R for Windows FAQ

Frequently Asked Questions on R for Windows

Version for

B. D. Ripley and D. J. Murdoch

Introduction
************

This FAQ is for the Windows port of R: it describes features specific to that version.  The main R FAQ can be found at

     http://CRAN.R-project.org/doc/FAQ/R-FAQ.html.

The information here applies only to recent versions of R for Windows, (2.5.0 or later).

Installation and Usage
**********************

Where can I find the latest version?
====================================

Go to any CRAN site (see http://cran.r-project.org/mirrors.html for a list), navigate to the bin/windows/base directory and collect the file(s) you need.  The current release is distributed as an installer win32.exe of about 30Mb.  This contains all the components and allows as complete as installation as you choose.

There are also links on that page to the r-patched and r-devel snapshots.  These are frequently updated builds of development versions of R.  The r-patched build includes bug fixes to the current release, and r-devel contains these as well as changes that will eventually make it into the next x.y.0 release.

How do I install R for Windows?
===============================

Versions of R as from 2.7.0 will only run on Windows 2000 or later.  (R 2.6.2 was the last version for Windows 95. 98, ME and NT4.)  There is no specific version for x64 Windows, but the standard 32-bit version works well enough.  We only test on versions of Windows currently supported by Microsoft, mainly on XP, Vista x64 and Windows Server 2003.

Your file system must allow case-honouring long file names (as is likely except perhaps for some network-mounted systems).  A full installation takes up about 60Mb of disk space and a minimal one less than 20Mb.

If you want to be able to build packages from sources, we recommend that you choose an installation path not containing spaces.  (Using a path with spaces in will probably work, but is little-tested.)  Users of Vista installing for a single user using an account with administrator rights (Non-administrator accounts will automatically be offered a default installation directory in the user area.) should consider installing into a non-system area (such as C:\R).  If you are installing to a network drive, you should consider changing the default form of help during the install not to be Compiled HTML help: see Help is not shown for some of the packages.  Installing to a network share (a filepath starting with \\machine\...) is not supported: such paths will need to mapped to a network drive.

To install use win32.exe.  Just double-click on the icon and follow the instructions.  If you installed R this way you can uninstall it from the Control Panel or Start Menu (unless you suppressed making a group for R).  If you have an account with Administrator privileges you will be able to install R in the Program Files area and to set all the optional registry entries; otherwise you will only be able to install R in your own file area.  On Windows Vista you may need to confirm that you want to proceed with installing a program from an `unidentified publisher'.

After installation you should choose a working directory for R.  You will have a shortcut to \bin\Rgui.exe on your desktop and/or somewhere on the Start menu file tree, and perhaps also in the Quick Launch part of the taskbar.  Right-click each shortcut, select Properties... and change the `Start in' field to your working directory.

You may also want to add command-line arguments at the end of the Target field (after any final double quote, and separated by a space), for example --sdi --max-mem-size=1Gb.  You can also set environment variables at the end of the Target field, for example R_LIBS=p:/myRlib, and if you want to ensure that menus and messages are in (American) English, LANGUAGE=en.

It is also possible to install from an MSI file, which will be of interest only for system administrators.  For how to build an MSI file, see the `R Installation and Administration Manual'.

How do I check an installation is not corrupt?
==============================================

Run the program bin\md5check.exe. This compares checksums on all the installed files with those put into the installer, and will report any changed or missing files.

(It only works if R was installed from the Inno Setup installer, and not the MSI installer.)

Can I customize the installation?
=================================

The normal way to customize the installation is by selecting components from the wizards shown.  However, sysadmins might like to install R from scripts, and the following command-line flags are available for use with the installer.

/SILENT
     only show the installation progress window and error messages.

/VERYSILENT
     only show error messages.

/DIR="x:\dirname"
     set the default installation directory

/GROUP="folder name"
     set the default Start-menu group name

/COMPONENTS="comma separated list of component names"
     set the initial list of components: Components are named main, chtml, html, latex, manuals, refman, libdocs, devel, tcl, Rd, latex and trans.

It is also possible to save the settings used to a file and later reload those settings using

/SAVEINF="filename"
     save the settings to the specified file.  Don't forget to use quotes if the filename contains spaces.

/LOADINF="filename"
     instructs the installer to load the settings from the specified file after having checked the command line.

A successful installation has exit code 0: unsuccessful ones may give 1, 2, 3, 4 or 5.  See the help for Inno Setup (http://jrsoftware.org/isinfo.php) for details.

We have some facilities for building a customized installer, in particular to add packages to the installer.  See the `R Installation and Administration' manual in the subsection `Building the installers'.

How do I run it?
================

Just double-click on the shortcut you prepared at installation.

If you want to set up another project, make a new shortcut or use the existing one and change the `Start in' field of the Properties.

You may if you prefer run R from the command line of any shell you use, for example a `Command Prompt' or a port of a Unix shell such as tcsh or bash. (The command line can be anything you would put in the Target field of a shortcut, and the starting directory will be the current working directory of the shell.)

Can I run R from a CD or USB drive?
===================================

Yes, with care.  A basic R installation is relocatable, so you can burn an image of the R installation on your hard disc or install directly onto a removable storage device such as a flash-memory USB drive.  (If you have installed packages into a private library, their absolute paths will appear in the HTML packages list.)

Running R does need access to a writable temporary directory and to a home directory, and in the last resort these are taken to be the current directory.  This should be no problem on a properly configured version of Windows, but otherwise does mean that it may not be possible to run R without creating a shortcut in a writable folder.

How do I UNinstall R?
=====================

Normally you can do this from the R group on the Start Menu or from the Add/Remove Programs (Programs and Features under Vista) in the Control Panel.  If it does not appear there or if you want to remove an old version, run unins000.exe in the top-level installation directory.  (There should be a separate uninstall item in the R group for each installed version of R. On Windows Vista, you may well be asked to confirm that you wish to run a program from an `unidentified publisher'.)

Uninstalling R only removes files from the initial installation, not (for example) packages you have installed or updated.

If all else fails, you can just delete the whole directory in which R was installed.

What's the best way to upgrade?
===============================

That's a matter of taste.  For most people the best thing to do is to uninstall R (see the previous Q), install the new version, copy any installed packages to the library folder in the new installation, run update.packages(checkBuilt=TRUE, ask=FALSE) in the new R and then delete anything left of the old installation.  Different versions of R are quite deliberately installed in parallel folders so you can keep old versions around if you wish.

For those with a personal library (folder R\win-library\X.Y of your home directory), you will need to update that too when the minor version of R changes (e.g. from 2.6.2 to 2.7.0).  A simple way to do so is to copy (say) R\win-library\2.6 to R\win-library\2.7 before running update.packages(checkBuilt=TRUE, ask=FALSE).

There seems to be a limit on the memory it uses!
================================================

Indeed there is.  It is set by the command-line flag --max-mem-size (see How do I install R for Windows?) and defaults to the smaller of the amount of physical RAM in the machine and 0.5Gb less than the limit of user virtual memory for a process (most often 2GB).  It can be set to any amount between 32Mb and 4095Mb.

Use ?Memory and ?memory.size for information about memory usage.  The limit can be raised by calling memory.limit within a running R session.

The executables Rgui.exe and Rterm.exe support up to 3Gb per process under suitably enabled versions of 32-bit Windows (see http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx and http://msdn2.microsoft.com/en-us/library/aa366778.aspx: where this is supported it may need to be specifically enabled).  On such systems, the default for --max-mem-size is the smaller of the amount of RAM and 2.5Gb.  On some 64-bit versions of Windows (e.g. Vista) the limit is 4GB, and there the default for --max-mem-size is the smaller of the amount of RAM and 3.5Gb.

How can I keep workspaces for different projects in different directories?
==========================================================================

Create a separate shortcut for each project: see Q2.5.  All the paths to files used by R are relative to the starting directory, so setting the `Start in' field automatically helps separate projects.

Alternatively, start R by double-clicking on a saved .RData file in the directory for the project you want to use, or drag-and-drop a file with extension .RData onto an R shortcut.  In either case, the working directory will be set to that containing the file.

How do I print from R?
======================

It depends what you want to print.

  * You can print the graphics window from its menu or by using dev.print with suitable arguments (see its help page: most likely dev.print(win.graph) will work).

  * You can print from the R console or pager by File | Print. (This will print the selection if there is one, otherwise the whole console or pager contents.)

  * You can print help files from the pager or HTML browser.

  * If you have configured RHOME\bin\helpPRINT.bat and have LaTeX installed you can print help files by help(fn_name, offline=TRUE).

Can I use R CMD BATCH?
======================

Yes: use R CMD BATCH --help or ?BATCH for full details.

You can set also up a batch file using Rterm.exe.  A sample batch file might contain (as one line)

     path_to_R\bin\Rterm.exe --no-restore --no-save < %1 > %1.out 2>&1

The purpose of 2>&1 is to redirect warnings and errors to the same file as normal output.

Can I use with ESS and (X)emacs?
================================

Yes.  All recent versions of ESS come with support for this version of R, and there is support for interrupting the R process from ESS (by C-c C-c).

For help with ESS, please send email to ESS-help@stat.ethz.ch, not the R mailing lists.

What are HOME and working directories?
======================================

Several places in the documentation use these terms.

The working directory is the directory from which Rgui or Rterm was launched, unless a shortcut was used when it is given by the `Start in' field of the shortcut's properties.  You can find this from R code by the call getwd().

The home directory is set as follows: If environment variable R_USER is set, its value is used.  Otherwise if environment variable HOME is set, its value is used.  After those two user-controllable settings, R tries to find system-defined home directories.  It first tries to use the Windows "personal" directory (typically C:\Documents and Settings\username\My Documents on Windows XP and C:\Users\username\Documents on Vista).  If that fails, if both environment variables HOMEDRIVE and HOMEPATH are set (and they normally are), the value is ${HOMEDRIVE}${HOMEPATH}.  If all of these fail, the current working directory is used.

You can find this from R code by Sys.getenv("R_USER").

How do I set environment variables?
===================================

Environment variables can be set for Rgui.exe and Rterm.exe in three different ways.

 1. On the command line as name=value pairs.  For example in the shortcut to Rgui you could have

          "path_to_R\bin\Rgui.exe" HOME=p:/ R_LIBS=p:/myRlib

 2. In an environment file .Renviron in the working directory or your home directory, for example containing the line

          R_LIBS=p:/myRlib

     If you have permission to do so, you can also create an environment file etc\Renviron.site and set environmental variables in that file in the same way.  This is useful for variables which should be set for all users and all usages of this R installation.  (Their values can be overridden in a .Renviron file or on the command line.)

     See ?Startup for more details of environment files.

 3. For all applications via Windows.  How you set an environment variable is system specific: under Windows 2000/XP/2003 you can use `System' in the control panel or the properties of `My Computer' (under the `Advanced' tab).  Under Vista, go to `User Accounts' in the Control Panel, and select your account and then `Change my environment variables'.

The order of precedence for environmental variables is the order in which these options are listed, that is the command line then .Renviron then the inherited environment.

R can't find my file, but I know it is there!
=============================================

How did you specify it?  Backslashes have to be doubled in R character strings, so for example one needs "d:\\\\library\\xgobi\\scripts\\xgobi.bat".  You can make life easier for yourself by using forward slashes as path separators: they do work under Windows.  You should include the file extension (e.g. "xgobi.bat" rather than just "xgobi"); sometimes this isn't shown in Windows, but it is necessary in R.

A simple way to avoid these problems is to use the function file.choose() to invoke the standard Windows file selection dialog.  If you select a file there, the name will be passed to R in the correct format.

Another possible source of grief is spaces in folder names.  We have tried to make R work on paths with spaces in, but many people writing packages for Unix do not bother.  So it is worth trying the alternative short name (something like PROGRA~1; you can get it as the `MS-DOS name' from the Properties of the file on some versions of Windows, and from dir /X in a Command Prompt window).

Does R use the Registry?
========================

No, not when R itself is running.

When you run the R installer, there are options (under `Select Additional Tasks') to `Save version number in registry' and `Associate R with .RData files'.

If you tick the first option, the following string entries are added to the Windows registry:

  * HKEY_LOCAL_MACHINE\Software\R-core\R\Current Version contains the version number, currently.

  * HKEY_LOCAL_MACHINE\Software\R-core\R\[version]\InstallPath (where [version] is currently) contains the path to the R home directory.

If you do not have administrative privileges on the machine while running the installer, then the entries are created under HKEY_CURRENT_USER.

If you tick the second option (`Associate R with .RData files') and have administrative privileges, then entries are created under HKEY_CLASSES_ROOT\.RData and HKEY_CLASSES_ROOT\RWorkspace.

After installation you can add the Registry entries in HKEY_LOCAL_MACHINE by running RSetReg.exe in the bin folder, and remove them by running this with argument /U.  Note that this requires administrative privileges and neither sets up nor removes the file associations.

Does R support automation (OLE, COM)?
=====================================

Directly, no.

There is a (D)COM server written by Thomas Baier available on CRAN (http://cran.r-project.org/other-software.html) which works with Rproxy.dll (in the R distribution) and R.dll to support transfer of data to and from R and remote execution of R commands, as well as embedding of an R graphics window.  An R-Excel interface making use of the (D)COM server is included in the distribution.

Thomas Baier also has a package rcom available on CRAN (in the usual way for a package) to provide COM client and server functionality from within R.

Another (D)COM server is available from http://www.omegahat.org/, which allows R objects to be exported as COM values.  That site also has packages RDCOMClient and SWinTypeLibs which allow R to act as a (D)COM client.

The Internet download functions fail.
=====================================

for example update.packages() and the menu items on the Packages menu.

We have had several reports of this, although they do work for us on all of our machines.  There are two known possible fixes.

(a) Use the alternative internet2.dll by starting R with the flag --internet2 (see How do I install R for Windows?) which uses the Internet Explorer internals (and so needs Internet Explorer 4 or later installed).  Note that this does not work with proxies that need authentication.

(b) A proxy needs to be set up: see ?download.file.  Here are two versions of an example (a real one, but from a machine that is only available locally) of a command-line in a short cut:

     "path_to_R\bin\Rgui.exe" http_proxy=http://user:pass@gannet:80/

     "path_to_R\bin\Rgui.exe" http_proxy=http://gannet/ http_proxy_user=ask

The second version will prompt the user for the proxy username and password when HTTP downloads are first used.

Another possibility is that firewall settings are blocking the R executables from contacting the Internet, but this should result in informative error messages from the firewall program.

Entering certain characters crashes Rgui.
=========================================

This has not been reported for a few years, but used to happen regularly.  All the occurrences we have solved have been traced to faulty versions of msvcrt.dll: we have installed a workaround that seems to avoid this.  A few other people have discovered this was caused by desktop switcher and keyboard macro programs, for example `Macro Magic' and `JS Pager'.

What does 'DLL attempted to change FPU control word' mean?
==========================================================

This is a warning which indicates that R has taken action to correct the action of some (non-R) DLL which has just been loaded and has changed the floating point control word (in its initialization code) to a setting incompatible with that needed for R.  This is not good practice on the part of the DLL, and often indicates that it needs to be updated.  (It was common with DLLs compiled in early versions of Visual C++.)

Unfortunately, because DLLs may load other DLLs it is not possible for R to track which DLL caused the problem.

See also ?dyn.load.

Other strange crashes.
======================

Some users have found that Rgui.exe fails to start, exiting with a ``Floating-point invalid operation'' or other low level error.  This error may also happen in the middle of a session.  In some cases where we have tracked this down, it was due to bugs in the video driver on the system in question: it makes changes to the floating point control word which are incompatible with R.  (Good practice would restore the control word to the state it was in when the driver code was called, and R tries hard to correct this before running its own code.)  For example, one user reported that the virtual screen manager JSP2 caused this crash.

These errors are essentially impossible for us to fix or work around beyond the measures already taken (which were increased in R 2.3.0). The only solution we know of is for the user to replace the buggy system component that is causing the error.

Why does R never use more than 50% of my CPU?
=============================================

This is a misreading of Windows' confusing Task Manager.  R's computation is single-threaded, and so it cannot use more than one CPU. What the task manager shows is not the usage in CPUs (as better written utilities do) but the usage as a percentage of the apparent total number of CPUs.  We say `apparent' as it treats so-called `hyperthreaded' CPUs as two CPUs even though there is only one physical CPU: dual-core CPUs will also show as two CPUs (which they genuinely are).

Many benchmarks show hyperthreading reduces the overall workload, so you may want to experiment with disabling it.

Does R run under Windows Vista?
===============================

It does.  A few issues have been reported that related to the way accounts and file permissions work.  (These are not specifically R issues, but changes in user experiences.)

Earlier versions of Windows had user and Administrator accounts, and user accounts could be give administrative privileges (by being added to the local Administrators group) and so write permission over system areas such as c:\Program Files.  R would be installed either by a user in his own file space or by an account with administrator privileges into a system area.  Sysadmins could set policies for user accounts, and you might for example have needed to be a `Power User' to install software at all.

Vista normally disables the Administrator account and expects software installation to done by an account which is in the local Administrator group with `admin approval mode' turned on.  (The Administrator account by default has it turned off.)  Unlike (say) Windows XP, such accounts do not run programs with full administrator privileges, and this is where the issues arise.  (For background information consult http://technet.microsoft.com/en-us/windowsvista/aa906021.aspx and http://windowsvistablog.com/blogs/windowsvista/archive/2007/01/23/security-features-vs-convenience.aspx.) Vista has the concept of `over-the-shoulder' credentials: if you are running without full administrator privileges and do something which needs them you may be prompted with one or more security-check dialog boxes, and may be required to provide administrator credentials or confirm that you really want to take that action.

Vista will report that the R installer has an `unidentified publisher' and ask if it should be run.  System administrators can disable installing applications from non-trusted sources, in which case you will have to persuade them that R is trustworthy, or digitally sign the R installer yourself, or (unless this is also disabled) run the installer from a standard account and install into your own file area. (The same issues apply to the .msi version of the installer.)

If you install R as a standard user into your own file space and use it under the same account, there are no known permission issues.

If you use the default Administrator account (without `admin approval mode' being turned on) and install/update packages (in the system area or elsewhere), no issues are known.

If you use an account in the local Administrators group in `admin approval mode' (which is the intended norm under Vista), installation will make use of `over-the-shoulder' credentials.  You will run into problems if you try installing (including updating) packages in the main R library.  (It would be nice if at that point R used over-the-shoulder credentials, but they apply to processes as a whole.  Vista disallows creating .chm and .dll files in the system area without credentials.)  There are several ways around this.

  * Run R with Administrator privileges in sessions where you want to install packages.  (Do so by right-clicking on the R shortcut and selecting 'Run as Administrator'.)

  * Transfer ownership of the R installation to the user which installed R. To do so, use the security tab on the Properties of the top-level R folder and give `Full Control' over this directory to the user (not just the Administrator group).

  * Install packages into a different library tree owned by the account used to install R.

     For an installation to be used by a single user, the simplest way is to make use of the `personal library' introduced in R 2.5.0: see I don't have permission to write to the \library directory.

     For a site installation, you can create a site-wide library directory anywhere convenient, and add it to the default package search path for all users via R_LIBS_SITE in etc\Renviron.site.  See What are HOME and working directories?.  There is a standard location for a site library, the site-library directory in the top-level R folder (which you would need to create with full control for the R installation account).  This will be used for installation in preference to the main library folder if it exists.

     This approach will not allow you to update the recommended packages unless you `Run as administrator': we suggest you use an R session running under Administrator privileges when updating those.

Another issue with Vista is that the standard POSIX ways that R uses (e.g. in file.info and file.access) to look at file permissions no longer work reliably.  file.access was re-written for R 2.5.1 to work with Windows NT-based security and the new version seems much more reliable with Vista.

On suitably recent hardware Vista can prevent the execution of code from data areas via `Data Execution Prevention' (from a tab in System Properties -> Advanced -> Performance), and sysadmins can turn this on for all programs.  R runs correctly with DEP enabled.

Quotes don't come out right on the console/terminal/pager.
==========================================================

R version 2.6.0 and later will make use of directional quotes that are not always rendered correctly by Windows.

Whether these are used in R output (from functions sQuote and dQuote) is controlled by getOption("useFancyQuotes") whose default is FALSE except for the Rgui console.  There are two potential problems with rendering directional quotes.  The first is that in European locales the `Windows Command Prompt' is by default set up to use MS-DOS and not Windows default encodings: this can be changed via chcp, with chcp 1252 being appropriate for Western European (including English) locales.  The other is that the default raster fonts only include directional single quotes and not directional double quotes (which will probably be rendered as a filled rectangle).

Directional quotes will also be used in text help which is normally displayed in R's internal pager: these may not be rendered correctly in an external pager.  They are also used in CHM and HTML help, where most browsers use fonts which render them correctly.

The font used can affect whether quotes are rendered correctly.  The default font in the Rgui console and internal pager is Courier New, which has directional quotes on all the systems we tried.  Lucida Console has elegant glyphs for directional quotes, but seems rather light on Windows XP (it looks better than Courier New on Vista).  Non-TrueType fonts such as Courier and FixedSys lack directional double quotes on all the systems we tried.

There is no tilde on my keyboard!
=================================

Often there is but it is not marked: also on all Windows versions you should be able to get tilde by holding the down the left Alt key and typing 0126 on the numeric keypad, then releasing the Alt key.

Where tilde does not appear on the main keyboard, it can normally be accessed by pressing AltGr (the right Alt key) plus some other key. This is ] in Canadian (multilingual), German and Scandinavian layouts, 1 in Eastern Europe, [ in Portuguese, 4 or 5 in Spanish, / in Francophone Belgian, and so on.  For some keyboards the uses of AltGr are at http://office.microsoft.com/en-us/word/HP052590631033.aspx: you can explore those for your keyboard via the `On-Screen Keyboard' (under Accessories, Accessibility on XP).

Languages and Internationalization
**********************************

The installer does not offer my language.
=========================================

Two things may be happening.  First, only languages which can be displayed using the current codepage are offered so you cannot install in Japanese unless running Windows in Japanese.

Second, only a limited range of languages is supported (but still wider than those for which R has translations), currently Brazilian Portuguese, Catalan, both Simplified and Traditional Chinese, Czech, Danish, Dutch, Finnish, French, German, Hungarian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Russian, Slovenian and Spanish (Spain).

I want R in English (and not in French/Chinese/...)!
====================================================

The default behaviour of R is to try to run in the language you run Windows in.  Apparently some users want Windows in their native language, but not R.  To do so, set LANGUAGE=en as discussed in Q2.2 and Q2.15, or in the Rconsole file.

I want to run R in Chinese/Japanese/Korean.
===========================================

All recent Windows versions of R support `East Asian' languages (with a suitable version of Windows -- e.g. Western installations of Windows XP do not by default have such support).

Both Rterm.exe and RGui.exe support single- and double-width characters.  It will be necessary to select suitable fonts in files Rconsole and Rdevga (see ?Rconsole or the comments in the files: the system versions are in the etc folder); in the latter you can replace Arial by Arial Unicode MS, and we tried FixedSys and MS Mincho in Rconsole.  (Note that Rdevga only applies to Windows graphics devices and not, say, to pdf.)

Note that it is important that the console font uses double-width characters for all CJK characters (as that is what the width table used assumes): this is true for the fonts intended for CJK locales but not for example for Lucida Console.

You do need to ensure that R is running in a suitable locale: use Sys.getlocale() to find out.  (CJK users may be used to their language characters always being available, which is the case for so-called `Unicode' Windows applications.  However, R used to run on Windows 9x and is not therefore `Unicode'.)  You can find suitable locale names from http://msdn.microsoft.com/library/default.asp?url=/library/en-us/vccore98/html/_crt_language_and_country_strings.asp: beware that "Chinese" is Traditional Chinese (code page 950, Big5) and "chs" is needed for Simplified Chinese (code page 936, GB2312).  Note that this can be rather tricky: on International versions of Windows XP there are several places to select the language under the `Regional and Language Options' part of the control panel, and the appropriate language has to be set under both the `Regional Options' and `Advanced' tabs.

When using Rterm the window in which it is run has to be set up to use a suitable font (e.g. Lucida Console, not the OEM raster fonts) and a suitable codepage (which for the Windows Cmd shell can be done by chcp).

I selected English for installation but R runs in Chinese.
==========================================================

Precisely, you selected English for installation!  The language of the installer has nothing to do with the language used to run R: this is completely standard Windows practice (and necessary as different users of the computer may use different languages).

The language R uses for menus and messages is determined by the locale: please read the appropriate manual (the R Installation and Administration Manual) for the details.  You can ensure that R uses English messages by appending LANGUAGE=en to the shortcut you use to start R, or setting it in the Rconsole file.

I would like to be able to use Japanese fonts.
==============================================

for example, in the console and to annotate graphs.  Similar comments apply to any non-Western European language.

With suitable fonts, this should just work.  You will need to set MS Mincho or MS Gothic as the console font to ensure that single- and double-width characters are handled correctly.  The default graphics fonts for the windows() graphics device can handle most common Japanese characters, but more specialized fonts may need to be set. (See Q3.5 for how to set fonts: the console font can also be set from the `GUI preferences' meny item.)  The help for windowsFonts has examples of selecting Japanese fonts for the windows() family of devices.

In addition, the Hershey vector fonts (see ?Hershey, ?Japanese and demo(Japanese)) can be used on any graphics device to display Japanese characters.

To use non-Latin-1 characters in the postscript graphics device, see its help page (which also applies to pdf).

I don't see characters with accents at the R console, for example in ?text.
===========================================================================

You need to specify a font in Rconsole (see Q3.5) that supports the encoding in use, in Western European languages Latin-1.  This used to be a problem in earlier versions of Windows, but now it is hard to find a font which does not.

Support for these characters within Rterm depends on the environment (the terminal window and shell, including locale and codepage settings) within which it is run as well as the font used by the terminal window.  Those are usually on legacy DOS settings and need to altered.

The dialog buttons are not translated.
======================================

In most cases they actually are, but by Windows.  Setting the locale or the LANGUAGE environment variable does not change the Windows setting of its `UI language'.  Under (international) Windows XP there are three tabs on the Regional and Language Options applet in the Control Panel.  The first tab controls the locale, the second the UI and the third the fonts used for `non-Unicode' programs (but apparently also for Unicode ones in many cases): see Q3.3.  Vista talks about the 'UI language' and the 'system locale' for setting the language used for `non-Unicode' programs.

If you have Windows running completely in say French or Chinese these settings are likely to be consistent.  However, if you try to run Windows in one language and R in another, you may find the way Windows handles internationalization slightly odd.  For further details see http://msdn.microsoft.com/library/default.asp?url=/library/en-us/intl/nls_0ddl.asp.

Packages
********

Can I install packages into libraries in this version?
======================================================

Yes, but you will need a lot of tools to do so, unless the author or the maintainers of the bin/windows/contrib section on CRAN have been kind enough to provide a pre-compiled version for Windows as a .zip file.

You can install pre-compiled packages either from CRAN or from a local .zip file by using install.packages: see its help page. There are menu items on the Packages menu to provide a point-and-click interface to package installation.  The packages for each minor (2.x) version will be stored in a separate area, so for R 2.7.? the files are in bin/windows/contrib/2.7.  You can try those compiled for earlier versions (but not before 2.0.0), at your own risk.

Note that the pre-compiled versions on CRAN are unsupported: see http://cran.r-project.org/bin/windows/contrib/ReadMe, which also gives the locations of a few other pre-compiled packages.

If there is not a pre-compiled version or that is not up-to-date or you prefer compiling from source, read the `R Installation and Administration' manual section on `Add-on Packages'.  You need to make sure you installed the necessary files, and you will need to collect and install several tools: you can download them via the portal at http://www.murdoch-sutherland.com/Rtools/.  Once you have done so, just run R CMD INSTALL pkgname.  To check the package (including running all the examples on its help pages and in its test suite, if any) use R CMD check pkgname: see the `Writing R Extensions' manual.

Note that setting up Windows to install a source package is rather tricky; please do ensure that you have followed the instructions exactly.  At least 90% of the questions asked are because people have not done so.

If you have a source package that is known to work on a Unix-alike system, you can try the automated Windows binary package builder documented at http://win-builder.r-project.org.

I don't have permission to write to the \library directory.
===========================================================

You can install packages anywhere and use the environment variable R_LIBS (see How do I set environment variables?) to point to the library location(s).

Suppose your packages are installed in p:\myRlib.  Then you can EITHER

     set the environment variable R_LIBS to p:\myRlib before starting R

OR use a package by, e.g.

     library(mypkg, lib.loc="p:/myRlib")

You can also have a personal library, which defaults to the directory R\win-library\X.Y of your home directory for versions X.Y.Z of R.  This location can be changed by setting the environment variable R_LIBS_USER, and can be found from inside R by running Sys.getenv("R_LIBS_USER").  This will only be used if it exists so you may need to create it: you can use

     dir.create(Sys.getenv("R_LIBS_USER"), recursive = TRUE)

to do so.  If you use install.packages and do not have permission to write to the main or site library, it should offer to create a personal library for you and install the packages there.  This will also happen if update.packages offers to update packages for you in a library where you do not have write permission.

There can be additional security issues under Windows Vista: see Does R run under Windows Vista?.  In particular, the detection that a standard user has suitable permissions appears to be unreliable under Vista, so we recommend that you do create a personal directory yourself.

The packages I installed do not appear in the HTML help system.
===============================================================

To update the HTML indices after you have installed a pre-compiled package, run at the R prompt.

     > link.html.help()

This is done automatically when installing from the Packages menu or by install.packages(), and when help.start is run, provided you have write permission on library.  If you do not have sufficient permission, you will get warnings and the packages you install will not appear in the list of packages or the search system.

My functions are not found by the HTML help search system.
==========================================================

The following conditions need to hold for functions in a package you installed.

  * the package contains a CONTENTS file in its top-level directory.

  * you updated the indices as described in the answer to Q4.3 after installing the package.

If those hold, this works for us.  Note that if you were unable to update the indices (for which you need write permission in the
} directory), only the functions in packages installed in
the main library will be found.

If the help search system does not work at all, this probably
indicates that Java support is either not installed or Java or
JavaScript is not enabled in your browser.  The search page contains a
link to the appropriate section in the R Installation and
Administration manual.

Loading a package fails.
========================

Is the package compiled for this version of R?   Many of the packages need to be compiled for a fairly recent version.

You can tell the version the package was compiled for by looking at the Built: line in its DESCRIPTION file or at the Version tab of its DLL in the libs directory. (Right-click on the DLL in Windows Explorer and select Version tab of the Properties, or use the DLL.version function inside R.)

Package TclTk does not work.
============================

For package tcltk to work (try demo(tkdensity) or demo(tkttest) after library(tcltk)) you need to have Tcl installed.  This is an optional part of the installation although it is selected by default.  If the message is

     Tcl/Tk support files were not installed

the optional files were not installed, and you need to go back to the installer and install them.

Alternatively, if you have the environment variable MY_TCLTK set to a non-empty value, it is assumed that you want to use a different Tcl/Tk 8.5.x installation with the path to its bin directory given by value of MY_TCLTK, and that this is set up correctly (with TCL_LIBRARY set if needed).  In that case you do not need the Tcl/Tk support files installed (but they can be).  Note that you do need 8.5.x and not 8.4.x.  (If you build R from the sources yourself you can configure it to use 8.4.x.)

Several package authors have suggested using ActiveTcl (http://www.activestate.com/Products/activetcl/) as a way to get Tcl/Tk extensions.  This could be used by setting (for a default install)

     MT_TCLTK=c:/Tcl/bin

but current versions (e.g. 8.5.1.0) do not contain any extra extensions.  Some extensions can be copied over from an ActiveTcl install of Tcl/Tk 8.4 or downloaded via the Teacup facility.

Hyperlinks in HTML sometimes do not work.
=========================================

They may well not work between packages installed in different libraries.  This is solved under Unix using symbolic links which Windows does not implement (except on NTFS file systems under Vista/Server 2008 -- where they may need Administrator privileges).

With HTML, help.start() fixes up links to the most of the standard packages if it has write permission in the main library tree. Not even these work for Compiled HTML help.

Currently links to the base, datasets, utils, grDevices, graphics, methods and stats packages are fixed.

update.packages() fails.
========================

You may not be able to update a package which is in use: Windows `locks' the package's DLL when it is loaded.  So use update.packages() (or the menu equivalent) in a new session.

If you put library(foo) in your .Rprofile you will need to start R with --vanilla to be able to update package foo. If you set R_DEFAULT_PACKAGES to include foo, you will need to unset it temporarily.

It has been reported that some other software has interfered with the installation process by preventing the renaming of temporary files, Google Desktop being a known example.

How do I add to the list of repositories?
=========================================

as shown in the Select repositories... item on the Packages menu?

This reads from the tab-delimited file R_HOME\etc\repositories, which you can edit, or put a modified copy at .R\repositories in your HOME directory (see What are HOME and working directories?).

Help is not shown for some of the packages
==========================================

Is this for Compiled HTML help (the default)?  If a help viewer appears but says the page cannot be displayed, this may be due to a Windows security patch (http://support.microsoft.com/kb/896358).  Either apply the workarounds given at that URL or choose another form of help as the default (on installation or by editing R_HOME\etc\Rprofile.site).

Windows Features
****************

What should I expect to behave differently from the Unix version of R?
======================================================================

  * R commands can be interrupted by Esc in Rgui.exe and Ctrl-break or Ctrl-C in Rterm.exe: Ctrl-C is used for copying in the GUI version.

  * Command-line editing is always available, but is simpler than the readline-based editing on Unix.  For Rgui.exe, the menu item `Help | Console' will give details.  For Rterm.exe see file README.rterm.

  * Using help.start() does not automatically send help requests to the browser: use options(htmlhelp=TRUE) to turn this on.

  * The HTML help system has limitations in supporting cross-library links.

  * Paths to files (e.g. in source()) can be specified with either "/" or "\\".

  * system() is slightly different: see its help page and that of shell().

I hear about some nifty features: please tell me about them!
============================================================

You have read the file README.}? There are file menus on
the R console, pager and graphics windows.  You can source and save from
those menus, and copy the graphics to png, jpeg,
bmp, postscript, PDF or metafile.  There are
right-click menus giving shortcuts to menu items, and optionally
toolbars with buttons giving shortcuts to frequent operations.

If you resize the R console the options(width=) is automatically
set to the console width (unless disabled in the configuration file).

The graphics has a history mechanism.  As README.} says:

     `The History menu allows the recording of plots.  When plots have been recorded they can be reviewed by PgUp and PgDn, saved and replaced.  Recording can be turned on automatically (the Recording item on the list) or individual plots can be added (Add or the INS key).  The whole plot history can be saved to or retrieved from an R variable in the global environment. The format of recorded plots may change between R versions. Recorded plots should not be used as a permanent storage format for R plots.

     There is only one graphics history shared by all the windows devices.'

The R console and graphics windows have configuration files stored in the RHOME\etc directory called Rconsole and Rdevga; you can keep personal copies in your HOME directory.  They contain comments which should suffice for you to edit them to your preferences.  For more details see ?Rconsole. There is a GUI preferences editor invoked from the Edit menu which can be used to edit the file Rconsole.

Circles appear as ovals on screen.
==================================

The graphics system asks Windows for the number of pixels per inch in the X and Y directions, and uses that to size graphics (which in R are in units of inches).  Sometimes the answer is a complete invention, and in any case Windows will not know exactly how the horizontal and vertical size have been set on a CRT.  You can specify correct values either in the call to windows or as options: see ?windows. (Typically these are of the order of 100.)

On one of our systems, the screen height was reported as 240mm, and the width as 300mm in 1280 x 1024 mode and 320mm in 1280 x 960 and 1600 x 1200 modes.  In fact it was a 21" monitor and 400mm x 300mm!

How do I move focus to a graphics window or the console?
========================================================

You may want to do this from within a function, for example when calling identify or readline.  Use the function bringToTop().  With its default argument it brings the active graphics window to the top and gives it focus.  With argument -1 it brings the console to the top and gives it focus.

This works for Rgui.exe in MDI and SDI modes, and can be used for graphics windows from Rterm.exe (although Windows may not always act on it).

What does TAB completion do?
============================

R 2.5.0 introduced TAB completion in both Rgui and Rterm.  Hitting TAB whilst entering a command line completes the current `word' as far as is unambiguously possible. Hitting TAB a second time then shows a list of possible completions (or the first few if there are many): the user can then enter one or more characters and hit TAB again.

What is it `completing'?  There are two modes: within an unterminated (single- or double-) quoted expression it completes file paths. Otherwise, it is completing R expressions: most obviously it will match visible R object names and keywords, so apr folloed by TAB will (in a vanilla session) complete to apropos.  After a function name and parenthesis (e.g. apropos() it will complete argument names (and =), and after $ or @ it will complete list components or slot names respectively.

This feature can be turned off: Rgui has two menu items to do so, and setting the environment variable R_COMPLETION to FALSE turns it off completely for both Rgui and Rterm.  Further, the behaviour can be fine-tuned: to see the settings available use

     ?rc.settings

which also explains how the various types of completion work.

This feature is very similar to the completion available in the readline-based command line interface on Unix-alikes: the Mac OS X Gui has a different completion scheme.

Workspaces
**********

My workspace gets saved in a strange place: how do I stop this?
===============================================================

Have you changed the working directory?: see Q6.2.

How do I store my workspace in a different place?
=================================================

Use the `File | Change Dir...' menu item to select a new working directory: this defaults to the last directory you loaded a file from.  The workspace is saved in the working directory.  You can also save a snapshot of the workspace from the `Save Workspace...' menu item.

From the command line you can change the working directory by the function setwd: see its help page.

Can I load workspaces saved under Unix/GNU-Linux or Mac OS?
===========================================================

Yes.  All ports of R use the same format for workspaces, so they are interchangeable (for the same 2.x.? version of R, at least).

Note though that character data in a workspace will be in a particular encoding that is not recorded in the workspace, so workspaces containing non-ASCII character data may not be interchangeable even on the same OS. Since R marks character data when it knows it to be in UTF-8 or Latin-1 (including its Windows superset, CP1252), strings in those encodings are likely to be transferred correctly: fortunately this covers most of the common cases (Mac OS X normally uses UTF-8, and Linux users are likely to use Latin-1 (its interpretation of the C locale) or UTF-8.)

The R Console
*************

When using Rgui the output to the console seems to be delayed.
==============================================================

This is deliberate: the console output is buffered and re-written in chunks to be faster and less distracting.  You can turn buffering off or on from the `Misc' menu or the right-click menu: Ctrl-W toggles the setting.

If you are sourcing R code or writing from a function, there is another option.  A call to the R function flush.console() will write out the buffer and so update the console.

Long lines in the console or pager are truncated.
=================================================

They only seem to be truncated: that $ at the end indicates you can scroll the window to see the rest of the line.  Use the horizontal scrollbar or the CTRL + left/right arrow keys to scroll horizontally. (The left/right arrow keys work in the pager too.)

Building from Source
********************

How can I compile R from source?
================================

To build R on 32-bit Windows you will need the tools from http://www.murdoch-sutherland.com/Rtools/ as well as some others.  See the `R Installation and Administration' manual.

It has been possible to cross-build R for Windows x64 using binutils and gcc with the x86_64-pc-mingw32 target, using suitable settings in src/gnuwin32/MkRules (see the comments there).  However, that toolchain is experimental and the support for Unicode file functions needed for R 2.7.x is at present incomplete.

You are of course welcome to try a commercial compiler, but we will not be distributing a port to which users cannot easily add packages.

Can I use a fast BLAS?
======================

Fast BLAS (Basic Linear Algebra Subprograms, http://www.netlib.org/blas/faq.html) routines are used to speed up numerical linear algebra.  There is support in the R sources for the `tuned' BLAS called ATLAS (http://math-atlas.sourceforge.net). The savings can be appreciable: on a 2.6GHz P4 and a 1000 x 1000 matrix svd took 16.2 sec with the standard BLAS and 7.8 sec with ATLAS. Because ATLAS is tuned to a particular chip we can't use it generally: the optimal routines for a P4 or an Athlon XP are quite different and neither will run at all on a PII.

BLAS support is supplied by the single DLL R_HOME\bin\Rblas.dll, and you can add a fast BLAS just by replacing that.  Replacements for some of the more common chips are available on CRAN in directory bin/windows/contrib/ATLAS.  See the  R Installation and Administration Manual for how to build an ATLAS Rblas.dll tuned to your system using the R sources.

How do I include compiled C code?
=================================

We strongly encourage you to do this via building an R package: see the `Writing R Extensions' manual.  In any event you should install the parts of the R system for building R packages (installed by default), and get and install the tools (including Perl) and compilers mentioned in the `R Installation and Administration' manual. Then you can use

     ...\bin\R CMD SHLIB foo.c bar.f

to make foo.dll.  Use ...\bin\R CMD SHLIB --help for further options, or see ?SHLIB.

If you want to use Visual C++, Borland C++ or other compilers, see the appropriate section in README.packages.

How do I debug code that I have compiled and dyn.load-ed?
=========================================================

You will need a suitable version of gdb: we normally use that from the Cygwin distribution.  Debugging under Windows is often a fraught process, and sometimes does not work at all.  If all you need is a just-in-time debugger to catch crashes, consider Dr. Mingw from the mingw-utils bundle on http://www.mingw.org (see also http://jrfonseca.dyndns.org/projects/gnu-win32/software/drmingw/). That will be able to pinpoint the error, most effectively if you build a version of R with debugging information as described below.

First, build a version of the R system with debugging information by

     make clean
     make DEBUG=T

and make a debug version of your package by either

     make pkgclean-mypkg
     make DEBUG=T pkg-mypkg

or

     Rcmd install -c mypkg
     set DEBUG=T
     Rcmd install mypkg

Then you can debug by

     gdb /path/to/bin/Rgui.exe

However, note

  * gdb will only be able to find the source code if we run in the location where the source was compiled (src/gnuwin32 for the main system, src/library/mypkg/src for a package), unless told otherwise by the directory command.  It is most convenient to set a list of code locations via directory commands in the file .gdbinit in the directory from which gdb is run.

  * It is only possible to set breakpoints in a DLL after the DLL has been loaded.  So a way to examine the function tukeyline in package stats might be

               gdb ../../../../bin/Rgui.exe
               (gdb) break WinMain
               (gdb) run
               [ stops with R.dll loaded ]
               (gdb) break R_ReadConsole
               (gdb) continue
               [ stops with console running ]
               (gdb) continue
               Rconsole> library(stats)
               (gdb) break tukeyline
               (gdb) clear R_ReadConsole
               (gdb) continue
               Rconsole> example(line)
               ...

     Alternatively, in Rgui you can use the `Misc|Break to debugger' menu item after your DLL is loaded.  The C function call breaktodebugger() will do the same thing.

  * Fortran symbols need an underline appended.

  * Windows has little support for signals, so the Unix idea of running a program under a debugger and sending it a signal to interrupt it and drop control back to the debugger does not work with a mingw version of gdb.  It does often work with the cygwin version.

  * Other debuggers than gdb can be used.  We have successfully used the insight front-end to gdb (see http://sources.redhat.com/insight/: there is a mingw port on their site), and Borland's debugger with a DLL compiled in a Borland compiler.

See http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/gdb.shtml for some further details.

How do I include C++ code?
==========================

You need to do two things:

(a) Write a wrapper to export the symbols you want to call from R as extern "C".

(b) Include the C++ libraries in the link to make the DLL.  Suppose X.cc contains your C++ code, and X_main.cc is the wrapper, as in the example in `Writing R Extensions'.  Then build the DLL by (gcc)

     ...\bin\R CMD SHLIB X.cc X_main.cc

or (VC++, which requires extension .cpp)

     cl /MT /c X.cpp X_main.cpp
     link /dll /out:X.dll /export:X_main X.obj X_main.obj

or (Borland C++, which also requires extension .cpp)

     bcc32 -u- -WDE X.cpp X_main.cpp

and call the entry point(s) in X_R, such as X_main. Construction of static variables will occur when the DLL is loaded, and destruction when the DLL is unloaded, usually when R terminates.

Note that you will not see the messages from this example in the GUI console: see the next section.

This example used to be in package cxx_0.0-x.tar.gz in the src/contrib/Devel section on CRAN, and could be compiled as a package in the usual way on Windows.

The output from my C code disappears. Why?
==========================================

The Rgui.exe console is a Windows application: writing to stdout or stderr will not produce output in the console.  (This will work with Rterm.exe.)  Use Rprintf or REprintf instead.  These are declared in header file R_ext/PrtUtil.h.

Note that output from the console is delayed (see The output to the console seems to be delayed), so that you will not normally see any output before returning to the R prompt.

The output from my Fortran code disappears. Why?
================================================

Writing to Fortran output writes to a file, not the Rgui console. Use one of the subroutines dblepr, intpr or realpr documented in the `Writing R Extensions' manual.

Note that output from the console is delayed (see The output to the console seems to be delayed), so that you will not normally see any output before returning to the R prompt even when using the xxxpr subroutines.

The console freezes when my compiled code is running.
=====================================================

The console, pagers and graphics window all run in the same thread as the R engine.  To allow the console etc to respond to Windows events, call R_ProcessEvents() periodically from your compiled code. If you want output to be updated on the console, call R_FlushConsole() and then R_ProcessEvents().

Last edited 2008-03-19: comments to <R-windows@r-project.org>