R for Windows FAQ

# R for Windows FAQ

## Version for `rw1031`

# Table of Contents

- 1 Introduction
- 2 Installation and Usage
  - 2.1 Where can I find the latest version?
  - 2.2 How do I install R for Windows?
  - 2.3 How do I run it?
  - 2.4 There seems to be a limit on the memory it uses!
  - 2.5 How can I keep workspaces for different projects in different directories?
  - 2.6 How do I print from R?
  - 2.7 Can I use `R BATCH`?
  - 2.8 Can I use rw1031 with ESS and emacs?
  - 2.9 What are HOME and working directories?
  - 2.10 R can't find my file, but I know it is there!
  - 2.11 Does R use the Registry?
  - 2.12 Entering certain characters crashes Rgui.
- 3 Packages
  - 3.1 Can I install packages (libraries) in this version?
  - 3.2 I don't have permission to write to the `rw1031\library` directory.
  - 3.3 The packages I installed do not appear in the HTML help system.
  - 3.4 My functions are not found by the HTML help search system.
  - 3.5 Loading a package fails.
  - 3.6 Package TclTk does not work.
  - 3.7 Hyperlinks in Compiled HTML sometimes do not work.
- 4 Windows Features
  - 4.1 What should I expect to behave differently from the Unix version of R?
  - 4.2 I hear about some nifty features: please tell me about them!
  - 4.3 Circles appear as ovals on screen
  - 4.4 How do I more focus to a graphics window or the console?
- 5 Workspaces
  - 5.1 My workspace gets saved in a strange place: how do I stop this?
  - 5.2 How do I store my workspace in a different place?
  - 5.3 Can I load workspaces saved under Unix/GNU-Linux?
- 6 The R Console and Fonts
  - 6.1 I would like to be able to use Japanese fonts
  - 6.2 I don't see characters with accents at the R console, for example in ?text.
  - 6.3 When using Rgui the output to the console seems to be delayed.
  - 6.4 Long lines in the console or pager are truncated.
- 7 Building from Source
  - 7.1 How can I compile R from source?
  - 7.2 How do I include compiled C code?
  - 7.3 How do I debug code that I have compiled and dyn.load-ed?
  - 7.4 How do I include C++ code?
  - 7.5 The output from my C code disappears. Why?
  - 7.6 The output from my Fortran code disappears. Why?
  - 7.7 The console freezes when my compiled code is running.
  - 7.8 The Perl scripts don't seem to work under Windows 9x/ME

# 1 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://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html.

The information here applies only to recent versions of R for Windows, (`rw1020` or later); the current version is often called something like `rw1031` (although not officially).

# 2 Installation and Usage

## 2.1 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 files you need. There are three possibilities.

1) `SetupR.exe`, is about 15Mb and gives a complete installation.

2) Directory `miniR` contains `miniR.exe` and six files `miniR-?.bin`. You can put `miniR.exe` and `miniR-1.bin` on one floppy and the remaining `miniR-?.bin` on a floppy each.

3) Via zip files in directory `zip`. You will need at least the files

          rw1031b1.zip rw1031b2.zip
          rw1031h.zip (text help) or rw1031ch.zip (Compiled HTML help)

and you may want `rw1031w.zip` (the HTML format help files), `rw1031l.zip` (the LaTeX format help files, used for offline printing), or `rw1031d?.zip` (the draft manuals, in PDF).

## 2.2 How do I install R for Windows?

First, you need Windows 95/98/ME/NT4/2000: Windows 3.11+win32s will not work. (Windows XP probably will.) Your file system must allow long file names (as is likely except perhaps for some network-mounted systems).

The simplest way is to use `SetupR.exe` or `miniR.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 supressed making a group for R).

For a manual installation, choose a location and unzip the zip files (with a tool that preserves long file names and the directory structure: we recommend the INFO-ZIP project's `unzip`). All the files will unpack into a directory `rw1031`.

Choose a working directory for R. Unless you used `SetupR.exe` or `miniR.exe` (which did this for you by default), make a shortcut to `rw1031\bin\Rgui.exe` on your desktop or somewhere on the Start menu file tree. Right-click the 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, for example `--sdi --max-mem-size=40M`. You can also set environment variables at the end of the Target field, for example `R_LIBS=p:/R/library`.

## 2.3 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.

## 2.4 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` and defaults to the smaller of the amount of physical RAM in the machine and 256Mb. It can be set to any amount over 10M. Be aware though that Windows has (in most versions) a maximum amount of user virtual memory of 2Gb, and parts of this can be reserved by processes but not used. R itself reserves 256Mb on startup. Because of the way the memory manager works, it is possible that there will be free memory but R will not be able to reserve it.

Use `?Memory` and `?memory.size` for information about memory usage.

R can be compiled to use a different memory manager which may be better at using large amounts of memory, but is substantially slower (making R several times slower on some tasks).

## 2.5 How can I keep workspaces for different projects in different directories?

Create a separate shortcut for each project: see Q2.3. 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.

## 2.6 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()`.
- 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)`.

## 2.7 Can I use `R BATCH`?

Yes, if you have Perl and the files for making source packages (from `SetupR.exe` or `rw1031sp.zip`) installed. The Windows analogue is `Rcmd BATCH`: use `Rcmd BATCH --help` for full details.

Otherwise you can set 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

## 2.8 Can I use rw1031 with ESS and emacs?

Yes. The latest versions of ESS (e.g. 5.1.18) 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.

## 2.9 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.
Otherwise if environment variables `HOMEDRIVE` and `HOMEPATH` are set, 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")`.

## 2.10 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:\\rw1031\\library\\xgobi\\scripts\\xgobi.bat"`. Make life easier for yourself by using forward slashes as path separators: they do work under Windows.

Another possible source of grief is spaces in folder names. We have tried to make R work on paths with spaces in, but lots of 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 most versions of Windows).

## 2.11 Does R use the Registry?

Not itself.

The installers set some entries to allow uninstallation. In addition they set a Registry key `LOCAL_MACHINE\Software\R-core\R` giving the version and install path. Again, this is not used by R itself, but it will be used by the DCOM interface (http://cran.r-project.org/other-software.html). Finally, a file association for extension `.RData` is set in the Registry.

You can add the Registry entries by running `RSetReg.exe` in the `bin` folder, and remove them by running this with argument `/U`. Note that the settings are all per machine and not per user, and that this neither sets up nor removes the file associations.

## 2.12 Entering certain characters crashes Rgui.

This seems to happen occasionally, and all the occurrences we have solved have been traced to faulty versions of `msvcrt.dll`. Try extracting the one to be found in the self-extracting archive ftp://ftp.microsoft.com/softlib/mslfiles/msvcrt.exe and put it in the `rw1031\bin` directory. Removing `msvcrt.dll` from that directory reverts to the standard behaviour.

This fix has solved other problems too, for example incorrect results in the date-time functions.

# 3 Packages

## 3.1 Can I install packages (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 has 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.

Note that the pre-compiled versions on CRAN are unsupported: see http://cran.r-project.org/bin/windows/contrib/ReadMe.

If there is not a pre-compiled version or that is not up-to-date or you prefer compiling from source, get `rw1031sp.zip` from the distribution (see Q1.1; you may already have installed this from `SetupR.exe`) and unpack it in the parent of `rw1031`. Then read the file `readme.packages`. You will need to collect and install several tools to use this. Once you have done so, just run `Rcmd INSTALL pkgname`. To check the package (including running all the examples on its help pages and in its test suite, if any) use `Rcmd check pkgname`: see the `Writing R Extensions' manual.

## 3.2 I don't have permission to write to the `rw1031\library` directory.

You can install packages anywhere and use the environment variable `R_LIBS` to point to the library location(s). You can also set the R variable `.lib.loc` in your `.Rprofile` or when running R.

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

    set the environment variable R_LIBS to p:\mylibs

OR put in the `.Rprofile` in the working directory or your home directory

    .lib.loc <- c("p:/mylibs", .Library)

OR use a package by, e.g.

    library(MASS, lib.loc="p:/mylibs")

How you set an environment variable is system specific: in Windows 9x you can set them in `autoexec.bat` or in an MS-DOS window from which you launch `Rgui` / `Rterm`. Under Windows NT/2000 you can use the control panel or the properties of `My Computer'. Under Windows Me you need to use the System Configuration Utility (under Programs, Accessories, System Tools on the Start menu). You can also set them on the command line, for example in the shortcut you could have

    path_to_R\bin\Rgui.exe R_LIBS=p:/mylibs

and you can set variables in a file `.Renviron` in the working directory or your home directory, for example

    R_LIBS=p:/mylibs

The order of precedence for environmental variables is the command line then `.Renviron` then the inherited environment.

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

The HTML search only works for packages installed in `rw1031\library`.

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()`.

## 3.4 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 is installed in `rw1031\library`.
- the package contains a `CONTENTS` file in its top-level directory.
- you updated the indices as described in the answer to Q3.3 after installing the package.

If those all hold true, this works for us.

## 3.5 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, and in particular a substantial minority need to be re-compiled for `rw1020` and later.

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 (if it has one) in the `libs` directory. (Right-click on the DLL in Windows Explorer, and select `Properties` or use the `DLL.version` function inside R.) If there is no `Built:` line or version tab, the package was compiled too long ago.

## 3.6 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. Download either ActiveTcl 8.3.3 from http://aspn.activestate.com/ASPN/Downloads/ActiveTcl/ or `tcl832.exe` from dev.scriptics.com and install it. (That will put the `bin` directory containing the Tcl and Tk DLLs in your path). You then need to set the environment variable `TCL_LIBRARY`, to something like `c:/Program Files/Tcl/lib/tcl8.3`. (The startup code for the package will warn you if this is unset, and Q3.2 explains how to set them. NB: do not quote the path, even if as here it contains spaces. If you forget, you can set the variable inside R by something like

        Sys.putenv("TCL_LIBRARY"="c:/Program Files/Tcl/lib/tcl8.3")

.)

## 3.7 Hyperlinks in Compiled HTML sometimes do not work.

Unfortunately, hyperlinks in compiled HTML files used from R are interpreted relative to the current working directory of the R process, not relative to the `pkg.chm` file. This was not discovered until `rw1021`: files made before that version work incorrectly. Remake the package to cure this.

# 4 Windows Features

## 4.1 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 can only access packages installed in the standard place.
- 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()`.

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

You have read the `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 the 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.

> 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 Preferences editor invoked from the `Edit` menu which can be used to edit the file `Rconsole`.

## 4.3 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 80.)

On one of our systems, the screen height is 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 is a 21" monitor and 400mm x 300mm!

## 4.4 How do I more focus to a graphics window or the console?

You may want to do this from within a function, for example when calling `idenitfy` 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`.

# 5 Workspaces

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

Have you changed the working directory?: see Q5.2.

## 5.2 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.

## 5.3 Can I load workspaces saved under Unix/GNU-Linux?

Yes. The converse (saving on Windows, loading on Unix) also works on almost all Unix systems, and workspaces can be interchanged with the Macintosh port too.

# 6 The R Console and Fonts

## 6.1 I would like to be able to use Japanese fonts

for example, in the console and to annotate graphs.

We believe this is possible by setting suitable fonts in the Rconsole and Rdevga configuration files (see Q4.2). You can specify additional fonts in Rdevga, and use them by

    par(font=, font.lab=, font.main=, font.sub=)

Nineteen fonts are specified (as 1 to 19) by default: you can add to these (up to 13 more) or replace them.

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

You need to specify a font in Rconsole (see Q4.2) that supports Latin1 encoding. The default, `Courier New`, does on our systems, as does `FixedSys`. This may be a problem in other locales, especially for non-Western European languages.

## 6.3 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 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.

## 6.4 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 message. Use the horizontal scrollbar or the <CTRL+arrow> keys to scroll horizontally.

# 7 Building from Source

## 7.1 How can I compile R from source?

Get the R sources. Suppose you want to compile R-1.3.1. Start in a directory whose path does not contain spaces, and run

    tar zxvf R-1.3.1.tgz
    cd R-1.3.1
    cd src\gnuwin32

Now read the `INSTALL` file and set up all the tools needed. Then you can just use `make`, sit back and wait. (A complete build takes about 15 minutes on a 300MHz PII with a fast local disc.)

You may need to compile under a case-honouring file system: we found that a `samba`-mounted file system (which maps all file names to lower case) did not work.

## 7.2 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 (in `SetupR.exe` or `rw1031sp.zip`), and get and install the tools (including Perl) and compilers mentioned in the file `readme.packages` contained therein. Then you can use

    ...\bin\Rcmd SHLIB foo.c bar.c

to make `foo.dll`. Use `...\bin\Rcmd 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`.

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

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

    make pkgclean-mypkg
    make DEBUG=T pkg-mypkg

Then you can debug by

    gdb /path/to/rw1031/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 (`rw1031/src/gnuwin32` for the main system, `rw1031/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 `eda` 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(eda)
           (gdb) break tukeyline
           (gdb) clear R_ReadConsole
           (gdb) continue

  Fortran symbols need an underline appended.

- Windows has little support for signals, so the usual 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 `mingw32` version of `gdb`. It does often work with the `cygwin` version.
- We have seen examples in debugging problems with Windows events that the `cygwin gdb` was able to catch but which terminated the `mingw32 gdb`.

If you have an X server available on the PC, there is a version of `DDD` available that runs under the cygwin emulation layer (follow the links at http://www.cygwin.com) and provides a graphical user interface to `gdb`. Another (Windows-native) GUI for `gdb` is `Insight`, part of the latest `cygwin` version of `gdb`.

## 7.4 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\Rcmd 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 is in package `cxx_0.0-x.tar.gz` in the `src/contrib/Devel` section on CRAN, and that can be compiled as a package in the usual way on Windows.

## 7.5 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.

## 7.6 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.

## 7.7 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()`.

## 7.8 The Perl scripts don't seem to work under Windows 9x/ME

This has been seen under some versions of Perl and Windows versions (95/98/ME) which use a 16-bit shell. Hopefully rw1030 and later are more robust in this respect: it may help to upgrade your Perl version (5.6.1, build 628 was current at the time of writing).