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<h1>R Installation and Administration</h1>

<p>This is a guide to installation and administration for R.

<p>The current version of this document is 1.4.1 (2002-01-30).

</ul>

<a name="Obtaining%20R"></a>

<h1>1 Obtaining R</h1>

<p>Sources, binaries and documentation for R can be obtained via
<small>CRAN</small>, the "Comprehensive R Archive Network".  See the file
<code>RESOURCES</code> for information on <small>CRAN</small>.

</ul>

<a name="Getting%20and%20unpacking%20the%20sources"></a>

<h2>1.1 Getting and unpacking the sources</h2>

<p>The simplest way is to download the most recent
<code>R-<var>x</var>.<var>y</var>.<var>z</var>.tgz</code> file, and unpack it with

<pre>tar xvfz R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
</pre>

<p>on systems that have GNU <code>tar</code> installed.  On other systems you
need at least to have the <code>gzip</code> program installed.  Then you
can use

<pre>gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tgz | tar xvf -
</pre>

<p>If you need to transport the sources on floppy disks, you can download
the <code>R-<var>x</var>.<var>y</var>.<var>z</var>.tgz-split.*</code> files and paste them
together at the destination with (Unix)

<pre>cat R-<var>x</var>.<var>y</var>.<var>z</var>-split.* &gt; R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
</pre>

<p>and proceed as above.  If you want the build to be usable by a group of
users, set <code>umask</code> before unpacking so that the files will be
readable by the target group (e.g., <code>umask 022</code> to be usable by all
users).

<p>Finally, for minor-minor releases (<code><var>x</var>.<var>y</var>.<var>z</var></code> with
<var>z</var> != 0), a patch against the preceding release is made available
in
<code>R-<var>x</var>.<var>y</var>.<var>{z-1}</var>-<var>x</var>.<var>y</var>.<var>z</var>.diff.gz</code>
(e.g., <code>R-1.2.2-1.2.3.diff.gz</code>), which is generally a much smaller
file that the <code>.tgz</code> files.  Such a file can be applied to the
sources of the previous version by changing to the top directory of it
and

<pre>gzip -dc /path/to/it/R-<var>x</var>.<var>y</var>.<var>{z-1}</var>-<var>x</var>.<var>y</var>.<var>z</var>.diff.gz | patch -E -p1
</pre>

<p>Beware that this does not necessarily work if the older sources have
been modified (e.g., by building in their directories).

<a name="Using%20rsync"></a>

<h2>1.2 Using rsync</h2>

<p>Sources are also available via anonymous rsync.  Use

<pre>rsync -rC rsync.r-project.org::<var>module</var> R
</pre>

<p>to create a copy of the source tree specified by <var>module</var> in the
subdirectory <code>R</code> of the current directory, where <var>module</var>
specifies one of the four existing flavors of the R sources, and can be
one of <code>r-release</code> (current released version), <code>r-patched</code>
(patched released version), and <code>r-devel</code> (development version,
less stable), and <code>r-ng</code> (next generation, unstable).  The rsync
trees are created directly from the master CVS archive and are updated
hourly.  The <code>-C</code> option in the <code>rsync</code> command is to
cause it to skip the CVS directories.  Further information on
<code>rsync</code> is available at <a href="http://rsync.samba.org/rsync/">http://rsync.samba.org/rsync/</a>.

<a name="Installing%20R%20under%20Unix"></a>

<h1>2 Installing R under Unix</h1>

<p>R will configure and build from source under a number of common
Unix-like platforms, including <code>i386-freebsd</code>,
<code>i386-linux-gnu</code>, <code>i386-sun-solaris</code>,
<code>powerpc-linux-gnu</code>, <code>powerpc-apple-darwin</code>,
<code>mips-sgi-irix</code>, <code>alpha-linux-gnu</code>, <code>alpha-dec-osf4</code>,
<code>rs6000-ibm-aix</code>, <code>hppa-hp-hpux</code>, <code>sparc-linux-gnu</code> and
<code>sparc-sun-solaris</code>.

<p>In addition, binary distributions are available for most common Linux
distributions, Compaq Alpha systems running OSF/Tru64, and for MacOS X
(Darwin) with X11.  See the <small>FAQ</small> for current details.  These
are installed in platform-specific ways.  So for the rest of this
chapter we consider only building from the sources.

</ul>

<a name="Simple%20compilation"></a>

<h2>2.1 Simple compilation</h2>

<p>First review the essential and useful tools and libraries in
<a href="#Essential%20and%20useful%20other%20programs">Essential and useful other programs</a>, and install those you want or
need.

<p>Choose a place to install the R tree (R is not just a binary, but
has additional data sets, help files, font metrics etc).  Let us call
this place <code>R_HOME</code>.  Untar the source code.  This should create
directories <code>src</code>, <code>doc</code>, and several more.  Issue the
following commands:

<pre>./configure
make
</pre>

<p>(See <a href="#Using%20make">Using make</a> if your make is not called <code>make</code>.)

<p>Then check the built system works correctly, by

<pre>make check
</pre>

<p>Failures are not necessarily problems as they might be caused by missing
functionality, but you should look carefully at any reported
discrepancies.  To re-run the tests you would need
<pre>make check FORCE=FORCE
</pre>

<p>If these commands execute successfully, the R binary will be copied
to the <code>${R_HOME}/bin</code> directory.  In addition, a shell-script
front-end called <code>R</code> will be created and copied to the same
directory.  You can copy this script to a place where users can invoke
it, for example to <code>/usr/local/bin/R</code>.  You could also copy the man
page <code>R.1</code> to a place where your <code>man</code> reader finds it,
such as <code>/usr/local/man/man1</code>.  If you want to install the complete
R tree to, e.g., <code>/usr/local/lib/R</code>, see <a href="#Installation">Installation</a>. 
Note: you do not <em>need</em> to install R: you can run it from where
it was built.

<p>You do not necessarily have to build R in the top-level source
directory (say, <code><var>TOP_SRCDIR</var></code>).  To build in
<code><var>BUILDDIR</var></code>, run

<pre>cd <var>BUILDDIR</var>
<var>TOP_SRCDIR</var>/configure
make
</pre>

<p>and so on, as described further below.  This has the advantage of always
keeping your source tree "clean".  (You may need GNU <code>make</code> to
allow this.)

<p>Make will also build plain text help pages as well as <small>HTML</small> and
LaTeX versions of the R object documentation (the three kinds can
also be generated separately using <code>make help</code>, <code>make html</code>
and <code>make latex</code>).  Note that you need Perl version 5: if this is
not available on your system, you can obtain PDF versions of the
documentation files via <small>CRAN</small>.

<p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
and the R <small>FAQ</small> (files <code>FAQ</code> or
<code>doc/html/faq.html</code>, or
<a href="http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html">http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html</a> which always has
the latest version).

<a name="Making%20the%20manuals"></a>

<h2>2.2 Making the manuals</h2>

<p>There is a set of manuals that can be built from the sources,

<dl>
<dt><code>refman</code>
<dd>Printed versions of all the help pages. 
<br><dt><code>R-FAQ</code>
<dd>R <small>FAQ</small> (which is already built for you). 
<br><dt><code>R-intro</code>
<dd>"An Introduction to R". 
<br><dt><code>R-data</code>
<dd>"R Data Import/Export". 
<br><dt><code>R-admin</code>
<dd>"R Installation and Administration", this manual. 
<br><dt><code>R-exts</code>
<dd>"Writing R Extensions". 
<br><dt><code>R-lang</code>
<dd>"The R Language Definition". 
</dl>

<p>To make these, use

<pre>make dvi      to create DVI versions
make pdf      to create PDF versions
make info     to create info files (not <code>refman</code>).
</pre>

<p>You will not be able to build the info files unless you have
<code>makeinfo</code> version 4 or later installed (and some Linux
distributions have 3.12).

<p>The DVI versions can be previewed and printed using standard programs
such as <code>xdvi</code> and <code>dvips</code>.  The PDF versions can be
viewed using Acrobat Reader or (recent versions of) ghostscript: they
have hyperlinks that can be followed in Acrobat Reader.  The info files
are suitable for reading online with Emacs or the standalone GNU Info.

<a name="Installation"></a>

<h2>2.3 Installation</h2>

<p>After

<pre>./configure
make
make check
</pre>

<p>have been completed successfully, you can install the complete R tree
to your system by typing

<pre>make install
</pre>

<p>This will install to the following directories:

<dl>
<dt><code>${prefix}/bin</code>
<dd>the front-end shell script
<br><dt><code>${prefix}/man/man1</code>
<dd>the man page
<br><dt><code>${prefix}/lib/R</code>
<dd>all the rest (libraries, on-line help system, <small>...</small>)
</dl>

<p>where <code>prefix</code> is determined during configuration (typically
<code>/usr/local</code>) and can be set by running <code>configure</code> with
the option <code>--prefix</code>, as in

<pre>./configure --prefix=/where/you/want/R/to/go
</pre>

<p>This causes <code>make install</code> to install the R executable to
<code>/where/you/want/R/to/go/bin</code>, and so on.  The prefix of the
installation directories can be seen in the status message that is
displayed at the end of <code>configure</code>.  You can install into
another directory by using

<pre>make prefix=/path/to/here install
</pre>

<p>To install DVI, info and PDF versions of the manuals, use one or more of

<pre>make install-dvi
make install-info
make install-pdf
</pre>

<p>To ensure that the installed tree is usable by the right group of users,
set <code>umask</code> appropriately (perhaps to <code>022</code>) before unpacking
the sources and throughout the build process.

<a name="Installing%20R%20under%20Windows"></a>

<h1>3 Installing R under Windows</h1>

<p>The <code>bin/windows</code> directory of a <small>CRAN</small> site contains
binaries for a base distribution and a large number of add-on packages
from <small>CRAN</small> to run on Windows 95, 98, NT4, 2000 and ME (at
least) on Intel and clones (but not on other platforms).

<p>You do need one of those Windows versions: Windows 3.11+win32s will not
work.

<p>Your file system must allow long file names (as is likely except
perhaps for some network-mounted systems).

<p>The simplest way is to use <code>SetupR.exe</code> or <code>miniR.exe</code>.  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 suppressed making a group for R).

<p>See the <a href="http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html">R Windows <small>FAQ</small></a> for more details.

</ul>

<a name="Building%20from%20source"></a>

<h2>3.1 Building from source</h2>

<p>If you want to build this port from the sources, see the file
<code>src/gnuwin32/INSTALL</code> in the source distribution.  You will need
to collect, install and test an extensive set of tools: see
<a href="http://www.stats.ox.ac.uk/pub/Rtools/">http://www.stats.ox.ac.uk/pub/Rtools/</a> for the current locations.

<p>You may need to compile under a case-honouring file system: we found
that a <code>samba</code>-mounted file system (which maps all file names to
lower case) did not work.  Open a commands window at a directory whose
path does not contain spaces, and run something like

<pre>tar zxvf R-1.3.0.tgz
cd R-1.3.0\src\gnuwin32
make
</pre>

<p>sit back and wait (for about 5 minutes on 1GHz PIII with a fast local
disc).

<p>For further details, including how to make the documentation and how to
cross-compile, see <code>src/gnuwin32/INSTALL</code>.

<a name="Installing%20R%20on%20Classic%20MacOS"></a>

<h1>4 Installing R on Classic MacOS</h1>

<p>The <code>bin/macos</code> directory of a <small>CRAN</small> site contains
<code>bin-hex</code>ed (<code>hqx</code>) and <code>stuffit</code> (<code>sit</code>)
archives for a base distribution and a large number of add-on packages
to run under MacOS 8.6 to MacOS 9.1 or MacOS X natively.  Just extract
one of these archives in a suitable folder using standard utilities like
Aladdin Stuffit Expander (tm).

<p>There is also a port to MacOS X which is considered to be a Unix variant
in this document.  You can find it in the <code>bin/macosx</code> directory at
of a <small>CRAN</small> site.

<a name="Add-on%20packages"></a>

<h1>5 Add-on packages</h1>

</ul>

<p>This chapter applies to Unix-like and Windows versions of R, but not
to the Classic MacOS port.

<p>It is helpful to use the correct terminology.  A <em>package</em> is
loaded from a <em>library</em> by the function <code>library</code>.  Thus a
library is a directory containing installed packages; the main library
is <code>R_HOME/library</code>, but others can be used, for example by setting
the environment variable <code>R_LIBS</code> or using the R function
<code>.libPaths()</code>.

<a name="Installing%20packages"></a>

<h2>5.1 Installing packages</h2>

<p>Note that you need to specify implicitly or explicitly the library to
which the package is to be installed.  This is only an issue if you have
more than one library, of course.

<p>To install packages from source on Unix use

<pre>R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> <small>...</small>
</pre>

<p>The part <code>-l /path/to/library</code> can be omitted, when the first
library in <code>R_LIBS</code> is used if set, otherwise the main library
<code>R_HOME/library</code>.

<p>The Windows equivalent is<a rel=footnote href="#fn-1"><sup>1</sup></a>

<pre>Rcmd INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> <small>...</small>
</pre>

<p>Alternatively, packages can be downloaded and installed from within
R.  First set the option <code>CRAN</code> to your nearest <small>CRAN</small>
mirror, for example

<pre>&gt; options(CRAN = "http://cran.us.r-project.org/")
</pre>

<p>Then download and install package <strong>foo</strong> by

<pre>&gt; install.packages("foo")
</pre>

<p>Unless the library is specified (argument <code>lib</code>) the first library
in the library search path is used.

<p>What this does is different on Unix and Windows.  On Unix it consults
the list of available source packages on <small>CRAN</small>, downloads the
latest version of the <strong>foo</strong> sources, and installs it (via <code>R
CMD INSTALL</code>).  On Windows it looks at the list of <em>binary</em>
versions of packages and downloads the latest version (if any).

<p>On Windows <code>install.packages</code> can also install a binary package
from a local <code>zip</code> file by setting argument <code>CRAN</code> to
<code>NULL</code>.   <code>RGui.exe</code> has a menu <code>Packages</code> with a GUI
interface to <code>install.packages</code>, <code>update.packages</code> and
<code>library</code>.

<a name="Updating%20packages"></a>

<h2>5.2 Updating packages</h2>

<p>The command <code>update.packages()</code> is the simplest way to ensure that
all the packages on your system are up to date.  Set the <code>CRAN</code>
option as in the previous section.  The <code>update.packages()</code>
downloads the list of available packages and their current versions,
compares it with those installed and offers to fetch and install any
that have later versions on <small>CRAN</small>.

<p>An alternative way of keeping packages up-to-date is provided by the
command <code>packageStatus()</code>, which returns an object with information
on all installed packages and packages available at multiple
repositories (CRAN, local archive, <small>...</small>). The <code>print</code> and
<code>summary</code> methods give an overview of installed and available
packages, the <code>upgrade</code> method offers to fetch and install outdated
packages.  This allows R to fetch packages from several repositories and
keep in sync with all of them, instead of only one CRAN mirror, and is
intended to become the default package manager for future versions of R.

<a name="Removing%20packages"></a>

<h2>5.3 Removing packages</h2>

<p>Packages can be removed in a number of ways.  From a command prompt they
can be removed by

<pre>R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> <small>...</small>
</pre>

<p>(Unix) or
<pre>Rcmd REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> <small>...</small>
</pre>

<p>(Windows).

<p>From a running R process they can be removed by

<pre>&gt; remove.packages(c("pkg1", "pkg2"),
                  lib = file.path("path", "to", "library"))
</pre>

<p>Finally, in most installations one can just remove the package directory
from the library.

<a name="Essential%20and%20useful%20other%20programs"></a>

<h1>Appendix A Essential and useful other programs</h1>

<p>This appendix gives details of programs you will need to build R on
Unix-like platforms, or which will be used by R if found by
<code>./configure</code>.

</ul>

<a name="Essential%20programs"></a>

<h2>A.1 Essential programs</h2>

<p>You need a means of compiling C and FORTRAN (see <a href="#Using%20FORTRAN">Using FORTRAN</a>). 
Some add-on packages also need a C++ compiler.

<p>You will need Perl version 5, available via
<a href="http://www.perl.com/CPAN/">http://www.perl.com/CPAN/</a>, to build any of the on-line
documentation.

<p>You will not be able to build the info files unless you have
<code>makeinfo</code> version 4 or later installed (and some Linux
distributions have 3.12).

<p>The typeset documentation needs <code>tex</code> and <code>latex</code>, or
<code>pdftex</code> and <code>pdflatex</code>.

<a name="Useful%20libraries%20and%20programs"></a>

<h2>A.2 Useful libraries and programs</h2>

<p>The command-line editing depends on the <code>readline</code> library
available from any GNU mirror: you will need a fairly recent version.

<p>Use of <code>gzfile</code> connections needs <code>zlib</code> (version 1.1.3 or later).

<p>The bitmapped graphics devices <code>jpeg()</code> and <code>png()</code> need the
appropriate libraries installed: <code>jpeg</code> (version 6b or later) or
<code>libpng</code> (version 1.0.5 or later)
and <code>zlib</code> (version 1.1.3 or later) respectively.

<p>The <code>bitmap</code> and <code>dev2bitmap</code> devices make use of ghostscript
(<a href="http://www.cs.wisc.edu/~ghost">http://www.cs.wisc.edu/~ghost</a>).

</ul>

<a name="Tcl%2fTk"></a>

<h3>A.2.1 Tcl/Tk</h3>

<p>The <strong>tcltk</strong> package needs Tcl/Tk installed: the sources are
available at <a href="http://dev.scriptics.com/">http://dev.scriptics.com/</a>.  To specify the locations
of the Tcl/Tk files you may need the configuration options

<dl>
<dt><code>--with-tcltk</code>
<dd>use Tcl/Tk, or specify its library directory
<br><dt><code>--with-tcl-config=<var>TCL_CONFIG</var></code>
<dd>specify location of <code>tclConfig.sh</code>
<br><dt><code>--with-tk-config=<var>TK_CONFIG</var></code>
<dd>specify location of <code>tkConfig.sh</code>
</dl>

<a name="Linear%20algebra"></a>

<h3>A.2.2 Linear algebra</h3>

<p>The linear algebra routines in R can make use of enhanced BLAS (Basic
Linear Algebra Subprograms, <a href="http://www.netlib.org/blas/faq.html">http://www.netlib.org/blas/faq.html</a>)
routines.  Some are compiler-system-specific (<code>libsunperf</code> on Sun
Sparc<a rel=footnote href="#fn-2"><sup>2</sup></a>, <code>libessl</code> on IBM) but ATLAS
(<a href="http://www.netlib.org/atlas/">http://www.netlib.org/atlas/</a>) is a `tuned' BLAS that runs on a
wide range of Unix-alike platforms.  If no more specific library is
found, a <code>libblas</code> library in the library path will be used.  You
can specify a specific BLAS library by the configuration option
<code>--with-blas</code> and not to use an external BLAS library by
<code>--without-blas</code>.

<p>Note that the BLAS library will be used for several add-on packages as
well as for R itself.  This means that it is better to use a shared
BLAS library, as most of a static library will be compiled into the R
executable and each BLAS-using package.

<p>You will need double-precision and double-complex versions of the BLAS,
but not single-precision nor complex routines.

<p>Optimized versions of LAPACK are available, but no provision is made for
using them with R as the likely performance gains are thought to be
small.

<p>As with all libraries, you need to ensure that they and R were
compiled with compatible compilers and flags.  For example, this means
that on Sun Sparc using the native compilers the flag <code>-dalign</code>
is needed so <code>libsunperf</code> can be used.

<p>An ATLAS `tuned' BLAS can also be used on Windows: see
<code>src/gnuwin32/INSTALL</code> for how to enable this.

<p>Note that if R is compiled against a non-default BLAS, then all
BLAS-using packages must also be.  So if R is re-built after ATLAS is
installed, then packages such as <strong>quantreg</strong> will need to be
re-installed.

<a name="Configuration%20on%20Unix"></a>

<h1>Appendix B Configuration on Unix</h1>

</ul>

<a name="Configuration%20options"></a>

<h2>B.1 Configuration options</h2>

<p><code>configure</code> has many options: running

<pre>./configure --help
</pre>

<p>will give a list.  Probably the most important ones not covered
elsewhere are (defaults in brackets)

<dl>
<dt><code>--with-x</code>
<dd>use the X Window System
<br><dt><code>--x-includes=<var>DIR</var></code>
<dd>X include files are in <var>DIR</var>
<br><dt><code>--x-libraries=<var>DIR</var></code>
<dd>X library files are in <var>DIR</var>
<br><dt><code>--with-readline</code>
<dd>use readline library (if available) [yes]
<br><dt><code>--enable-R-profiling</code>
<dd>attempt to compile support for <code>Rprof()</code> [yes]
<br><dt><code>--enable-R-shlib</code>
<dd>build R as a shared library [no]
</dl>

<p>You can use <code>--without-foo</code> or <code>--disable-foo</code> for the
negatives.

<p>You will want to use <code>--disable-R-profiling</code> if you are building
a profiled executable of R (e.g. with <code>-pg)</code>.

<p>Flag <code>--enable-R-shlib</code> causes the make process to build R as a
shared library, typically called <code>libR.so</code>, and to take
considerably longer, so you probably only want this if you will be using
an application which embeds R.

<a name="Configuration%20variables"></a>

<h2>B.2 Configuration variables</h2>

<p>If you need or want to set certain configure variables to something
other than their default, you can do that by either editing the file
<code>config.site</code> (which documents all the variables you might want to
set) or on the command line as

<pre>VAR="..." ./configure              # Bourne shell compatibles
(setenv VAR "..."; ./configure)    # C shell
</pre>

<p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to
<code>a4</code>, not <code>letter</code>.

<p>If you have libraries and header files, e.g., for GNU readline, in
non-system directories, use the variables <code>LIBS</code> (for libraries)
and <code>CPPFLAGS</code> (for header files), respectively, to specify these
locations.  These default to <code>/usr/local/lib</code> and
<code>/usr/local/include</code> to catch the most common cases.  If libraries
are still not found, then maybe your compiler/linker does not support
re-ordering of <code>-L</code> and <code>-l</code> flags (this has been reported
to be a problem on HP-UX with the native <code>cc</code>).  In this case,
use a different compiler (or a front end shell script which does the
re-ordering).

<p>If you find you need to alter configure variables, it is worth noting
that some settings are cached in the file <code>config.cache</code>, and it is
a good idea to remove that file before re-configuring.

<a name="Using%20make"></a>

<h2>B.3 Using make</h2>

<p>To compile R, you will most likely find it easiest to use GNU
<code>make</code>.  On Solaris 2.6/7/8 in particular, you need a version of
GNU <code>make</code> different from 3.77; 3.79 works fine, as does the Sun
<code>make</code>.  The native <code>make</code> is reported to fail on SGI
Irix 6.5.

<p>To build in a separate directory you need a <code>make</code> that uses the
<code>VPATH</code> variable, for example GNU <code>make</code>, or Sun
<code>make</code> on Solaris 2.7/8 (but not earlier).

<p>If you want to use a <code>make</code> by another name, for example if your
GNU <code>make</code> is called <code>gmake</code>, you need to set the
environment variable <code>MAKE</code> at configure time, for example

<pre>MAKE=gmake ./configure        (sh, bash)
env MAKE=gmake ./configure    (csh)
</pre>

<a name="Using%20FORTRAN"></a>

<h2>B.4 Using FORTRAN</h2>

<p>To compile R, you need a FORTRAN compiler or <code>f2c</code>, the
FORTRAN-to-C converter (<a href="http://www.netlib.org/f2c">http://www.netlib.org/f2c</a>).  The default
is to search for <code>g77</code>, <code>f77</code>, <code>xlf</code>,
<code>cf77</code>, <code>cft77</code>, <code>pgf77</code>, <code>fl32</code>,
<code>af77</code>, <code>fort77</code>, <code>f90</code>, <code>xlf90</code>,
<code>pgf90</code>, <code>epcf90</code>, <code>f95</code>, <code>xlf95</code>,
<code>lf9</code>5, <code>g95</code>, and <code>fc</code> (in that
order)<a rel=footnote href="#fn-3"><sup>3</sup></a>, and
then for <code>f2c</code>, and use whichever is found first; if none is
found, R cannot be compiled.  The search mechanism can be changed
using the <code>--with-g77</code>, <code>--with-f77</code>, and
<code>--with-f2c</code> command line options to <code>configure</code>.  If
your FORTRAN compiler is in a non-standard location, you should set the
environment variable <code>PATH</code> accordingly before running
<code>configure</code>.

<p>If your FORTRAN libraries are in slightly peculiar places, you should
also look at <code>LD_LIBRARY_PATH</code> or your system's equivalent to make
sure that all libraries are on this path.

<p>You must set whatever compilation flags (if any) are needed to ensure
that FORTRAN <code>integer</code> is equivalent to a C <code>int</code> pointer and
FORTRAN <code>double precision</code> is equivalent to a C <code>double</code>
pointer.  This is checked during the configuration process.

<p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
is a FORTRAN 90 extension.  This is checked for at configure
time<a rel=footnote href="#fn-4"><sup>4</sup></a>, but you may need to avoid
compiler flags<a rel=footnote href="#fn-5"><sup>5</sup></a> asserting
FORTRAN 77 compliance.

<p>For performance reasons<a rel=footnote href="#fn-6"><sup>6</sup></a> you may want to choose a FORTRAN 90/95 compiler.

<p>If you use <code>f2c</code> you may need to ensure that the FORTRAN type
<code>integer</code> is translated to the C type <code>int</code>.  Normally
<code>f2c.h</code> contains <code>typedef long int integer;</code>, which will
work on a 32-bit platform but not on a 64-bit platform.

<a name="Compile%20and%20load%20flags"></a>

<h2>B.5 Compile and load flags</h2>

<p>A wide range of flags can be set in the file <code>config.site</code> or via
environment variables.  We have already mentioned

<dl>
<dt><code>CPPFLAGS</code>
<dd>extra include flags
<br><dt><code>LIBS</code>
<dd>libraries and <code>-L/lib/path</code> flags
</dl>

<p>and others include

<dl>
<dt><code>CFLAGS</code>
<dd>debugging and optimization flags, C
<br><dt><code>MAIN_CFLAGS</code>
<dd>ditto, for compiling the main program
<br><dt><code>SHLIB_CFLAGS</code>
<dd>for shared libraries
<br><dt><code>FFLAGS</code>
<dd>debugging and optimization flags, FORTRAN
<br><dt><code>MAIN_FFLAGS</code>
<dd>ditto, for compiling the main program
<br><dt><code>SHLIB_FFLAGS</code>
<dd>for shared libraries
<br><dt><code>MAIN_LDFLAGS</code>
<dd>additional flags for the main link
<br><dt><code>SHLIB_LDFLAGS</code>
<dd>additional flags for linking the shared libraries
</dl>

<p>Library paths specified as <code>-L/lib/path</code> in <code>LIBS</code> are
collected together and prepended to <code>LD_LIBRARY_PATH</code> (or your
system's equivalent), so there should be no need for <code>-R</code> or
<code>-rpath</code> flags.

<p>To compile a profiling version of R, one might for example want to
use <code>MAIN_CFLAGS=-pg</code>, <code>MAIN_FFLAGS=-pg</code>,
<code>MAIN_LDFLAGS=-pg</code> on platforms where <code>-pg</code> cannot be used
with position-independent code.

<p><strong>Beware:</strong> it may be necessary to set <code>CFLAGS</code> and
<code>FFLAGS</code> in ways compatible with the libraries to be used: one
possible issue is the alignment of doubles, another is the way
structures are passed.

<a name="Building%20the%20GNOME%20interface"></a>

<h2>B.6 Building the <small>GNOME</small> interface</h2>

<p>This interface is experimental and incomplete.  It provides a console
and two graphics devices named <code>gtk()</code> and <code>gnome()</code>.  The
console offers a basic command line editing and history mechanism, along
with tool and button bars that give a point-and-click interface to some
R commands.  Many of the features of the console are currently
stubs. The <code>gtk()</code> graphics device is a port of the <code>x11()</code>
device to <small>GDK</small> (the GIMP Drawing Kit). The <code>gnome()</code>
device uses the <small>GNOME</small> canvas.

<p>Due to its experimental nature, the <small>GNOME</small> interface for R
will not be built automatically.  You must specify it by running
configure with the <code>--with-gnome</code> option.  For example, you might
run

<pre>./configure --with-gnome
</pre>

<p>but please check you have all the requirements first. The
<small>GNOME</small> interface for R is currently being developed under
<small>GNOME</small> 1.4, and is not guaranteed to work with previous
versions.  You therefore need at least the following libraries installed

<pre>audiofile-0.2.1
esound-0.2.23
glib-1.2.10
gtk+-1.2.10
imlib-1.9.10
ORBit-0.5.12
gnome-libs-1.4.1.2
libxml-1.8.16
libglade-0.17
</pre>

<p>It is preferable to have a complete installation of the <small>GNOME</small>
desktop environment.  If you use Linux, then this should be provided
with your distribution.  In addition, packaged binary distributions of
GNOME are available from <a href="http://www.ximian.com">http://www.ximian.com</a> for the most
popular Linux distributions and for Solaris.

<p>Remember that some package management systems (such as <small>RPM</small> and
deb) make a distinction between the user version of a package and the
developer version. The latter usually has the same name but with the
extension "-devel". If you use a pre-packaged version of <small>GNOME</small>
then you must have the developer versions of the above packages in order
to compile the R-GNOME interface.

<p>The full list of <small>GNOME</small> options to configure is

<dl>
<dt><code>--with-gnome</code>
<dd>use <small>GNOME</small>, or specify its prefix [no]
<br><dt><code>--with-gnome-includes=<var>DIR</var></code>
<dd>specify location of <small>GNOME</small> headers
<br><dt><code>--with-gnome-libs=<var>DIR</var></code>
<dd>specify location of <small>GNOME</small> libs
<br><dt><code>--with-libglade-config=<var>LIBGLADE_CONFIG</var></code>
<dd>specify location of <code>libglade-config</code>
</dl>

<a name="Platform%20notes"></a>

<h2>B.7 Platform notes</h2>

<p>This section provides some notes on building R on different Unix-like
platforms.  These notes are based on tests run on one or two systems
in each case with particular sets of compilers and support libraries. 
Success in building R depends on the proper installation and functioning
of support software; your results may differ if you have other versions
of compilers and support libraries.

</ul>

<a name="MacOS%20X"></a>

<h3>B.7.1 MacOS X</h3>

<p>You can build R as a Unix application on MacOS X.  You will need the
DevTools, <code>f2c</code> or <code>g77</code>, and the <code>dlcompat</code>
library.  You will also need to install an X sub-system or configure
with <code>--without-x</code>.

<p><code>f2c</code>, <code>g77</code>, the <code>dlcompat</code> library, and X server
and support libraries are available from the Fink project
(<a href="http://fink.sourceforge.net">http://fink.sourceforge.net</a>).  At the time of writing
<code>f2c</code> and <code>g77</code> were not available as part of the Fink
binary distribution and needed to be installed directly; for example for
<code>g77</code> use
<pre>fink install g77
</pre>

<p>Fink prefers to install in <code>/sw</code> so <code>CPPFLAGS</code>, <code>LDFLAGS</code>
need to be set accordingly.  If you want to use Tcl/Tk, also available
from Fink, then you will also need to use the <code>configure</code>
options to specify the Tcl and Tk config locations.

<a name="Solaris"></a>

<h3>B.7.2 Solaris on Sparc</h3>

<p>R has been built successfully on Solaris 2.7 using
<code>gcc</code>/<code>g77</code> and the SunPro WorkShop&nbsp;6 compilers, and
less regularly on 2.5.1, 2.6 and 8.  GNU <code>make</code> is needed prior
to 2.7 for building other than in the source tree, and perhaps even
then.

<p>When using the SunPro compilers do <em>not</em> specify <code>-fast</code>, as
this disables <small>IEEE</small> arithmetic and <code>make check</code> will
fail.  The maximal set of optimization options known to work is

<pre>-xlibmil -xO5 -dalign
</pre>

<p>We have found little performance difference between <code>gcc</code> and
<code>cc</code> but considerable benefit from using a SunPro Fortran
compiler: the <code>gcc</code>/<code>f77</code> combination works well.

<p>To compile for a 64-bit target on Solaris (which needs an UltraSparc
chip and for support to be enabled in the OS) we used
<pre>CC="cc -xarch=v9"
CFLAGS="-xO5 -xlibmil -dalign"
FC="f95 -xarch=v9"
FFLAGS="-xO5 -xlibmil -dalign"
CXX=CC
CXXFLAGS="-xO5 -xlibmil -dalign -xarch=v9"
</pre>

<p>in <code>config.site</code>.  Note that using <code>f95</code> allows the Sun
performance library to be selected: it will not work with <code>f77</code>,
nor with <code>g77</code>.

<p>Some care is needed to ensure that libraries found by <code>configure</code>
are compatible with the R executable and modules, as the testing
process will not detect many of the possible problems.  For 32-bit
builds under <code>cc</code> the flag <code>-dalign</code> is needed for some of
the Sun libraries: fortunately the equivalent flag for <code>gcc</code>,
<code>-munaligned-doubles</code>, is the default.  In theory, libraries such
as <code>libpng</code>, <code>libjpeg</code>, <code>zlib</code> and the ATLAS libraries
need to be built with a <code>pic</code> or <code>PIC</code> flag, which could be
a problem if static libraries are used.  In practice this seems to
give little problem for 32-bit builds, but seems essential for 64-bit
builds.

<p>For a 64-bit build, 64-bit libraries must be used.  As the
configuration process starts with <code>LIBS=/usr/local/lib</code> you may
need to reset it to avoid finding 32-bit addons.

<a name="HPUX"></a>

<h3>B.7.3 HPUX</h3>

<p>R has been built successfully on HPUX 10.2 and HPUX 11.0 using both
native compilers and <code>gcc</code>.  By default, R is configured to use
<code>gcc</code> and <code>g77</code> on HPUX (if available).  Some
installations of <code>g77</code> only install a static version of the
<code>g2c</code> library that cannot be linked into a shared library since
its files have not been compiled with the appropriate flag for producing
position independent code (<small>PIC</small>).  This will result in
<code>make</code> failing with a linker error complaining that code needs
to be compiled with a <code>+z</code> or <code>+Z</code> flag, the native
<code>cc</code> <small>PIC</small> flag.  If this is the case you either need to
modify your <code>g77</code> installation or configure with the

<pre>--with-f77=fort77
</pre>

<p>flag to specify use of the native <small>POSIX</small>-compliant FORTRAN 77
compiler.

<p>You may find that <code>configure</code> detects other libraries, such as
BLAS, that R needs to use as shared libraries but are only available as
static libraries.  If you cannot install shared versions you will need
to tell <code>configure</code> not to use these libraries.

<p>Some versions of <code>gcc</code> may contain what appears to be a bug at
the <code>-O2</code> optimization level that causes
<pre>&gt; 2 %/% 2
[1] 1
&gt; 1:2 %/% 2
[1] 0 0     # wrong!!
</pre>

<p>which will cause <code>make check</code> to fail.  If this is the case, you
should use <code>CFLAGS</code> to specify <code>-O</code> as the optimization
level to use.

<p>Some systems running HPUX 11.0 may have a <code>gcc</code> that was
installed under HPUX 10.2.  Between versions 10.2 and 11.0 HPUX changed
its support functions for <small>IEEE</small> arithmetic from the recommended
functions of the <small>IEEE</small> standard to the ones specified in the
C9x draft standard.  In particular, this means that <code>finite</code> has
been replaced by <code>isfinite</code>.  A <code>gcc</code> configured for HPUX
10.2 run on 11.0 will not find <code>isfinite</code>, and as a result
<code>configure</code> does not recognize the machine as fully supporting
<small>IEEE</small> arithmetic and does not define <code>IEEE_754</code> when
compiling C code.  This results in a failure in <code>make check</code>. 
The best solution is to install a properly configured <code>gcc</code>.  An
alternative work-around is to add <code>-DIEEE_754</code> to the
<code>CFLAGS</code> variable.

<p>You can configure R to use both the native <code>cc</code> and
<code>fort77</code> with (assuming you are using a <code>csh</code> shell)
<pre>env CC=cc ./configure --with-f77=fort77
</pre>

<a name="IRIX"></a>

<h3>B.7.4 IRIX</h3>

<p>R has been built successfully on IRIX64 6.5 using
<code>gcc</code>/<code>f77</code> or <code>cc</code>/<code>f77</code> for 32-bit
executables and the native compilers for a 64-bit executable.  The
command
<pre>env CC="cc -64" ./configure --with-f77="f77 -64" --with-tcltk=no
</pre>

<p>was used to create the 64-bit executable.  It was necessary to
explicitly omit Tcl/Tk because <code>configure</code> would find the 32-bit
version but not detect that is was incompatible with a 64-bit build.

<p>A 32-bit build using <code>gcc</code>/<code>g77</code> passed <code>make
check</code> but failed <code>make test-all-extras</code> in the complex LAPACK
tests.

<a name="Alpha%2fOSF1"></a>

<h3>B.7.5 Alpha/OSF1</h3>

<p>R has been built successfully on an Alpha running OSF1 V4.0 using
<code>gcc</code>/<code>g77</code> and <code>cc</code>/<code>f77</code>.  Mixing
<code>cc</code> and <code>g77</code> fails to configure.  The
<code>configure</code> option <code>--without-blas</code> was used since the
native blas seems not to have been built with the flags needed to
suppress <code>SIGFPE</code>'s.  Currently R does not set a signal handler for
<code>SIGFPE</code> on platforms that support <small>IEEE</small> arithmetic, so
these are fatal.

<p><code>make check</code> passes with no problems.  <code>make
test-all-extras</code> in the <code>tests</code> directory fails at the end of
<code>reg-tests-1.R</code> since this system does not have <code>vsnprintf</code>. 
As currently written, the test at the end of <code>reg-tests-1.R</code> causes
a segfault in this case.  You can complete the tests by executing
<pre>touch reg-tests-1.Rout
</pre>

<a name="Alpha%2fFreeBSD"></a>

<h3>B.7.6 Alpha/FreeBSD</h3>

<p>Attempts to build R on an Alpha with FreeBSD 4.3 have been only
partly successful.  Configuring with <code>-mieee</code> added to both
<code>CFLAGS</code> and <code>FFLAGS</code> builds successfully, but tests fail with
<code>SIGFPE</code>'s.  It would appear that <code>-mieee</code> only defers these
rather than suppressing them entirely.  Advice on how to complete this
port would be greatly appreciated.

<a name="New%20platforms"></a>

<h1>Appendix C New platforms</h1>

<p>There are a number of sources of problems when installing R on a new
hardware/OS platform.  These include

<p><strong>Floating Point Arithmetic</strong>: R supports the <small>POSIX</small>,
SVID and <small>IEEE</small> models for floating point arithmetic.  The
<small>POSIX</small> and SVID models provide no problems.  The <small>IEEE</small>
model however can be a pain.  The problem is that there is no agreement
on how to set the signalling behaviour; Sun/Sparc, SGI/IRIX and ix86
Linux require no special action, FreeBSD requires a call to (the macro)
<code>fpsetmask(0)</code> and OSF1 requires that computation be done with a
<code>-ieee_with_inexact</code> flag etc.  On a new platform you must find
out the magic recipe and add some code to make it work.  This can often
be done via the file <code>config.site</code> which resides in the top level
directory.

<p>Beware of using high levels of optimization, at least initially.  On
many compilers these reduce the degree of compliance to the
<small>IEEE</small> model.  For example, using <code>-fast</code> on the Solaris
SunPro compilers causes R's <code>NaN</code> to be set incorrectly.

<p><strong>Shared Libraries</strong>: There seems to be very little agreement
across platforms on what needs to be done to build shared libraries. 
there are many different combinations of flags for the compilers and
loaders.  GNU libtool cannot be used (yet), as it currently does not
fully support FORTRAN (and will most likely never support <code>f2c</code>:
one would need a shell wrapper for this).  The technique we use is to
first interrogate the X window system about what it does (using
<code>xmkmf</code>), and then override this in situations where we know
better (for tools from the GNU Compiler Collection and/or platforms we
know about).  This typically works, but you may have to manually
override the results.  Scanning the <code>cc(1)</code> and <code>ld(1)</code>
manual entries usually reveals the correct incantation.  Once you know
the recipe you can modify the file <code>config.site</code> (following the
instructions therein) so that the build will use these options.

<p>If you do manage to get R running on a new platform please let us
know about it so we can modify the configuration procedures to include
that platform.

<p>If you are having trouble getting R to work on your platform please
feel free to get in touch to ask questions.  We've had a fair amount
of practice at porting R to new platforms <small>...</small>.

<a name="Function%20and%20variable%20index"></a>

<h1>Function and variable index</h1>

<ul compact>
<li><code>configure</code>: <a href="#Using%20make">Using make</a>, <a href="#Configuration%20variables">Configuration variables</a>, <a href="#Installation">Installation</a>, <a href="#Simple%20compilation">Simple compilation</a>
<li><code>install.packages</code>: <a href="#Installing%20packages">Installing packages</a>
<li><code>make</code>: <a href="#Using%20make">Using make</a>
<li><code>R_HOME</code>: <a href="#Simple%20compilation">Simple compilation</a>
<li><code>remove.packages</code>: <a href="#Removing%20packages">Removing packages</a>
<li><code>rsync</code>: <a href="#Using%20rsync">Using rsync</a>
<li><code>update.packages</code>: <a href="#Updating%20packages">Updating packages</a>
</ul>
<a name="Concept%20index"></a>

<h1>Concept index</h1>

<ul compact>
<li>FORTRAN: <a href="#Using%20FORTRAN">Using FORTRAN</a>
<li>Help pages: <a href="#Simple%20compilation">Simple compilation</a>
<li>Installation: <a href="#Installation">Installation</a>
<li>Installing under MacOS: <a href="#Installing%20R%20on%20Classic%20MacOS">Installing R on Classic MacOS</a>
<li>Installing under Unix: <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
<li>Installing under Windows: <a href="#Installing%20R%20under%20Windows">Installing R under Windows</a>
<li>Linux: <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
<li>MacOS X: <a href="#Installing%20R%20on%20Classic%20MacOS">Installing R on Classic MacOS</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
<li>Manuals: <a href="#Making%20the%20manuals">Making the manuals</a>
<li>Manuals, installing: <a href="#Installation">Installation</a>
<li>Obtaining R: <a href="#Obtaining%20R">Obtaining R</a>
<li>Packages: <a href="#Add-on%20packages">Add-on packages</a>
<li>Packages, installing: <a href="#Installing%20packages">Installing packages</a>
<li>Packages, removing: <a href="#Removing%20packages">Removing packages</a>
<li>Packages, updating: <a href="#Updating%20packages">Updating packages</a>
<li>Patch files: <a href="#Getting%20and%20unpacking%20the%20sources">Getting and unpacking the sources</a>
<li>Sources for R: <a href="#Getting%20and%20unpacking%20the%20sources">Getting and unpacking the sources</a>
</ul>


<hr><h4>Footnotes</h4>
<ol type="1">
<li><a name="fn-1"></a>
<p>if you have Perl and the source-code
package files installed</p>

<li><a name="fn-2"></a>
<p>Using the SunPro <code>cc</code> and <code>f95</code>
compilers</p>

<li><a name="fn-3"></a>
<p>On HPUX <code>fort77</code> is the <small>POSIX</small>
compliant FORTRAN compiler, and comes second in the search list.</p>

<li><a name="fn-4"></a>
<p>as well as its equivalence to the <code>Rcomplex</code>
structure defined in <code>R_ext/Complex.h</code>.</p>

<li><a name="fn-5"></a>
<p>In particular, avoid <code>g77</code>'s
<code>-pedantic</code>, which gives confusing error messages.</p>

<li><a name="fn-6"></a>
<p>e.g., to use an optimized BLAS on
Sun/Sparc</p>

</ol><hr>

</body></html>