynamically changed by appending/removing thenames of any new/closed windowConfigAllow InterruptIt is equivalent to set the option "Interrupt=TRUE" in the .Renvironment config file but this can be changed at runtime.This menu is syncronizedwith the option you select in the Preference pane.On Open SourceIt 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 syncronizedwith the option you select in the Preference pane.Preferences (under Mac OS only)Opens the R Preferences paneHelpR Help? It is equivalent to "help.start()"Help On TopicOpens a dialog where the user can specify an item he orshe wants to see. equivalent to "help(topic)" or"?topic"Search Help On Opens a dialog where the user can specify an argument tohave 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 shewants to run anexample of. It is equivalentto "example(topic)".Link Packages HelpAfter 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 fontused.For non fixed fonts the algorithm can fail so the window can resulta bit larger or smaller then needed.R windows are opened in cascade for each class (edit windows, fileshow windows and graphic windows). This functionality does not work onMacOS X yet.APPLE SCRIPT SUPPORTFrom 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 ofapplescript that interacts with R.set CommandLine to "R.Version()"trytell application "R" activate with timeout of 90000 seconds cmd CommandLine cmd "Sys.getenv()" end timeout end tellend tryWhere 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 , 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. EXTERNAL EDITOR INTERACTIONFrom release 7.4.1 of the famous Alpha editor, there is a (tcl) modecalled 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 menubar the "S+/R" menu. Of this menu you can use "Process File" or "ProcessSelection" to interact with R. By default Alpha sends an `open' commandto R and by default R opens a file in a non editable window (equivalentto the `File Show' menu). If you want R to source a file you should modifyactivate the option "OnOpenSource" thatis set by default to "FALSE". You can changethis 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/MEMORYUnder 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 ofmemory if for some reason R went out of memory. To do this, go to the Finderand select the R aplication icon. Then with CMD+I key obtain the Informationfor R. Select "Memory" and the fix the amount of memory you need. UnderMacOS X, there is no need to reserve memory to R. R will use as muchmemory as it needs.SPECIFYING OPTIONS: the Preferences paneThe 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 thepreferences.If you have different logins under OS X, remember that each user should set its own preferences.SPECIFYING ENVIRONMENT VARIABLES: the .Renviron fileIn this file you can specify some of options or environment variables. This is not standardfor 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 theenviroment 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 separateline 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 beginningof a line means that this is a commented out line.You can find more details on that in the .Renviron file itself.THE NEW USER MENUThe 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 anyitem 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 numberget.num.cmd(menunum)returns the R Command associated to menu item number "menunum" and the corresponding menu labeldel.menu.cmd("label")removes the menu item "label" from the User menudel.num.cmd(menunum)removes the menu item numbered "menunum" from the User menudel.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"R HELPERS* If you want to use an external editor we suggest you to use Alphaversion 7.4.1 or newer that contains a S+/R mode. Alpha home pageis located at http://www.kelehers.org/alpha/.SYSTEM REQUIREMENTSTo run the R application you need at least 42MB of free memory for theapplication itself you work under MacOS but there is no limitations underMacOS 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. KNOWN BUGSThis 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.SHORT FAQ (in the MAC-FAQ)QHow can I manage invisible files under MacOS X ?AUnder Unix it is typical that invisible files are files starting with a "." (dot) in the filename. MacOS X conforms to this convention. So it could happen that your preferred editor doesn't allow you to open and or write files like .Rprofile or .Renviron under MacOS X (this is the case of BBedit as reported by one user). You have several options: one of this is toa file like "some_file" with your editor or R, and then use the system() commandto change its name as follows system("mv some_file .some_file"). Then usesystem("ls -al") to see if all went right. QOn exit: Why I can't save the workspace image via file dialog under MacOS X ?AAs before, files starting with a dot, such as ".RData" cannot be manageddirectly via standard dialogs (you can see invisible files but you can't specify them as filenames !)To save the workspace image, youcan either save it with a different name (e.g. "RData", but in thisthe workspace image will not be reloaded the next you start R), or yousave it beofre quitting R: type "save.image()" from the R Console and then "q()" replying "n" when R asks for "Save workspace image? [y/n/c]:".QHow can I work on a separate directory for each of my projects?AUnder Unix you usually create a directory, go into it and launch R. Under MacOS you can create a directory and put all the files that you needthere. You then (or before) run R in its own directory and use themenu item "Tools->Change Working Directory" to change the currentworking directory to directory you have created. You can then workas you do in Unix. You can save/load workspace image to this directory,as well as the command history files. You can then reload these nexttime you work.QHow can I interrupt lengthy operations or output ?AYou can now use the standard Macintosh control break sequence, that is you should press "Cmd option" and "." (dot). This will interrupt any R loops. The "Esc" key gives you the same result.QHow can I change memory settings for R ? (MacOS pre X only)AYou cannot use the standard settings as on other platforms. You should assign memory to R from the Finder/Information dialog for R application. See Section "Memory" above.QWhen I use to send R output to a file like "my_file", R seems to work on this file butI cannot find it. What happened ? (MacOS X only)AOn MacOS X it is important to specify correctly the file names. If you want the file to be created in your current working directory you have toput a ":" before file name, such as ":myfile" otherwise the file will be createdas "/my_file", i.e. in the root "/" directory. This is in particular important when you specify directories relative to your current workingdirectory.REMERCIEMENTSI would like to thank among the others (only few I can remember due to my brain volatility...) some of the peoplewho have contantly sent me feedback on this Macintosh port of R or simply suggetested me some possibiledirections. So, merci, in random order, to P. Macdonald, P. Flint, R. Gill, K. Pflugshaupt, J. DeLeeuw, G. Sawitzki and half of the R-Core.Last edited 2002 Sep 7th, Stefano M. 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