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R for Mac OS X FAQ

Frequently Asked Questions on R for Mac OS X

Version 3.1.1 2014-07-11, R.app 1.65

1 Introduction

This document contains a user guide to the R.app version of R, andinformation on using R on OS X which supplements the main Rmanuals. As from R 3.0.0 most of the information has been moved tothose manuals, the latest versions of which can be found athttp://cran.r-project.org/manuals.html.

In this document R refers to the core, command-line-based R systemwhile R.app refers to the GUI-based Mac OS application that controlsthe underlying R.

This `R for Mac OS X FAQ' is rather incomplete at the moment and requirescontributions from users. Anything specific to the R language can befound in the main R-FAQ (seehttp://cran.r-project.org/doc/FAQ/R-FAQ.html). Please send anyrequests/questions you would like answers to theR-SIG-Macmailing list (after subscribing) as well as comments on this FAQ.

The last section of this document contains the most frequently askedquestions that don't fit strictly into any of the categories above – itis usually a good idea to always look into that section if your issuedoesn't fit any of the above or was not answered in one of the specificsections. Always read this FAQ before asking for help onR-SIG-Mac!

1.1 How many versions of R for Mac OS X?

There is only one version of R for Mac OS X. However, R on Mac OS Xcan be used either on the command-line as on other Unix systems, or viathe R.app GUI (see R.app). The second approach is mostlypreferred by Macintosh users.

Prior to R 3.0.0 there were separate 32- and 64-bit version ofR.app: nowadays only 64-bit builds are supported in binary form.

1.2 What machines does R for Mac OS X run on?

64-bit Intel-based Macs, that is any machine made since mid 2008.

1.3 How can R for Mac OS X be obtained and installed?

R is available on CRAN in the form of an Installer packagecontaining the R framework and the R.app GUI. The package is usuallynamed R.pkg with an optional version number.

The installation is done by double-clicking on the Installerpackage. The Installer will guide you through the necessary steps. Notethat it will require password or login of an account with administratorprivileges. The installation can be customized, but the default issuitable for most users.

Snapshots of the R-patched and R-devel flavours are available athttp://r.research.att.com/, packaged in the same way.

Further details, including uninstallation and building R from thesources, are in the `R Installation and Administration Manual'.

2 R.app

R.app is the name of the GUI for Mac OS X that was introduced in R2.0.0. It appears as an icon labeled R, but to avoid confusionwith general R, we prefer to use the name as it appears when usingGet Info on the GUI: R.app This stands for Rapplication.

Internally R.app is a Cocoa program (hence written in Objective C)which links to embedded R installed as a framework.

2.1 How to get R.app

R.app is part of the binary distribution of R for Mac OS X availablefrom CRAN. That distribution consists of one package containing the Rframework and R.app.

Development versions of R.app are made available on daily basis in theform of a disk image containing the R.app itself. See the Mac OS Xpages on CRAN for detail how to obtain such snapshots (currently athttp://R.research.att.com/).

2.2 How to install the R.app

R.app is installed the same way as the R framework, namely usingbinary package provided on CRAN. The bin/macosx directory of aCRAN site contains a standard Apple installer package namedR.pkg (optionally containing the version number). Download anddouble-click the package icon.

Please, carefully read the note on the usage of tcltk and Fortran on the bin/macosx directory of a CRAN site.

2.3 The R Console

In this section you'll find general information on the R.app. For specific R tasks thatcan be done via the R.app using menus you should read below (see The Menus).

2.3.1 The Input and the Output

The current design of the R Console is to have a single frame for input (user) and output (R).

2.3.2 Copy and Paste

Copy and paste works in R as in any other Macintosh application.

If you want high resolution graphic exports, you can save the PDF format using the File/Save as menu item (see Quartz device). Or you can use supported formats in R through pdf(), jpeg() etc. (type ?capabilities to get more details).

2.3.3 The current and startup working directories

If not otherwise specified in the Preferences (see Preferences), or if the specified path is no longer available, then the default working directory at startup is the user home. The working directory can be changed using the setwd R command or using the Misc menu item Change working directory. Finally it is possible to use a specific directory for a single R session by dragging a folder onto the R.app icon. If R.app is not running, this will cause R.app to be started in the directory corresponding to the folder dragged. The same can be achieved on the command line – for example open -a R . causes R.app to be started using the current directory as the startup working directory.

This feature is useful if you want different startup procedures defined by the .Rprofile; you canedit a .Rprofile (containing you personal initialization R commands) in a particular directory and usethe Preferences (or any other method mentioned above) to change the startup directory. Next time you launch R.app the .Rprofile is read and executed by R at startup. This is the equivalent on Unix (or the command line) to launch R from different directories.

2.3.4 Resizing the R Console

When the R Console Window is resized, the R option width is set appropriately so that any futureoutput will fit the window size.

2.3.5 R Console text colors

Use the Preferences window to set the R Console text colors (see Preferences).

2.4 General Features

2.4.1 Editor

R.app provides an integrated editor for editing of R code. It sports a number of features designed to help developing code inside R. The probably most often used function is the ability to execute code directly from the editor by pressing <Command>-<Return>. Other features include syntax highlighting, brace-matching, code completion and function indexing.

2.4.2 Editor undo and line numbers

The editor supports undo/redo operations on an appropriate level of granularity (used tobe all or nothing). The editor has an optional facility to show line numbers. These help withlocating error messages. The editor also responds to the 'Go to Line' Edit menu function. Theassociated Preference Pane allows enabling/disabling of the line numbers, as well as setting linenumber gutter width (to fit larger line numbers) and text margin width.

2.4.3 Editor text completion

Completion of typed input (both file names and R code) in the editor is available through the Edit menu 'Complete' or by typing <Control>-<.> (same as is Xcode). It uses the same facilities as the console window (for compatibility the console responds to both <Tab> and <Control>-<.>).

2.4.4 Editor function list

The editor maintains a popup list of functions defined in the edited document. The list is available in the toolbar and is updated as you type. Selecting a function from that list causes the cursor to jump to the beginning of the function.

2.4.5 Editor syntax coloring

The editor supports syntax-highlighting for R code. It is possible to change the syntax highlighting colors using the Syntax Color Preference Pane (see below). Starting with R.app version 1.17 lazy syntax highlighting is used, which means that changes influencing the entire file (such as typing a single or double quote) no longer apply to the entire file, but only a few lines. This temporary state is usually recovered by closing the quote, but in some rare instances it may persist until a change is made to the first line of the offending quote. However, lazy highlighting brings huge speedup when editing large files.

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2.4.6 Editor (internal and external)

By default, the editor used is incorporated into R.app, the Mac OS X GUI for R. It is arelatively simple multi-document editor that supports the features listed above. Additionally,two powerful commands are available to source the file being edited in its entirety (Command-E)or to source the current selection to R (Command-Return). Using R's edit() function, allowsediting of R objects or files while R is kept waiting for the edit session to finish.

It is possible to 'redirect' all R requests to an external editor, which runsoutside R.app. In that case, it is not possible to keep R waiting if edit() is used. UsingAppleScript it is easy to implement Command-E and Command-Return like functionality.

2.4.7 Editor help

The editor contains a light-weight help system in form of a search filed placed inside the toolbar. It is possible to use either an exact or approximate search.

2.4.8 Drag & drop

Drag and drop of a directory on the R.app icon while R.app is notrunning will start R.app and set the working directory. By default.RData and the history file (default name .Rapp.history)are fetched from this working directory. If a file is dropped on theR.app icon while R.app is not running, R.app is started, the fileis either restored (if it is a saved workspace), sourced into R.app oropened in the selected editor. Whether the file is opened or sourced isspecified by a Preference setting in the StartUp Preference Pane.

Note: At this point opening a file in the editor before R.app is finishedloading will crash R.app.

While R.app is running, drag & drop of a directory updates the workingdirectory. Drag & drop of a file sources or opens the file in theselected editor. Double clicking on files bound to ('Open With ...') R,if R.app is not running, R.app is started and the file is sourced oropened in editor. If R.app is running, the file is opened in theeditor.

2.4.9 Help system

The Help screen allows a user to go back or forward to previous helppages. It is possible to print help pages. If a help topic is notfound, a pop-up window allows to exit the help search or expand thesearch to a fuzzy/approximate search.

2.4.10 History

R.app uses history files that are (superset) compatible with historyfiles created by R. Multiline support remains available from insideR.app. Multiline is particularly useful when using the<Command>-<Return> feature while editing an Rscript. Import and export allows storing and importing history fromfiles visible in the Mac OS Finder. Multiline is preserved. This can beset through the StartUp Preference Panel. Default number of kept historyentries is 250. A variety of history entry cleanup modes is possible. At a minimum it is suggested to select 'Cleanup history entries'. It'soptional to select removal of duplicate entries and strip comments.

Note: Command-line R stores history in a file usually called.Rhistory. It is suggested to use a different name for theR.app history file, and the default is .Rapp.history.

Note that the functions loadhistory(), savehistory() andhence history() are not currently supported in R.app.

2.4.11 Authentication and .libPaths

The official CRAN binaries come pre-packaged in such a way thatadministrator have sufficient privileges to update R and installpackages system-wide. However, the default Unix build requiresroot-authentication for package installation and other administrativetasks. As it is not feasible to run the GUI as root, we provide thepossibility to authenticate system commands issued from the GUI. Theauthentication requires an administrator login and causes all subsequentsystem commands to be executed as root. Use with care!

In order to allow non-administrators to maintain their own set ofpackages, R.app optionally adds ~/Library/R/x.y/library to the.libPaths (see start-up preferences, x.y denotes the Rversion without patch level). It is possible to use the PackageInstaller to install packages either globally (admin users only) or forthe current user only. (This is the same mechanism for personal librarydirectories described in the main R documentation, but with a locationspecific to CRAN-like builds of R on OS X.)

Note that user-local packages are only used when the correspondingpreference option is enabled. The default for admin users is to usesystem-wide directories, for non-admin users the personal librarydirectory will be used.

2.5 The Menus

2.5.1 Application Menu

The Application menu is the first one after the main Apple Menu: it islabelled R.

With this menu you can access three items: 1. the About box, which tellsyou which version of R is currently in use, 2. Check for updates, whichsearch on CRAN if a new version of the binary distribution of Rfor Mac OS X is available (you need an Internet connection), 3. you canaccess the Preferences (see Preferences).

2.5.2 File Menu

This menu provides standard functionalities. The open command is associated to the action Source R code, which means that you can select a file, which is a script, and it will be executedin R. This is a interface to the R source command source.

2.5.3 Misc Menu

Apart for standard functionalities, the only relevant item in this menuis Edit Object which is an interface to the Reditfunction.

2.5.4 Misc Menu

With this menu you can load and save the history of commands typed in the R Console or view what's currently inside. You can also change the current working directory, let R show you the current working directory or set it back to thestartup directory. From release 1.9.0 of R the current working directory is also shown on the main window bar.

2.5.5 Workspace Menu

Here you find self explanatory menu items for manage your workspace inR. You can either load and save the workspace also by specifying filename. All of these are interfaces to the load andsaveR commands. The only relevant item, which is specificto this GUI, is Browse workspace which invokes thebrowseEnv() function in R. This will open a window with asummary description of the objects in your workspace. Recursive objects(like lists, data.frame etc) can be expanded (one level only though).

2.5.6 Packages Menu

Using this menu you can have access to the list of packages anddata-sets installed on your system and to the ones on CRAN or on theBioconductor site.

With the first two menus you can load and detach packages andwheres CRAN uses binary packages. Only the CRAN build isguaranteed to be compatible with the package binaries on CRAN (orBioconductor).

10.10 Why is R.home() in the R framework not versioned?

In the command line version of R, R.home() always points to theResources directory symbolic link inside the R framework whichpoints to Versions/Current/Resource which is turn points to theactual home – a versioned directory such as for exampleVersions/3.0/Resources. This is how framework versioning worksin Mac OS X and is defined by Apple (seeFramework Anatomy).

The advantage of this setup is that it is possible to install multiple Rversions in parallel and they all will be fully functional as long asthe Current symbolic link points to the currently usedversion. There is even a small GUI utility RSwitch available fromthe R for Mac devel page that allowsyou to select the desired version. In addition, any applicationembedding R can choose to use a specific R version (in most cases) orany version. Note that R.app is compiled against a particular versionof R and it may crash if RSwitch is used to change the versionof R in use.

Although it is possible to set R_HOME directly to the versionedpath in the R shell scripts (and thus be able to run different versionin parallel without changing the symbolic link), there are severaldangers lurking there so we don't recommend it. One problem is thatbuilding packages from source won't work. The linker is always linkingagainst the current version of the framework and therefore only thecurrently active version of R can compile packages. Further, packagesmay have used the value of R.home() at install time and thus maynot work with incorrect setting. Finally, if such an R start scripthappens to get copied and the R version changes, it will stop working.

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10.11 R.app GUI crashes on startup!

If your R.app GUI crashes on startup, there are two common causes forthis: a saved workspace or a corrupted history file. (Another is amismatch between R.app and R if either has been updated orRSwitch has been used.)

Saved workspaces can contain commands that implicitly load packageswhich in turn can trigger bugs in packages or feed R with incorrectstarting values (especially if it was saved using another R). Tryremoving or renaming your workspace – it's called .RData. If youdid not change your startup settings, you can e.g. use

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to move it aside and load later manually for inspection using load('~/workspace.RData').

Second most common cause of crashes on startup is a history file thatwas not created using the R.app GUI. Again, move it aside to see ifthat's the issue: for the default file this could be done by

Although we are trying to recover from invalid history files, they canstill crash R.app due to issues in the internal handling of strings inMac OS X. We are currently working on preventing this issue.

If you did both of the above and R.app still crashes, please select`1' in the menu after the crash (if you get the crash menu in theconsole) and send us the resulting crash report (see see R.app Bugsabove).

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10.12 Why is the GUI not saving my history?

R.app will by default save the history in a .Rapp.history filewhereas command line R will use .Rhistory. So the savedhistory is only used in subsequent R.app sessions and not command-lineR, and conversely.

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Note that calling savehistory() in R.app does not currentlysave the history of the R.app session: this means thathistory() will show an empty window.

10.13 I get “command not found” in the GUI yet it works in the Terminal – why?

When executing system commands (for example directly via system or indirectly via functions that call other programs such as install.packages) the locations in which the shell is looking for programs is governed by the PATH environment variable. That variable may be set differently for R started from an interactive shell and for R started in the GUI. You can use Sys.getenv('PATH') to verify the current setting.

When R is started from a shell (e.g., on the command line of the Terminal), it will inherit settings from that shell. Those are typically modified by shell-specific configuration files, such as .profile or .bashrc. Those apply only to the shell, not to the system as a whole. In addition, some installers (such as MacTeX) will modify global shell settings to make user's life more comfortable on the command line, but, again, those do not apply to programs not started from the shell – such as GUIs. See Apple Technical Q&A QA1067 for what Apple says about the topic.

In order to standardize your PATH setting in R, you can set it inyour .Renviron file (in your home directory – see ?Startupin R for details on how R uses configuration files on startup). Thissetting will apply to R regardless of how it is started. You can alsoadd more elaborate constructs to .Rprofile instead if you wish toselectively modify the existing PATH variable viaSys.getenv and Sys.setenv.

10.14 I see no text in a Quartz plot!

Typically this means that you have corrupted fonts in your system. Openthe Font Book application (in Applications) and check thefonts that you are using (for example the default font in Quartz iscurrently “Arial”). Corrupted fonts will have no glyphs (text will notappear as it should), remove such fonts.