The R Project SVN – R – Diff – /trunk/src/gnuwin32/rw-FAQ.texi


\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
@end ifinfo
@ifhtml
@html
<hr>
@end html
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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                                @*
 
@sp 2
@end ifinfo
 
@ifhtml
@html
<h2>Version for <tt>@value{VERSION}</tt></h2>
<address>B. D. Ripley</address>
<hr>
@end html
@end ifhtml
 
@paragraphindent 0
 
@contents
 
@ifinfo
@sp 1
@end ifinfo
 
 
@node Top, Introduction, (dir), (dir)
 
@menu
* Introduction::
* Installation and Usage::
* Packages::
* Windows Features::
* Workspaces::
* The R Console and Fonts::
* 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://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html}.
@end display
 
The information here applies only to recent versions of R for Windows,
(@code{1.9.0} or later); the current version is often called something like
@code{@value{VERSION}} (although not officially).
 
 
 
@newchap{}
@node Installation and Usage, Packages, Introduction, Top
@chapter Installation and Usage
 
@menu
* Where can I find the latest version?::
* How do I install R for Windows?::
* Can I customize the installation?::
* How do I run it?::
* 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 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.::
* Other strange crashes.::
@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 @code{bin/windows/base}
directory and collect the files you need.  There are two versions of
the distribution.
 
1) @code{@RWVER@.exe} is about 21Mb.  This contains all the components
and allows as complete as installation as you choose.
 
2) Directory @code{miniR} contains @code{miniR.exe} and eight files
@code{miniR-?.bin}.  You can put @code{miniR.exe} and @code{miniR-1.bin}
on one floppy and the remaining @code{miniR-?.bin} on a floppy each.
This is a small installation, containing the text and compiled HTML
versions of the help files and the @emph{An Introduction to R} and
@emph{Data Import/Export} manuals in PDF.  There is no support for
@code{tcltk} in this version.
 
 
 
@node How do I install R for Windows?, Can I customize the installation?, Where can I find the latest version?, Installation and Usage
@section How do I install R for Windows?
 
You need Windows 95/98/ME/NT4/2000/XP: 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).
 
If you want 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.)
 
To use @code{@RWVER@.exe} or @code{miniR.exe}.  Just double-click on the
icon and follow the instructions.  If you installed R this way you can
uninstall it from the Control Panel or Start Menu (unless you supressed
making a group for R).
 
Choose a working directory for R.  If you installed manually, make a
shortcut to @code{@RWVER@\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 (@emph{after} any final double quote), for example @code{--sdi
--max-mem-size=200M}.  You can also set environment variables at the end
of the Target field, for example @code{R_LIBS=p:/myRlib}.
 
@node Can I customize the installation?, How do I run it?, How do I install R for Windows?, 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
either 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.  This is only useful with
@code{@RWVER@.exe}, which has components @code{main}, @code{chtml},
@code{html}, @code{latex}, @code{manuals}, @code{devel} and @code{tcl}.
@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 4
(@uref{http://jrsoftware.org/isinfo.php}) for details.
 
 
@node How do I run it?, How do I UNinstall R?, 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 an `MS-DOS window' (Windows 9x/ME), a `Command Prompt'
(Windows 2000/XP) or a port of a Unix shell such as @code{tcsh} or
@code{bash}. (The command line can be anything you would put in the
Target field of a shortcut, and the starting directory will be the
currect working directory of the shell.)
 
 
@node How do I UNinstall R?, What's the best way to upgrade?, How do I run it?, 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
@code{Add/Remove Programs} 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 for each installed version of R.)
 
Uninstalling R only removes files from the initial installation, not
(for example) packages you have installed.
 
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()} in the new R (`Update packages from CRAN' from
the Packages menu, if you prefer) 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.
 
 
@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
1Gb.  It can be set to any amount over 10M. (R will not run in less.)
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.  The version of the memory manager used from R
1.9.0 allocates large objects in their own memory areas and so is better
able to make use of fragmented virtual memory than that used from 1.2.0
to 1.8.x.
 
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.
 
R can be compiled to use a different memory manager which might be better
at using large amounts of memory, but is substantially slower (making R
several times slower on some tasks).
 
If you are running a version of Windows which supports more than 2Gb per
process, you can let the R executables use it by marking their headers
suitably.  If you have Visual Studio use
@smallexample
editbin /LARGEADDRESSAWARE \path\to\rwxxxx\bin\Rgui.exe
editbin /LARGEADDRESSAWARE \path\to\rwxxxx\bin\Rterm.exe
@end smallexample
and check this by
@smallexample
dumpbin /headers \path\to\rwxxxx\bin\Rgui.exe
dumpbin /headers \path\to\rwxxxx\bin\Rterm.exe
@end smallexample
You should see a line like
@smallexample
                   Application can handle large (>2GB) addresses
@end smallexample
 
 
@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 Q2.3.  All the paths to
files used by R are relative to the starting directory, so setting the
`Start in' field automatically helps separate projects.
 
Alternatively, start R by double-clicking on a saved @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 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 @code{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 configured @code{RHOME\bin\helpPRINT.bat} and have
LaTeX installed you can print help files by @code{help(fn_name, offline=TRUE)}.
@end itemize
 
 
@node Can I use R 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 BATCH}?
 
Yes.  The Windows analogue is @code{Rcmd BATCH}: use @code{Rcmd BATCH
--help} for full details.  (Perl is no longer required.)
 
You can set also up a batch file using @code{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, and users of Windows 95/98/ME's default
@code{command.com} `shell' will need to omit it. (That program has no
means to redirect @file{stderr}, and @code{Rterm.exe} sends warnings and
errors to the normal output file on such systems.)
 
 
@node Can I use @RWVER@ with ESS and (X)emacs?, What are HOME and working directories?, Can I use R BATCH?, Installation and Usage
@section Can I use @RWVER@ with ESS and (X)emacs?
 
Yes.  Recent versions of ESS (e.g. 5.1.20) 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
@code{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.@*
Otherwise if environment variables @env{HOMEDRIVE} and @env{HOMEPATH}
are set, the value is @code{$@{HOMEDRIVE@}$@{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 in R in three different ways.
@enumerate
@item
On the command line as name=value pairs.  For example in the shortcut to
@code{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} 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: in Windows 9x
you can set them in @file{autoexec.bat} or in an MS-DOS window from
which you launch @code{Rgui} / @code{Rterm}.  Under Windows NT/2000/XP you
can use the control panel or the properties of `My Computer'.  Under
Windows ME you can use the System Configuration Utility (under
Programs, Accessories, System Tools on the Start menu).  You may have to
log out or reboot for such changes to take effect.
@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
@code{"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.
 
Another possible source of grief is spaces in folder names.  We have
tried to make R work on paths with spaces in, but lots of people writing
packages for Unix do not bother.  So it is worth trying the alternative
short name (something like @code{PROGRA~1}; you can get it as the
`MS-DOS name' from the Properties of the file on most versions of
Windows, and from @code{dir /X} in a @code{Command Prompt} window on 2000/XP).
 
 
@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?
 
Not itself.
 
The installers set some entries to allow uninstallation.  In addition
(by default, but this can be de-selected) they set a Registry key
@code{LOCAL_MACHINE\Software\R-core\R} giving the version and install
path.  Again, this is not used by R itself, but it will be used by the
DCOM interface (@uref{http://cran.r-project.org/other-software.html}).
Finally, a file association for extension @code{.RData} is set in the
Registry.
 
You can add the Registry entries by running @code{RSetReg.exe} in the
@code{bin} folder, and remove them by running this with argument
@code{/U}.  Note that the settings are all per machine and not per user,
and that this 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
@code{Rproxy.dll} (in the R distribution) and @code{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 DCOM server is included in the distribution.  @strong{NOTE:}
You should ensure that the @code{@RWVER@/bin} directory is in your
path when using this software, so that the R library DLLs are found.
 
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.
 
 
@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 @code{internet2.dll} by starting R with the flag
@option{--internet2} (@pxref{How do I install R for Windows?}) which uses
the Internet Explorer internals (and so needs Internet Explorer 4 or
later installed).  Note that this does not work with proxies that need
authentication.
 
(b) A proxy needs to be set up: see @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:
 
@smallexample
/R/@RWVER@/bin/RGui.exe http_proxy=http://user:pass@@gannet:80/
 
/R/@RWVER@/bin/RGui.exe http_proxy=http://gannet/ http_proxy_user=ask
@end smallexample
 
@noindent
The second version will prompt the user for the proxy username and
password when HTTP downloads are first used.
 
 
@node Entering certain characters crashes Rgui., Other strange crashes., The internet download functions fail., Installation and Usage
@section Entering certain characters crashes Rgui.
 
This used to happen occasionally, and 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'.
 
If it still happens, try extracting the one to be found in the
self-extracting archive
@uref{ftp://ftp.microsoft.com/softlib/mslfiles/msvcrt.exe} and put it in
the @code{@RWVER@\bin} directory.  Removing @samp{msvcrt.dll} from that
directory reverts to the standard behaviour.
It seems that on some versions of Windows (but not 2000/XP) you also
need to put the @code{@RWVER@\bin} directory early in your path.
 
This fix has solved other problems too, for example incorrect results in
the date-time functions.  However, you are probably better off
re-installing Windows.
 
 
 
@node Other strange crashes.,  , Entering certain characters crashes Rgui., 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.) 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.
The only solution we know of is for the user to replace the buggy driver
that is causing the error.
 
 
 
@newchap{}
@node Packages, Windows Features, Installation and Usage, Top
@chapter Packages
 
 
@menu
* Can I install packages (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 Compiled HTML do not work.::
* update.packages() fails::
@end menu
 
 
@node Can I install packages (libraries) in this version?, I don't have permission to write to the @RWVER@\library directory, Packages, Packages
@section Can I install packages (libraries) in this version?
 
Yes, but you will need a lot of tools to do so, unless the author or the
maintainers of the @code{bin/windows/contrib} section on CRAN have been
kind enough to provide a pre-compiled version for Windows as a
@code{.zip} file.
 
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 (1.x) version will be stored in a separate area, so for R
1.9.? the files are in @code{bin/windows/contrib/1.9}.  You can try
those compiled for earlier versions, at your own risk.
 
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 precompiled packages.
 
If there is not a pre-compiled version or that is not up-to-date or
you prefer compiling from source, make sure you installed the
necessary files from @code{@RWVER@.exe}.  Then read the file
@file{readme.packages}.  You will need to collect and install several
tools to use this: you can download them via the portal at
@uref{http://www.stats.ox.ac.uk/pub/Rtools/}.  Once you have done so,
just run @code{Rcmd INSTALL pkgname}.  To check the package (including
running all the examples on its help pages and in its test suite, if
any) use @code{Rcmd check pkgname}: see the @emph{`Writing R
Extensions'} manual.
 
Note that this 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.
 
 
@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 (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 @code{p:\myRlib}.  Then you can
EITHER
 
@example
set the environment variable R_LIBS to p:\myRlib
@end example
@noindent
OR use a package by, e.g.
 
@example
library(mypkg, lib.loc="p:/myRlib")
@end example
 
 
 
@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.
 
To update the HTML indices after you have installed a pre-compiled
package, run at the R prompt.
 
@example
> link.html.help()
@end example
 
This is done automatically when installing from the Packages menu or
by @code{install.packages()}, and when @code{help.start} is run,
provided you have write permission in @file{@RWVER@}.
 
 
@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.
 
The following conditions need to hold for functions in a package you installed.
 
@itemize @bullet
@item the package is installed in @file{@RWVER@\library}.
@item the package contains a @file{CONTENTS} file in its top-level directory.
@item you updated the indices as described in the answer to Q3.3 after
installing the package.
@end itemize
@noindent
If those all hold true, this works for us.
 
If the help search system does not work @emph{at all}, this probably
indicates that Java support is either not installed or not enabled in
your browser.  Recent versions of browsers have made Java support
optional: for example it is optional in Netscape 6/7 and in Opera, and
may not be installed for IE6 on Windows XP.  You also need JavaScript
enabled.
 
@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
@code{Built:} line in its @file{DESCRIPTION} file or at the
@code{Version} tab of its DLL (if it has one) in the @file{libs}
directory.  (Right-click on the DLL in Windows Explorer and select
@code{Version} tab of the @code{Properties}, or use the
@code{DLL.version} function inside R.)
 
 
 
@node Package TclTk does not work., Hyperlinks in Compiled 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 by
@code{@value{VERSION}.exe}, although it is selected by default.
If the message is
@smallexample
Tcl/Tk support files were not installed
@end smallexample
the optional files were not installed, and you need to go back to the
installer and install them.  (Note: package @code{tcltk} is not part of
the @code{miniR} installer.)
 
Alternatively, if you have the environment variable @code{MY_TCLTK} set
to a non-empty value, it is assumed that you want to use a different
Tcl/Tk 8.4.x installation, and that this is set up correctly (with the
DLLs in your path and @code{TCL_LIBRARY} set).  In that case you do not
need the Tcl/Tk support files installed (but they can be).  Note that
you do need 8.4.x and not 8.3.x.  (If you build R from the sources
yourself you can configure it to use 8.3.x.)
 
 
@node  Hyperlinks in Compiled HTML do not work., update.packages() fails, Package TclTk does not work., Packages
@section Hyperlinks in Compiled HTML sometimes do not work.
 
They may well not work between packages installed in different
libraries.  This is solved under Unix using symbolic links which Windows
does not implement.
 
@node update.packages() fails,  , Hyperlinks in Compiled 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 @code{R_DEFAULT_PACKAGES} to include @code{foo}, you will
need to unset it temporarily.
 
@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?::
@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 @code{Rgui.exe}
and @key{Ctrl-break} or @key{Ctrl-C} in @code{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 @code{Rgui.exe}, the menu item `Help |
Console' will give details.  For @code{Rterm.exe} see file
@file{README.rterm}.
 
@item Using @code{help.start()} does not automatically send help
requests to the browser: use @code{options(htmlhelp=TRUE)} to turn this on.
 
@item The HTML help system has limitations in supporting cross-library links.
 
@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 @code{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 @code{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.
 
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 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 80.)
 
On one of our systems, the screen height is reported as 240mm, and the
width as 300mm in 1280 x 1024 mode and 320mm in 1280 x 960 and 1600 x 1200
modes.  In fact it is a 21" monitor and 400mm x 300mm!
 
@node How do I move focus to a graphics window or the console?,  , 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 @samp{Rgui.exe} in MDI and SDI modes, and can be used for
graphics windows from @samp{Rterm.exe} (although Windows may not always
act on it).
 
@newchap{}
@node Workspaces, The R Console and Fonts, 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 MacOS?::
@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 Q5.2.
 
 
@node How do I store my workspace in a different place?, Can I load workspaces saved under Unix/GNU-Linux or MacOS?, 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 MacOS?,  , How do I store my workspace in a different place?, Workspaces
@section Can I load workspaces saved under Unix/GNU-Linux or MacOS?
 
Yes.  All ports of R use the same format for workspaces, so they are
interchangeable (for the same 1.x.? version of R, at least).
 
 
@newchap{}
@node The R Console and Fonts, Building from Source, Workspaces, Top
@chapter The R Console and Fonts
 
 
@menu
* I would like to be able to use Japanese fonts::
* I don't see characters with accents at the R console::
* The output to the console seems to be delayed::
* Long lines seem to be truncated.::
@end menu
 
 
@node I would like to be able to use Japanese fonts, I don't see characters with accents at the R console, The R Console and Fonts, The R Console and Fonts
@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.
 
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
 
@example
par(font=, font.lab=, font.main=, font.sub=)
@end example
 
Nineteen fonts are specified (as 1 to 19) by default: you can add to these
(up to 13 more) or replace them.
 
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.
 
 
@node I don't see characters with accents at the R console, The output to the console seems to be delayed, I would like to be able to use Japanese fonts, The R Console and Fonts
@section 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, @code{Courier New}, does on our systems, as does
@code{FixedSys}.  This may be a problem in other locales, especially for
non-Western European languages.
 
Support for these characters within @code{Rterm} depends on the
environment (the terminal window and shell, including locale settings)
within which it is run as well as the font used by the terminal window.
 
If you are using a non-Latin1 language, you do need to ensure that the
fonts you selected support the language.  For example, it was found by
one Czech user (under Windows 98) that he had to select @code{Times New
Roman CE} or @code{Courier} (not @code{Courier New}) to get certain
Czech characters displayed correctly.
 
@node The output to the console seems to be delayed, Long lines seem to be truncated., I don't see characters with accents at the R console, The R Console and Fonts
@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 and Fonts
@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 and Fonts, 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?
 
Get the R sources.  Suppose you want to compile R-@value{RVERSION}.
Start in a directory whose path does not contain spaces, and run
 
@example
tar zxvf R-@value{RVERSION}.tgz
cd R-@value{RVERSION}
cd src\gnuwin32
@end example
@noindent
Now read the @file{INSTALL} file and set up all the tools needed.  Then you
can just use @code{make}, sit back and wait.  (A complete build takes about
5 minutes on a 2.4GHz P4 with a fast local disc.)
 
You may need to compile under a case-honouring file system: we found
that a @code{samba}-mounted file system (which maps all file names to lower
case) did not work.
 
@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 PIII or an Athlon XP are quite different and
neither will not 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}.
 
If you are building R from source, in the file @file{MkRules} there
are macros @code{USE_ATLAS} and @code{ATLAS_PATH}.  Set
@code{USE_ATLAS = YES} and @code{ATLAS_PATH} to where the ATLAS
libraries are located.  You will need to make the libraries yourself:
none of the binaries we have seen are compiled for the correct
compiler.
 
Even faster hand-coded routines are available as DLLs from Kazushige
Goto for certain CPUs (Pentium III and 4 and Opteron).  He does not
allow redistribution: they are currently available @emph{via}
@uref{http://www.cs.utexas.edu/users/kgoto/signup_first.html} and there
is support in the R sources to build @file{R_HOME\bin\Rblas.dll} to link
to one of his DLLs.  On the @code{svd} problem they took 6.8 sec.
 
 
@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 (in
@code{@RWVER@.exe}), and get and install the tools (including Perl) and
compilers mentioned in the file @file{readme.packages} contained
therein.  Then you can use
@example
...\bin\Rcmd SHLIB foo.c bar.f
@end example
@noindent
to make @code{foo.dll}.  Use @code{...\bin\Rcmd 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 @code{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} (see also
@uref{http://jrfonseca.dyndns.org/projects/gnu-win32/software/drmingw/}).
That will be able to pinpoint the error, most effectively if you build a
version of R with debugging information as described below.
 
First, build a version of the R system with debugging information by
 
@example
make clean
make DEBUG=T
@end example
@noindent
 
and make a debug version of your package by
 
@example
make pkgclean-mypkg
make DEBUG=T pkg-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
@code{gdb} will only be able to find the source code if we run in the
location where the source was compiled (@code{@RWVER@/src/gnuwin32} for
the main system, @code{@RWVER@/src/library/mypkg/src} for a package),
unless told otherwise by the @code{directory} command.  It is most
convenient to set a list of code locations via @code{directory} commands
in the file @file{.gdbinit} in the directory from which @code{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{eda} 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(eda)
     (gdb) break tukeyline
     (gdb) clear R_ReadConsole
     (gdb) continue
@end example
 
Fortran symbols need an underline appended.
 
@item
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 a @code{mingw}
version of @code{gdb}.  It does often work with the @code{cygwin} version.
 
@end itemize
 
 
@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
(@code{gcc})
 
@example
...\bin\Rcmd 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 is in package @code{cxx_0.0-x.tar.gz} in the
@file{src/contrib/Devel} section on CRAN, and that can 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 @code{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 @code{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 @code{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()}.
 
 
@ifhtml
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<address>
Last edited 2004 January 20 by Professor B. D. Ripley
<code><a href="mailto:ripley@@stats.ox.ac.uk">ripley@@stats.ox.ac.uk</a></code>
</address>
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@ifinfo
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Last edited 2004 January 20 by Professor B. D. Ripley <ripley@@stats.ox.ac.uk>
@end ifinfo
 
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