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<title>R Installation and Administration</title>
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<h1 class="settitle">R Installation and Administration</h1>
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<a name="Top"></a>
14184 ripley 20 
 
24001 hornik 21 
<h2 class="unnumbered">R Installation and Administration</h2>
14184 ripley 22 
 
26591 hornik 23 
<p>This is a guide to installation and administration for R.
14184 ripley 24 
 
28362 murdoch 25 
   <p>The current version of this document is 1.9.0 (2004-02-18).
14184 ripley 26 
 
26882 ripley 27 
   ISBN 3-900051-02-X
19393 hornik 28 
 
14185 ripley 29 
<a name="Obtaining%20R"></a>
14184 ripley 30 
 
24001 hornik 31 
<h2 class="chapter">1 Obtaining R</h2>
14184 ripley 32 
 
26591 hornik 33 
<p>Sources, binaries and documentation for R can be obtained via
14307 ripley 34 
<small>CRAN</small>, the "Comprehensive R Archive Network".  See the file
18887 hornik 35 
<code>RESOURCES</code> in the R distribution for information on
36 
<small>CRAN</small>.
14184 ripley 37 
 
14307 ripley 38 
<a name="Getting%20and%20unpacking%20the%20sources"></a>
14184 ripley 39 
 
24001 hornik 40 
<h3 class="section">1.1 Getting and unpacking the sources</h3>
14184 ripley 41 
 
26591 hornik 42 
<p>The simplest way is to download the most recent
24001 hornik 43 
<code>R-</code><var>x</var><code>.</code><var>y</var><code>.</code><var>z</var><code>.tgz</code> file, and unpack it with
14307 ripley 44 
 
24001 hornik 45 
<pre class="smallexample">     tar xvfz R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
46 
     </pre>
14184 ripley 47 
 
14307 ripley 48 
<p>on systems that have GNU <code>tar</code> installed.  On other systems you
49 
need at least to have the <code>gzip</code> program installed.  Then you
50 
can use
51 
 
24001 hornik 52 
<pre class="smallexample">     gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tgz | tar xvf -
53 
     </pre>
14184 ripley 54 
 
24001 hornik 55 
   <p>If you need to transport the sources on floppy disks, you can download
56 
the <code>R-</code><var>x</var><code>.</code><var>y</var><code>.</code><var>z</var><code>.tgz-split.*</code> files and paste them
14307 ripley 57 
together at the destination with (Unix)
58 
 
24001 hornik 59 
<pre class="smallexample">     cat R-<var>x</var>.<var>y</var>.<var>z</var>-split.* &gt; R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
60 
     </pre>
14184 ripley 61 
 
14307 ripley 62 
<p>and proceed as above.  If you want the build to be usable by a group of
63 
users, set <code>umask</code> before unpacking so that the files will be
64 
readable by the target group (e.g., <code>umask 022</code> to be usable by all
14184 ripley 65 
users).
66 
 
14185 ripley 67 
<a name="Using%20rsync"></a>
14184 ripley 68 
 
24001 hornik 69 
<h3 class="section">1.2 Using rsync</h3>
14184 ripley 70 
 
26591 hornik 71 
<p>Sources are also available via anonymous rsync.  Use
14184 ripley 72 
 
24001 hornik 73 
<pre class="smallexample">     rsync -rC rsync.r-project.org::<var>module</var> R
74 
     </pre>
14184 ripley 75 
 
76 
<p>to create a copy of the source tree specified by <var>module</var> in the
77 
subdirectory <code>R</code> of the current directory, where <var>module</var>
15508 pd 78 
specifies one of the four existing flavors of the R sources, and can be
15168 pd 79 
one of <code>r-release</code> (current released version), <code>r-patched</code>
28261 murdoch 80 
(patched released version), and <code>r-devel</code> (development version).
24354 hornik 81 
(These flavors are described in the R FAQ,
82 
<a href="http://www.ci.tuwien.ac.at/~hornik/R/">http://www.ci.tuwien.ac.at/~hornik/R/</a>.)  The rsync trees are
28261 murdoch 83 
created directly from the master CVS archive and are updated hourly.
24354 hornik 84 
The <code>-C</code> option in the <code>rsync</code> command is to cause it to
85 
skip the CVS directories.  Further information on <code>rsync</code> is
86 
available at <a href="http://rsync.samba.org/rsync/">http://rsync.samba.org/rsync/</a>.
14184 ripley 87 
 
14185 ripley 88 
<a name="Installing%20R%20under%20Unix"></a>
14184 ripley 89 
 
24001 hornik 90 
<h2 class="chapter">2 Installing R under Unix</h2>
14184 ripley 91 
 
26591 hornik 92 
<p>R will configure and build under a number of common Unix platforms
21394 pd 93 
including i386-freebsd, <var>cpu</var>-linux-gnu for the i386, alpha, arm,
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hppa, ia64, m68k, powerpc, and sparc CPUs (see e.g.
21394 pd 95 
<a href="http://buildd.debian.org/build.php?&amp;pkg=r-base">http://buildd.debian.org/build.php?&amp;pkg=r-base</a>),
96 
i386-sun-solaris, powerpc-apple-darwin, mips-sgi-irix, alpha-dec-osf4,
97 
rs6000-ibm-aix, hppa-hp-hpux, and sparc-sun-solaris.
14184 ripley 98 
 
24001 hornik 99 
   <p>In addition, binary distributions are available for most common Linux
23621 hornik 100 
distributions, and for MacOS X (Darwin) with X11.  See the <small>FAQ</small>
101 
for current details.  These are installed in platform-specific ways.  So
102 
for the rest of this chapter we consider only building from the sources.
14184 ripley 103 
 
14307 ripley 104 
<a name="Simple%20compilation"></a>
14184 ripley 105 
 
24001 hornik 106 
<h3 class="section">2.1 Simple compilation</h3>
14184 ripley 107 
 
26591 hornik 108 
<p>First review the essential and useful tools and libraries in
14307 ripley 109 
<a href="#Essential%20and%20useful%20other%20programs">Essential and useful other programs</a>, and install those you want or
110 
need.
14184 ripley 111 
 
24001 hornik 112 
   <p>Choose a place to install the R tree (R is not just a binary, but
14184 ripley 113 
has additional data sets, help files, font metrics etc).  Let us call
18887 hornik 114 
this place <var>R_HOME</var>.  Untar the source code.  This should create
14184 ripley 115 
directories <code>src</code>, <code>doc</code>, and several more.  Issue the
116 
following commands:
117 
 
24001 hornik 118 
<pre class="smallexample">     ./configure
119 
     make
120 
     </pre>
14184 ripley 121 
 
122 
<p>(See <a href="#Using%20make">Using make</a> if your make is not called <code>make</code>.)
123 
 
24001 hornik 124 
   <p>Then check the built system works correctly, by
14184 ripley 125 
 
24001 hornik 126 
<pre class="smallexample">     make check
127 
     </pre>
14184 ripley 128 
 
129 
<p>Failures are not necessarily problems as they might be caused by missing
14307 ripley 130 
functionality, but you should look carefully at any reported
14328 ripley 131 
discrepancies.  To re-run the tests you would need
18887 hornik 132 
 
24001 hornik 133 
<pre class="smallexample">     make check FORCE=FORCE
134 
     </pre>
14184 ripley 135 
 
24001 hornik 136 
   <p>More comprehensive testing can be done by
23859 hornik 137 
 
24001 hornik 138 
<pre class="smallexample">     make check-devel
139 
     </pre>
23859 hornik 140 
 
141 
<p>or
142 
 
24001 hornik 143 
<pre class="smallexample">     make check-all
144 
     </pre>
23859 hornik 145 
 
146 
<p>see <code>tests/README</code>.
147 
 
24001 hornik 148 
   <p>If these commands execute successfully, the R binary will be copied
149 
to the <code></code><var>R_HOME</var><code>/bin</code> directory.  In addition, a shell-script
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front-end called <code>R</code> will be created and copied to the same
151 
directory.  You can copy this script to a place where users can invoke
152 
it, for example to <code>/usr/local/bin/R</code>.  You could also copy the man
14307 ripley 153 
page <code>R.1</code> to a place where your <code>man</code> reader finds it,
154 
such as <code>/usr/local/man/man1</code>.  If you want to install the complete
28261 murdoch 155 
R tree to, e.g., <code>/usr/local/lib/R</code>, see <a href="#Installation">Installation</a>.
14307 ripley 156 
Note: you do not <em>need</em> to install R: you can run it from where
157 
it was built.
14184 ripley 158 
 
24001 hornik 159 
   <p>You do not necessarily have to build R in the top-level source
160 
directory (say, <code></code><var>TOP_SRCDIR</var><code></code>).  To build in
161 
<code></code><var>BUILDDIR</var><code></code>, run
14307 ripley 162 
 
24001 hornik 163 
<pre class="smallexample">     cd <var>BUILDDIR</var>
164 
     <var>TOP_SRCDIR</var>/configure
165 
     make
166 
     </pre>
14184 ripley 167 
 
168 
<p>and so on, as described further below.  This has the advantage of always
14307 ripley 169 
keeping your source tree "clean".  (You may need GNU <code>make</code> to
170 
allow this.)
14184 ripley 171 
 
24001 hornik 172 
   <p>Make will also build plain text help pages as well as <small>HTML</small> and
14307 ripley 173 
LaTeX versions of the R object documentation (the three kinds can
174 
also be generated separately using <code>make help</code>, <code>make html</code>
175 
and <code>make latex</code>).  Note that you need Perl version 5: if this is
176 
not available on your system, you can obtain PDF versions of the
14184 ripley 177 
documentation files via <small>CRAN</small>.
178 
 
24001 hornik 179 
   <p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
14307 ripley 180 
and the R <small>FAQ</small> (files <code>FAQ</code> or
181 
<code>doc/html/faq.html</code>, or
182 
<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
183 
the latest version).
14184 ripley 184 
 
14307 ripley 185 
<a name="Making%20the%20manuals"></a>
14184 ripley 186 
 
24001 hornik 187 
<h3 class="section">2.2 Making the manuals</h3>
14184 ripley 188 
 
26591 hornik 189 
<p>There is a set of manuals that can be built from the sources,
14184 ripley 190 
 
24001 hornik 191 
     <dl>
14184 ripley 192 
<dt><code>refman</code>
28261 murdoch 193 
     <dd>Printed versions of all the help pages.
14184 ripley 194 
<br><dt><code>R-FAQ</code>
28261 murdoch 195 
     <dd>R <small>FAQ</small> (which is already built for you).
14184 ripley 196 
<br><dt><code>R-intro</code>
28261 murdoch 197 
     <dd>"An Introduction to R".
14184 ripley 198 
<br><dt><code>R-data</code>
28261 murdoch 199 
     <dd>"R Data Import/Export".
14184 ripley 200 
<br><dt><code>R-admin</code>
28261 murdoch 201 
     <dd>"R Installation and Administration", this manual.
14184 ripley 202 
<br><dt><code>R-exts</code>
28261 murdoch 203 
     <dd>"Writing R Extensions".
14184 ripley 204 
<br><dt><code>R-lang</code>
28261 murdoch 205 
     <dd>"The R Language Definition".
14184 ripley 206 
</dl>
207 
 
14698 hornik 208 
<p>To make these, use
14184 ripley 209 
 
24001 hornik 210 
<pre class="smallexample">     make dvi      to create DVI versions
211 
     make pdf      to create PDF versions
212 
     make info     to create info files (not <code>refman</code>).
213 
     </pre>
14184 ripley 214 
 
24001 hornik 215 
   <p>You will not be able to build the info files unless you have
14184 ripley 216 
<code>makeinfo</code> version 4 or later installed (and some Linux
217 
distributions have 3.12).
218 
 
24001 hornik 219 
   <p>The DVI versions can be previewed and printed using standard programs
14307 ripley 220 
such as <code>xdvi</code> and <code>dvips</code>.  The PDF versions can be
221 
viewed using Acrobat Reader or (recent versions of) ghostscript: they
222 
have hyperlinks that can be followed in Acrobat Reader.  The info files
223 
are suitable for reading online with Emacs or the standalone GNU Info.
14184 ripley 224 
 
14185 ripley 225 
<a name="Installation"></a>
14184 ripley 226 
 
24001 hornik 227 
<h3 class="section">2.3 Installation</h3>
14184 ripley 228 
 
26591 hornik 229 
<p>After
14307 ripley 230 
 
24001 hornik 231 
<pre class="smallexample">     ./configure
232 
     make
233 
     make check
234 
     </pre>
14184 ripley 235 
 
236 
<p>have been completed successfully, you can install the complete R tree
237 
to your system by typing
14307 ripley 238 
 
24001 hornik 239 
<pre class="smallexample">     make install
240 
     </pre>
14184 ripley 241 
 
242 
<p>This will install to the following directories:
243 
 
24001 hornik 244 
     <dl>
245 
<dt><code></code><var>prefix</var><code>/bin</code>
246 
     <dd>the front-end shell script
247 
<br><dt><code></code><var>prefix</var><code>/man/man1</code>
248 
     <dd>the man page
249 
<br><dt><code></code><var>prefix</var><code>/lib/R</code>
250 
     <dd>all the rest (libraries, on-line help system, <small class="dots">...</small>)
14184 ripley 251 
</dl>
252 
 
18887 hornik 253 
<p>where <var>prefix</var> is determined during configuration (typically
14307 ripley 254 
<code>/usr/local</code>) and can be set by running <code>configure</code> with
255 
the option <code>--prefix</code>, as in
256 
 
24001 hornik 257 
<pre class="smallexample">     ./configure --prefix=/where/you/want/R/to/go
258 
     </pre>
14184 ripley 259 
 
14328 ripley 260 
<p>This causes <code>make install</code> to install the R executable to
261 
<code>/where/you/want/R/to/go/bin</code>, and so on.  The prefix of the
14698 hornik 262 
installation directories can be seen in the status message that is
14328 ripley 263 
displayed at the end of <code>configure</code>.  You can install into
264 
another directory by using
14184 ripley 265 
 
24001 hornik 266 
<pre class="smallexample">     make prefix=/path/to/here install
267 
     </pre>
14184 ripley 268 
 
24001 hornik 269 
   <p>To install DVI, info and PDF versions of the manuals, use one or more of
14307 ripley 270 
 
24001 hornik 271 
<pre class="smallexample">     make install-dvi
272 
     make install-info
273 
     make install-pdf
274 
     </pre>
14184 ripley 275 
 
276 
<p>To ensure that the installed tree is usable by the right group of users,
14307 ripley 277 
set <code>umask</code> appropriately (perhaps to <code>022</code>) before unpacking
278 
the sources and throughout the build process.
14184 ripley 279 
 
14185 ripley 280 
<a name="Installing%20R%20under%20Windows"></a>
14184 ripley 281 
 
24001 hornik 282 
<h2 class="chapter">3 Installing R under Windows</h2>
14184 ripley 283 
 
26591 hornik 284 
<p>The <code>bin/windows</code> directory of a <small>CRAN</small> site contains
14184 ripley 285 
binaries for a base distribution and a large number of add-on packages
20580 hornik 286 
from <small>CRAN</small> to run on Windows 95, 98, NT4, 2000, ME and XP (at
14184 ripley 287 
least) on Intel and clones (but not on other platforms).
288 
 
24001 hornik 289 
   <p>You do need one of those Windows versions: Windows 3.11+win32s will not
14184 ripley 290 
work.
291 
 
24001 hornik 292 
   <p>Your file system must allow long file names (as is likely except
14184 ripley 293 
perhaps for some network-mounted systems).
294 
 
26591 hornik 295 
   <p>The simplest way is to use <code>rw1090dev.exe</code> or
21924 ripley 296 
<code>miniR.exe</code>.  Just double-click on the icon and follow the
297 
instructions.  If you installed R this way you can uninstall it from the
22570 ripley 298 
Control Panel.
14184 ripley 299 
 
24001 hornik 300 
   <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.
14184 ripley 301 
 
14307 ripley 302 
<a name="Building%20from%20source"></a>
14184 ripley 303 
 
24001 hornik 304 
<h3 class="section">3.1 Building from source</h3>
14184 ripley 305 
 
26591 hornik 306 
<p>If you want to build this port from the sources, see the file
14307 ripley 307 
<code>src/gnuwin32/INSTALL</code> in the source distribution.  You will need
308 
to collect, install and test an extensive set of tools: see
14184 ripley 309 
<a href="http://www.stats.ox.ac.uk/pub/Rtools/">http://www.stats.ox.ac.uk/pub/Rtools/</a> for the current locations.
310 
 
24001 hornik 311 
   <p>You may need to compile under a case-honouring file system: we found
14184 ripley 312 
that a <code>samba</code>-mounted file system (which maps all file names to
19393 hornik 313 
lower case) did not work.  Open a commands window at a directory <em>whose
314 
path does not contain spaces</em>, and run something like
14307 ripley 315 
 
26591 hornik 316 
<pre class="smallexample">     tar zxvf R-1.9.0.tgz
317 
     cd R-1.9.0\src\gnuwin32
24001 hornik 318 
     make
319 
     </pre>
14184 ripley 320 
 
14307 ripley 321 
<p>sit back and wait (for about 5 minutes on 1GHz PIII with a fast local
322 
disc).
14184 ripley 323 
 
24001 hornik 324 
   <p>For further details, including how to make the documentation and how to
14184 ripley 325 
cross-compile, see <code>src/gnuwin32/INSTALL</code>.
326 
 
14307 ripley 327 
<a name="Add-on%20packages"></a>
14184 ripley 328 
 
24070 ripley 329 
<h2 class="chapter">4 Add-on packages</h2>
14184 ripley 330 
 
26591 hornik 331 
<p>This chapter applies to Unix-like and Windows versions of R.
14184 ripley 332 
 
24001 hornik 333 
   <p>It is helpful to use the correct terminology.  A <em>package</em> is
18887 hornik 334 
loaded from a <em>library</em> by the function <code>library()</code>.  Thus a
14184 ripley 335 
library is a directory containing installed packages; the main library
24001 hornik 336 
is <code></code><var>R_HOME</var><code>/library</code>, but others can be used, for example by
18887 hornik 337 
setting the environment variable <code>R_LIBS</code> or using the R function
16988 hornik 338 
<code>.libPaths()</code>.
14184 ripley 339 
 
14185 ripley 340 
<a name="Installing%20packages"></a>
14184 ripley 341 
 
24070 ripley 342 
<h3 class="section">4.1 Installing packages</h3>
14184 ripley 343 
 
28261 murdoch 344 
<p>Packages may be distributed in source form or compiled binary form.
24594 ripley 345 
Installing source packages requires that compilers and tools
346 
(including Perl 5.004 or later) be installed.  Binary packages
347 
are platform specific and generally need
348 
no special tools to install, but see the documentation for
349 
your platform for details.
19459 pd 350 
 
24001 hornik 351 
   <p>Note that you need to specify implicitly or explicitly the library to
14184 ripley 352 
which the package is to be installed.  This is only an issue if you have
353 
more than one library, of course.
354 
 
24001 hornik 355 
   <p>To install packages from source on Unix use
14307 ripley 356 
 
24001 hornik 357 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
358 
     </pre>
14184 ripley 359 
 
20580 hornik 360 
<p>The part <code>-l /path/to/library</code> can be omitted, in which case the
361 
first library in <code>R_LIBS</code> is used if set, otherwise the main
24001 hornik 362 
library <code></code><var>R_HOME</var><code>/library</code> is used.  (<code>R_LIBS</code> is looked
20580 hornik 363 
for in the environment: <code>.Renviron</code> is not read by <code>R CMD</code>.)
14184 ripley 364 
 
24001 hornik 365 
   <p>The Windows equivalent is<a rel="footnote" href="#fn-1"><sup>1</sup></a>
14307 ripley 366 
 
28261 murdoch 367 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
24001 hornik 368 
     </pre>
14184 ripley 369 
 
24001 hornik 370 
   <p>Alternatively, packages can be downloaded and installed from within
14307 ripley 371 
R.  First set the option <code>CRAN</code> to your nearest <small>CRAN</small>
372 
mirror, for example
373 
 
24001 hornik 374 
<pre class="smallexample">     &gt; options(CRAN = "http://cran.us.r-project.org/")
375 
     </pre>
14184 ripley 376 
 
14307 ripley 377 
<p>Then download and install package <strong>foo</strong> by
378 
 
24001 hornik 379 
<pre class="smallexample">     &gt; install.packages("foo")
380 
     </pre>
14184 ripley 381 
 
382 
<p>Unless the library is specified (argument <code>lib</code>) the first library
16988 hornik 383 
in the library search path is used.
14184 ripley 384 
 
24001 hornik 385 
   <p>What this does is different on Unix and Windows.  On Unix it consults
14307 ripley 386 
the list of available source packages on <small>CRAN</small>, downloads the
387 
latest version of the <strong>foo</strong> sources, and installs it (via <code>R
14184 ripley 388 
CMD INSTALL</code>).  On Windows it looks at the list of <em>binary</em>
389 
versions of packages and downloads the latest version (if any).
390 
 
24001 hornik 391 
   <p>On Windows <code>install.packages</code> can also install a binary package
14307 ripley 392 
from a local <code>zip</code> file by setting argument <code>CRAN</code> to
14754 ripley 393 
<code>NULL</code>.   <code>RGui.exe</code> has a menu <code>Packages</code> with a GUI
394 
interface to <code>install.packages</code>, <code>update.packages</code> and
395 
<code>library</code>.
14184 ripley 396 
 
14185 ripley 397 
<a name="Updating%20packages"></a>
14184 ripley 398 
 
24070 ripley 399 
<h3 class="section">4.2 Updating packages</h3>
14184 ripley 400 
 
26591 hornik 401 
<p>The command <code>update.packages()</code> is the simplest way to ensure that
14307 ripley 402 
all the packages on your system are up to date.  Set the <code>CRAN</code>
403 
option as in the previous section.  The <code>update.packages()</code>
14184 ripley 404 
downloads the list of available packages and their current versions,
405 
compares it with those installed and offers to fetch and install any
406 
that have later versions on <small>CRAN</small>.
407 
 
24001 hornik 408 
   <p>An alternative way of keeping packages up-to-date is provided by the
17276 pd 409 
command <code>packageStatus()</code>, which returns an object with information
410 
on all installed packages and packages available at multiple
24001 hornik 411 
repositories (CRAN, local archive, <small class="dots">...</small>). The <code>print</code> and
17276 pd 412 
<code>summary</code> methods give an overview of installed and available
413 
packages, the <code>upgrade</code> method offers to fetch and install outdated
414 
packages.  This allows R to fetch packages from several repositories and
415 
keep in sync with all of them, instead of only one CRAN mirror, and is
416 
intended to become the default package manager for future versions of R.
417 
 
14185 ripley 418 
<a name="Removing%20packages"></a>
14184 ripley 419 
 
24070 ripley 420 
<h3 class="section">4.3 Removing packages</h3>
14184 ripley 421 
 
26591 hornik 422 
<p>Packages can be removed in a number of ways.  From a command prompt they
14184 ripley 423 
can be removed by
424 
 
24001 hornik 425 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
426 
     </pre>
14184 ripley 427 
 
428 
<p>(Unix) or
22426 hornik 429 
 
28261 murdoch 430 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
24001 hornik 431 
     </pre>
14184 ripley 432 
 
433 
<p>(Windows).
434 
 
24001 hornik 435 
   <p>From a running R process they can be removed by
14698 hornik 436 
 
24001 hornik 437 
<pre class="smallexample">     &gt; remove.packages(c("pkg1", "pkg2"),
438 
                       lib = file.path("path", "to", "library"))
439 
     </pre>
14184 ripley 440 
 
24001 hornik 441 
   <p>Finally, in most installations one can just remove the package directory
14184 ripley 442 
from the library.
443 
 
24001 hornik 444 
   <p><strong>Note:</strong> whereas it is currently possible to install package
18887 hornik 445 
<em>bundles</em>, one cannot remove these as such--the packages contained
446 
in the bundle have to removed individually.
447 
 
14307 ripley 448 
<a name="Essential%20and%20useful%20other%20programs"></a>
14184 ripley 449 
 
24001 hornik 450 
<h2 class="appendix">Appendix A Essential and useful other programs</h2>
14184 ripley 451 
 
26591 hornik 452 
<p>This appendix gives details of programs you will need to build R on
14184 ripley 453 
Unix-like platforms, or which will be used by R if found by
18887 hornik 454 
<code>configure</code>.
14184 ripley 455 
 
27252 ripley 456 
   <p>Remember that some package management systems (such as <small>RPM</small> and
457 
deb) make a distinction between the user version of a package and the
458 
development version.  The latter usually has the same name but with the
459 
extension <code>-devel</code> or <code>-dev</code>: you need both versions
460 
installed.
461 
 
14307 ripley 462 
<a name="Essential%20programs"></a>
14184 ripley 463 
 
24001 hornik 464 
<h3 class="section">A.1 Essential programs</h3>
14184 ripley 465 
 
26591 hornik 466 
<p>You need a means of compiling C and FORTRAN 77 (see <a href="#Using%20FORTRAN">Using FORTRAN</a>).  Some add-on packages also need a C++ compiler.
14184 ripley 467 
 
27252 ripley 468 
   <p>Unless you do not want to view graphs on-screen you need <code>X11</code>
469 
installed, including its headers and client libraries.  (On RedHat Linux
470 
this means the <code>XFree86-devel</code> and <code>XFree86-libs</code> RPMs, for
471 
example.)
472 
 
24001 hornik 473 
   <p>You will need Perl version 5.004 or later, available via
14184 ripley 474 
<a href="http://www.perl.com/CPAN/">http://www.perl.com/CPAN/</a>, to build any of the on-line
24650 hornik 475 
documentation.
14184 ripley 476 
 
24001 hornik 477 
   <p>You will not be able to build the info files unless you have
23859 hornik 478 
<code>makeinfo</code> version 4 or later installed.
14184 ripley 479 
 
24001 hornik 480 
   <p>The typeset documentation needs <code>tex</code> and <code>latex</code>, or
14184 ripley 481 
<code>pdftex</code> and <code>pdflatex</code>.
482 
 
14307 ripley 483 
<a name="Useful%20libraries%20and%20programs"></a>
14184 ripley 484 
 
24001 hornik 485 
<h3 class="section">A.2 Useful libraries and programs</h3>
14184 ripley 486 
 
26591 hornik 487 
<p>The command-line editing depends on the <code>readline</code> library
14184 ripley 488 
available from any GNU mirror: you will need a fairly recent version.
489 
 
24001 hornik 490 
   <p>The bitmapped graphics devices <code>jpeg()</code> and <code>png()</code> need the
23859 hornik 491 
appropriate headers and libraries installed: <code>jpeg</code> (version 6b
492 
or later) or <code>libpng</code> (version 1.2.3 or later) and <code>zlib</code>
493 
(version 1.1.3 or later) respectively.
14184 ripley 494 
 
24001 hornik 495 
   <p>The <code>bitmap</code> and <code>dev2bitmap</code> devices make use of ghostscript
14184 ripley 496 
(<a href="http://www.cs.wisc.edu/~ghost">http://www.cs.wisc.edu/~ghost</a>).
497 
 
26882 ripley 498 
   <p>If you have them installed (including the appropriate headers and of
499 
late enough versions), <code>zlib</code>, <code>libbz2</code> and PCRE will be used
500 
if specified by <code>--with-zlib</code>, <code>--with-bzlib</code> or
501 
<code>--with-pcre</code>: otherwise versions in the R sources will be
502 
compiled in.  As the latter suffice and are tested with R you should
503 
not need to change this.
18664 ripley 504 
 
14185 ripley 505 
<a name="Tcl%2fTk"></a>
14184 ripley 506 
 
26591 hornik 507 
<h3 class="subsection">A.2.1 Tcl/Tk</h4>
14184 ripley 508 
 
26591 hornik 509 
<p>The <strong>tcltk</strong> package needs Tcl/Tk installed: the sources are
21609 ripley 510 
available at <a href="http://www.scriptics.com/">http://www.scriptics.com/</a>.  To specify the locations
14307 ripley 511 
of the Tcl/Tk files you may need the configuration options
512 
 
24001 hornik 513 
     <dl>
14184 ripley 514 
<dt><code>--with-tcltk</code>
24001 hornik 515 
     <dd>use Tcl/Tk, or specify its library directory
516 
<br><dt><code>--with-tcl-config=</code><var>TCL_CONFIG</var><code></code>
517 
     <dd>specify location of <code>tclConfig.sh</code>
518 
<br><dt><code>--with-tk-config=</code><var>TK_CONFIG</var><code></code>
519 
     <dd>specify location of <code>tkConfig.sh</code>
14184 ripley 520 
</dl>
521 
 
18887 hornik 522 
<p>or use the configure variables <code>TCLTK_LIBS</code> and
523 
<code>TCLTK_CPPFLAGS</code> to specify the flags needed for linking against
524 
the Tcl and Tk libraries and for finding the <code>tcl.h</code> and
525 
<code>tk.h</code> headers, respectively.
526 
 
27252 ripley 527 
   <p>Versions of Tcl/TK from 8.3 to 8.4.4 have been used successfully: 8.0 is
528 
no longer supported.
21609 ripley 529 
 
14307 ripley 530 
<a name="Linear%20algebra"></a>
14184 ripley 531 
 
26591 hornik 532 
<h3 class="subsection">A.2.2 Linear algebra</h4>
14184 ripley 533 
 
26591 hornik 534 
<p>The linear algebra routines in R can make use of enhanced BLAS (Basic
22181 ripley 535 
Linear Algebra Subprograms, <a href="http://www.netlib.org/blas/faq.html">http://www.netlib.org/blas/faq.html</a>)
536 
routines.  Some are compiler-system-specific (<code>libsunperf</code> on Sun
24001 hornik 537 
Sparc<a rel="footnote" href="#fn-2"><sup>2</sup></a>, <code>libessl</code> on IBM, <code>vecLib</code> on MacOS
23148 ripley 538 
X) but ATLAS (<a href="http://math-atlas.sourceforge.net/">http://math-atlas.sourceforge.net/</a>) is a "tuned"
539 
BLAS that runs on a wide range of Unix-alike platforms.  If no more
540 
specific library is found, a <code>libblas</code> library in the library path
541 
will be used.  You can specify a specific BLAS library by the
542 
configuration option <code>--with-blas</code> and not to use an external
543 
BLAS library by <code>--without-blas</code>.
14184 ripley 544 
 
27252 ripley 545 
   <p>For systems with multiple processors it is possible to use a
546 
multi-threaded version of ATLAS.  (Prior to R 1.8.0 this was not
25780 hornik 547 
supported since <code>SIGINT</code> signals sent to the process and handled by
27252 ripley 548 
the wrong thread could result in segfaults.)  A remaining issue is that
549 
R profiling, which uses the <code>SIGPROF</code> signal, may cause
550 
problems.  You may want to disable profiling if you use a multi-threaded
551 
version of ATLAS.  You can use a multi-threaded ATLAS by specifying
24001 hornik 552 
<pre class="smallexample">     --with-blas="-lptf77blas -lpthread -latlas"
553 
     </pre>
19031 hornik 554 
 
27343 hornik 555 
   <p>Another tuned BLAS which is available for some processors under Linux is
556 
by Kazushige Goto, currently available at
557 
<a href="http://www.cs.utexas.edu/users/flame/goto/">http://www.cs.utexas.edu/users/flame/goto/</a>.  Once this is is
558 
installed, it can be used by one of
559 
<pre class="smallexample">     --with-blas=goto
560 
     --with-blas=-lgoto
561 
     </pre>
562 
   Multi-threaded versions of Goto's BLAS are available, so please note the
563 
<em>caveat</em> in the previous paragraph.
564 
 
27441 ripley 565 
   <p>For Intel processors under Linux, Intel's Math Kernel Library
566 
<a href="http://www.intel.com/software/products/mkl/">http://www.intel.com/software/products/mkl/</a>
567 
can be used by
568 
<pre class="smallexample">     --with-blas="-lmkl -lguide -lpthread"
569 
     </pre>
570 
   with the same caveat on multi-threading.  (Thanks to Andy Liaw for the
571 
information.)
572 
 
24001 hornik 573 
   <p>Note that the BLAS library will be used for several add-on packages as
14307 ripley 574 
well as for R itself.  This means that it is better to use a shared
575 
BLAS library, as most of a static library will be compiled into the R
22142 ripley 576 
executable and each BLAS-using package.  In any case, the BLAS library
27252 ripley 577 
must be usable with dynamically-loadable code: this can be a problem
578 
with ATLAS that is not by default built with position-independent code.
14184 ripley 579 
 
24001 hornik 580 
   <p>You will need double-precision and double-complex versions of the BLAS,
14215 ripley 581 
but not single-precision nor complex routines.
582 
 
27252 ripley 583 
   <p>Provision is made for using an external LAPACK library, principally to
584 
cope with BLAS libraries which contain a copy of LAPACK (such as
28261 murdoch 585 
<code>libsunperf</code> on Solaris and <code>vecLib</code> on MacOS 10.2.2).
27252 ripley 586 
However, the likely performance gains are thought to be small (and may
587 
be negative), and the default is not to search for a suitable LAPACK
588 
library.  You can specify a specific LAPACK library or a search for a
589 
generic library by the configuration option <code>--with-lapack</code>.  The
590 
default for <code>--with-lapack</code> is to check the BLAS library and then
591 
look for an external library <code>-llapack</code>.  Sites searching for the
592 
fastest possible linear algebra may want to build a LAPACK library using
593 
the ATLAS-optimized subset of LAPACK.  To do so specify something like
24001 hornik 594 
<pre class="smallexample">     --with-lapack="-L/path/to/libs -llapack -lcblas"
595 
     </pre>
14215 ripley 596 
 
23273 hornik 597 
<p>since the ATLAS subset of LAPACK depends on <code>libcblas</code>.
598 
 
24001 hornik 599 
   <p>If you do use <code>--with-lapack</code>, be aware of potential problems
22570 ripley 600 
with bugs in the LAPACK 3.0 sources (or in the posted corrections to those
601 
sources).  In particular, bugs in <code>DGEEV</code> and <code>DGESDD</code> have
602 
resulted in error messages such as
24001 hornik 603 
<pre class="smallexample">     DGEBRD gave error code -10
604 
     </pre>
22570 ripley 605 
 
23148 ripley 606 
<p>(from the Debian <code>-llapack</code> which was current in late 2002).  Other
607 
potential problems are incomplete versions of the libraries: for example
608 
<code>libsunperf</code> from Sun Forte 6.x was missing the entry point for
609 
<code>DLANGE</code> and <code>vecLib</code> has omitted the BLAS routine
610 
<code>LSAME</code>.
22570 ripley 611 
 
24001 hornik 612 
   <p>As with all libraries, you need to ensure that they and R were
14754 ripley 613 
compiled with compatible compilers and flags.  For example, this means
17472 ripley 614 
that on Sun Sparc using the native compilers the flag <code>-dalign</code>
615 
is needed so <code>libsunperf</code> can be used.
14754 ripley 616 
 
24001 hornik 617 
   <p>An ATLAS `tuned' BLAS can also be used on Windows: see
20580 hornik 618 
<code>src/gnuwin32/INSTALL</code> for how to enable this when building from
28261 murdoch 619 
source, and <a href="http://www.stats.ox.ac.uk/pub/R/rw-FAQ.html">R Windows <small>FAQ</small></a> for adding pre-compiled support to binary versions.
27916 hornik 620 
Goto's BLAS can also be used when building from source.
15508 pd 621 
 
24001 hornik 622 
   <p>Note that under Unix (but not under Windows) if R is compiled
28261 murdoch 623 
against a non-default BLAS, then all BLAS-using packages must also be.
19393 hornik 624 
So if R is re-built after ATLAS is installed, then packages such as
625 
<strong>quantreg</strong> will need to be re-installed.
17472 ripley 626 
 
14185 ripley 627 
<a name="Configuration%20on%20Unix"></a>
14184 ripley 628 
 
24001 hornik 629 
<h2 class="appendix">Appendix B Configuration on Unix</h2>
14184 ripley 630 
 
14185 ripley 631 
<a name="Configuration%20options"></a>
14184 ripley 632 
 
24001 hornik 633 
<h3 class="section">B.1 Configuration options</h3>
14184 ripley 634 
 
26591 hornik 635 
<p><code>configure</code> has many options: running
14307 ripley 636 
 
24001 hornik 637 
<pre class="smallexample">     ./configure --help
638 
     </pre>
14184 ripley 639 
 
14307 ripley 640 
<p>will give a list.  Probably the most important ones not covered
641 
elsewhere are (defaults in brackets)
642 
 
24001 hornik 643 
     <dl>
14307 ripley 644 
<dt><code>--with-x</code>
24001 hornik 645 
     <dd>use the X Window System
646 
<br><dt><code>--x-includes=</code><var>DIR</var><code></code>
647 
     <dd>X include files are in <var>DIR</var>
648 
<br><dt><code>--x-libraries=</code><var>DIR</var><code></code>
649 
     <dd>X library files are in <var>DIR</var>
14307 ripley 650 
<br><dt><code>--with-readline</code>
24001 hornik 651 
     <dd>use readline library (if available) [yes]
14307 ripley 652 
<br><dt><code>--enable-R-profiling</code>
24001 hornik 653 
     <dd>attempt to compile support for <code>Rprof()</code> [yes]
14307 ripley 654 
<br><dt><code>--enable-R-shlib</code>
24001 hornik 655 
     <dd>build R as a shared library [no]
14307 ripley 656 
</dl>
657 
 
658 
<p>You can use <code>--without-foo</code> or <code>--disable-foo</code> for the
14184 ripley 659 
negatives.
660 
 
24001 hornik 661 
   <p>You will want to use <code>--disable-R-profiling</code> if you are building
14307 ripley 662 
a profiled executable of R (e.g. with <code>-pg)</code>.
14184 ripley 663 
 
24001 hornik 664 
   <p>Flag <code>--enable-R-shlib</code> causes the make process to build R as a
14698 hornik 665 
shared library, typically called <code>libR.so</code>, and to take
666 
considerably longer, so you probably only want this if you will be using
667 
an application which embeds R.
14184 ripley 668 
 
14185 ripley 669 
<a name="Configuration%20variables"></a>
14184 ripley 670 
 
24001 hornik 671 
<h3 class="section">B.2 Configuration variables</h3>
14184 ripley 672 
 
26591 hornik 673 
<p>If you need or want to set certain configure variables to something
14184 ripley 674 
other than their default, you can do that by either editing the file
14307 ripley 675 
<code>config.site</code> (which documents all the variables you might want to
676 
set) or on the command line as
14184 ripley 677 
 
24001 hornik 678 
<pre class="smallexample">     ./configure VAR=<var>value</var>
679 
     </pre>
14184 ripley 680 
 
18887 hornik 681 
<p>These variables are <em>precious</em>, implying that they do not have to
682 
be exported to the environment, are kept in the cache even if not
683 
specified on the command line and checked for consistency between two
684 
configure runs (provided that caching is used), and are kept during
685 
automatic reconfiguration as if having been passed as command line
686 
arguments, even if no cache is used.
687 
 
24001 hornik 688 
   <p>See the variable output section of <code>configure --help</code> for a list of
18887 hornik 689 
all these variables.
690 
 
24001 hornik 691 
   <p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to
19611 ripley 692 
<code>a4</code>, not <code>letter</code>.  (Valid values are <code>a4</code>,
693 
<code>letter</code>, <code>legal</code> and <code>executive</code>.)
14184 ripley 694 
 
24001 hornik 695 
   <p>If you have libraries and header files, e.g., for GNU readline, in
18887 hornik 696 
non-system directories, use the variables <code>LDFLAGS</code> (for libraries,
697 
using <code>-L</code> flags to be passed to the linker) and <code>CPPFLAGS</code>
698 
(for header files, using <code>-I</code> flags to be passed to the C/C++
699 
preprocessors), respectively, to specify these locations.  These default
700 
to <code>/usr/local/lib</code> and <code>/usr/local/include</code> to catch the most
701 
common cases.  If libraries are still not found, then maybe your
702 
compiler/linker does not support re-ordering of <code>-L</code> and
703 
<code>-l</code> flags (this has been reported to be a problem on HP-UX with
704 
the native <code>cc</code>).  In this case, use a different compiler (or a
705 
front end shell script which does the re-ordering).
14184 ripley 706 
 
24001 hornik 707 
   <p>Another precious variable is <code>R_BROWSER</code>, the default browser, which
22313 ripley 708 
should take a value of an executable in the user's path or specify
709 
a full path.
710 
 
24001 hornik 711 
   <p>If you find you need to alter configure variables, it is worth noting
18887 hornik 712 
that some settings may be cached in the file <code>config.cache</code>, and it
28261 murdoch 713 
is a good idea to remove that file (if it exists) before re-configuring.
18887 hornik 714 
Note that caching is turned <em>off</em> by default; use the command line
715 
option <code>--config-cache</code> (or <code>-C</code>) to enable caching.
14184 ripley 716 
 
14185 ripley 717 
<a name="Using%20make"></a>
14184 ripley 718 
 
24001 hornik 719 
<h3 class="section">B.3 Using make</h3>
14184 ripley 720 
 
26591 hornik 721 
<p>To compile R, you will most likely find it easiest to use GNU
14184 ripley 722 
<code>make</code>.  On Solaris 2.6/7/8 in particular, you need a version of
21609 ripley 723 
GNU <code>make</code> different from 3.77; 3.79.1 works fine, as does the Sun
17302 ripley 724 
<code>make</code>.  The native <code>make</code> is reported to fail on SGI
20580 hornik 725 
Irix 6.5 and Alpha/OSF1 (aka Tru64).
14184 ripley 726 
 
24001 hornik 727 
   <p>To build in a separate directory you need a <code>make</code> that uses the
14307 ripley 728 
<code>VPATH</code> variable, for example GNU <code>make</code>, or Sun
729 
<code>make</code> on Solaris 2.7/8 (but not earlier).
14184 ripley 730 
 
24001 hornik 731 
   <p>If you want to use a <code>make</code> by another name, for example if your
18887 hornik 732 
GNU <code>make</code> is called <code>gmake</code>, you need to set the variable
733 
<code>MAKE</code> at configure time, for example
14307 ripley 734 
 
24001 hornik 735 
<pre class="smallexample">     ./configure MAKE=gmake
736 
     </pre>
14184 ripley 737 
 
14307 ripley 738 
<a name="Using%20FORTRAN"></a>
14184 ripley 739 
 
24001 hornik 740 
<h3 class="section">B.4 Using FORTRAN</h3>
14184 ripley 741 
 
26591 hornik 742 
<p>To compile R, you need a FORTRAN compiler or <code>f2c</code>, the
14307 ripley 743 
FORTRAN-to-C converter (<a href="http://www.netlib.org/f2c">http://www.netlib.org/f2c</a>).  The default
744 
is to search for <code>g77</code>, <code>f77</code>, <code>xlf</code>,
21630 hornik 745 
<code>frt</code>, <code>pgf77</code>, <code>fl32</code>, <code>af77</code>,
746 
<code>fort77</code>, <code>f90</code>, <code>xlf90</code>, <code>pgf90</code>,
747 
<code>epcf90</code>, <code>f95</code>, <code>fort</code>, <code>xlf95</code>,
748 
<code>lf95</code>, <code>g95</code>, and <code>fc</code> (in that
24001 hornik 749 
order)<a rel="footnote" href="#fn-3"><sup>3</sup></a>, and
14307 ripley 750 
then for <code>f2c</code>, and use whichever is found first; if none is
751 
found, R cannot be compiled.  The search mechanism can be changed
19221 hornik 752 
using the configure variables <code>F77</code> and <code>F2C</code> which specify
753 
the commands that run the FORTRAN 77 compiler and FORTRAN-to-C
754 
converter, respectively.  If <code>F77</code> is given, it is used to compile
755 
FORTRAN; otherwise, if <code>F2C</code> is given, f2c is used even if a
756 
FORTRAN compiler would be be available.  If your FORTRAN compiler is in
757 
a non-standard location, you should set the environment variable
18887 hornik 758 
<code>PATH</code> accordingly before running <code>configure</code>, or use the
759 
configure variable <code>F77</code> to specify its full path.
14184 ripley 760 
 
24001 hornik 761 
   <p>If your FORTRAN libraries are in slightly peculiar places, you should
14698 hornik 762 
also look at <code>LD_LIBRARY_PATH</code> or your system's equivalent to make
763 
sure that all libraries are on this path.
14184 ripley 764 
 
24001 hornik 765 
   <p>You must set whatever compilation flags (if any) are needed to ensure
14307 ripley 766 
that FORTRAN <code>integer</code> is equivalent to a C <code>int</code> pointer and
767 
FORTRAN <code>double precision</code> is equivalent to a C <code>double</code>
14184 ripley 768 
pointer.  This is checked during the configuration process.
769 
 
24001 hornik 770 
   <p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
14307 ripley 771 
is a FORTRAN 90 extension.  This is checked for at configure
24001 hornik 772 
time<a rel="footnote" href="#fn-4"><sup>4</sup></a>, but you may need to avoid
773 
compiler flags<a rel="footnote" href="#fn-5"><sup>5</sup></a> asserting
14307 ripley 774 
FORTRAN 77 compliance.
14215 ripley 775 
 
24001 hornik 776 
   <p>For performance reasons<a rel="footnote" href="#fn-6"><sup>6</sup></a> you may want to choose a FORTRAN 90/95 compiler.
14215 ripley 777 
 
24001 hornik 778 
   <p>If you use <code>f2c</code> you may need to ensure that the FORTRAN type
17302 ripley 779 
<code>integer</code> is translated to the C type <code>int</code>.  Normally
18887 hornik 780 
<code>f2c.h</code> contains <code>typedef long int integer;</code>, which will work
781 
on a 32-bit platform but not on a 64-bit platform.
17302 ripley 782 
 
14307 ripley 783 
<a name="Compile%20and%20load%20flags"></a>
14184 ripley 784 
 
24001 hornik 785 
<h3 class="section">B.5 Compile and load flags</h3>
14184 ripley 786 
 
26591 hornik 787 
<p>A wide range of flags can be set in the file <code>config.site</code> or as
18887 hornik 788 
configure variables on the command line.  We have already mentioned
14307 ripley 789 
 
24001 hornik 790 
     <dl>
14184 ripley 791 
<dt><code>CPPFLAGS</code>
24001 hornik 792 
     <dd>header file search directory (<code>-I</code>) and any other miscellaneous
18887 hornik 793 
options for the C and C++ preprocessors and compilers
794 
<br><dt><code>LDFLAGS</code>
24001 hornik 795 
     <dd>path (<code>-L</code>), stripping (<code>-s</code>) and any other miscellaneous
18887 hornik 796 
options for the linker
14184 ripley 797 
</dl>
798 
 
799 
<p>and others include
14307 ripley 800 
 
24001 hornik 801 
     <dl>
14184 ripley 802 
<dt><code>CFLAGS</code>
24001 hornik 803 
     <dd>debugging and optimization flags, C
14184 ripley 804 
<br><dt><code>MAIN_CFLAGS</code>
24001 hornik 805 
     <dd>ditto, for compiling the main program
14184 ripley 806 
<br><dt><code>SHLIB_CFLAGS</code>
24001 hornik 807 
     <dd>for shared libraries
14184 ripley 808 
<br><dt><code>FFLAGS</code>
24001 hornik 809 
     <dd>debugging and optimization flags, FORTRAN
14184 ripley 810 
<br><dt><code>MAIN_FFLAGS</code>
24001 hornik 811 
     <dd>ditto, for compiling the main program
14184 ripley 812 
<br><dt><code>SHLIB_FFLAGS</code>
24001 hornik 813 
     <dd>for shared libraries
14184 ripley 814 
<br><dt><code>MAIN_LDFLAGS</code>
24001 hornik 815 
     <dd>additional flags for the main link
14184 ripley 816 
<br><dt><code>SHLIB_LDFLAGS</code>
24001 hornik 817 
     <dd>additional flags for linking the shared libraries
14184 ripley 818 
</dl>
819 
 
18887 hornik 820 
<p>Library paths specified as <code>-L/lib/path</code> in <code>LDFLAGS</code> are
14698 hornik 821 
collected together and prepended to <code>LD_LIBRARY_PATH</code> (or your
822 
system's equivalent), so there should be no need for <code>-R</code> or
823 
<code>-rpath</code> flags.
14184 ripley 824 
 
24001 hornik 825 
   <p>To compile a profiling version of R, one might for example want to
14184 ripley 826 
use <code>MAIN_CFLAGS=-pg</code>, <code>MAIN_FFLAGS=-pg</code>,
827 
<code>MAIN_LDFLAGS=-pg</code> on platforms where <code>-pg</code> cannot be used
828 
with position-independent code.
829 
 
24001 hornik 830 
   <p><strong>Beware:</strong> it may be necessary to set <code>CFLAGS</code> and
14754 ripley 831 
<code>FFLAGS</code> in ways compatible with the libraries to be used: one
832 
possible issue is the alignment of doubles, another is the way
833 
structures are passed.
834 
 
14307 ripley 835 
<a name="Building%20the%20GNOME%20interface"></a>
14184 ripley 836 
 
24001 hornik 837 
<h3 class="section">B.6 Building the <small>GNOME</small> interface</h3>
14184 ripley 838 
 
26591 hornik 839 
<p>This interface is experimental and incomplete.  It provides a console
17276 pd 840 
and two graphics devices named <code>gtk()</code> and <code>gnome()</code>.  The
841 
console offers a basic command line editing and history mechanism, along
842 
with tool and button bars that give a point-and-click interface to some
843 
R commands.  Many of the features of the console are currently
844 
stubs. The <code>gtk()</code> graphics device is a port of the <code>x11()</code>
845 
device to <small>GDK</small> (the GIMP Drawing Kit). The <code>gnome()</code>
846 
device uses the <small>GNOME</small> canvas.
14184 ripley 847 
 
24001 hornik 848 
   <p>Due to its experimental nature, the <small>GNOME</small> interface for R
17276 pd 849 
will not be built automatically.  You must specify it by running
850 
configure with the <code>--with-gnome</code> option.  For example, you might
851 
run
14307 ripley 852 
 
24001 hornik 853 
<pre class="smallexample">     ./configure --with-gnome
854 
     </pre>
14184 ripley 855 
 
21609 ripley 856 
<p>but please check you have all the requirements first. You need at least
857 
the following libraries (or later) installed
14307 ripley 858 
 
24001 hornik 859 
<pre class="smallexample">     audiofile-0.2.1
860 
     esound-0.2.23
861 
     glib-1.2.10
862 
     gtk+-1.2.10
863 
     imlib-1.9.10
864 
     ORBit-0.5.12
865 
     gnome-libs-1.4.1.2
866 
     libxml-1.8.16
867 
     libglade-0.17
868 
     </pre>
14184 ripley 869 
 
17276 pd 870 
<p>It is preferable to have a complete installation of the <small>GNOME</small>
871 
desktop environment.  If you use Linux, then this should be provided
872 
with your distribution.  In addition, packaged binary distributions of
873 
GNOME are available from <a href="http://www.ximian.com">http://www.ximian.com</a> for the most
874 
popular Linux distributions and for Solaris.
14307 ripley 875 
 
24001 hornik 876 
   <p>Remember that some package management systems (such as <small>RPM</small> and
17276 pd 877 
deb) make a distinction between the user version of a package and the
18887 hornik 878 
developer version.  The latter usually has the same name but with the
879 
extension <code>-devel</code>.  If you use a pre-packaged version of
880 
<small>GNOME</small> then you must have the developer versions of the above
881 
packages in order to compile the R-GNOME interface.
14184 ripley 882 
 
24001 hornik 883 
   <p>The full list of <small>GNOME</small> options to configure is
14184 ripley 884 
 
24001 hornik 885 
     <dl>
14184 ripley 886 
<dt><code>--with-gnome</code>
24001 hornik 887 
     <dd>use <small>GNOME</small>, or specify its prefix [no]
888 
<br><dt><code>--with-gnome-includes=</code><var>DIR</var><code></code>
889 
     <dd>specify location of <small>GNOME</small> headers
890 
<br><dt><code>--with-gnome-libs=</code><var>DIR</var><code></code>
891 
     <dd>specify location of <small>GNOME</small> libs
892 
<br><dt><code>--with-libglade-config=</code><var>LIBGLADE_CONFIG</var><code></code>
893 
     <dd>specify location of <code>libglade-config</code>
14184 ripley 894 
</dl>
895 
 
17472 ripley 896 
<a name="Platform%20notes"></a>
897 
 
24001 hornik 898 
<h3 class="section">B.7 Platform notes</h3>
17472 ripley 899 
 
26591 hornik 900 
<p>This section provides some notes on building R on different Unix-like
18887 hornik 901 
platforms.  These notes are based on tests run on one or two systems in
28261 murdoch 902 
each case with particular sets of compilers and support libraries.
17472 ripley 903 
Success in building R depends on the proper installation and functioning
904 
of support software; your results may differ if you have other versions
905 
of compilers and support libraries.
906 
 
27252 ripley 907 
<a name="Linux"></a>
908 
 
909 
<h3 class="subsection">B.7.1 Linux</h4>
910 
 
911 
<p>Linux is the main development platform for R, so compilation from the
912 
sources is normally straightforward.
913 
 
914 
   <p>Remember that some package management systems (such as <small>RPM</small> and
915 
deb) make a distinction between the user version of a package and the
916 
developer version.  The latter usually has the same name but with the
917 
extension <code>-devel</code> or  <code>-dev</code>: you need both versions
918 
installed.  So please check the <code>configure</code> output to see if the
919 
expected features are detected: if for example <code>readline</code> is
920 
missing add the package containing its headers.
921 
 
922 
   <p>When R has been installed from a binary distribution there are
923 
sometimes problems with missing components such as the Fortran
924 
compiler.  Searching the <code>R-help</code> archives will normally reveal
925 
what is needed.
926 
 
927 
   <p>It seems that the <code>gcc</code> compilers normally produce PIC code on
928 
<code>ix86</code> Linux but do not necessarily do so on 64-bit versions such
929 
as that for AMD Opteron.  So care can be needed with BLAS libraries and
930 
when building R as a shared library to ensure that
931 
position-independent code is used in any static libraries (such as the
932 
Tcl/Tk libraries, <code>libpng</code>, <code>libjpeg</code> and <code>zlib</code>) which
933 
might be linked against.  Fortunately these are normally built as shared
934 
libraries with the exception of the ATLAS BLAS libraries.
935 
 
17472 ripley 936 
<a name="MacOS%20X"></a>
937 
 
27252 ripley 938 
<h3 class="subsection">B.7.2 MacOS X</h4>
17472 ripley 939 
 
26591 hornik 940 
<p>You can build R as a Unix application on MacOS X.  You will need the
17472 ripley 941 
DevTools, <code>f2c</code> or <code>g77</code>, and the <code>dlcompat</code>
942 
library.  You will also need to install an X sub-system or configure
943 
with <code>--without-x</code>.
944 
 
24001 hornik 945 
   <p><code>f2c</code>, <code>g77</code>, the <code>dlcompat</code> library, and X server
17472 ripley 946 
and support libraries are available from the Fink project
947 
(<a href="http://fink.sourceforge.net">http://fink.sourceforge.net</a>).  At the time of writing
948 
<code>f2c</code> and <code>g77</code> were not available as part of the Fink
949 
binary distribution and needed to be installed directly; for example for
950 
<code>g77</code> use
18887 hornik 951 
 
24001 hornik 952 
<pre class="smallexample">     fink install g77
953 
     </pre>
17472 ripley 954 
 
24001 hornik 955 
   <p>The <code>vecLib</code> library of MacOS &gt;= 10.2.2 can be used <em>via</em> the
22570 ripley 956 
configuration options
24001 hornik 957 
<pre class="smallexample">     --with-blas="-framework vecLib" --with-lapack
958 
     </pre>
22570 ripley 959 
 
28261 murdoch 960 
<p>to provide higher-performance versions of the BLAS and LAPACK routines.
24173 ripley 961 
With <code>gcc 3.1</code> that appears to be the only way to build R, as
962 
the Fortran support routines in <code>libg2c</code> cannot be linked into a
963 
dynmaic library.  (We have had reports of success with pre-release
964 
versions of <code>gcc 3.3</code>.)
22570 ripley 965 
 
17472 ripley 966 
<a name="Solaris"></a>
967 
 
27252 ripley 968 
<h3 class="subsection">B.7.3 Solaris on Sparc</h4>
17472 ripley 969 
 
26591 hornik 970 
<p>R has been built successfully on Solaris 8 aka Solaris 2.8 aka SunOS
23148 ripley 971 
5.8 using <code>gcc</code>/<code>g77</code> and the SunPro WorkShop&nbsp;6 (aka
972 
Forte 6) compilers and the `Sun ONE Studio 7 Compiler Suite' (aka Forte
973 
7), and less regularly on Solaris 2.5.1, 2.6, 2.7 and 9.  GNU
24449 ripley 974 
<code>make</code> is needed prior to Solaris 2.7 for building other than in
975 
the source tree, and perhaps even then.
17472 ripley 976 
 
24449 ripley 977 
   <p>The Solaris versions of several of the tools needed to build R
978 
(e.g. <code>make</code>, <code>ar</code> and <code>ld</code>) are in
979 
<code>/usr/ccs/bin</code>, so if using those tools ensure this is in your
980 
path.
981 
 
24001 hornik 982 
   <p><code>gcc</code> 3.2.1 and 3.2.2 generate incorrect code on 32-bit Solaris
27252 ripley 983 
builds with optimization, but versions 3.1, 3.2, 3.2.3  and 3.3.x work
24173 ripley 984 
correctly.  At least files <code>src/main/engine.c</code>,
985 
<code>src/main/graphics.c</code> and <code>src/modules/devX11.c</code> are affected.
22118 ripley 986 
 
24001 hornik 987 
   <p>If using <code>gcc</code>, do ensure that the compiler was compiled for the
22570 ripley 988 
version of Solaris in use.  (This can be ascertained from <code>gcc
19611 ripley 989 
-v</code>.)  <code>gcc</code> makes modified versions of some header files, and
990 
so (for example) <code>gcc</code> compiled under Solaris 2.6 will not
991 
compile R under Solaris 2.7.  Also, do ensure that it was compiled
992 
for the assembler/loader in use.  If you download <code>gcc</code> from
993 
<a href="http://www.sunfreeware.com">http://www.sunfreeware.com</a> then you need to download
994 
<code>binutils</code> too.  To avoid all these pitfalls we strongly
995 
recommended you compile <code>gcc</code> from the sources yourself.
19393 hornik 996 
 
24001 hornik 997 
   <p>When using the SunPro compilers do <em>not</em> specify <code>-fast</code>, as
17472 ripley 998 
this disables <small>IEEE</small> arithmetic and <code>make check</code> will
999 
fail.  The maximal set of optimization options known to work is
1000 
 
24001 hornik 1001 
<pre class="smallexample">     -xlibmil -xO5 -dalign
1002 
     </pre>
17472 ripley 1003 
 
24001 hornik 1004 
   <p>We have found little performance difference between <code>gcc</code> and
17472 ripley 1005 
<code>cc</code> but considerable benefit from using a SunPro Fortran
23148 ripley 1006 
compiler: the <code>gcc</code>/<code>f77</code> combination works well.  For
1007 
many C++ applications (e.g. package <strong>Matrix</strong>) Forte 7 requires
1008 
<code>-lCstd</code>, which the configure script will add to
1009 
<code>SHLIB_CXXLDFLAGS</code> if it identifies the compiler correctly.
17472 ripley 1010 
 
24001 hornik 1011 
   <p>To compile for a 64-bit target on Solaris (which needs an UltraSparc
23148 ripley 1012 
chip and for support to be enabled in the OS) with the Forte 6 and 7
21058 ripley 1013 
compilers we used
18887 hornik 1014 
 
24001 hornik 1015 
<pre class="smallexample">     CC="cc -xarch=v9"
1016 
     CFLAGS="-xO5 -xlibmil -dalign"
1017 
     F77="f95 -xarch=v9"
1018 
     FFLAGS="-xO5 -xlibmil -dalign"
1019 
     CXX="CC -xarch=v9"
1020 
     CXXFLAGS="-xO5 -xlibmil -dalign"
1021 
     </pre>
17472 ripley 1022 
 
22181 ripley 1023 
<p>in <code>config.site</code>.
1024 
 
27252 ripley 1025 
   <p>For 64-bit compilation with <code>gcc</code> 3.2.x and 3.3.x we used
21058 ripley 1026 
 
24001 hornik 1027 
<pre class="smallexample">     CC="gcc -m64"
1028 
     FFLAGS="-m64 -g -O2"
1029 
     CXXFLAGS="-m64 -g -O2"
1030 
     LDFLAGS="-L/usr/local/lib/sparcv9 -L/usr/local/lib"
1031 
     </pre>
21058 ripley 1032 
 
27252 ripley 1033 
   <p>Note that <code>/usr/local/lib/sparcv9</code> will need to be in the
1034 
<code>LD_LIBRARY_PATH</code> during configuration.
22142 ripley 1035 
 
27252 ripley 1036 
   <p>Note that using <code>f95</code> allows the Sun performance library
1037 
<code>libsunperf</code> to be selected: it will not work with <code>f77</code>,
1038 
nor with <code>g77</code>.  <code>libsunperf</code> contains both BLAS and LAPACK
1039 
code, and <code>--with-lapack</code> is recommended for 32-bit builds using
1040 
<code>f95</code>, but not for 64-bit builds where on our test system it
1041 
failed in both Forte 6U1 and 7, albeit in different ways.  Our
1042 
experience has been that ATLAS's BLAS is faster than <code>libsunperf</code>,
1043 
especially for complex numbers.
1044 
 
24001 hornik 1045 
   <p>Some care is needed to ensure that libraries found by
18887 hornik 1046 
<code>configure</code> are compatible with the R executable and modules, as
1047 
the testing process will not detect many of the possible problems.  For
1048 
32-bit builds under <code>cc</code> the flag <code>-dalign</code> is needed for
1049 
some of the Sun libraries: fortunately the equivalent flag for
27252 ripley 1050 
<code>gcc</code>, <code>-mno-unaligned-doubles</code>, is the default.  In
1051 
theory, libraries such as <code>libpng</code>, <code>libjpeg</code>, <code>zlib</code> and
1052 
the ATLAS libraries need to be built with a <code>pic</code> or <code>PIC</code>
1053 
flag, which could be a problem if static libraries are used.  In
1054 
practice this seems to give little problem for 32-bit builds.
17472 ripley 1055 
 
24001 hornik 1056 
   <p>For a 64-bit build, 64-bit libraries must be used.  As the configuration
21058 ripley 1057 
process by default sets <code>LDFLAGS</code> to <code>-L/usr/local/lib</code>,
1058 
you may need to set it to avoid finding 32-bit addons (as in the
28023 ripley 1059 
<code>gcc -m64</code> example above).  It is possible to build Tcl/Tk as
1060 
64-bit libraries with the configure option <code>--enable-64bit</code>, but
1061 
only with the Forte compiler (and not with <code>gcc</code>) as of Tcl/Tk 8.4.5.
17472 ripley 1062 
 
22181 ripley 1063 
<a name="HP-UX"></a>
17472 ripley 1064 
 
27252 ripley 1065 
<h3 class="subsection">B.7.4 HP-UX</h4>
17472 ripley 1066 
 
26591 hornik 1067 
<p>R has been built successfully on HP-UX 10.2 and HP-UX 11.0 using both
19393 hornik 1068 
native compilers and <code>gcc</code>.  However, 10.2 has not been tested
1069 
since R 1.4.0.  By default, R is configured to use <code>gcc</code> and
22181 ripley 1070 
<code>g77</code> on HP-UX (if available).  Some installations of
19393 hornik 1071 
<code>g77</code> only install a static version of the <code>g2c</code> library
1072 
that cannot be linked into a shared library since its files have not
1073 
been compiled with the appropriate flag for producing position
1074 
independent code (<small>PIC</small>).  This will result in <code>make</code>
22181 ripley 1075 
failing with a linker error similar to
17472 ripley 1076 
 
24001 hornik 1077 
<pre class="smallexample">     ld: CODE_ONE_SYM fixup to non-code subspace in file foo.o -
1078 
     shared library must be position independent. Use +z or +Z to recompile.
1079 
     </pre>
22181 ripley 1080 
 
1081 
<p>(<code>+z</code> and <code>+Z</code> are the <small>PIC</small> flags for the native
1082 
compiler <code>cc</code>.)  If this is the case you either need to modify
1083 
your <code>g77</code> installation or configure with
1084 
 
24001 hornik 1085 
<pre class="smallexample">     F77=fort77
1086 
     </pre>
17472 ripley 1087 
 
18887 hornik 1088 
<p>to specify use of the native <small>POSIX</small>-compliant FORTRAN 77
17472 ripley 1089 
compiler.
1090 
 
24001 hornik 1091 
   <p>You may find that <code>configure</code> detects other libraries that R
22181 ripley 1092 
needs to use as shared libraries but are only available as static
1093 
libraries.  If you cannot install shared versions you will need to tell
1094 
<code>configure</code> not to use these libraries, or make sure they are
1095 
not in the library path.  The symptom will the linker error shown in the
1096 
last paragraph.  Static libraries that might be found and would cause
1097 
problems are
22426 hornik 1098 
 
24001 hornik 1099 
<pre class="smallexample">     BLAS                   use --without-blas
1100 
     Tcl/Tk                 use --without-tcltk
1101 
     GNOME                  not built by default
1102 
     libpng                 use --without-libpng
1103 
     jpeg                   use --without-jpeglib
1104 
     zlib                   use --without-zlib
1105 
     </pre>
17472 ripley 1106 
 
22181 ripley 1107 
<p>and <code>bzip2</code> and <code>pcre</code> are problematic when building
22270 ripley 1108 
<code>libR.so</code>, only.  These can be avoided by <code>--without-bzlib</code>
27343 hornik 1109 
and <code>--without-pcre</code> respectively, but these are the defaults.
22181 ripley 1110 
 
24001 hornik 1111 
   <p>Some versions of <code>gcc</code> may contain what appears to be a bug at
17472 ripley 1112 
the <code>-O2</code> optimization level that causes
18887 hornik 1113 
 
24001 hornik 1114 
<pre class="smallexample">     &gt; 2 %/% 2
1115 
     [1] 1
1116 
     &gt; 1:2 %/% 2
1117 
     [1] 0 0     # wrong!!
1118 
     </pre>
17472 ripley 1119 
 
1120 
<p>which will cause <code>make check</code> to fail.  If this is the case, you
1121 
should use <code>CFLAGS</code> to specify <code>-O</code> as the optimization
1122 
level to use.
1123 
 
24001 hornik 1124 
   <p>Some systems running HP-UX 11.0 may have a <code>gcc</code> that was
22181 ripley 1125 
installed under HP-UX 10.2.  Between versions 10.2 and 11.0 HP-UX
1126 
changed its support functions for <small>IEEE</small> arithmetic from the
1127 
recommended functions of the <small>IEEE</small> standard to the ones
1128 
specified in the C9x draft standard.  In particular, this means that
1129 
<code>finite</code> has been replaced by <code>isfinite</code>.  A <code>gcc</code>
1130 
configured for HP-UX 10.2 run on 11.0 will not find <code>isfinite</code>, and
1131 
as a result <code>configure</code> does not recognize the machine as fully
1132 
supporting <small>IEEE</small> arithmetic and does not define <code>IEEE_754</code>
1133 
when compiling C code.  This results in a failure in <code>make
1134 
check</code>.  The best solution is to install a properly configured
1135 
<code>gcc</code>.  An alternative work-around is to add <code>-DIEEE_754</code>
1136 
to the <code>CFLAGS</code> variable.
17472 ripley 1137 
 
24001 hornik 1138 
   <p>You can configure R to use both the native <code>cc</code> and
18887 hornik 1139 
<code>fort77</code> with
1140 
 
24001 hornik 1141 
<pre class="smallexample">     ./configure CC=cc F77=fort77
1142 
     </pre>
17472 ripley 1143 
 
24001 hornik 1144 
   <p><code>f90</code> insists on linking against a static <code>libF90.a</code> which
18887 hornik 1145 
typically resides in a non-standard directory (e.g.,
1146 
<code>/opt/fortran90/lib</code>).  Hence, to use <code>f90</code> one needs to
1147 
add this directory to the linker path via the configure variable
1148 
<code>LDFLAGS</code> (e.g., <code>./configure F77=f90
1149 
LDFLAGS=/opt/fortran90/lib</code>).
1150 
 
17472 ripley 1151 
<a name="IRIX"></a>
1152 
 
27252 ripley 1153 
<h3 class="subsection">B.7.5 IRIX</h4>
17472 ripley 1154 
 
26591 hornik 1155 
<p>R has been built successfully on IRIX64 6.5 using
17472 ripley 1156 
<code>gcc</code>/<code>f77</code> or <code>cc</code>/<code>f77</code> for 32-bit
1157 
executables and the native compilers for a 64-bit executable.  The
1158 
command
18887 hornik 1159 
 
24001 hornik 1160 
<pre class="smallexample">     ./configure CC="cc -64" F77="f77 -64" --with-tcltk=no
1161 
     </pre>
17472 ripley 1162 
 
1163 
<p>was used to create the 64-bit executable.  It was necessary to
1164 
explicitly omit Tcl/Tk because <code>configure</code> would find the 32-bit
1165 
version but not detect that is was incompatible with a 64-bit build.
1166 
 
24001 hornik 1167 
   <p>A 32-bit build using <code>gcc</code>/<code>g77</code> passed <code>make
17472 ripley 1168 
check</code> but failed <code>make test-all-extras</code> in the complex LAPACK
1169 
tests.
1170 
 
1171 
<a name="Alpha%2fOSF1"></a>
1172 
 
27252 ripley 1173 
<h3 class="subsection">B.7.6 Alpha/OSF1</h4>
17472 ripley 1174 
 
26591 hornik 1175 
<p>R has been built successfully on an Alpha running OSF1 V4.0 using
17472 ripley 1176 
<code>gcc</code>/<code>g77</code> and <code>cc</code>/<code>f77</code>.  Mixing
1177 
<code>cc</code> and <code>g77</code> fails to configure.  The
1178 
<code>configure</code> option <code>--without-blas</code> was used since the
1179 
native blas seems not to have been built with the flags needed to
1180 
suppress <code>SIGFPE</code>'s.  Currently R does not set a signal handler for
1181 
<code>SIGFPE</code> on platforms that support <small>IEEE</small> arithmetic, so
1182 
these are fatal.
1183 
 
1184 
<a name="Alpha%2fFreeBSD"></a>
1185 
 
27252 ripley 1186 
<h3 class="subsection">B.7.7 Alpha/FreeBSD</h4>
17472 ripley 1187 
 
26591 hornik 1188 
<p>Attempts to build R on an Alpha with FreeBSD 4.3 have been only
17472 ripley 1189 
partly successful.  Configuring with <code>-mieee</code> added to both
1190 
<code>CFLAGS</code> and <code>FFLAGS</code> builds successfully, but tests fail with
1191 
<code>SIGFPE</code>'s.  It would appear that <code>-mieee</code> only defers these
1192 
rather than suppressing them entirely.  Advice on how to complete this
1193 
port would be greatly appreciated.
1194 
 
19031 hornik 1195 
<a name="AIX"></a>
1196 
 
27252 ripley 1197 
<h3 class="subsection">B.7.8 AIX</h4>
19031 hornik 1198 
 
26591 hornik 1199 
<p>On AIX 4.3.3 and AIX 5.1, it was found that the use of "run time
19031 hornik 1200 
linking" (as opposed to normal AIX style linking) was required.  For
1201 
this, the R main program must be linked to the runtime linker with the
1202 
<code>-brtl</code> linker option, and shareable objects must be enabled for
1203 
runtime linking with the <code>-G</code> linker option.  Without these
1204 
options, the AIX linker will not automatically link to any shared object
1205 
with a <code>.so</code> extension.  Also, the R main program is unable to
1206 
dynamically load modules (such as X11) with the <code>dlopen</code> call.
1207 
 
24001 hornik 1208 
   <p>When setting <code>MAIN_LDFLAGS</code> and <code>SHLIB_LDFLAGS</code> accordingly,
19031 hornik 1209 
note that linker flags must be escaped using <code>-Wl,</code> if
1210 
<code>gcc</code> is used for linking: use <code>MAIN_LDFLAGS="-Wl,brtl"</code>
1211 
and <code>SHLIB_LDFLAGS="-Wl,-G"</code> in this case.
1212 
 
28194 hornik 1213 
   <p>Harald Servat Gelabert &lt;harald at cepba dot upc dot es&gt; reported
1214 
success building R 1.7.0 under AIX 5.1 with
24354 hornik 1215 
 
1216 
<pre class="smallexample">     CC=xlc
1217 
     F77=xlf
1218 
     CXX=xlC
1219 
     CFLAGS=-O3 -qstrict -qmaxmem=8192
1220 
     FFLAGS=-O3 -qstrict -qmaxmem=8192
1221 
     CXXFLAGS=-O2 -qmaxmem=8192
1222 
     MAIN_LDFLAGS=-Wl,-brtl
1223 
     SHLIB_LDFLAGS=-Wl,-G
1224 
     </pre>
1225 
 
1226 
<p>but was unable to use the X libraries or the native BLAS (ESSL) and so
1227 
used <code>--without-x --without-blas</code>.
1228 
 
14307 ripley 1229 
<a name="New%20platforms"></a>
14184 ripley 1230 
 
24001 hornik 1231 
<h2 class="appendix">Appendix C New platforms</h2>
14184 ripley 1232 
 
26591 hornik 1233 
<p>There are a number of sources of problems when installing R on a new
17472 ripley 1234 
hardware/OS platform.  These include
14184 ripley 1235 
 
24001 hornik 1236 
   <p><strong>Floating Point Arithmetic</strong>: R supports the <small>POSIX</small>,
14307 ripley 1237 
SVID and <small>IEEE</small> models for floating point arithmetic.  The
1238 
<small>POSIX</small> and SVID models provide no problems.  The <small>IEEE</small>
1239 
model however can be a pain.  The problem is that there is no agreement
1240 
on how to set the signalling behaviour; Sun/Sparc, SGI/IRIX and ix86
1241 
Linux require no special action, FreeBSD requires a call to (the macro)
1242 
<code>fpsetmask(0)</code> and OSF1 requires that computation be done with a
1243 
<code>-ieee_with_inexact</code> flag etc.  On a new platform you must find
1244 
out the magic recipe and add some code to make it work.  This can often
1245 
be done via the file <code>config.site</code> which resides in the top level
1246 
directory.
14184 ripley 1247 
 
24001 hornik 1248 
   <p>Beware of using high levels of optimization, at least initially.  On
14328 ripley 1249 
many compilers these reduce the degree of compliance to the
17472 ripley 1250 
<small>IEEE</small> model.  For example, using <code>-fast</code> on the Solaris
14328 ripley 1251 
SunPro compilers causes R's <code>NaN</code> to be set incorrectly.
1252 
 
24001 hornik 1253 
   <p><strong>Shared Libraries</strong>: There seems to be very little agreement
28261 murdoch 1254 
across platforms on what needs to be done to build shared libraries.
14307 ripley 1255 
there are many different combinations of flags for the compilers and
17472 ripley 1256 
loaders.  GNU libtool cannot be used (yet), as it currently does not
1257 
fully support FORTRAN (and will most likely never support <code>f2c</code>:
1258 
one would need a shell wrapper for this).  The technique we use is to
1259 
first interrogate the X window system about what it does (using
1260 
<code>xmkmf</code>), and then override this in situations where we know
1261 
better (for tools from the GNU Compiler Collection and/or platforms we
1262 
know about).  This typically works, but you may have to manually
18887 hornik 1263 
override the results.  Scanning the manual entries for <code>cc</code> and
1264 
<code>ld</code> usually reveals the correct incantation.  Once you know the
1265 
recipe you can modify the file <code>config.site</code> (following the
17472 ripley 1266 
instructions therein) so that the build will use these options.
14184 ripley 1267 
 
24001 hornik 1268 
   <p>If you do manage to get R running on a new platform please let us
14307 ripley 1269 
know about it so we can modify the configuration procedures to include
1270 
that platform.
14184 ripley 1271 
 
24001 hornik 1272 
   <p>If you are having trouble getting R to work on your platform please
18887 hornik 1273 
feel free to get in touch to ask questions.  We have had a fair amount
24001 hornik 1274 
of practice at porting R to new platforms <small class="enddots">....</small>
14184 ripley 1275 
 
14185 ripley 1276 
<a name="Function%20and%20variable%20index"></a>
14184 ripley 1277 
 
24001 hornik 1278 
<h2 class="unnumbered">Function and variable index</h2>
14184 ripley 1279 
 
24001 hornik 1280 
<ul class="index-vr" compact>
14307 ripley 1281 
<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>
14184 ripley 1282 
<li><code>install.packages</code>: <a href="#Installing%20packages">Installing packages</a>
1283 
<li><code>make</code>: <a href="#Using%20make">Using make</a>
14307 ripley 1284 
<li><code>R_HOME</code>: <a href="#Simple%20compilation">Simple compilation</a>
14184 ripley 1285 
<li><code>remove.packages</code>: <a href="#Removing%20packages">Removing packages</a>
1286 
<li><code>rsync</code>: <a href="#Using%20rsync">Using rsync</a>
1287 
<li><code>update.packages</code>: <a href="#Updating%20packages">Updating packages</a>
26591 hornik 1288 
</ul>
14185 ripley 1289 
<a name="Concept%20index"></a>
14184 ripley 1290 
 
24001 hornik 1291 
<h2 class="unnumbered">Concept index</h2>
14184 ripley 1292 
 
24001 hornik 1293 
<ul class="index-cp" compact>
22142 ripley 1294 
<li>AIX: <a href="#AIX">AIX</a>
22570 ripley 1295 
<li>BLAS library: <a href="#Solaris">Solaris</a>, <a href="#MacOS%20X">MacOS X</a>, <a href="#Using%20FORTRAN">Using FORTRAN</a>, <a href="#Linear%20algebra">Linear algebra</a>
14307 ripley 1296 
<li>FORTRAN: <a href="#Using%20FORTRAN">Using FORTRAN</a>
1297 
<li>Help pages: <a href="#Simple%20compilation">Simple compilation</a>
22181 ripley 1298 
<li>HP-UX: <a href="#HP-UX">HP-UX</a>
14184 ripley 1299 
<li>Installation: <a href="#Installation">Installation</a>
1300 
<li>Installing under Unix: <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
1301 
<li>Installing under Windows: <a href="#Installing%20R%20under%20Windows">Installing R under Windows</a>
22142 ripley 1302 
<li>IRIS: <a href="#IRIX">IRIX</a>
22570 ripley 1303 
<li>LAPACK library: <a href="#Solaris">Solaris</a>, <a href="#MacOS%20X">MacOS X</a>, <a href="#Linear%20algebra">Linear algebra</a>
27252 ripley 1304 
<li>Linux: <a href="#Linux">Linux</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
24070 ripley 1305 
<li>MacOS X: <a href="#MacOS%20X">MacOS X</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
14307 ripley 1306 
<li>Manuals: <a href="#Making%20the%20manuals">Making the manuals</a>
14184 ripley 1307 
<li>Manuals, installing: <a href="#Installation">Installation</a>
1308 
<li>Obtaining R: <a href="#Obtaining%20R">Obtaining R</a>
14307 ripley 1309 
<li>Packages: <a href="#Add-on%20packages">Add-on packages</a>
14184 ripley 1310 
<li>Packages, installing: <a href="#Installing%20packages">Installing packages</a>
1311 
<li>Packages, removing: <a href="#Removing%20packages">Removing packages</a>
1312 
<li>Packages, updating: <a href="#Updating%20packages">Updating packages</a>
22142 ripley 1313 
<li>Solaris: <a href="#Solaris">Solaris</a>
14307 ripley 1314 
<li>Sources for R: <a href="#Getting%20and%20unpacking%20the%20sources">Getting and unpacking the sources</a>
26591 hornik 1315 
</ul>
14184 ripley 1316 
 
1317 
 
24001 hornik 1318 
   <div class="footnote">
1319 
<hr>
1320 
<h4>Footnotes</h4>
14184 ripley 1321 
<ol type="1">
1322 
<li><a name="fn-1"></a>
19459 pd 1323 
<p>if you have the source-code package
1324 
files installed</p>
14184 ripley 1325 
 
24001 hornik 1326 
   <li><a name="fn-2"></a>
23148 ripley 1327 
<p>Using the SunPro aka Forte aka Sun ONE <code>cc</code> and
1328 
<code>f95</code> compilers</p>
14184 ripley 1329 
 
24001 hornik 1330 
   <li><a name="fn-3"></a>
22181 ripley 1331 
<p>On HP-UX <code>fort77</code> is the <small>POSIX</small>
17472 ripley 1332 
compliant FORTRAN compiler, and comes second in the search list.</p>
14184 ripley 1333 
 
24001 hornik 1334 
   <li><a name="fn-4"></a>
14215 ripley 1335 
<p>as well as its equivalence to the <code>Rcomplex</code>
1336 
structure defined in <code>R_ext/Complex.h</code>.</p>
1337 
 
24001 hornik 1338 
   <li><a name="fn-5"></a>
14215 ripley 1339 
<p>In particular, avoid <code>g77</code>'s
1340 
<code>-pedantic</code>, which gives confusing error messages.</p>
1341 
 
24001 hornik 1342 
   <li><a name="fn-6"></a>
14698 hornik 1343 
<p>e.g., to use an optimized BLAS on
14215 ripley 1344 
Sun/Sparc</p>
1345 
 
24001 hornik 1346 
   </ol><hr></div>
14184 ripley 1347 
 
24001 hornik 1348 
   </body></html>
14184 ripley 1349