\input texinfo
@c %**start of header
@setfilename rw-FAQ.info
@settitle R for Windows FAQ
@setchapternewpage on
@set VERSION @RWVER@
@set RVERSION @RVER@
@c %**end of header
@documentlanguage en
@documentencoding ISO-8859-1

@finalout

@macro newchap{}
@ifinfo
@sp 1
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@titlepage
@title R for Windows FAQ
@subtitle Frequently Asked Questions on R for Windows
@subtitle Version @value{VERSION}
@author B. D. Ripley and D. J. Murdoch
@end titlepage

@ifinfo
R for Windows FAQ                           @*
Frequently Asked Questions on R for Windows @*
Version for @value{VERSION}                 @*
B. D. Ripley and D. J. Murdoch              @*

@sp 2
@end ifinfo

@ifhtml
@html
<h2>Version for <tt>@value{VERSION}</tt></h2>
<address>B. D. Ripley and D. J. Murdoch</address>
<hr>
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@paragraphindent 0

@contents

@ifinfo
@sp 1
@end ifinfo


@node Top, Introduction, (dir), (dir)

@menu
* Introduction::                
* Installation and Usage::      
* Languages and Internationalization::  
* Packages::                    
* Windows Features::            
* Workspaces::                  
* The R Console::               
* Building from Source::        
@end menu


@newchap{}
@node Introduction, Installation and Usage, Top, Top
@chapter 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

@display
@uref{http://CRAN.R-project.org/doc/FAQ/R-FAQ.html}.
@end display

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


@newchap{}
@node Installation and Usage, Languages and Internationalization, Introduction, Top
@chapter Installation and Usage

@menu
* Where can I find the latest version?::  
* How do I install R for Windows?::  
* How do I check an installation?::  
* Can I customize the installation?::  
* How do I run it?::            
* Can I run R from a CD or USB drive?::  
* How do I UNinstall R?::       
* What's the best way to upgrade?::  
* There seems to be a limit on the memory it uses!::  
* How can I keep workspaces for different projects in different directories?::  
* How do I print from R?::      
* Can I use R CMD BATCH?::      
* Can I use @RWVER@ with ESS and (X)emacs?::  
* What are HOME and working directories?::  
* How do I set environment variables?::  
* R can't find my file::        
* Does R use the Registry?::    
* Does R support automation?::  
* The Internet download functions fail.::  
* Entering certain characters crashes Rgui.::  
* What does 'DLL attempted to change FPU control word' mean?::  
* Other strange crashes.::      
* Why does R never use more than 50% of my CPU?::  
* Does R run under Windows Vista?::  
* Quotes don't come out right on the console/terminal/pager::  
* There is no tilde on my keyboard::  
@end menu


@node Where can I find the latest version?, How do I install R for Windows?, Installation and Usage, Installation and Usage
@section Where can I find the latest version?

Go to any CRAN site (see @uref{http://cran.r-project.org/mirrors.html}
for a list), navigate to the @file{bin/windows/base} directory and
collect the file(s) you need.  The current release is distributed as an
installer @samp{@RWVER@-win32.exe} of about 32Mb.  This contains all the
components and allows as complete as installation as you choose.

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

@node How do I install R for Windows?, How do I check an installation?, Where can I find the latest version?, Installation and Usage
@section How do I install R for Windows?

Current binary versions of R run on Windows 2000 or later.@footnote{R
2.6.2 was the last version for Windows 95. 98, ME and NT4.}  There is no
specific binary@footnote{See @ref{How can I compile R from source?} for
the possibility of building one from the sources.} 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
32-bit XP SP3 and 64-bit Vista and Windows Server 2008.

Your file system must allow case-honouring long file names (as is likely
except perhaps for some network-mounted systems).  A typical install
takes 50Mb of disk space, a full installation about 65Mb and a
minimal one about 29Mb.

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/Windows 7 installing for a single user using an account with
administrator rights@footnote{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
@file{C:\R}).  Installing to a network share (a filepath starting
with @code{\\machine\...}) is not supported: such paths will need to
mapped to a network drive.

To install use @samp{@RWVER@-win32.exe}.  Just double-click on the icon
and follow the instructions.  If you have an account with Administrator
privileges you will be able to install R in the @file{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 recent versions of
Windows 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 @file{@RWVER@\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 (@emph{after} any final double quote, and separated by a
space), for example @code{--sdi --max-mem-size=1G}.  You can also set
environment variables at the end of the Target field, for example
@code{R_LIBS=p:/myRlib}, and if you want to ensure that menus and
messages are in (American) English, @code{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'.


@node How do I check an installation?, Can I customize the installation?, How do I install R for Windows?, Installation and Usage
@section How do I check an installation is not corrupt?

Run the program @file{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.)

@node Can I customize the installation?, How do I run it?, How do I check an installation?, Installation and Usage
@section 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.

@table @samp
@item /SILENT
only show the installation progress window and error messages.
@item /VERYSILENT
only show error messages.
@item /DIR="x:\dirname"
set the default installation directory
@item /GROUP="folder name"
set the default Start-menu group name
@item /COMPONENTS="comma separated list of component names"
set the initial list of components: Components are named @samp{main},
@samp{html}, @samp{manuals}, @samp{manuals/basic},
@samp{manuals/technical}, @samp{manuals/refman}, @samp{libdocs},
@samp{tcl}, @samp{tcl/chm}, @samp{trans} and @code{tests}.
@end table

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

@table @samp
@item /SAVEINF="filename"
save the settings to the specified file.  Don't forget to use quotes if
the filename contains spaces.
@item /LOADINF="filename"
instructs the installer to load the settings from the specified file
after having checked the command line.
@end table

A successful installation has exit code 0: unsuccessful ones may give 1,
2, 3, 4 or 5.  See the help for Inno Setup
(@uref{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'.

@node How do I run it?, Can I run R from a CD or USB drive?, Can I customize the installation?, Installation and Usage
@section 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
@command{tcsh} or @command{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.)

@node Can I run R from a CD or USB drive?, How do I UNinstall R?, How do I run it?, Installation and Usage
@section 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.


@node How do I UNinstall R?, What's the best way to upgrade?, Can I run R from a CD or USB drive?, Installation and Usage
@section How do I UNinstall R?

Normally you can do this from the R group on the Start Menu or from the
@samp{Add/Remove Programs} or @samp{Programs and Features} group in the
Control Panel.  If it does not appear there or if you want to remove an
old version, run @file{unins000.exe} in the top-level installation
directory.  (There should be a separate uninstall item in the R group on
the Start Menu for each installed version of R.  On recent versions of
Windows 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.


@node What's the best way to upgrade?, There seems to be a limit on the memory it uses!, How do I UNinstall R?, Installation and Usage
@section 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
@code{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 @file{R\win-library\@var{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) @file{R\win-library\2.6} to
@file{R\win-library\2.7} before running
@code{update.packages(checkBuilt=TRUE, ask=FALSE)}.


@node There seems to be a limit on the memory it uses!, How can I keep workspaces for different projects in different directories?, What's the best way to upgrade?, Installation and Usage
@section There seems to be a limit on the memory it uses!

Indeed there is.  It is set by the command-line flag
@option{--max-mem-size} (@pxref{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 @code{?Memory} and @code{?memory.size} for information about memory
usage.  The limit can be raised by calling @code{memory.limit} within a
running R session.

The executables @file{Rgui.exe} and @file{Rterm.exe} support up to 3GB
of user address space per process under suitably enabled versions of
32-bit Windows (see
@uref{http://www.microsoft.com/whdc/system/platform/server/PAE/PAEmem.mspx},
@uref{http://msdn.microsoft.com/en-us/library/bb613473%28VS.85%29.aspx};
this is not enabled by default).  On such systems, the default for
@code{--max-mem-size} is the smaller of the amount of RAM and 2.5GB.  On
some 64-bit versions of Windows the user address space for a 32-bit
process is 4GB, and there the default for @code{--max-mem-size} is the
smaller of the amount of RAM and 3.5GB.

@c limits are documented at http://msdn.microsoft.com/en-us/library/aa366778%28VS.85%29.aspx

@node How can I keep workspaces for different projects in different directories?, How do I print from R?, There seems to be a limit on the memory it uses!, Installation and Usage
@section 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 @file{.RData} file
in the directory for the project you want to use, or drag-and-drop a
file with extension @file{.RData} onto an R shortcut.  In either case,
the working directory will be set to that containing the file.


@node How do I print from R?, Can I use R CMD BATCH?, How can I keep workspaces for different projects in different directories?, Installation and Usage
@section How do I print from R?

It depends what you want to print.

@itemize @bullet
@item
You can print the graphics window from its menu or by using
@code{dev.print} with suitable arguments (see its help page: most likely
@code{dev.print(win.graph)} will work).

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

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

@item
If you have LaTeX installed and a PostScript or PDF printing system you
can print help files by @code{help(fn_name, help_type="postscript")} (or
@code{"PDF"}).
@end itemize


@node Can I use R CMD BATCH?, Can I use @RWVER@ with ESS and (X)emacs?, How do I print from R?, Installation and Usage
@section Can I use @code{R CMD BATCH}?

Yes: use @code{R CMD BATCH --help} or @code{?BATCH} for full details.

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

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

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


@node Can I use @RWVER@ with ESS and (X)emacs?, What are HOME and working directories?, Can I use R CMD BATCH?, Installation and Usage
@section Can I use @RWVER@ 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
@code{C-c C-c}).

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


@node What are HOME and working directories?, How do I set environment variables?, Can I use @RWVER@ with ESS and (X)emacs?, Installation and Usage
@section What are HOME and working directories?

Several places in the documentation use these terms.

The working directory is the directory from which @code{Rgui} or
@command{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 @code{getwd()}.

The home directory is set as follows: If environment variable
@env{R_USER} is set, its value is used.  Otherwise if environment
variable @env{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 @file{C:\Documents and Settings\username\My Documents} on
Windows XP and @file{C:\Users\username\Documents} on Vista).  If that
fails, if both environment variables @env{HOMEDRIVE} and @env{HOMEPATH}
are set (and they normally are), the value is
@file{$@{HOMEDRIVE@}$@{HOMEPATH@}}.  If all of these fail, the current
working directory is used.

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

@node How do I set environment variables?, R can't find my file, What are HOME and working directories?, Installation and Usage
@section How do I set environment variables?

Environment variables can be set for @command{Rgui.exe} and
@command{Rterm.exe} in three different ways.
@enumerate
@item
On the command line as name=value pairs.  For example in the shortcut to
@command{Rgui} you could have

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

@item
In an environment file @file{.Renviron} in the working directory
or your home directory, for example containing the line

@example
R_LIBS=p:/myRlib
@end example

If you have permission to do so, you can also create an environment file
@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 @file{.Renviron} file or on the command line.)

See @code{?Startup} for more details of environment files.

@item
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'.
@end enumerate

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


@node R can't find my file, Does R use the Registry?, How do I set environment variables?, Installation and Usage
@section 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
@samp{"d:\\@RWVER@\\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.@: @samp{"xgobi.bat"} rather than just @samp{"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
@code{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 @samp{PROGRA~1}; you can get it as the
`MS-DOS name' from the Properties of the file on some versions of
Windows, and from @command{dir /X} in a @samp{Command Prompt} window).


@node Does R use the Registry?, Does R support automation?, R can't find my file, Installation and Usage
@section 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:
@itemize @bullet
@item  @code{HKEY_LOCAL_MACHINE\Software\R-core\R\Current Version}  
    contains the version number, currently @RVER@.
@item @code{HKEY_LOCAL_MACHINE\Software\R-core\R\[version]\InstallPath}
    (where @code{[version]} is currently @RVER@) contains the path to the R 
    home directory.
@end itemize
If you do not have administrative privileges on the machine while running
the installer, then the entries are created under @code{HKEY_CURRENT_USER}.

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

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


@node Does R support automation?, The Internet download functions fail., Does R use the Registry?, Installation and Usage
@section Does R support automation (OLE, COM)?

Directly, no.

There is a (D)COM server written by Thomas Baier available on CRAN
(@uref{http://cran.r-project.org/other-software.html}) which works with
@file{Rproxy.dll} (in the R distribution) and @file{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 @code{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 @uref{http://www.omegahat.org/},
which allows R objects to be exported as COM values.  That site also
has packages @code{RDCOMClient} and @code{SWinTypeLibs} which allow R
to act as a (D)COM client.  However, they are normally not available as
pre-compiled packages for Windows.


@node The Internet download functions fail., Entering certain characters crashes Rgui., Does R support automation?, Installation and Usage
@section The Internet download functions fail.

for example @code{update.packages()} and the menu items on the Packages menu.

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

(a) Use the alternative @file{internet2.dll} by starting R with the flag
@option{--internet2} (@pxref{How do I install R for Windows?}) or
calling @code{setInternet2(TRUE)}.  These cause R to use the Internet
Explorer internals.@footnote{and so may need Internet Explorer installed,
althought these are part of recent versions of Windows}.  Note that this
does not work with proxies that need authentication.

(b) A proxy needs to be set up: see @code{?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:

@example
"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
@end example

@noindent
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.


@node Entering certain characters crashes Rgui., What does 'DLL attempted to change FPU control word' mean?, The Internet download functions fail., Installation and Usage
@section 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 @samp{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'.

@node What does 'DLL attempted to change FPU control word' mean?, Other strange crashes., Entering certain characters crashes Rgui., Installation and Usage
@section What does 'DLL attempted to change FPU control word' mean?

This is a @emph{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 @code{?dyn.load}.

@node Other strange crashes., Why does R never use more than 50% of my CPU?, What does 'DLL attempted to change FPU control word' mean?, Installation and Usage
@section Other strange crashes.

Some users have found that @code{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.


@node Why does R never use more than 50% of my CPU?, Does R run under Windows Vista?, Other strange crashes., Installation and Usage
@section 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.


@node Does R run under Windows Vista?, Quotes don't come out right on the console/terminal/pager, Why does R never use more than 50% of my CPU?, Installation and Usage
@section Does R run under Windows Vista/7/Server 2008?

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.)

The comments here apply to Windows Vista, Server 2008 and Windows 7.

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 @file{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
@url{http://technet.microsoft.com/en-us/windowsvista/aa906021.aspx}
and
@url{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 @file{.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 @code{.chm} and @code{.dll} files in
the system area without credentials.)  There are several ways around
this.

@itemize
@item
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'.)

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

@item
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: @xref{I don't
have permission to write to the @RWVER@\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 @env{R_LIBS_SITE} in @file{etc\Renviron.site}.  @xref{What
are HOME and working directories?}.  There is a standard location for a
site library, the @file{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.
@end itemize


Another issue with Vista is that the standard POSIX ways that R uses
(e.g.@: in @code{file.info} and @code{file.access}) to look at file
permissions no longer work reliably.  @code{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 (but still not 100% correct).

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.


@node Quotes don't come out right on the console/terminal/pager, There is no tilde on my keyboard, Does R run under Windows Vista?, Installation and Usage
@section 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 @code{sQuote} and
@code{dQuote}) is controlled by @code{getOption("useFancyQuotes")} whose
default is @code{FALSE} except for the @code{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 @command{chcp}, with @command{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 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 @code{Rgui} console and internal pager is
@code{Courier New}, which has directional quotes on all the systems we
tried.  @code{Lucida Console} has elegant glyphs for directional quotes,
but seems rather light on Windows XP (it looks better than @code{Courier
New} on Vista).  Non-TrueType fonts such as @code{Courier} and
@code{FixedSys} lack directional double quotes on all the systems we
tried.

@node There is no tilde on my keyboard,  , Quotes don't come out right on the console/terminal/pager, Installation and Usage
@section 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 @code{]} in Canadian (multilingual), German and Scandinavian
layouts, @code{1} in Eastern Europe, @code{[} in Portuguese, @code{4} or
@code{5} in Spanish, @code{/} in Francophone Belgian, and so on.  For
some keyboards the uses of AltGr are at
@url{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).

@newchap{}
@node Languages and Internationalization, Packages, Installation and Usage, Top
@chapter Languages and Internationalization

@menu
* The installer does not offer my language::  
* I want R in English!::        
* I want to run R in Chinese/Japanese/Korean::  
* I selected English for installation but R runs in Chinese::  
* I would like to be able to use Japanese fonts::  
* I don't see characters with accents at the R console::  
* The dialog buttons are not translated::  
@end menu

@node The installer does not offer my language, I want R in English!, Languages and Internationalization, Languages and Internationalization
@section The installer does not offer my language.

Two things may be happening.  First, in earlier version only languages
which can be displayed using the current codepage were offered so you
could install in Japanese unless running Windows in Japanese: this
changed in mid-2009 in time for R 2.10.0

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).

@node I want R in English!, I want to run R in Chinese/Japanese/Korean, The installer does not offer my language, Languages and Internationalization
@section 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 @code{LANGUAGE=en} as discussed in Q2.2 and
Q2.15, or in the @file{Rconsole} file.

@node I want to run R in Chinese/Japanese/Korean, I selected English for installation but R runs in Chinese, I want R in English!, Languages and Internationalization
@section 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 @command{Rterm.exe} and @command{RGui.exe} support single- and
double-width characters.  It will be necessary to select suitable fonts
in files @file{Rconsole} and @file{Rdevga} (see @code{?Rconsole} or the
comments in the files: the system versions are in the @file{etc}
folder); in the latter you can replace @code{Arial} by @code{Arial
Unicode MS}, and we tried @code{FixedSys} and @code{MS Mincho} in
@file{Rconsole}.  (Note that @file{Rdevga} only applies to Windows
graphics devices and not, say, to @code{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
@code{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
@uref{http://msdn.microsoft.com/library/default.asp?url=/library/en-us/vccore98/html/_crt_language_and_country_strings.asp}:
beware that @code{"Chinese"} is Traditional Chinese (code page 950,
Big5) and @code{"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 @emph{both} the `Regional
Options' and `Advanced' tabs.

When using @command{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 @command{chcp}).

@node I selected English for installation but R runs in Chinese, I would like to be able to use Japanese fonts, I want to run R in Chinese/Japanese/Korean, Languages and Internationalization
@section I selected English for installation but R runs in Chinese.

Precisely, you selected English @strong{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
@emph{locale}: please read the appropriate manual (the @emph{R
Installation and Administration Manual}) for the details.  You can
ensure that R uses English messages by appending @code{LANGUAGE=en} to
the shortcut you use to start R, or setting it in the @file{Rconsole} file.

@node I would like to be able to use Japanese fonts, I don't see characters with accents at the R console, I selected English for installation but R runs in Chinese, Languages and Internationalization
@section 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 @code{windows()} graphics device can handle most common
Japanese characters, but more specialized fonts may need to be set.
(See Q5.2 for how to set fonts: the console font can also be set from
the `GUI preferences' menu item.)  The help for @code{windowsFonts} has
examples of selecting Japanese fonts for the @code{windows()} family of
devices.

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

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

@node I don't see characters with accents at the R console, The dialog buttons are not translated, I would like to be able to use Japanese fonts, Languages and Internationalization
@section I don't see characters with accents at the R console, for example in ?text.

You need to specify a font in @file{Rconsole} (see Q5.2) 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 @command{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.

@node The dialog buttons are not translated,  , I don't see characters with accents at the R console, Languages and Internationalization
@section The dialog buttons are not translated.

In most cases they actually are, but by Windows.  Setting the locale
or the @code{LANGUAGE} environment variable does not change the
Windows setting of its `UI language'.  Under (international) Windows
XP there are three tabs on the @emph{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
@uref{http://msdn.microsoft.com/library/default.asp?url=/library/en-us/intl/nls_0ddl.asp}.

@newchap{}
@node Packages, Windows Features, Languages and Internationalization, Top
@chapter Packages


@menu
* Can I install packages into libraries in this version?::  
* I don't have permission to write to the @RWVER@\library directory::  
* The packages I installed do not appear in the HTML help system::  
* My functions are not found by the HTML help search system.::  
* Loading a package fails.::    
* Package TclTk does not work.::  
* Hyperlinks in HTML do not work.::  
* update.packages() fails::     
* How do I add to the list of repositories?::  
* Help is not shown for some of the packages::  
@end menu


@node Can I install packages into libraries in this version?, I don't have permission to write to the @RWVER@\library directory, Packages, Packages
@section 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 @file{bin/windows/contrib} section on CRAN have been
kind enough to provide a pre-compiled version for Windows as a
@code{.zip} file, or the package is a simple one involving no compiled
code (and pre-compiled versions are usually available for simple
packages).

You can install pre-compiled packages either from CRAN or from a local
@code{.zip} file by using @code{install.packages}: see its help page.
There are menu items on the @code{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 @file{bin/windows/contrib/2.7}.  You can try
those compiled for earlier versions, at your own risk, but help may well
not work correctly with those installed before R 2.10.0.

Note that the pre-compiled versions on CRAN are unsupported: see
@uref{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'.  Source packages
which contain no C/C++/Fortran code which needs compilation can simply
be installed by @code{install.packages(type = "source")} or @command{R
CMD INSTALL pkgname}.  Otherwise you will need to collect and install
several tools: you can download them via the portal at
@uref{http://www.murdoch-sutherland.com/Rtools/}.  Once you have done
so, just run @command{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 @command{R CMD check pkgname} (which needs Perl
installed): see the @emph{`Writing R Extensions'} manual.

Note that setting up Windows to install a source package that needs
compilation is rather tricky; please do ensure that you have followed
the instructions @strong{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 @url{http://win-builder.r-project.org}.

@node I don't have permission to write to the @RWVER@\library directory, The packages I installed do not appear in the HTML help system, Can I install packages into libraries in this version?, Packages
@section I don't have permission to write to the @file{@RWVER@\library} directory.

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

Suppose your packages are installed in @file{p:\myRlib}.  Then you can
EITHER

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

OR use a package by, e.g.@:

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

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

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

@noindent
to do so.  If you use @code{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 @code{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 and later:
@xref{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.


@node The packages I installed do not appear in the HTML help system, My functions are not found by the HTML help search system., I don't have permission to write to the @RWVER@\library directory, Packages
@section The packages I installed do not appear in the HTML help system.

This question applied to the pre-2.10.0 HTML help system, which has been
replaced.


@node My functions are not found by the HTML help search system., Loading a package fails., The packages I installed do not appear in the HTML help system, Packages
@section My functions are not found by the HTML help search system.

This question applied to the pre-2.10.0 search system, which has been
replaced.


@node Loading a package fails., Package TclTk does not work., My functions are not found by the HTML help search system., Packages
@section 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
@samp{Built:} line in its @file{DESCRIPTION} file or at the
@samp{Version} tab of its DLL in the @file{libs} directory.
(Right-click on the DLL in Windows Explorer and select @samp{Version}
tab of the @samp{Properties}, or use the @code{DLL.version} function
inside R.)


@node Package TclTk does not work., Hyperlinks in HTML do not work., Loading a package fails., Packages
@section Package TclTk does not work.

For package @code{tcltk} to work (try @code{demo(tkdensity)} or
@code{demo(tkttest)} after @code{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
@example
Tcl/Tk support files were not installed
@end example
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 @env{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 @file{bin} directory
given by value of @env{MY_TCLTK}, and that this is set up correctly
(with @env{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 or 8.6.0.

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

@example
MY_TCLTK=c:/Tcl/bin
@end example

@noindent
@strong{but} current versions 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 @code{Teacup} facility.


@node  Hyperlinks in HTML do not work., update.packages() fails, Package TclTk does not work., Packages
@section Hyperlinks in HTML sometimes do not work.

This question was much more relevant prior to version 2.10.0.

They may still not work between packages installed in different libraries
if the HTTP server has been disabled: the remedy is not to do that!



@node update.packages() fails, How do I add to the list of repositories?, Hyperlinks in HTML do not work., Packages
@section @code{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 @code{update.packages()}
(or the menu equivalent) in a new session.

If you put @code{library(foo)} in your @file{.Rprofile} you will need to
start R with @option{--vanilla} to be able to update package @code{foo}.
If you set @env{R_DEFAULT_PACKAGES} to include @code{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,
@emph{Google Desktop} being a known example.


@node How do I add to the list of repositories?, Help is not shown for some of the packages, update.packages() fails, Packages
@section How do I add to the list of repositories?

as shown in the @code{Select repositories...} item on the
@code{Packages} menu?

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

@node Help is not shown for some of the packages,  , How do I add to the list of repositories?, Packages
@section Help is not shown for some of the packages

This was about Compiled HTML help, which is not longer supported.


@newchap{}
@node Windows Features, Workspaces, Packages, Top
@chapter Windows Features

@menu
* What should I expect to behave differently from the Unix version::  
* I hear about some nifty features.::  
* Circles appear as ovals on screen::  
* How do I move focus to a graphics window or the console?::  
* What does TAB completion do?::  
@end menu


@node  What should I expect to behave differently from the Unix version, I hear about some nifty features., Windows Features, Windows Features
@section  What should I expect to behave differently from the Unix version of R?

@itemize @bullet
@item R commands can be interrupted by @key{Esc} in @command{Rgui.exe}
and @key{Ctrl-break} or @key{Ctrl-C} in @command{Rterm.exe}:
@key{Ctrl-C} is used for copying in the GUI version.

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

@item Paths to files (e.g.@: in @code{source()}) can be specified with
either "/" or "\\".

@item @code{system()} is slightly different: see its help page and that
of @code{shell()}.
@end itemize


@node I hear about some nifty features., Circles appear as ovals on screen, What should I expect to behave differently from the Unix version, Windows Features
@section I hear about some nifty features: please tell me about them!

You have read the file @file{README.@RWVER@}? 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 @code{png}, @code{jpeg},
@code{bmp}, @code{postscript}, @code{PDF} or @code{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 @code{options(width=)} is automatically
set to the console width (unless disabled in the configuration file).

The graphics has a history mechanism.  As @file{README.@RWVER@} says:

@quotation
`The History menu allows the recording of plots.  When plots have been
recorded they can be reviewed by @key{PgUp} and @key{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 @key{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 @strong{not} be used as a permanent
  storage format for R plots.

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

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


@node Circles appear as ovals on screen, How do I move focus to a graphics window or the console?, I hear about some nifty features., Windows Features
@section 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 @code{windows} or as options: see @code{?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!

@node How do I move focus to a graphics window or the console?, What does TAB completion do?, Circles appear as ovals on screen, Windows Features
@section 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
@samp{identify} or @samp{readline}.  Use the function
@samp{bringToTop()}.  With its default argument it brings the active
graphics window to the top and gives it focus.  With argument @samp{-1}
it brings the console to the top and gives it focus.

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


@node What does TAB completion do?,  , How do I move focus to a graphics window or the console?, Windows Features
@section What does TAB completion do?

R 2.5.0 introduced @kbd{TAB} completion in both @command{Rgui} and
@command{Rterm}.  Hitting @kbd{TAB} whilst entering a command line
completes the current `word' as far as is unambiguously possible.
Hitting @kbd{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 @kbd{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 @kbd{apr} folloed by @kbd{TAB}
will (in a vanilla session) complete to @code{apropos}.  After a
function name and parenthesis (e.g.@: @kbd{apropos(}) it will complete
argument names (and @kbd{=}), and after @kbd{$} or @kbd{@@} it will
complete list components or slot names respectively.

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

@example
?rc.settings
@end example

@noindent
which also explains how the various types of completion work.

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

@newchap{}
@node Workspaces, The R Console, Windows Features, Top
@chapter Workspaces


@menu
* My workspace gets saved in a strange place.  How do I stop this?::  
* How do I store my workspace in a different place?::  
* Can I load workspaces saved under Unix/GNU-Linux or Mac OS?::  
@end menu


@node My workspace gets saved in a strange place.  How do I stop this?, How do I store my workspace in a different place?, Workspaces, Workspaces
@section My workspace gets saved in a strange place: how do I stop this?

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


@node How do I store my workspace in a different place?, Can I load workspaces saved under Unix/GNU-Linux or Mac OS?, My workspace gets saved in a strange place.  How do I stop this?, Workspaces
@section 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 @code{setwd}: see its help page.


@node Can I load workspaces saved under Unix/GNU-Linux or Mac OS?,  , How do I store my workspace in a different place?, Workspaces
@section 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 UTF-8 or perhaps Latin-1 (which used to be used for English).)


@newchap{}
@node The R Console, Building from Source, Workspaces, Top
@chapter The R Console


@menu
* The output to the console seems to be delayed::  
* Long lines seem to be truncated.::  
@end menu




@node The output to the console seems to be delayed, Long lines seem to be truncated., The R Console, The R Console
@section 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: @key{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 @code{flush.console()} will write out
the buffer and so update the console.


@node Long lines seem to be truncated.,  , The output to the console seems to be delayed, The R Console
@section Long lines in the console or pager are truncated.

They only @strong{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 @key{CTRL + left/right arrow} keys to scroll
horizontally. (The @key{left/right arrow} keys work in the pager too.)



@newchap{}
@node Building from Source,  , The R Console, Top
@chapter Building from Source

@menu
* How can I compile R from source?::  
* Can I use a fast BLAS?::      
* How do I include compiled C code?::  
* How do I debug code that I have compiled and dyn.load-ed?::  
* How do I include C++ code?::  
* The output from my C code disappears.::  
* The output from my Fortran code disappears.::  
* The console freezes when my compiled code is running::  
@end menu


@node How can I compile R from source?, Can I use a fast BLAS?, Building from Source, Building from Source
@section How can I compile R from source?

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

To build a 64-bit version on 64-bit Windows you will need a suitable
compiler, and experiments with the Mingw64 port of @code{binutils} and
@code{gcc} have failed to produce a working version on R.  You are of
course welcome to try a commercial compiler@footnote{such as those from
Intel and PGI: there is no Fortran compiler in the Microsoft set, but
@code{f2c} could be used.}, and pre-compiled versions using such
compilers are available from R redistributors.

@node Can I use a fast BLAS?, How do I include compiled C code?, How can I compile R from source?, Building from Source
@section  Can I use a fast BLAS?

Fast BLAS (Basic Linear Algebra Subprograms,
@uref{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 (@uref{http://math-atlas.sourceforge.net}).
The savings can be appreciable: on a 2.6GHz P4 and a 1000 x 1000 matrix
@code{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 @file{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
@file{bin/windows/contrib/ATLAS}.  See the  @emph{R
Installation and Administration Manual} for how to build an ATLAS
@file{Rblas.dll} tuned to your system using the R sources.

@node  How do I include compiled C code?, How do I debug code that I have compiled and dyn.load-ed?, Can I use a fast BLAS?, Building from Source
@section How do I include compiled C code?

We strongly encourage you to do this @emph{via} building an R package:
see the @emph{`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 and compilers mentioned in the
@emph{`R Installation and Administration'} manual.  Then you can use
@example
...\bin\R CMD SHLIB foo.c bar.f
@end example
@noindent
to make @file{foo.dll}.  Use @command{...\bin\R CMD SHLIB --help} for
further options, or see @code{?SHLIB}.

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



@node How do I debug code that I have compiled and dyn.load-ed?, How do I include C++ code?, How do I include compiled C code?, Building from Source
@section How do I debug code that I have compiled and dyn.load-ed?

You will need a suitable version of @command{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 @emph{just-in-time} debugger to catch crashes, consider
@code{Dr. Mingw} from the @code{mingw-utils} bundle on
@uref{http://www.mingw.org}.  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

@example
make clean
make DEBUG=T
@end example

@noindent
and make a debug version of your package by either

@example
make pkgclean-mypkg
make DEBUG=T pkg-mypkg
@end example

@noindent
or

@example
Rcmd install -c mypkg
set DEBUG=T
Rcmd install mypkg
@end example

@noindent
Then you can debug by

@example
gdb /path/to/@RWVER@/bin/Rgui.exe
@end example

@noindent
However, note

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

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

@example
     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)
     ...
@end example

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

@item
Fortran symbols need an underline appended.

@item
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 @code{mingw}
version of @command{gdb}.  It does often work with the @code{cygwin} version.

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

@end itemize

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


@node  How do I include C++ code?, The output from my C code disappears., How do I debug code that I have compiled and dyn.load-ed?, Building from Source
@section  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
 @code{extern "C"}.

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

@example
...\bin\R CMD SHLIB X.cc X_main.cc
@end example

@noindent
or (VC++, which requires extension @code{.cpp})

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

@noindent
or (Borland C++, which also requires extension @code{.cpp})

@example
bcc32 -u- -WDE X.cpp X_main.cpp
@end example

@noindent
and call the entry point(s) in @code{X_R}, such as @code{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 @file{cxx_0.0-x.tar.gz} in the
@file{src/contrib/Devel} section on CRAN, and could be compiled as a
package in the usual way on Windows.


@node  The output from my C code disappears., The output from my Fortran code disappears., How do I include C++ code?, Building from Source
@section  The output from my C code disappears.  Why?

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

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


@node  The output from my Fortran code disappears., The console freezes when my compiled code is running, The output from my C code disappears., Building from Source
@section  The output from my Fortran code disappears.  Why?

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

Note that output from the console is delayed (@pxref{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 @code{xxxpr}
subroutines.


@node  The console freezes when my compiled code is running,  , The output from my Fortran code disappears., Building from Source
@section 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 @code{R_ProcessEvents()} periodically from your compiled code.
If you want output to be updated on the console, call
@code{R_FlushConsole()} and then @code{R_ProcessEvents()}.

@set LASTEDIT 2009-02-04
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Last edited @value{LASTEDIT}: comments to
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