R BATCH?
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,
(rw1000 or later); the current version is often called something like
rw1011 (although not officially).
Go to any CRAN site (see http://cran.r-project.org/mirrors.html
for a list), navigate to the bin/windows/windows-NT/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.
First, you need Windows 95 or 98 or NT4 or 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. We use --vsize=10M --nsize=400k. You can also set
environment variables at the end of the Target field, for
example R_LIBS=e:/R/library.
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.
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.
It depends what you want to print.
dev.print().
File | Print.
RHOME\bin\helpPRINT.bat and have
latex installed you can print help files by help(fn_name, offline=TRUE).
R BATCH?No, but 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 --vsize=10M --nsize=500k --no-restore --no-save < %1 > %1.out
Yes. The latest versions of ESS (e.g. 5.1.13) 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.
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 getenv("R_USER").
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/windows-NT/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 cd src\gnuwin32
and read README.packages. You will need to collect and install
several tools to use this. Once you have done so, installation is easy:
just run make pkg-pkgname. To check the package (run all the examples
on its help pages) use make pkgcheck-pkgname.
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 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'. 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.
You can also build packages from anywhere to anywhere, but may be simpler to install a private copy of R to do the building.
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
The following conditions need to hold for functions in a package you installed.
rwXxxx\library.
CONTENTS file in top-level directory
(a few of the binary distributions do not).
If those all hold true, this works for us.
Rgui.exe
and <Ctrl-break> or <Ctrl-C> in Rterm.exe: <Ctrl-C>
is used for copying in the GUI version.
Rgui.exe, the menu item `Help |
Console' will give details.
help.start() does not automatically send help
requests to the browser: use options(htmlhelp=T) to turn this on.
source()) can be specified with
either "/" or "\\".
system() is slightly different: see its help page and that
of shell().
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 <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. From rw1010
there is a Preferences editor invoked from the Edit menu which
can be used to edit the file Rconsole.
Have you changed the working directory?: see Q5.2.
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 Image' menu item.
Yes. The converse (saving on Windows, loading on Unix) also works.
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.
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.
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.
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.
Get the R sources. Suppose you want to compile R-1.1.0.
tar zxvf R-1.1.0.tgz cd R-1.1.0 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.
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 DEBUG=T pkg-mypkg
Then you can debug by
gdb /path/to/rwXxxx/bin/Rgui.exe
However, note
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.
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.
mingw32
version of gdb. It does often work with the cygwin version.
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://sources.redhat.com/cygwin) and provides a
graphical user interface to gdb. Another (Windows-native) GUI
for gdb is Insight, part of the latest cygwin
version of gdb
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-2.95)
g++ -c X.cc X_main.cc dlltool --export-all-symbols --output-def X.def X_main.o dllwrap -o X.dll --def X.def X.o X_main.o -lstdc++
or if you have --shared (mingw32 gcc-2.95.1 or
cygwin 1.1)
g++ -shared -o X.dll 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.
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.
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.
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().
ripley@stats.ox.ac.uk