R for Windows FAQ Frequently Asked Questions on R for Windows Version for rw1022 Brian Ripley 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 rwXxxx 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! 3 Packages 3.1 Can I install packages (libraries) in this version? 3.2 I don't have permission to write to the `rwXxxx/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! 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 debug code that I have compiled and dyn.load-ed? 7.3 How do I include C++ code? 7.4 The output from my C code disappears. Why? 7.5 The output from my Fortran code disappears. Why? 7.6 The console freezes when my compiled code is running. 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 `rw1022' (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. You will need at least the files rwXxxxb1.zip rwXxxxb2.zip rwXxxxh.zip (text help) or rwXxxxch.zip (Compiled HTML help) and you may want `rwXxxxwh.zip' (the Windows help files) or `rwXxxxw.zip' (the HTML format help files), `rwXxxxl.zip' (the LaTeX format help files, used for offline printing), or `rwXxxxd?.zip' (the draft manuals, in PDF). Optionally, you can download the installer, `rwinst.exe'. 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. Your file system must allow long file names (as is likely except perhaps for some network-mounted systems). The simplest way is to run the installer (double-click on the icon for `rwinst.exe' and navigate its wizard-like pages). Alternatively, 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 called `rwXxxx', for some `Xxxx'. Choose a working directory for R. Make a shortcut to `rwXxxx\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 `--max-mem-size=40M'. You can also set environment variables at the end of the Target field, for example `R_LIBS=e:/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. 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 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 rwXxxx 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 , 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:\\rw1021\\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 for Unix do not bother. So it is worth trying the alternative short name (something like `PROGRA~1'; you can get if from the Properties). 3 Packages ********** 3.1 Can I install packages (libraries) in this version? ======================================================= Yes, of course. The easy way is to see if a pre-compiled binary version of the package is available: look on CRAN at `bin/windows/contrib'. If there is, download the zip file and unpack it in the `rwXxxx\library' directory, using `unzip' or similar, or using the installer `rwinst.exe'. Perhaps even easier is to use the R function `install.packages()': check out its help page. If there is not a binary version or that is not up-to-date or you prefer compiling from source, get `rwXxxxsp.zip' from the distribution (see Q1.1) and unpack it in `rwXxxx'. Then read the `readme.packages'. You will need to collect and install several tools to use this. Once you have done so, installation is easy: just run `Rcmd INSTALL pkgname'. To check the package (run all the examples on its help pages and in its test suite, if any) use `Rcmd check pkgname'. 3.2 I don't have permission to write to the `rwXxxx/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 --vsize=10M R_LIBS=e:/R/library and you can set variables in a file `.Renviron' in the working directory or your home directory, for example R_LIBS=e:/R/library R_VSIZE=10M R_NSIZE=400k The order of precedence is the command line (flags before variables) then `.Renviron' then the inherited environment. 3.3 The packages I installed do not appear in the HTML help system. =================================================================== HTML help only works for packages installed in `rwXxxx\library'. To update the HTML help files after you have installed a binary package, run at the R prompt. > link.html.help() (Using `install.packages()' does this for you. The source-code installation also does this automatically, and if you have that installed you can use (preferably) cd rwXxxx\src\gnuwin32\help make indices instead.) 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 `rwXxxx\library'. * the package contains a `CONTENTS' file in 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'. 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)') you need to have Tcl installed. Download `tcl832.exe' (or use `tcl831.exe' if you already have it) from 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.) 3.7 Hyperlinks in Compiled HTML sometimes do not work. ====================================================== Unfortunately, hyperlinks in compiled HTML files used from R are being interpreted relative to the current working directory of the R process, not relative to the `pkg.chm' file. This was not discovered until `rw1021', so only files made with that version are working correctly. Remake the package under `rw1021' or later to cure this. If you explore the installed `.chm' from Windows Explorer, the links will work. 4 Windows Features ****************** 4.1 What should I expect to behave differently from the Unix version of R? ========================================================================== * R commands can be interrupted by in `Rgui.exe' and or in `Rterm.exe': 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. * Using `help.start()' does not automatically send help requests to the browser: use `options(htmlhelp=T)' 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' 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 and , saved and replaced. Recording can be turned on automatically (the Recording item on the list) or individual plots can be added (Add or the 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'. 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. 5.3 Can I load workspaces saved under Unix/GNU-Linux? ===================================================== Yes. The converse (saving on Windows, loading on Unix) also works. 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: 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 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-1.2.1. tar zxvf R-1.2.1.tgz cd R-1.2.1 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 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/rwXxxx/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 (`rwXxxx/src/gnuwin32' for the main system, `rwXxxx/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' 7.3 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_0.0-0.tar.gz' in the `src/contrib/Devel' section on CRAN, and that can be compiled as package in the usual way on Windows. 7.4 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 (*note The output to the console seems to be delayed::), so that you will not normally see any output before returning to the R prompt. 7.5 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. 7.6 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 2001 January 3 by Brian Ripley