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<body>
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<h1 class="settitle">R Installation and Administration</h1>
 18 
<h1 class="settitle">R Installation and Administration</h1>
19 
<a name="Top"></a>
 19 
<a name="Top"></a>
20 
 
 20 
 
21 
<h2 class="unnumbered">R Installation and Administration</h2>
 21 
<h2 class="unnumbered">R Installation and Administration</h2>
22 
 
 22 
 
23 
<p>This is a guide to installation and administration for R.
 23 
<p>This is a guide to installation and administration for R.
24 
 
 24 
 
25 
   <p>The current version of this document is 1.9.0 (2004-02-04).
 25 
   <p>The current version of this document is 1.9.0 (2004-02-18).
26 
 
 26 
 
27 
   ISBN 3-900051-02-X
 27 
   ISBN 3-900051-02-X
28 
 
 28 
 
29 
<a name="Obtaining%20R"></a>
 29 
<a name="Obtaining%20R"></a>
30 
 
 30 
 
31 
<h2 class="chapter">1 Obtaining R</h2>
 31 
<h2 class="chapter">1 Obtaining R</h2>
32 
 
 32 
 
33 
<p>Sources, binaries and documentation for R can be obtained via
 33 
<p>Sources, binaries and documentation for R can be obtained via
34 
<small>CRAN</small>, the "Comprehensive R Archive Network".  See the file
 34 
<small>CRAN</small>, the "Comprehensive R Archive Network".  See the file
35 
<code>RESOURCES</code> in the R distribution for information on
 35 
<code>RESOURCES</code> in the R distribution for information on
36 
<small>CRAN</small>.
 36 
<small>CRAN</small>.
37 
 
 37 
 
38 
<a name="Getting%20and%20unpacking%20the%20sources"></a>
 38 
<a name="Getting%20and%20unpacking%20the%20sources"></a>
39 
 
 39 
 
40 
<h3 class="section">1.1 Getting and unpacking the sources</h3>
 40 
<h3 class="section">1.1 Getting and unpacking the sources</h3>
41 
 
 41 
 
42 
<p>The simplest way is to download the most recent
 42 
<p>The simplest way is to download the most recent
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
 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
44 
 
 44 
 
45 
<pre class="smallexample">     tar xvfz R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
 45 
<pre class="smallexample">     tar xvfz R-<var>x</var>.<var>y</var>.<var>z</var>.tgz
46 
     </pre>
 46 
     </pre>
47 
 
 47 
 
48 
<p>on systems that have GNU <code>tar</code> installed.  On other systems you
 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
 49 
need at least to have the <code>gzip</code> program installed.  Then you
50 
can use
 50 
can use
51 
 
 51 
 
52 
<pre class="smallexample">     gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tgz | tar xvf -
 52 
<pre class="smallexample">     gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tgz | tar xvf -
53 
     </pre>
 53 
     </pre>
54 
 
 54 
 
55 
   <p>If you need to transport the sources on floppy disks, you can download
 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
 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
57 
together at the destination with (Unix)
 57 
together at the destination with (Unix)
58 
 
 58 
 
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
 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>
 60 
     </pre>
61 
 
 61 
 
62 
<p>and proceed as above.  If you want the build to be usable by a group of
 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
 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
 64 
readable by the target group (e.g., <code>umask 022</code> to be usable by all
65 
users).
 65 
users).
66 
 
 66 
 
67 
<a name="Using%20rsync"></a>
 67 
<a name="Using%20rsync"></a>
68 
 
 68 
 
69 
<h3 class="section">1.2 Using rsync</h3>
 69 
<h3 class="section">1.2 Using rsync</h3>
70 
 
 70 
 
71 
<p>Sources are also available via anonymous rsync.  Use
 71 
<p>Sources are also available via anonymous rsync.  Use
72 
 
 72 
 
73 
<pre class="smallexample">     rsync -rC rsync.r-project.org::<var>module</var> R
 73 
<pre class="smallexample">     rsync -rC rsync.r-project.org::<var>module</var> R
74 
     </pre>
 74 
     </pre>
75 
 
 75 
 
76 
<p>to create a copy of the source tree specified by <var>module</var> in the
 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>
 77 
subdirectory <code>R</code> of the current directory, where <var>module</var>
78 
specifies one of the four existing flavors of the R sources, and can be
 78 
specifies one of the four existing flavors of the R sources, and can be
79 
one of <code>r-release</code> (current released version), <code>r-patched</code>
 79 
one of <code>r-release</code> (current released version), <code>r-patched</code>
80 
(patched released version), and <code>r-devel</code> (development version).
 80 
(patched released version), and <code>r-devel</code> (development version).
81 
(These flavors are described in the R FAQ,
 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
 82 
<a href="http://www.ci.tuwien.ac.at/~hornik/R/">http://www.ci.tuwien.ac.at/~hornik/R/</a>.)  The rsync trees are
83 
created directly from the master CVS archive and are updated hourly.
 83 
created directly from the master CVS archive and are updated hourly.
84 
The <code>-C</code> option in the <code>rsync</code> command is to cause it to
 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
 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>.
 86 
available at <a href="http://rsync.samba.org/rsync/">http://rsync.samba.org/rsync/</a>.
87 
 
 87 
 
88 
<a name="Installing%20R%20under%20Unix"></a>
 88 
<a name="Installing%20R%20under%20Unix"></a>
89 
 
 89 
 
90 
<h2 class="chapter">2 Installing R under Unix</h2>
 90 
<h2 class="chapter">2 Installing R under Unix</h2>
91 
 
 91 
 
92 
<p>R will configure and build under a number of common Unix platforms
 92 
<p>R will configure and build under a number of common Unix platforms
93 
including i386-freebsd, <var>cpu</var>-linux-gnu for the i386, alpha, arm,
 93 
including i386-freebsd, <var>cpu</var>-linux-gnu for the i386, alpha, arm,
94 
hppa, ia64, m68k, powerpc, and sparc CPUs (see e.g.
 94 
hppa, ia64, m68k, powerpc, and sparc CPUs (see e.g.
95 
<a href="http://buildd.debian.org/build.php?&amp;pkg=r-base">http://buildd.debian.org/build.php?&amp;pkg=r-base</a>),
 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,
 96 
i386-sun-solaris, powerpc-apple-darwin, mips-sgi-irix, alpha-dec-osf4,
97 
rs6000-ibm-aix, hppa-hp-hpux, and sparc-sun-solaris.
 97 
rs6000-ibm-aix, hppa-hp-hpux, and sparc-sun-solaris.
98 
 
 98 
 
99 
   <p>In addition, binary distributions are available for most common Linux
 99 
   <p>In addition, binary distributions are available for most common Linux
100 
distributions, and for MacOS X (Darwin) with X11.  See the <small>FAQ</small>
 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
 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.
 102 
for the rest of this chapter we consider only building from the sources.
103 
 
 103 
 
104 
<a name="Simple%20compilation"></a>
 104 
<a name="Simple%20compilation"></a>
105 
 
 105 
 
106 
<h3 class="section">2.1 Simple compilation</h3>
 106 
<h3 class="section">2.1 Simple compilation</h3>
107 
 
 107 
 
108 
<p>First review the essential and useful tools and libraries in
 108 
<p>First review the essential and useful tools and libraries in
109 
<a href="#Essential%20and%20useful%20other%20programs">Essential and useful other programs</a>, and install those you want or
 109 
<a href="#Essential%20and%20useful%20other%20programs">Essential and useful other programs</a>, and install those you want or
110 
need.
 110 
need.
111 
 
 111 
 
112 
   <p>Choose a place to install the R tree (R is not just a binary, but
 112 
   <p>Choose a place to install the R tree (R is not just a binary, but
113 
has additional data sets, help files, font metrics etc).  Let us call
 113 
has additional data sets, help files, font metrics etc).  Let us call
114 
this place <var>R_HOME</var>.  Untar the source code.  This should create
 114 
this place <var>R_HOME</var>.  Untar the source code.  This should create
115 
directories <code>src</code>, <code>doc</code>, and several more.  Issue the
 115 
directories <code>src</code>, <code>doc</code>, and several more.  Issue the
116 
following commands:
 116 
following commands:
117 
 
 117 
 
118 
<pre class="smallexample">     ./configure
 118 
<pre class="smallexample">     ./configure
119 
     make
 119 
     make
120 
     </pre>
 120 
     </pre>
121 
 
 121 
 
122 
<p>(See <a href="#Using%20make">Using make</a> if your make is not called <code>make</code>.)
 122 
<p>(See <a href="#Using%20make">Using make</a> if your make is not called <code>make</code>.)
123 
 
 123 
 
124 
   <p>Then check the built system works correctly, by
 124 
   <p>Then check the built system works correctly, by
125 
 
 125 
 
126 
<pre class="smallexample">     make check
 126 
<pre class="smallexample">     make check
127 
     </pre>
 127 
     </pre>
128 
 
 128 
 
129 
<p>Failures are not necessarily problems as they might be caused by missing
 129 
<p>Failures are not necessarily problems as they might be caused by missing
130 
functionality, but you should look carefully at any reported
 130 
functionality, but you should look carefully at any reported
131 
discrepancies.  To re-run the tests you would need
 131 
discrepancies.  To re-run the tests you would need
132 
 
 132 
 
133 
<pre class="smallexample">     make check FORCE=FORCE
 133 
<pre class="smallexample">     make check FORCE=FORCE
134 
     </pre>
 134 
     </pre>
135 
 
 135 
 
136 
   <p>More comprehensive testing can be done by
 136 
   <p>More comprehensive testing can be done by
137 
 
 137 
 
138 
<pre class="smallexample">     make check-devel
 138 
<pre class="smallexample">     make check-devel
139 
     </pre>
 139 
     </pre>
140 
 
 140 
 
141 
<p>or
 141 
<p>or
142 
 
 142 
 
143 
<pre class="smallexample">     make check-all
 143 
<pre class="smallexample">     make check-all
144 
     </pre>
 144 
     </pre>
145 
 
 145 
 
146 
<p>see <code>tests/README</code>.
 146 
<p>see <code>tests/README</code>.
147 
 
 147 
 
148 
   <p>If these commands execute successfully, the R binary will be copied
 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
 149 
to the <code></code><var>R_HOME</var><code>/bin</code> directory.  In addition, a shell-script
150 
front-end called <code>R</code> will be created and copied to the same
 150 
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
 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
 152 
it, for example to <code>/usr/local/bin/R</code>.  You could also copy the man
153 
page <code>R.1</code> to a place where your <code>man</code> reader finds it,
 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
 154 
such as <code>/usr/local/man/man1</code>.  If you want to install the complete
155 
R tree to, e.g., <code>/usr/local/lib/R</code>, see <a href="#Installation">Installation</a>.
 155 
R tree to, e.g., <code>/usr/local/lib/R</code>, see <a href="#Installation">Installation</a>.
156 
Note: you do not <em>need</em> to install R: you can run it from where
 156 
Note: you do not <em>need</em> to install R: you can run it from where
157 
it was built.
 157 
it was built.
158 
 
 158 
 
159 
   <p>You do not necessarily have to build R in the top-level source
 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
 160 
directory (say, <code></code><var>TOP_SRCDIR</var><code></code>).  To build in
161 
<code></code><var>BUILDDIR</var><code></code>, run
 161 
<code></code><var>BUILDDIR</var><code></code>, run
162 
 
 162 
 
163 
<pre class="smallexample">     cd <var>BUILDDIR</var>
 163 
<pre class="smallexample">     cd <var>BUILDDIR</var>
164 
     <var>TOP_SRCDIR</var>/configure
 164 
     <var>TOP_SRCDIR</var>/configure
165 
     make
 165 
     make
166 
     </pre>
 166 
     </pre>
167 
 
 167 
 
168 
<p>and so on, as described further below.  This has the advantage of always
 168 
<p>and so on, as described further below.  This has the advantage of always
169 
keeping your source tree "clean".  (You may need GNU <code>make</code> to
 169 
keeping your source tree "clean".  (You may need GNU <code>make</code> to
170 
allow this.)
 170 
allow this.)
171 
 
 171 
 
172 
   <p>Make will also build plain text help pages as well as <small>HTML</small> and
 172 
   <p>Make will also build plain text help pages as well as <small>HTML</small> and
173 
LaTeX versions of the R object documentation (the three kinds can
 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>
 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
 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
 176 
not available on your system, you can obtain PDF versions of the
177 
documentation files via <small>CRAN</small>.
 177 
documentation files via <small>CRAN</small>.
178 
 
 178 
 
179 
   <p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
 179 
   <p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
180 
and the R <small>FAQ</small> (files <code>FAQ</code> or
 180 
and the R <small>FAQ</small> (files <code>FAQ</code> or
181 
<code>doc/html/faq.html</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
 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).
 183 
the latest version).
184 
 
 184 
 
185 
<a name="Making%20the%20manuals"></a>
 185 
<a name="Making%20the%20manuals"></a>
186 
 
 186 
 
187 
<h3 class="section">2.2 Making the manuals</h3>
 187 
<h3 class="section">2.2 Making the manuals</h3>
188 
 
 188 
 
189 
<p>There is a set of manuals that can be built from the sources,
 189 
<p>There is a set of manuals that can be built from the sources,
190 
 
 190 
 
191 
     <dl>
 191 
     <dl>
192 
<dt><code>refman</code>
 192 
<dt><code>refman</code>
193 
     <dd>Printed versions of all the help pages.
 193 
     <dd>Printed versions of all the help pages.
194 
<br><dt><code>R-FAQ</code>
 194 
<br><dt><code>R-FAQ</code>
195 
     <dd>R <small>FAQ</small> (which is already built for you).
 195 
     <dd>R <small>FAQ</small> (which is already built for you).
196 
<br><dt><code>R-intro</code>
 196 
<br><dt><code>R-intro</code>
197 
     <dd>"An Introduction to R".
 197 
     <dd>"An Introduction to R".
198 
<br><dt><code>R-data</code>
 198 
<br><dt><code>R-data</code>
199 
     <dd>"R Data Import/Export".
 199 
     <dd>"R Data Import/Export".
200 
<br><dt><code>R-admin</code>
 200 
<br><dt><code>R-admin</code>
201 
     <dd>"R Installation and Administration", this manual.
 201 
     <dd>"R Installation and Administration", this manual.
202 
<br><dt><code>R-exts</code>
 202 
<br><dt><code>R-exts</code>
203 
     <dd>"Writing R Extensions".
 203 
     <dd>"Writing R Extensions".
204 
<br><dt><code>R-lang</code>
 204 
<br><dt><code>R-lang</code>
205 
     <dd>"The R Language Definition".
 205 
     <dd>"The R Language Definition".
206 
</dl>
 206 
</dl>
207 
 
 207 
 
208 
<p>To make these, use
 208 
<p>To make these, use
209 
 
 209 
 
210 
<pre class="smallexample">     make dvi      to create DVI versions
 210 
<pre class="smallexample">     make dvi      to create DVI versions
211 
     make pdf      to create PDF versions
 211 
     make pdf      to create PDF versions
212 
     make info     to create info files (not <code>refman</code>).
 212 
     make info     to create info files (not <code>refman</code>).
213 
     </pre>
 213 
     </pre>
214 
 
 214 
 
215 
   <p>You will not be able to build the info files unless you have
 215 
   <p>You will not be able to build the info files unless you have
216 
<code>makeinfo</code> version 4 or later installed (and some Linux
 216 
<code>makeinfo</code> version 4 or later installed (and some Linux
217 
distributions have 3.12).
 217 
distributions have 3.12).
218 
 
 218 
 
219 
   <p>The DVI versions can be previewed and printed using standard programs
 219 
   <p>The DVI versions can be previewed and printed using standard programs
220 
such as <code>xdvi</code> and <code>dvips</code>.  The PDF versions can be
 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
 221 
viewed using Acrobat Reader or (recent versions of) ghostscript: they
222 
have hyperlinks that can be followed in Acrobat Reader.  The info files
 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.
 223 
are suitable for reading online with Emacs or the standalone GNU Info.
224 
 
 224 
 
225 
<a name="Installation"></a>
 225 
<a name="Installation"></a>
226 
 
 226 
 
227 
<h3 class="section">2.3 Installation</h3>
 227 
<h3 class="section">2.3 Installation</h3>
228 
 
 228 
 
229 
<p>After
 229 
<p>After
230 
 
 230 
 
231 
<pre class="smallexample">     ./configure
 231 
<pre class="smallexample">     ./configure
232 
     make
 232 
     make
233 
     make check
 233 
     make check
234 
     </pre>
 234 
     </pre>
235 
 
 235 
 
236 
<p>have been completed successfully, you can install the complete R tree
 236 
<p>have been completed successfully, you can install the complete R tree
237 
to your system by typing
 237 
to your system by typing
238 
 
 238 
 
239 
<pre class="smallexample">     make install
 239 
<pre class="smallexample">     make install
240 
     </pre>
 240 
     </pre>
241 
 
 241 
 
242 
<p>This will install to the following directories:
 242 
<p>This will install to the following directories:
243 
 
 243 
 
244 
     <dl>
 244 
     <dl>
245 
<dt><code></code><var>prefix</var><code>/bin</code>
 245 
<dt><code></code><var>prefix</var><code>/bin</code>
246 
     <dd>the front-end shell script
 246 
     <dd>the front-end shell script
247 
<br><dt><code></code><var>prefix</var><code>/man/man1</code>
 247 
<br><dt><code></code><var>prefix</var><code>/man/man1</code>
248 
     <dd>the man page
 248 
     <dd>the man page
249 
<br><dt><code></code><var>prefix</var><code>/lib/R</code>
 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>)
 250 
     <dd>all the rest (libraries, on-line help system, <small class="dots">...</small>)
251 
</dl>
 251 
</dl>
252 
 
 252 
 
253 
<p>where <var>prefix</var> is determined during configuration (typically
 253 
<p>where <var>prefix</var> is determined during configuration (typically
254 
<code>/usr/local</code>) and can be set by running <code>configure</code> with
 254 
<code>/usr/local</code>) and can be set by running <code>configure</code> with
255 
the option <code>--prefix</code>, as in
 255 
the option <code>--prefix</code>, as in
256 
 
 256 
 
257 
<pre class="smallexample">     ./configure --prefix=/where/you/want/R/to/go
 257 
<pre class="smallexample">     ./configure --prefix=/where/you/want/R/to/go
258 
     </pre>
 258 
     </pre>
259 
 
 259 
 
260 
<p>This causes <code>make install</code> to install the R executable to
 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
 261 
<code>/where/you/want/R/to/go/bin</code>, and so on.  The prefix of the
262 
installation directories can be seen in the status message that is
 262 
installation directories can be seen in the status message that is
263 
displayed at the end of <code>configure</code>.  You can install into
 263 
displayed at the end of <code>configure</code>.  You can install into
264 
another directory by using
 264 
another directory by using
265 
 
 265 
 
266 
<pre class="smallexample">     make prefix=/path/to/here install
 266 
<pre class="smallexample">     make prefix=/path/to/here install
267 
     </pre>
 267 
     </pre>
268 
 
 268 
 
269 
   <p>To install DVI, info and PDF versions of the manuals, use one or more of
 269 
   <p>To install DVI, info and PDF versions of the manuals, use one or more of
270 
 
 270 
 
271 
<pre class="smallexample">     make install-dvi
 271 
<pre class="smallexample">     make install-dvi
272 
     make install-info
 272 
     make install-info
273 
     make install-pdf
 273 
     make install-pdf
274 
     </pre>
 274 
     </pre>
275 
 
 275 
 
276 
<p>To ensure that the installed tree is usable by the right group of users,
 276 
<p>To ensure that the installed tree is usable by the right group of users,
277 
set <code>umask</code> appropriately (perhaps to <code>022</code>) before unpacking
 277 
set <code>umask</code> appropriately (perhaps to <code>022</code>) before unpacking
278 
the sources and throughout the build process.
 278 
the sources and throughout the build process.
279 
 
 279 
 
280 
<a name="Installing%20R%20under%20Windows"></a>
 280 
<a name="Installing%20R%20under%20Windows"></a>
281 
 
 281 
 
282 
<h2 class="chapter">3 Installing R under Windows</h2>
 282 
<h2 class="chapter">3 Installing R under Windows</h2>
283 
 
 283 
 
284 
<p>The <code>bin/windows</code> directory of a <small>CRAN</small> site contains
 284 
<p>The <code>bin/windows</code> directory of a <small>CRAN</small> site contains
285 
binaries for a base distribution and a large number of add-on packages
 285 
binaries for a base distribution and a large number of add-on packages
286 
from <small>CRAN</small> to run on Windows 95, 98, NT4, 2000, ME and XP (at
 286 
from <small>CRAN</small> to run on Windows 95, 98, NT4, 2000, ME and XP (at
287 
least) on Intel and clones (but not on other platforms).
 287 
least) on Intel and clones (but not on other platforms).
288 
 
 288 
 
289 
   <p>You do need one of those Windows versions: Windows 3.11+win32s will not
 289 
   <p>You do need one of those Windows versions: Windows 3.11+win32s will not
290 
work.
 290 
work.
291 
 
 291 
 
292 
   <p>Your file system must allow long file names (as is likely except
 292 
   <p>Your file system must allow long file names (as is likely except
293 
perhaps for some network-mounted systems).
 293 
perhaps for some network-mounted systems).
294 
 
 294 
 
295 
   <p>The simplest way is to use <code>rw1090dev.exe</code> or
 295 
   <p>The simplest way is to use <code>rw1090dev.exe</code> or
296 
<code>miniR.exe</code>.  Just double-click on the icon and follow the
 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
 297 
instructions.  If you installed R this way you can uninstall it from the
298 
Control Panel.
 298 
Control Panel.
299 
 
 299 
 
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.
 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.
301 
 
 301 
 
302 
<a name="Building%20from%20source"></a>
 302 
<a name="Building%20from%20source"></a>
303 
 
 303 
 
304 
<h3 class="section">3.1 Building from source</h3>
 304 
<h3 class="section">3.1 Building from source</h3>
305 
 
 305 
 
306 
<p>If you want to build this port from the sources, see the file
 306 
<p>If you want to build this port from the sources, see the file
307 
<code>src/gnuwin32/INSTALL</code> in the source distribution.  You will need
 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
 308 
to collect, install and test an extensive set of tools: see
309 
<a href="http://www.stats.ox.ac.uk/pub/Rtools/">http://www.stats.ox.ac.uk/pub/Rtools/</a> for the current locations.
 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 
 
 310 
 
311 
   <p>You may need to compile under a case-honouring file system: we found
 311 
   <p>You may need to compile under a case-honouring file system: we found
312 
that a <code>samba</code>-mounted file system (which maps all file names to
 312 
that a <code>samba</code>-mounted file system (which maps all file names to
313 
lower case) did not work.  Open a commands window at a directory <em>whose
 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
 314 
path does not contain spaces</em>, and run something like
315 
 
 315 
 
316 
<pre class="smallexample">     tar zxvf R-1.9.0.tgz
 316 
<pre class="smallexample">     tar zxvf R-1.9.0.tgz
317 
     cd R-1.9.0\src\gnuwin32
 317 
     cd R-1.9.0\src\gnuwin32
318 
     make
 318 
     make
319 
     </pre>
 319 
     </pre>
320 
 
 320 
 
321 
<p>sit back and wait (for about 5 minutes on 1GHz PIII with a fast local
 321 
<p>sit back and wait (for about 5 minutes on 1GHz PIII with a fast local
322 
disc).
 322 
disc).
323 
 
 323 
 
324 
   <p>For further details, including how to make the documentation and how to
 324 
   <p>For further details, including how to make the documentation and how to
325 
cross-compile, see <code>src/gnuwin32/INSTALL</code>.
 325 
cross-compile, see <code>src/gnuwin32/INSTALL</code>.
326 
 
 326 
 
327 
<a name="Add-on%20packages"></a>
 327 
<a name="Add-on%20packages"></a>
328 
 
 328 
 
329 
<h2 class="chapter">4 Add-on packages</h2>
 329 
<h2 class="chapter">4 Add-on packages</h2>
330 
 
 330 
 
331 
<p>This chapter applies to Unix-like and Windows versions of R.
 331 
<p>This chapter applies to Unix-like and Windows versions of R.
332 
 
 332 
 
333 
   <p>It is helpful to use the correct terminology.  A <em>package</em> is
 333 
   <p>It is helpful to use the correct terminology.  A <em>package</em> is
334 
loaded from a <em>library</em> by the function <code>library()</code>.  Thus a
 334 
loaded from a <em>library</em> by the function <code>library()</code>.  Thus a
335 
library is a directory containing installed packages; the main library
 335 
library is a directory containing installed packages; the main library
336 
is <code></code><var>R_HOME</var><code>/library</code>, but others can be used, for example by
 336 
is <code></code><var>R_HOME</var><code>/library</code>, but others can be used, for example by
337 
setting the environment variable <code>R_LIBS</code> or using the R function
 337 
setting the environment variable <code>R_LIBS</code> or using the R function
338 
<code>.libPaths()</code>.
 338 
<code>.libPaths()</code>.
339 
 
 339 
 
340 
<a name="Installing%20packages"></a>
 340 
<a name="Installing%20packages"></a>
341 
 
 341 
 
342 
<h3 class="section">4.1 Installing packages</h3>
 342 
<h3 class="section">4.1 Installing packages</h3>
343 
 
 343 
 
344 
<p>Packages may be distributed in source form or compiled binary form.
 344 
<p>Packages may be distributed in source form or compiled binary form.
345 
Installing source packages requires that compilers and tools
 345 
Installing source packages requires that compilers and tools
346 
(including Perl 5.004 or later) be installed.  Binary packages
 346 
(including Perl 5.004 or later) be installed.  Binary packages
347 
are platform specific and generally need
 347 
are platform specific and generally need
348 
no special tools to install, but see the documentation for
 348 
no special tools to install, but see the documentation for
349 
your platform for details.
 349 
your platform for details.
350 
 
 350 
 
351 
   <p>Note that you need to specify implicitly or explicitly the library to
 351 
   <p>Note that you need to specify implicitly or explicitly the library to
352 
which the package is to be installed.  This is only an issue if you have
 352 
which the package is to be installed.  This is only an issue if you have
353 
more than one library, of course.
 353 
more than one library, of course.
354 
 
 354 
 
355 
   <p>To install packages from source on Unix use
 355 
   <p>To install packages from source on Unix use
356 
 
 356 
 
357 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
 357 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
358 
     </pre>
 358 
     </pre>
359 
 
 359 
 
360 
<p>The part <code>-l /path/to/library</code> can be omitted, in which case the
 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
 361 
first library in <code>R_LIBS</code> is used if set, otherwise the main
362 
library <code></code><var>R_HOME</var><code>/library</code> is used.  (<code>R_LIBS</code> is looked
 362 
library <code></code><var>R_HOME</var><code>/library</code> is used.  (<code>R_LIBS</code> is looked
363 
for in the environment: <code>.Renviron</code> is not read by <code>R CMD</code>.)
 363 
for in the environment: <code>.Renviron</code> is not read by <code>R CMD</code>.)
364 
 
 364 
 
365 
   <p>The Windows equivalent is<a rel="footnote" href="#fn-1"><sup>1</sup></a>
 365 
   <p>The Windows equivalent is<a rel="footnote" href="#fn-1"><sup>1</sup></a>
366 
 
 366 
 
367 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
 367 
<pre class="smallexample">     R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
368 
     </pre>
 368 
     </pre>
369 
 
 369 
 
370 
   <p>Alternatively, packages can be downloaded and installed from within
 370 
   <p>Alternatively, packages can be downloaded and installed from within
371 
R.  First set the option <code>CRAN</code> to your nearest <small>CRAN</small>
 371 
R.  First set the option <code>CRAN</code> to your nearest <small>CRAN</small>
372 
mirror, for example
 372 
mirror, for example
373 
 
 373 
 
374 
<pre class="smallexample">     &gt; options(CRAN = "http://cran.us.r-project.org/")
 374 
<pre class="smallexample">     &gt; options(CRAN = "http://cran.us.r-project.org/")
375 
     </pre>
 375 
     </pre>
376 
 
 376 
 
377 
<p>Then download and install package <strong>foo</strong> by
 377 
<p>Then download and install package <strong>foo</strong> by
378 
 
 378 
 
379 
<pre class="smallexample">     &gt; install.packages("foo")
 379 
<pre class="smallexample">     &gt; install.packages("foo")
380 
     </pre>
 380 
     </pre>
381 
 
 381 
 
382 
<p>Unless the library is specified (argument <code>lib</code>) the first library
 382 
<p>Unless the library is specified (argument <code>lib</code>) the first library
383 
in the library search path is used.
 383 
in the library search path is used.
384 
 
 384 
 
385 
   <p>What this does is different on Unix and Windows.  On Unix it consults
 385 
   <p>What this does is different on Unix and Windows.  On Unix it consults
386 
the list of available source packages on <small>CRAN</small>, downloads the
 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
 387 
latest version of the <strong>foo</strong> sources, and installs it (via <code>R
388 
CMD INSTALL</code>).  On Windows it looks at the list of <em>binary</em>
 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).
 389 
versions of packages and downloads the latest version (if any).
390 
 
 390 
 
391 
   <p>On Windows <code>install.packages</code> can also install a binary package
 391 
   <p>On Windows <code>install.packages</code> can also install a binary package
392 
from a local <code>zip</code> file by setting argument <code>CRAN</code> to
 392 
from a local <code>zip</code> file by setting argument <code>CRAN</code> to
393 
<code>NULL</code>.   <code>RGui.exe</code> has a menu <code>Packages</code> with a GUI
 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
 394 
interface to <code>install.packages</code>, <code>update.packages</code> and
395 
<code>library</code>.
 395 
<code>library</code>.
396 
 
 396 
 
397 
<a name="Updating%20packages"></a>
 397 
<a name="Updating%20packages"></a>
398 
 
 398 
 
399 
<h3 class="section">4.2 Updating packages</h3>
 399 
<h3 class="section">4.2 Updating packages</h3>
400 
 
 400 
 
401 
<p>The command <code>update.packages()</code> is the simplest way to ensure that
 401 
<p>The command <code>update.packages()</code> is the simplest way to ensure that
402 
all the packages on your system are up to date.  Set the <code>CRAN</code>
 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>
 403 
option as in the previous section.  The <code>update.packages()</code>
404 
downloads the list of available packages and their current versions,
 404 
downloads the list of available packages and their current versions,
405 
compares it with those installed and offers to fetch and install any
 405 
compares it with those installed and offers to fetch and install any
406 
that have later versions on <small>CRAN</small>.
 406 
that have later versions on <small>CRAN</small>.
407 
 
 407 
 
408 
   <p>An alternative way of keeping packages up-to-date is provided by the
 408 
   <p>An alternative way of keeping packages up-to-date is provided by the
409 
command <code>packageStatus()</code>, which returns an object with information
 409 
command <code>packageStatus()</code>, which returns an object with information
410 
on all installed packages and packages available at multiple
 410 
on all installed packages and packages available at multiple
411 
repositories (CRAN, local archive, <small class="dots">...</small>). The <code>print</code> and
 411 
repositories (CRAN, local archive, <small class="dots">...</small>). The <code>print</code> and
412 
<code>summary</code> methods give an overview of installed and available
 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
 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
 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
 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.
 416 
intended to become the default package manager for future versions of R.
417 
 
 417 
 
418 
<a name="Removing%20packages"></a>
 418 
<a name="Removing%20packages"></a>
419 
 
 419 
 
420 
<h3 class="section">4.3 Removing packages</h3>
 420 
<h3 class="section">4.3 Removing packages</h3>
421 
 
 421 
 
422 
<p>Packages can be removed in a number of ways.  From a command prompt they
 422 
<p>Packages can be removed in a number of ways.  From a command prompt they
423 
can be removed by
 423 
can be removed by
424 
 
 424 
 
425 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
 425 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
426 
     </pre>
 426 
     </pre>
427 
 
 427 
 
428 
<p>(Unix) or
 428 
<p>(Unix) or
429 
 
 429 
 
430 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
 430 
<pre class="smallexample">     R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
431 
     </pre>
 431 
     </pre>
432 
 
 432 
 
433 
<p>(Windows).
 433 
<p>(Windows).
434 
 
 434 
 
435 
   <p>From a running R process they can be removed by
 435 
   <p>From a running R process they can be removed by
436 
 
 436 
 
437 
<pre class="smallexample">     &gt; remove.packages(c("pkg1", "pkg2"),
 437 
<pre class="smallexample">     &gt; remove.packages(c("pkg1", "pkg2"),
438 
                       lib = file.path("path", "to", "library"))
 438 
                       lib = file.path("path", "to", "library"))
439 
     </pre>
 439 
     </pre>
440 
 
 440 
 
441 
   <p>Finally, in most installations one can just remove the package directory
 441 
   <p>Finally, in most installations one can just remove the package directory
442 
from the library.
 442 
from the library.
443 
 
 443 
 
444 
   <p><strong>Note:</strong> whereas it is currently possible to install package
 444 
   <p><strong>Note:</strong> whereas it is currently possible to install package
445 
<em>bundles</em>, one cannot remove these as such--the packages contained
 445 
<em>bundles</em>, one cannot remove these as such--the packages contained
446 
in the bundle have to removed individually.
 446 
in the bundle have to removed individually.
447 
 
 447 
 
448 
<a name="Essential%20and%20useful%20other%20programs"></a>
 448 
<a name="Essential%20and%20useful%20other%20programs"></a>
449 
 
 449 
 
450 
<h2 class="appendix">Appendix A Essential and useful other programs</h2>
 450 
<h2 class="appendix">Appendix A Essential and useful other programs</h2>
451 
 
 451 
 
452 
<p>This appendix gives details of programs you will need to build R on
 452 
<p>This appendix gives details of programs you will need to build R on
453 
Unix-like platforms, or which will be used by R if found by
 453 
Unix-like platforms, or which will be used by R if found by
454 
<code>configure</code>.
 454 
<code>configure</code>.
455 
 
 455 
 
456 
   <p>Remember that some package management systems (such as <small>RPM</small> and
 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
 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
 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
 459 
extension <code>-devel</code> or <code>-dev</code>: you need both versions
460 
installed.
 460 
installed.
461 
 
 461 
 
462 
<a name="Essential%20programs"></a>
 462 
<a name="Essential%20programs"></a>
463 
 
 463 
 
464 
<h3 class="section">A.1 Essential programs</h3>
 464 
<h3 class="section">A.1 Essential programs</h3>
465 
 
 465 
 
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.
 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.
467 
 
 467 
 
468 
   <p>Unless you do not want to view graphs on-screen you need <code>X11</code>
 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
 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
 470 
this means the <code>XFree86-devel</code> and <code>XFree86-libs</code> RPMs, for
471 
example.)
 471 
example.)
472 
 
 472 
 
473 
   <p>You will need Perl version 5.004 or later, available via
 473 
   <p>You will need Perl version 5.004 or later, available via
474 
<a href="http://www.perl.com/CPAN/">http://www.perl.com/CPAN/</a>, to build any of the on-line
 474 
<a href="http://www.perl.com/CPAN/">http://www.perl.com/CPAN/</a>, to build any of the on-line
475 
documentation.
 475 
documentation.
476 
 
 476 
 
477 
   <p>You will not be able to build the info files unless you have
 477 
   <p>You will not be able to build the info files unless you have
478 
<code>makeinfo</code> version 4 or later installed.
 478 
<code>makeinfo</code> version 4 or later installed.
479 
 
 479 
 
480 
   <p>The typeset documentation needs <code>tex</code> and <code>latex</code>, or
 480 
   <p>The typeset documentation needs <code>tex</code> and <code>latex</code>, or
481 
<code>pdftex</code> and <code>pdflatex</code>.
 481 
<code>pdftex</code> and <code>pdflatex</code>.
482 
 
 482 
 
483 
<a name="Useful%20libraries%20and%20programs"></a>
 483 
<a name="Useful%20libraries%20and%20programs"></a>
484 
 
 484 
 
485 
<h3 class="section">A.2 Useful libraries and programs</h3>
 485 
<h3 class="section">A.2 Useful libraries and programs</h3>
486 
 
 486 
 
487 
<p>The command-line editing depends on the <code>readline</code> library
 487 
<p>The command-line editing depends on the <code>readline</code> library
488 
available from any GNU mirror: you will need a fairly recent version.
 488 
available from any GNU mirror: you will need a fairly recent version.
489 
 
 489 
 
490 
   <p>The bitmapped graphics devices <code>jpeg()</code> and <code>png()</code> need the
 490 
   <p>The bitmapped graphics devices <code>jpeg()</code> and <code>png()</code> need the
491 
appropriate headers and libraries installed: <code>jpeg</code> (version 6b
 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>
 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.
 493 
(version 1.1.3 or later) respectively.
494 
 
 494 
 
495 
   <p>The <code>bitmap</code> and <code>dev2bitmap</code> devices make use of ghostscript
 495 
   <p>The <code>bitmap</code> and <code>dev2bitmap</code> devices make use of ghostscript
496 
(<a href="http://www.cs.wisc.edu/~ghost">http://www.cs.wisc.edu/~ghost</a>).
 496 
(<a href="http://www.cs.wisc.edu/~ghost">http://www.cs.wisc.edu/~ghost</a>).
497 
 
 497 
 
498 
   <p>If you have them installed (including the appropriate headers and of
 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
 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
 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
 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
 502 
compiled in.  As the latter suffice and are tested with R you should
503 
not need to change this.
 503 
not need to change this.
504 
 
 504 
 
505 
<a name="Tcl%2fTk"></a>
 505 
<a name="Tcl%2fTk"></a>
506 
 
 506 
 
507 
<h3 class="subsection">A.2.1 Tcl/Tk</h4>
 507 
<h3 class="subsection">A.2.1 Tcl/Tk</h4>
508 
 
 508 
 
509 
<p>The <strong>tcltk</strong> package needs Tcl/Tk installed: the sources are
 509 
<p>The <strong>tcltk</strong> package needs Tcl/Tk installed: the sources are
510 
available at <a href="http://www.scriptics.com/">http://www.scriptics.com/</a>.  To specify the locations
 510 
available at <a href="http://www.scriptics.com/">http://www.scriptics.com/</a>.  To specify the locations
511 
of the Tcl/Tk files you may need the configuration options
 511 
of the Tcl/Tk files you may need the configuration options
512 
 
 512 
 
513 
     <dl>
 513 
     <dl>
514 
<dt><code>--with-tcltk</code>
 514 
<dt><code>--with-tcltk</code>
515 
     <dd>use Tcl/Tk, or specify its library directory
 515 
     <dd>use Tcl/Tk, or specify its library directory
516 
<br><dt><code>--with-tcl-config=</code><var>TCL_CONFIG</var><code></code>
 516 
<br><dt><code>--with-tcl-config=</code><var>TCL_CONFIG</var><code></code>
517 
     <dd>specify location of <code>tclConfig.sh</code>
 517 
     <dd>specify location of <code>tclConfig.sh</code>
518 
<br><dt><code>--with-tk-config=</code><var>TK_CONFIG</var><code></code>
 518 
<br><dt><code>--with-tk-config=</code><var>TK_CONFIG</var><code></code>
519 
     <dd>specify location of <code>tkConfig.sh</code>
 519 
     <dd>specify location of <code>tkConfig.sh</code>
520 
</dl>
 520 
</dl>
521 
 
 521 
 
522 
<p>or use the configure variables <code>TCLTK_LIBS</code> and
 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
 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
 524 
the Tcl and Tk libraries and for finding the <code>tcl.h</code> and
525 
<code>tk.h</code> headers, respectively.
 525 
<code>tk.h</code> headers, respectively.
526 
 
 526 
 
527 
   <p>Versions of Tcl/TK from 8.3 to 8.4.4 have been used successfully: 8.0 is
 527 
   <p>Versions of Tcl/TK from 8.3 to 8.4.4 have been used successfully: 8.0 is
528 
no longer supported.
 528 
no longer supported.
529 
 
 529 
 
530 
<a name="Linear%20algebra"></a>
 530 
<a name="Linear%20algebra"></a>
531 
 
 531 
 
532 
<h3 class="subsection">A.2.2 Linear algebra</h4>
 532 
<h3 class="subsection">A.2.2 Linear algebra</h4>
533 
 
 533 
 
534 
<p>The linear algebra routines in R can make use of enhanced BLAS (Basic
 534 
<p>The linear algebra routines in R can make use of enhanced BLAS (Basic
535 
Linear Algebra Subprograms, <a href="http://www.netlib.org/blas/faq.html">http://www.netlib.org/blas/faq.html</a>)
 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
 536 
routines.  Some are compiler-system-specific (<code>libsunperf</code> on Sun
537 
Sparc<a rel="footnote" href="#fn-2"><sup>2</sup></a>, <code>libessl</code> on IBM, <code>vecLib</code> on MacOS
 537 
Sparc<a rel="footnote" href="#fn-2"><sup>2</sup></a>, <code>libessl</code> on IBM, <code>vecLib</code> on MacOS
538 
X) but ATLAS (<a href="http://math-atlas.sourceforge.net/">http://math-atlas.sourceforge.net/</a>) is a "tuned"
 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
 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
 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
 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
 542 
configuration option <code>--with-blas</code> and not to use an external
543 
BLAS library by <code>--without-blas</code>.
 543 
BLAS library by <code>--without-blas</code>.
544 
 
 544 
 
545 
   <p>For systems with multiple processors it is possible to use a
 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
 546 
multi-threaded version of ATLAS.  (Prior to R 1.8.0 this was not
547 
supported since <code>SIGINT</code> signals sent to the process and handled by
 547 
supported since <code>SIGINT</code> signals sent to the process and handled by
548 
the wrong thread could result in segfaults.)  A remaining issue is that
 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
 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
 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
 551 
version of ATLAS.  You can use a multi-threaded ATLAS by specifying
552 
<pre class="smallexample">     --with-blas="-lptf77blas -lpthread -latlas"
 552 
<pre class="smallexample">     --with-blas="-lptf77blas -lpthread -latlas"
553 
     </pre>
 553 
     </pre>
554 
 
 554 
 
555 
   <p>Another tuned BLAS which is available for some processors under Linux is
 555 
   <p>Another tuned BLAS which is available for some processors under Linux is
556 
by Kazushige Goto, currently available at
 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
 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
 558 
installed, it can be used by one of
559 
<pre class="smallexample">     --with-blas=goto
 559 
<pre class="smallexample">     --with-blas=goto
560 
     --with-blas=-lgoto
 560 
     --with-blas=-lgoto
561 
     </pre>
 561 
     </pre>
562 
   Multi-threaded versions of Goto's BLAS are available, so please note the
 562 
   Multi-threaded versions of Goto's BLAS are available, so please note the
563 
<em>caveat</em> in the previous paragraph.
 563 
<em>caveat</em> in the previous paragraph.
564 
 
 564 
 
565 
   <p>For Intel processors under Linux, Intel's Math Kernel Library
 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>
 566 
<a href="http://www.intel.com/software/products/mkl/">http://www.intel.com/software/products/mkl/</a>
567 
can be used by
 567 
can be used by
568 
<pre class="smallexample">     --with-blas="-lmkl -lguide -lpthread"
 568 
<pre class="smallexample">     --with-blas="-lmkl -lguide -lpthread"
569 
     </pre>
 569 
     </pre>
570 
   with the same caveat on multi-threading.  (Thanks to Andy Liaw for the
 570 
   with the same caveat on multi-threading.  (Thanks to Andy Liaw for the
571 
information.)
 571 
information.)
572 
 
 572 
 
573 
   <p>Note that the BLAS library will be used for several add-on packages as
 573 
   <p>Note that the BLAS library will be used for several add-on packages as
574 
well as for R itself.  This means that it is better to use a shared
 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
 575 
BLAS library, as most of a static library will be compiled into the R
576 
executable and each BLAS-using package.  In any case, the BLAS library
 576 
executable and each BLAS-using package.  In any case, the BLAS library
577 
must be usable with dynamically-loadable code: this can be a problem
 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.
 578 
with ATLAS that is not by default built with position-independent code.
579 
 
 579 
 
580 
   <p>You will need double-precision and double-complex versions of the BLAS,
 580 
   <p>You will need double-precision and double-complex versions of the BLAS,
581 
but not single-precision nor complex routines.
 581 
but not single-precision nor complex routines.
582 
 
 582 
 
583 
   <p>Provision is made for using an external LAPACK library, principally to
 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
 584 
cope with BLAS libraries which contain a copy of LAPACK (such as
585 
<code>libsunperf</code> on Solaris and <code>vecLib</code> on MacOS 10.2.2).
 585 
<code>libsunperf</code> on Solaris and <code>vecLib</code> on MacOS 10.2.2).
586 
However, the likely performance gains are thought to be small (and may
 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
 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
 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
 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
 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
 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
 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
 593 
the ATLAS-optimized subset of LAPACK.  To do so specify something like
594 
<pre class="smallexample">     --with-lapack="-L/path/to/libs -llapack -lcblas"
 594 
<pre class="smallexample">     --with-lapack="-L/path/to/libs -llapack -lcblas"
595 
     </pre>
 595 
     </pre>
596 
 
 596 
 
597 
<p>since the ATLAS subset of LAPACK depends on <code>libcblas</code>.
 597 
<p>since the ATLAS subset of LAPACK depends on <code>libcblas</code>.
598 
 
 598 
 
599 
   <p>If you do use <code>--with-lapack</code>, be aware of potential problems
 599 
   <p>If you do use <code>--with-lapack</code>, be aware of potential problems
600 
with bugs in the LAPACK 3.0 sources (or in the posted corrections to those
 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
 601 
sources).  In particular, bugs in <code>DGEEV</code> and <code>DGESDD</code> have
602 
resulted in error messages such as
 602 
resulted in error messages such as
603 
<pre class="smallexample">     DGEBRD gave error code -10
 603 
<pre class="smallexample">     DGEBRD gave error code -10
604 
     </pre>
 604 
     </pre>
605 
 
 605 
 
606 
<p>(from the Debian <code>-llapack</code> which was current in late 2002).  Other
 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
 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
 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
 609 
<code>DLANGE</code> and <code>vecLib</code> has omitted the BLAS routine
610 
<code>LSAME</code>.
 610 
<code>LSAME</code>.
611 
 
 611 
 
612 
   <p>As with all libraries, you need to ensure that they and R were
 612 
   <p>As with all libraries, you need to ensure that they and R were
613 
compiled with compatible compilers and flags.  For example, this means
 613 
compiled with compatible compilers and flags.  For example, this means
614 
that on Sun Sparc using the native compilers the flag <code>-dalign</code>
 614 
that on Sun Sparc using the native compilers the flag <code>-dalign</code>
615 
is needed so <code>libsunperf</code> can be used.
 615 
is needed so <code>libsunperf</code> can be used.
616 
 
 616 
 
617 
   <p>An ATLAS `tuned' BLAS can also be used on Windows: see
 617 
   <p>An ATLAS `tuned' BLAS can also be used on Windows: see
618 
<code>src/gnuwin32/INSTALL</code> for how to enable this when building from
 618 
<code>src/gnuwin32/INSTALL</code> for how to enable this when building from
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.
 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.
620 
Goto's BLAS can also be used when building from source.
 620 
Goto's BLAS can also be used when building from source.
621 
 
 621 
 
622 
   <p>Note that under Unix (but not under Windows) if R is compiled
 622 
   <p>Note that under Unix (but not under Windows) if R is compiled
623 
against a non-default BLAS, then all BLAS-using packages must also be.
 623 
against a non-default BLAS, then all BLAS-using packages must also be.
624 
So if R is re-built after ATLAS is installed, then packages such as
 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.
 625 
<strong>quantreg</strong> will need to be re-installed.
626 
 
 626 
 
627 
<a name="Configuration%20on%20Unix"></a>
 627 
<a name="Configuration%20on%20Unix"></a>
628 
 
 628 
 
629 
<h2 class="appendix">Appendix B Configuration on Unix</h2>
 629 
<h2 class="appendix">Appendix B Configuration on Unix</h2>
630 
 
 630 
 
631 
<a name="Configuration%20options"></a>
 631 
<a name="Configuration%20options"></a>
632 
 
 632 
 
633 
<h3 class="section">B.1 Configuration options</h3>
 633 
<h3 class="section">B.1 Configuration options</h3>
634 
 
 634 
 
635 
<p><code>configure</code> has many options: running
 635 
<p><code>configure</code> has many options: running
636 
 
 636 
 
637 
<pre class="smallexample">     ./configure --help
 637 
<pre class="smallexample">     ./configure --help
638 
     </pre>
 638 
     </pre>
639 
 
 639 
 
640 
<p>will give a list.  Probably the most important ones not covered
 640 
<p>will give a list.  Probably the most important ones not covered
641 
elsewhere are (defaults in brackets)
 641 
elsewhere are (defaults in brackets)
642 
 
 642 
 
643 
     <dl>
 643 
     <dl>
644 
<dt><code>--with-x</code>
 644 
<dt><code>--with-x</code>
645 
     <dd>use the X Window System
 645 
     <dd>use the X Window System
646 
<br><dt><code>--x-includes=</code><var>DIR</var><code></code>
 646 
<br><dt><code>--x-includes=</code><var>DIR</var><code></code>
647 
     <dd>X include files are in <var>DIR</var>
 647 
     <dd>X include files are in <var>DIR</var>
648 
<br><dt><code>--x-libraries=</code><var>DIR</var><code></code>
 648 
<br><dt><code>--x-libraries=</code><var>DIR</var><code></code>
649 
     <dd>X library files are in <var>DIR</var>
 649 
     <dd>X library files are in <var>DIR</var>
650 
<br><dt><code>--with-readline</code>
 650 
<br><dt><code>--with-readline</code>
651 
     <dd>use readline library (if available) [yes]
 651 
     <dd>use readline library (if available) [yes]
652 
<br><dt><code>--enable-R-profiling</code>
 652 
<br><dt><code>--enable-R-profiling</code>
653 
     <dd>attempt to compile support for <code>Rprof()</code> [yes]
 653 
     <dd>attempt to compile support for <code>Rprof()</code> [yes]
654 
<br><dt><code>--enable-R-shlib</code>
 654 
<br><dt><code>--enable-R-shlib</code>
655 
     <dd>build R as a shared library [no]
 655 
     <dd>build R as a shared library [no]
656 
</dl>
 656 
</dl>
657 
 
 657 
 
658 
<p>You can use <code>--without-foo</code> or <code>--disable-foo</code> for the
 658 
<p>You can use <code>--without-foo</code> or <code>--disable-foo</code> for the
659 
negatives.
 659 
negatives.
660 
 
 660 
 
661 
   <p>You will want to use <code>--disable-R-profiling</code> if you are building
 661 
   <p>You will want to use <code>--disable-R-profiling</code> if you are building
662 
a profiled executable of R (e.g. with <code>-pg)</code>.
 662 
a profiled executable of R (e.g. with <code>-pg)</code>.
663 
 
 663 
 
664 
   <p>Flag <code>--enable-R-shlib</code> causes the make process to build R as a
 664 
   <p>Flag <code>--enable-R-shlib</code> causes the make process to build R as a
665 
shared library, typically called <code>libR.so</code>, and to take
 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
 666 
considerably longer, so you probably only want this if you will be using
667 
an application which embeds R.
 667 
an application which embeds R.
668 
 
 668 
 
669 
<a name="Configuration%20variables"></a>
 669 
<a name="Configuration%20variables"></a>
670 
 
 670 
 
671 
<h3 class="section">B.2 Configuration variables</h3>
 671 
<h3 class="section">B.2 Configuration variables</h3>
672 
 
 672 
 
673 
<p>If you need or want to set certain configure variables to something
 673 
<p>If you need or want to set certain configure variables to something
674 
other than their default, you can do that by either editing the file
 674 
other than their default, you can do that by either editing the file
675 
<code>config.site</code> (which documents all the variables you might want to
 675 
<code>config.site</code> (which documents all the variables you might want to
676 
set) or on the command line as
 676 
set) or on the command line as
677 
 
 677 
 
678 
<pre class="smallexample">     ./configure VAR=<var>value</var>
 678 
<pre class="smallexample">     ./configure VAR=<var>value</var>
679 
     </pre>
 679 
     </pre>
680 
 
 680 
 
681 
<p>These variables are <em>precious</em>, implying that they do not have to
 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
 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
 683 
specified on the command line and checked for consistency between two
684 
configure runs (provided that caching is used), and are kept during
 684 
configure runs (provided that caching is used), and are kept during
685 
automatic reconfiguration as if having been passed as command line
 685 
automatic reconfiguration as if having been passed as command line
686 
arguments, even if no cache is used.
 686 
arguments, even if no cache is used.
687 
 
 687 
 
688 
   <p>See the variable output section of <code>configure --help</code> for a list of
 688 
   <p>See the variable output section of <code>configure --help</code> for a list of
689 
all these variables.
 689 
all these variables.
690 
 
 690 
 
691 
   <p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to
 691 
   <p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to
692 
<code>a4</code>, not <code>letter</code>.  (Valid values are <code>a4</code>,
 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>.)
 693 
<code>letter</code>, <code>legal</code> and <code>executive</code>.)
694 
 
 694 
 
695 
   <p>If you have libraries and header files, e.g., for GNU readline, in
 695 
   <p>If you have libraries and header files, e.g., for GNU readline, in
696 
non-system directories, use the variables <code>LDFLAGS</code> (for libraries,
 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>
 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++
 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
 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
 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
 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
 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
 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
 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).
 705 
front end shell script which does the re-ordering).
706 
 
 706 
 
707 
   <p>Another precious variable is <code>R_BROWSER</code>, the default browser, which
 707 
   <p>Another precious variable is <code>R_BROWSER</code>, the default browser, which
708 
should take a value of an executable in the user's path or specify
 708 
should take a value of an executable in the user's path or specify
709 
a full path.
 709 
a full path.
710 
 
 710 
 
711 
   <p>If you find you need to alter configure variables, it is worth noting
 711 
   <p>If you find you need to alter configure variables, it is worth noting
712 
that some settings may be cached in the file <code>config.cache</code>, and it
 712 
that some settings may be cached in the file <code>config.cache</code>, and it
713 
is a good idea to remove that file (if it exists) before re-configuring.
 713 
is a good idea to remove that file (if it exists) before re-configuring.
714 
Note that caching is turned <em>off</em> by default; use the command line
 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.
 715 
option <code>--config-cache</code> (or <code>-C</code>) to enable caching.
716 
 
 716 
 
717 
<a name="Using%20make"></a>
 717 
<a name="Using%20make"></a>
718 
 
 718 
 
719 
<h3 class="section">B.3 Using make</h3>
 719 
<h3 class="section">B.3 Using make</h3>
720 
 
 720 
 
721 
<p>To compile R, you will most likely find it easiest to use GNU
 721 
<p>To compile R, you will most likely find it easiest to use GNU
722 
<code>make</code>.  On Solaris 2.6/7/8 in particular, you need a version of
 722 
<code>make</code>.  On Solaris 2.6/7/8 in particular, you need a version of
723 
GNU <code>make</code> different from 3.77; 3.79.1 works fine, as does the Sun
 723 
GNU <code>make</code> different from 3.77; 3.79.1 works fine, as does the Sun
724 
<code>make</code>.  The native <code>make</code> is reported to fail on SGI
 724 
<code>make</code>.  The native <code>make</code> is reported to fail on SGI
725 
Irix 6.5 and Alpha/OSF1 (aka Tru64).
 725 
Irix 6.5 and Alpha/OSF1 (aka Tru64).
726 
 
 726 
 
727 
   <p>To build in a separate directory you need a <code>make</code> that uses the
 727 
   <p>To build in a separate directory you need a <code>make</code> that uses the
728 
<code>VPATH</code> variable, for example GNU <code>make</code>, or Sun
 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).
 729 
<code>make</code> on Solaris 2.7/8 (but not earlier).
730 
 
 730 
 
731 
   <p>If you want to use a <code>make</code> by another name, for example if your
 731 
   <p>If you want to use a <code>make</code> by another name, for example if your
732 
GNU <code>make</code> is called <code>gmake</code>, you need to set the variable
 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
 733 
<code>MAKE</code> at configure time, for example
734 
 
 734 
 
735 
<pre class="smallexample">     ./configure MAKE=gmake
 735 
<pre class="smallexample">     ./configure MAKE=gmake
736 
     </pre>
 736 
     </pre>
737 
 
 737 
 
738 
<a name="Using%20FORTRAN"></a>
 738 
<a name="Using%20FORTRAN"></a>
739 
 
 739 
 
740 
<h3 class="section">B.4 Using FORTRAN</h3>
 740 
<h3 class="section">B.4 Using FORTRAN</h3>
741 
 
 741 
 
742 
<p>To compile R, you need a FORTRAN compiler or <code>f2c</code>, the
 742 
<p>To compile R, you need a FORTRAN compiler or <code>f2c</code>, the
743 
FORTRAN-to-C converter (<a href="http://www.netlib.org/f2c">http://www.netlib.org/f2c</a>).  The default
 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>,
 744 
is to search for <code>g77</code>, <code>f77</code>, <code>xlf</code>,
745 
<code>frt</code>, <code>pgf77</code>, <code>fl32</code>, <code>af77</code>,
 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>,
 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>,
 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
 748 
<code>lf95</code>, <code>g95</code>, and <code>fc</code> (in that
749 
order)<a rel="footnote" href="#fn-3"><sup>3</sup></a>, and
 749 
order)<a rel="footnote" href="#fn-3"><sup>3</sup></a>, and
750 
then for <code>f2c</code>, and use whichever is found first; if none is
 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
 751 
found, R cannot be compiled.  The search mechanism can be changed
752 
using the configure variables <code>F77</code> and <code>F2C</code> which specify
 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
 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
 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
 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
 756 
FORTRAN compiler would be be available.  If your FORTRAN compiler is in
757 
a non-standard location, you should set the environment variable
 757 
a non-standard location, you should set the environment variable
758 
<code>PATH</code> accordingly before running <code>configure</code>, or use the
 758 
<code>PATH</code> accordingly before running <code>configure</code>, or use the
759 
configure variable <code>F77</code> to specify its full path.
 759 
configure variable <code>F77</code> to specify its full path.
760 
 
 760 
 
761 
   <p>If your FORTRAN libraries are in slightly peculiar places, you should
 761 
   <p>If your FORTRAN libraries are in slightly peculiar places, you should
762 
also look at <code>LD_LIBRARY_PATH</code> or your system's equivalent to make
 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.
 763 
sure that all libraries are on this path.
764 
 
 764 
 
765 
   <p>You must set whatever compilation flags (if any) are needed to ensure
 765 
   <p>You must set whatever compilation flags (if any) are needed to ensure
766 
that FORTRAN <code>integer</code> is equivalent to a C <code>int</code> pointer and
 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>
 767 
FORTRAN <code>double precision</code> is equivalent to a C <code>double</code>
768 
pointer.  This is checked during the configuration process.
 768 
pointer.  This is checked during the configuration process.
769 
 
 769 
 
770 
   <p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
 770 
   <p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
771 
is a FORTRAN 90 extension.  This is checked for at configure
 771 
is a FORTRAN 90 extension.  This is checked for at configure
772 
time<a rel="footnote" href="#fn-4"><sup>4</sup></a>, but you may need to avoid
 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
 773 
compiler flags<a rel="footnote" href="#fn-5"><sup>5</sup></a> asserting
774 
FORTRAN 77 compliance.
 774 
FORTRAN 77 compliance.
775 
 
 775 
 
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.
 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.
777 
 
 777 
 
778 
   <p>If you use <code>f2c</code> you may need to ensure that the FORTRAN type
 778 
   <p>If you use <code>f2c</code> you may need to ensure that the FORTRAN type
779 
<code>integer</code> is translated to the C type <code>int</code>.  Normally
 779 
<code>integer</code> is translated to the C type <code>int</code>.  Normally
780 
<code>f2c.h</code> contains <code>typedef long int integer;</code>, which will work
 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.
 781 
on a 32-bit platform but not on a 64-bit platform.
782 
 
 782 
 
783 
<a name="Compile%20and%20load%20flags"></a>
 783 
<a name="Compile%20and%20load%20flags"></a>
784 
 
 784 
 
785 
<h3 class="section">B.5 Compile and load flags</h3>
 785 
<h3 class="section">B.5 Compile and load flags</h3>
786 
 
 786 
 
787 
<p>A wide range of flags can be set in the file <code>config.site</code> or as
 787 
<p>A wide range of flags can be set in the file <code>config.site</code> or as
788 
configure variables on the command line.  We have already mentioned
 788 
configure variables on the command line.  We have already mentioned
789 
 
 789 
 
790 
     <dl>
 790 
     <dl>
791 
<dt><code>CPPFLAGS</code>
 791 
<dt><code>CPPFLAGS</code>
792 
     <dd>header file search directory (<code>-I</code>) and any other miscellaneous
 792 
     <dd>header file search directory (<code>-I</code>) and any other miscellaneous
793 
options for the C and C++ preprocessors and compilers
 793 
options for the C and C++ preprocessors and compilers
794 
<br><dt><code>LDFLAGS</code>
 794 
<br><dt><code>LDFLAGS</code>
795 
     <dd>path (<code>-L</code>), stripping (<code>-s</code>) and any other miscellaneous
 795 
     <dd>path (<code>-L</code>), stripping (<code>-s</code>) and any other miscellaneous
796 
options for the linker
 796 
options for the linker
797 
</dl>
 797 
</dl>
798 
 
 798 
 
799 
<p>and others include
 799 
<p>and others include
800 
 
 800 
 
801 
     <dl>
 801 
     <dl>
802 
<dt><code>CFLAGS</code>
 802 
<dt><code>CFLAGS</code>
803 
     <dd>debugging and optimization flags, C
 803 
     <dd>debugging and optimization flags, C
804 
<br><dt><code>MAIN_CFLAGS</code>
 804 
<br><dt><code>MAIN_CFLAGS</code>
805 
     <dd>ditto, for compiling the main program
 805 
     <dd>ditto, for compiling the main program
806 
<br><dt><code>SHLIB_CFLAGS</code>
 806 
<br><dt><code>SHLIB_CFLAGS</code>
807 
     <dd>for shared libraries
 807 
     <dd>for shared libraries
808 
<br><dt><code>FFLAGS</code>
 808 
<br><dt><code>FFLAGS</code>
809 
     <dd>debugging and optimization flags, FORTRAN
 809 
     <dd>debugging and optimization flags, FORTRAN
810 
<br><dt><code>MAIN_FFLAGS</code>
 810 
<br><dt><code>MAIN_FFLAGS</code>
811 
     <dd>ditto, for compiling the main program
 811 
     <dd>ditto, for compiling the main program
812 
<br><dt><code>SHLIB_FFLAGS</code>
 812 
<br><dt><code>SHLIB_FFLAGS</code>
813 
     <dd>for shared libraries
 813 
     <dd>for shared libraries
814 
<br><dt><code>MAIN_LDFLAGS</code>
 814 
<br><dt><code>MAIN_LDFLAGS</code>
815 
     <dd>additional flags for the main link
 815 
     <dd>additional flags for the main link
816 
<br><dt><code>SHLIB_LDFLAGS</code>
 816 
<br><dt><code>SHLIB_LDFLAGS</code>
817 
     <dd>additional flags for linking the shared libraries
 817 
     <dd>additional flags for linking the shared libraries
818 
</dl>
 818 
</dl>
819 
 
 819 
 
820 
<p>Library paths specified as <code>-L/lib/path</code> in <code>LDFLAGS</code> are
 820 
<p>Library paths specified as <code>-L/lib/path</code> in <code>LDFLAGS</code> are
821 
collected together and prepended to <code>LD_LIBRARY_PATH</code> (or your
 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
 822 
system's equivalent), so there should be no need for <code>-R</code> or
823 
<code>-rpath</code> flags.
 823 
<code>-rpath</code> flags.
824 
 
 824 
 
825 
   <p>To compile a profiling version of R, one might for example want to
 825 
   <p>To compile a profiling version of R, one might for example want to
826 
use <code>MAIN_CFLAGS=-pg</code>, <code>MAIN_FFLAGS=-pg</code>,
 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
 827 
<code>MAIN_LDFLAGS=-pg</code> on platforms where <code>-pg</code> cannot be used
828 
with position-independent code.
 828 
with position-independent code.
829 
 
 829 
 
830 
   <p><strong>Beware:</strong> it may be necessary to set <code>CFLAGS</code> and
 830 
   <p><strong>Beware:</strong> it may be necessary to set <code>CFLAGS</code> and
831 
<code>FFLAGS</code> in ways compatible with the libraries to be used: one
 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
 832 
possible issue is the alignment of doubles, another is the way
833 
structures are passed.
 833 
structures are passed.
834 
 
 834 
 
835 
<a name="Building%20the%20GNOME%20interface"></a>
 835 
<a name="Building%20the%20GNOME%20interface"></a>
836 
 
 836 
 
837 
<h3 class="section">B.6 Building the <small>GNOME</small> interface</h3>
 837 
<h3 class="section">B.6 Building the <small>GNOME</small> interface</h3>
838 
 
 838 
 
839 
<p>This interface is experimental and incomplete.  It provides a console
 839 
<p>This interface is experimental and incomplete.  It provides a console
840 
and two graphics devices named <code>gtk()</code> and <code>gnome()</code>.  The
 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
 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
 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
 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>
 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>
 845 
device to <small>GDK</small> (the GIMP Drawing Kit). The <code>gnome()</code>
846 
device uses the <small>GNOME</small> canvas.
 846 
device uses the <small>GNOME</small> canvas.
847 
 
 847 
 
848 
   <p>Due to its experimental nature, the <small>GNOME</small> interface for R
 848 
   <p>Due to its experimental nature, the <small>GNOME</small> interface for R
849 
will not be built automatically.  You must specify it by running
 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
 850 
configure with the <code>--with-gnome</code> option.  For example, you might
851 
run
 851 
run
852 
 
 852 
 
853 
<pre class="smallexample">     ./configure --with-gnome
 853 
<pre class="smallexample">     ./configure --with-gnome
854 
     </pre>
 854 
     </pre>
855 
 
 855 
 
856 
<p>but please check you have all the requirements first. You need at least
 856 
<p>but please check you have all the requirements first. You need at least
857 
the following libraries (or later) installed
 857 
the following libraries (or later) installed
858 
 
 858 
 
859 
<pre class="smallexample">     audiofile-0.2.1
 859 
<pre class="smallexample">     audiofile-0.2.1
860 
     esound-0.2.23
 860 
     esound-0.2.23
861 
     glib-1.2.10
 861 
     glib-1.2.10
862 
     gtk+-1.2.10
 862 
     gtk+-1.2.10
863 
     imlib-1.9.10
 863 
     imlib-1.9.10
864 
     ORBit-0.5.12
 864 
     ORBit-0.5.12
865 
     gnome-libs-1.4.1.2
 865 
     gnome-libs-1.4.1.2
866 
     libxml-1.8.16
 866 
     libxml-1.8.16
867 
     libglade-0.17
 867 
     libglade-0.17
868 
     </pre>
 868 
     </pre>
869 
 
 869 
 
870 
<p>It is preferable to have a complete installation of the <small>GNOME</small>
 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
 871 
desktop environment.  If you use Linux, then this should be provided
872 
with your distribution.  In addition, packaged binary distributions of
 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
 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.
 874 
popular Linux distributions and for Solaris.
875 
 
 875 
 
876 
   <p>Remember that some package management systems (such as <small>RPM</small> and
 876 
   <p>Remember that some package management systems (such as <small>RPM</small> and
877 
deb) make a distinction between the user version of a package and the
 877 
deb) make a distinction between the user version of a package and the
878 
developer version.  The latter usually has the same name but with the
 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
 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
 880 
<small>GNOME</small> then you must have the developer versions of the above
881 
packages in order to compile the R-GNOME interface.
 881 
packages in order to compile the R-GNOME interface.
882 
 
 882 
 
883 
   <p>The full list of <small>GNOME</small> options to configure is
 883 
   <p>The full list of <small>GNOME</small> options to configure is
884 
 
 884 
 
885 
     <dl>
 885 
     <dl>
886 
<dt><code>--with-gnome</code>
 886 
<dt><code>--with-gnome</code>
887 
     <dd>use <small>GNOME</small>, or specify its prefix [no]
 887 
     <dd>use <small>GNOME</small>, or specify its prefix [no]
888 
<br><dt><code>--with-gnome-includes=</code><var>DIR</var><code></code>
 888 
<br><dt><code>--with-gnome-includes=</code><var>DIR</var><code></code>
889 
     <dd>specify location of <small>GNOME</small> headers
 889 
     <dd>specify location of <small>GNOME</small> headers
890 
<br><dt><code>--with-gnome-libs=</code><var>DIR</var><code></code>
 890 
<br><dt><code>--with-gnome-libs=</code><var>DIR</var><code></code>
891 
     <dd>specify location of <small>GNOME</small> libs
 891 
     <dd>specify location of <small>GNOME</small> libs
892 
<br><dt><code>--with-libglade-config=</code><var>LIBGLADE_CONFIG</var><code></code>
 892 
<br><dt><code>--with-libglade-config=</code><var>LIBGLADE_CONFIG</var><code></code>
893 
     <dd>specify location of <code>libglade-config</code>
 893 
     <dd>specify location of <code>libglade-config</code>
894 
</dl>
 894 
</dl>
895 
 
 895 
 
896 
<a name="Platform%20notes"></a>
 896 
<a name="Platform%20notes"></a>
897 
 
 897 
 
898 
<h3 class="section">B.7 Platform notes</h3>
 898 
<h3 class="section">B.7 Platform notes</h3>
899 
 
 899 
 
900 
<p>This section provides some notes on building R on different Unix-like
 900 
<p>This section provides some notes on building R on different Unix-like
901 
platforms.  These notes are based on tests run on one or two systems in
 901 
platforms.  These notes are based on tests run on one or two systems in
902 
each case with particular sets of compilers and support libraries.
 902 
each case with particular sets of compilers and support libraries.
903 
Success in building R depends on the proper installation and functioning
 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
 904 
of support software; your results may differ if you have other versions
905 
of compilers and support libraries.
 905 
of compilers and support libraries.
906 
 
 906 
 
907 
<a name="Linux"></a>
 907 
<a name="Linux"></a>
908 
 
 908 
 
909 
<h3 class="subsection">B.7.1 Linux</h4>
 909 
<h3 class="subsection">B.7.1 Linux</h4>
910 
 
 910 
 
911 
<p>Linux is the main development platform for R, so compilation from the
 911 
<p>Linux is the main development platform for R, so compilation from the
912 
sources is normally straightforward.
 912 
sources is normally straightforward.
913 
 
 913 
 
914 
   <p>Remember that some package management systems (such as <small>RPM</small> and
 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
 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
 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
 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
 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
 919 
expected features are detected: if for example <code>readline</code> is
920 
missing add the package containing its headers.
 920 
missing add the package containing its headers.
921 
 
 921 
 
922 
   <p>When R has been installed from a binary distribution there are
 922 
   <p>When R has been installed from a binary distribution there are
923 
sometimes problems with missing components such as the Fortran
 923 
sometimes problems with missing components such as the Fortran
924 
compiler.  Searching the <code>R-help</code> archives will normally reveal
 924 
compiler.  Searching the <code>R-help</code> archives will normally reveal
925 
what is needed.
 925 
what is needed.
926 
 
 926 
 
927 
   <p>It seems that the <code>gcc</code> compilers normally produce PIC code on
 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
 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
 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
 930 
when building R as a shared library to ensure that
931 
position-independent code is used in any static libraries (such as the
 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
 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
 933 
might be linked against.  Fortunately these are normally built as shared
934 
libraries with the exception of the ATLAS BLAS libraries.
 934 
libraries with the exception of the ATLAS BLAS libraries.
935 
 
 935 
 
936 
<a name="MacOS%20X"></a>
 936 
<a name="MacOS%20X"></a>
937 
 
 937 
 
938 
<h3 class="subsection">B.7.2 MacOS X</h4>
 938 
<h3 class="subsection">B.7.2 MacOS X</h4>
939 
 
 939 
 
940 
<p>You can build R as a Unix application on MacOS X.  You will need the
 940 
<p>You can build R as a Unix application on MacOS X.  You will need the
941 
DevTools, <code>f2c</code> or <code>g77</code>, and the <code>dlcompat</code>
 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
 942 
library.  You will also need to install an X sub-system or configure
943 
with <code>--without-x</code>.
 943 
with <code>--without-x</code>.
944 
 
 944 
 
945 
   <p><code>f2c</code>, <code>g77</code>, the <code>dlcompat</code> library, and X server
 945 
   <p><code>f2c</code>, <code>g77</code>, the <code>dlcompat</code> library, and X server
946 
and support libraries are available from the Fink project
 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
 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
 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
 949 
binary distribution and needed to be installed directly; for example for
950 
<code>g77</code> use
 950 
<code>g77</code> use
951 
 
 951 
 
952 
<pre class="smallexample">     fink install g77
 952 
<pre class="smallexample">     fink install g77
953 
     </pre>
 953 
     </pre>
954 
 
 954 
 
955 
   <p>The <code>vecLib</code> library of MacOS &gt;= 10.2.2 can be used <em>via</em> the
 955 
   <p>The <code>vecLib</code> library of MacOS &gt;= 10.2.2 can be used <em>via</em> the
956 
configuration options
 956 
configuration options
957 
<pre class="smallexample">     --with-blas="-framework vecLib" --with-lapack
 957 
<pre class="smallexample">     --with-blas="-framework vecLib" --with-lapack
958 
     </pre>
 958 
     </pre>
959 
 
 959 
 
960 
<p>to provide higher-performance versions of the BLAS and LAPACK routines.
 960 
<p>to provide higher-performance versions of the BLAS and LAPACK routines.
961 
With <code>gcc 3.1</code> that appears to be the only way to build R, as
 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
 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
 963 
dynmaic library.  (We have had reports of success with pre-release
964 
versions of <code>gcc 3.3</code>.)
 964 
versions of <code>gcc 3.3</code>.)
965 
 
 965 
 
966 
<a name="Solaris"></a>
 966 
<a name="Solaris"></a>
967 
 
 967 
 
968 
<h3 class="subsection">B.7.3 Solaris on Sparc</h4>
 968 
<h3 class="subsection">B.7.3 Solaris on Sparc</h4>
969 
 
 969 
 
970 
<p>R has been built successfully on Solaris 8 aka Solaris 2.8 aka SunOS
 970 
<p>R has been built successfully on Solaris 8 aka Solaris 2.8 aka SunOS
971 
5.8 using <code>gcc</code>/<code>g77</code> and the SunPro WorkShop&nbsp;6 (aka
 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
 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
 973 
7), and less regularly on Solaris 2.5.1, 2.6, 2.7 and 9.  GNU
974 
<code>make</code> is needed prior to Solaris 2.7 for building other than in
 974 
<code>make</code> is needed prior to Solaris 2.7 for building other than in
975 
the source tree, and perhaps even then.
 975 
the source tree, and perhaps even then.
976 
 
 976 
 
977 
   <p>The Solaris versions of several of the tools needed to build R
 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
 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
 979 
<code>/usr/ccs/bin</code>, so if using those tools ensure this is in your
980 
path.
 980 
path.
981 
 
 981 
 
982 
   <p><code>gcc</code> 3.2.1 and 3.2.2 generate incorrect code on 32-bit Solaris
 982 
   <p><code>gcc</code> 3.2.1 and 3.2.2 generate incorrect code on 32-bit Solaris
983 
builds with optimization, but versions 3.1, 3.2, 3.2.3  and 3.3.x work
 983 
builds with optimization, but versions 3.1, 3.2, 3.2.3  and 3.3.x work
984 
correctly.  At least files <code>src/main/engine.c</code>,
 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.
 985 
<code>src/main/graphics.c</code> and <code>src/modules/devX11.c</code> are affected.
986 
 
 986 
 
987 
   <p>If using <code>gcc</code>, do ensure that the compiler was compiled for the
 987 
   <p>If using <code>gcc</code>, do ensure that the compiler was compiled for the
988 
version of Solaris in use.  (This can be ascertained from <code>gcc
 988 
version of Solaris in use.  (This can be ascertained from <code>gcc
989 
-v</code>.)  <code>gcc</code> makes modified versions of some header files, and
 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
 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
 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
 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
 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
 994 
<code>binutils</code> too.  To avoid all these pitfalls we strongly
995 
recommended you compile <code>gcc</code> from the sources yourself.
 995 
recommended you compile <code>gcc</code> from the sources yourself.
996 
 
 996 
 
997 
   <p>When using the SunPro compilers do <em>not</em> specify <code>-fast</code>, as
 997 
   <p>When using the SunPro compilers do <em>not</em> specify <code>-fast</code>, as
998 
this disables <small>IEEE</small> arithmetic and <code>make check</code> will
 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
 999 
fail.  The maximal set of optimization options known to work is
1000 
 
 1000 
 
1001 
<pre class="smallexample">     -xlibmil -xO5 -dalign
 1001 
<pre class="smallexample">     -xlibmil -xO5 -dalign
1002 
     </pre>
 1002 
     </pre>
1003 
 
 1003 
 
1004 
   <p>We have found little performance difference between <code>gcc</code> and
 1004 
   <p>We have found little performance difference between <code>gcc</code> and
1005 
<code>cc</code> but considerable benefit from using a SunPro Fortran
 1005 
<code>cc</code> but considerable benefit from using a SunPro Fortran
1006 
compiler: the <code>gcc</code>/<code>f77</code> combination works well.  For
 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
 1007 
many C++ applications (e.g. package <strong>Matrix</strong>) Forte 7 requires
1008 
<code>-lCstd</code>, which the configure script will add to
 1008 
<code>-lCstd</code>, which the configure script will add to
1009 
<code>SHLIB_CXXLDFLAGS</code> if it identifies the compiler correctly.
 1009 
<code>SHLIB_CXXLDFLAGS</code> if it identifies the compiler correctly.
1010 
 
 1010 
 
1011 
   <p>To compile for a 64-bit target on Solaris (which needs an UltraSparc
 1011 
   <p>To compile for a 64-bit target on Solaris (which needs an UltraSparc
1012 
chip and for support to be enabled in the OS) with the Forte 6 and 7
 1012 
chip and for support to be enabled in the OS) with the Forte 6 and 7
1013 
compilers we used
 1013 
compilers we used
1014 
 
 1014 
 
1015 
<pre class="smallexample">     CC="cc -xarch=v9"
 1015 
<pre class="smallexample">     CC="cc -xarch=v9"
1016 
     CFLAGS="-xO5 -xlibmil -dalign"
 1016 
     CFLAGS="-xO5 -xlibmil -dalign"
1017 
     F77="f95 -xarch=v9"
 1017 
     F77="f95 -xarch=v9"
1018 
     FFLAGS="-xO5 -xlibmil -dalign"
 1018 
     FFLAGS="-xO5 -xlibmil -dalign"
1019 
     CXX="CC -xarch=v9"
 1019 
     CXX="CC -xarch=v9"
1020 
     CXXFLAGS="-xO5 -xlibmil -dalign"
 1020 
     CXXFLAGS="-xO5 -xlibmil -dalign"
1021 
     </pre>
 1021 
     </pre>
1022 
 
 1022 
 
1023 
<p>in <code>config.site</code>.
 1023 
<p>in <code>config.site</code>.
1024 
 
 1024 
 
1025 
   <p>For 64-bit compilation with <code>gcc</code> 3.2.x and 3.3.x we used
 1025 
   <p>For 64-bit compilation with <code>gcc</code> 3.2.x and 3.3.x we used
1026 
 
 1026 
 
1027 
<pre class="smallexample">     CC="gcc -m64"
 1027 
<pre class="smallexample">     CC="gcc -m64"
1028 
     FFLAGS="-m64 -g -O2"
 1028 
     FFLAGS="-m64 -g -O2"
1029 
     CXXFLAGS="-m64 -g -O2"
 1029 
     CXXFLAGS="-m64 -g -O2"
1030 
     LDFLAGS="-L/usr/local/lib/sparcv9 -L/usr/local/lib"
 1030 
     LDFLAGS="-L/usr/local/lib/sparcv9 -L/usr/local/lib"
1031 
     </pre>
 1031 
     </pre>
1032 
 
 1032 
 
1033 
   <p>Note that <code>/usr/local/lib/sparcv9</code> will need to be in the
 1033 
   <p>Note that <code>/usr/local/lib/sparcv9</code> will need to be in the
1034 
<code>LD_LIBRARY_PATH</code> during configuration.
 1034 
<code>LD_LIBRARY_PATH</code> during configuration.
1035 
 
 1035 
 
1036 
   <p>Note that using <code>f95</code> allows the Sun performance library
 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>,
 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
 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
 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
 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
 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>,
 1042 
experience has been that ATLAS's BLAS is faster than <code>libsunperf</code>,
1043 
especially for complex numbers.
 1043 
especially for complex numbers.
1044 
 
 1044 
 
1045 
   <p>Some care is needed to ensure that libraries found by
 1045 
   <p>Some care is needed to ensure that libraries found by
1046 
<code>configure</code> are compatible with the R executable and modules, as
 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
 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
 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
 1049 
some of the Sun libraries: fortunately the equivalent flag for
1050 
<code>gcc</code>, <code>-mno-unaligned-doubles</code>, is the default.  In
 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
 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>
 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
 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.
 1054 
practice this seems to give little problem for 32-bit builds.
1055 
 
 1055 
 
1056 
   <p>For a 64-bit build, 64-bit libraries must be used.  As the configuration
 1056 
   <p>For a 64-bit build, 64-bit libraries must be used.  As the configuration
1057 
process by default sets <code>LDFLAGS</code> to <code>-L/usr/local/lib</code>,
 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
 1058 
you may need to set it to avoid finding 32-bit addons (as in the
1059 
<code>gcc -m64</code> example above).  It is possible to build Tcl/Tk as
 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
 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.
 1061 
only with the Forte compiler (and not with <code>gcc</code>) as of Tcl/Tk 8.4.5.
1062 
 
 1062 
 
1063 
<a name="HP-UX"></a>
 1063 
<a name="HP-UX"></a>
1064 
 
 1064 
 
1065 
<h3 class="subsection">B.7.4 HP-UX</h4>
 1065 
<h3 class="subsection">B.7.4 HP-UX</h4>
1066 
 
 1066 
 
1067 
<p>R has been built successfully on HP-UX 10.2 and HP-UX 11.0 using both
 1067 
<p>R has been built successfully on HP-UX 10.2 and HP-UX 11.0 using both
1068 
native compilers and <code>gcc</code>.  However, 10.2 has not been tested
 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
 1069 
since R 1.4.0.  By default, R is configured to use <code>gcc</code> and
1070 
<code>g77</code> on HP-UX (if available).  Some installations of
 1070 
<code>g77</code> on HP-UX (if available).  Some installations of
1071 
<code>g77</code> only install a static version of the <code>g2c</code> library
 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
 1072 
that cannot be linked into a shared library since its files have not
1073 
been compiled with the appropriate flag for producing position
 1073 
been compiled with the appropriate flag for producing position
1074 
independent code (<small>PIC</small>).  This will result in <code>make</code>
 1074 
independent code (<small>PIC</small>).  This will result in <code>make</code>
1075 
failing with a linker error similar to
 1075 
failing with a linker error similar to
1076 
 
 1076 
 
1077 
<pre class="smallexample">     ld: CODE_ONE_SYM fixup to non-code subspace in file foo.o -
 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.
 1078 
     shared library must be position independent. Use +z or +Z to recompile.
1079 
     </pre>
 1079 
     </pre>
1080 
 
 1080 
 
1081 
<p>(<code>+z</code> and <code>+Z</code> are the <small>PIC</small> flags for the native
 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
 1082 
compiler <code>cc</code>.)  If this is the case you either need to modify
1083 
your <code>g77</code> installation or configure with
 1083 
your <code>g77</code> installation or configure with
1084 
 
 1084 
 
1085 
<pre class="smallexample">     F77=fort77
 1085 
<pre class="smallexample">     F77=fort77
1086 
     </pre>
 1086 
     </pre>
1087 
 
 1087 
 
1088 
<p>to specify use of the native <small>POSIX</small>-compliant FORTRAN 77
 1088 
<p>to specify use of the native <small>POSIX</small>-compliant FORTRAN 77
1089 
compiler.
 1089 
compiler.
1090 
 
 1090 
 
1091 
   <p>You may find that <code>configure</code> detects other libraries that R
 1091 
   <p>You may find that <code>configure</code> detects other libraries that R
1092 
needs to use as shared libraries but are only available as static
 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
 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
 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
 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
 1096 
last paragraph.  Static libraries that might be found and would cause
1097 
problems are
 1097 
problems are
1098 
 
 1098 
 
1099 
<pre class="smallexample">     BLAS                   use --without-blas
 1099 
<pre class="smallexample">     BLAS                   use --without-blas
1100 
     Tcl/Tk                 use --without-tcltk
 1100 
     Tcl/Tk                 use --without-tcltk
1101 
     GNOME                  not built by default
 1101 
     GNOME                  not built by default
1102 
     libpng                 use --without-libpng
 1102 
     libpng                 use --without-libpng
1103 
     jpeg                   use --without-jpeglib
 1103 
     jpeg                   use --without-jpeglib
1104 
     zlib                   use --without-zlib
 1104 
     zlib                   use --without-zlib
1105 
     </pre>
 1105 
     </pre>
1106 
 
 1106 
 
1107 
<p>and <code>bzip2</code> and <code>pcre</code> are problematic when building
 1107 
<p>and <code>bzip2</code> and <code>pcre</code> are problematic when building
1108 
<code>libR.so</code>, only.  These can be avoided by <code>--without-bzlib</code>
 1108 
<code>libR.so</code>, only.  These can be avoided by <code>--without-bzlib</code>
1109 
and <code>--without-pcre</code> respectively, but these are the defaults.
 1109 
and <code>--without-pcre</code> respectively, but these are the defaults.
1110 
 
 1110 
 
1111 
   <p>Some versions of <code>gcc</code> may contain what appears to be a bug at
 1111 
   <p>Some versions of <code>gcc</code> may contain what appears to be a bug at
1112 
the <code>-O2</code> optimization level that causes
 1112 
the <code>-O2</code> optimization level that causes
1113 
 
 1113 
 
1114 
<pre class="smallexample">     &gt; 2 %/% 2
 1114 
<pre class="smallexample">     &gt; 2 %/% 2
1115 
     [1] 1
 1115 
     [1] 1
1116 
     &gt; 1:2 %/% 2
 1116 
     &gt; 1:2 %/% 2
1117 
     [1] 0 0     # wrong!!
 1117 
     [1] 0 0     # wrong!!
1118 
     </pre>
 1118 
     </pre>
1119 
 
 1119 
 
1120 
<p>which will cause <code>make check</code> to fail.  If this is the case, you
 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
 1121 
should use <code>CFLAGS</code> to specify <code>-O</code> as the optimization
1122 
level to use.
 1122 
level to use.
1123 
 
 1123 
 
1124 
   <p>Some systems running HP-UX 11.0 may have a <code>gcc</code> that was
 1124 
   <p>Some systems running HP-UX 11.0 may have a <code>gcc</code> that was
1125 
installed under HP-UX 10.2.  Between versions 10.2 and 11.0 HP-UX
 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
 1126 
changed its support functions for <small>IEEE</small> arithmetic from the
1127 
recommended functions of the <small>IEEE</small> standard to the ones
 1127 
recommended functions of the <small>IEEE</small> standard to the ones
1128 
specified in the C9x draft standard.  In particular, this means that
 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>
 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
 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
 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>
 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
 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
 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>
 1135 
<code>gcc</code>.  An alternative work-around is to add <code>-DIEEE_754</code>
1136 
to the <code>CFLAGS</code> variable.
 1136 
to the <code>CFLAGS</code> variable.
1137 
 
 1137 
 
1138 
   <p>You can configure R to use both the native <code>cc</code> and
 1138 
   <p>You can configure R to use both the native <code>cc</code> and
1139 
<code>fort77</code> with
 1139 
<code>fort77</code> with
1140 
 
 1140 
 
1141 
<pre class="smallexample">     ./configure CC=cc F77=fort77
 1141 
<pre class="smallexample">     ./configure CC=cc F77=fort77
1142 
     </pre>
 1142 
     </pre>
1143 
 
 1143 
 
1144 
   <p><code>f90</code> insists on linking against a static <code>libF90.a</code> which
 1144 
   <p><code>f90</code> insists on linking against a static <code>libF90.a</code> which
1145 
typically resides in a non-standard directory (e.g.,
 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
 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
 1147 
add this directory to the linker path via the configure variable
1148 
<code>LDFLAGS</code> (e.g., <code>./configure F77=f90
 1148 
<code>LDFLAGS</code> (e.g., <code>./configure F77=f90
1149 
LDFLAGS=/opt/fortran90/lib</code>).
 1149 
LDFLAGS=/opt/fortran90/lib</code>).
1150 
 
 1150 
 
1151 
<a name="IRIX"></a>
 1151 
<a name="IRIX"></a>
1152 
 
 1152 
 
1153 
<h3 class="subsection">B.7.5 IRIX</h4>
 1153 
<h3 class="subsection">B.7.5 IRIX</h4>
1154 
 
 1154 
 
1155 
<p>R has been built successfully on IRIX64 6.5 using
 1155 
<p>R has been built successfully on IRIX64 6.5 using
1156 
<code>gcc</code>/<code>f77</code> or <code>cc</code>/<code>f77</code> for 32-bit
 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
 1157 
executables and the native compilers for a 64-bit executable.  The
1158 
command
 1158 
command
1159 
 
 1159 
 
1160 
<pre class="smallexample">     ./configure CC="cc -64" F77="f77 -64" --with-tcltk=no
 1160 
<pre class="smallexample">     ./configure CC="cc -64" F77="f77 -64" --with-tcltk=no
1161 
     </pre>
 1161 
     </pre>
1162 
 
 1162 
 
1163 
<p>was used to create the 64-bit executable.  It was necessary to
 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
 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.
 1165 
version but not detect that is was incompatible with a 64-bit build.
1166 
 
 1166 
 
1167 
   <p>A 32-bit build using <code>gcc</code>/<code>g77</code> passed <code>make
 1167 
   <p>A 32-bit build using <code>gcc</code>/<code>g77</code> passed <code>make
1168 
check</code> but failed <code>make test-all-extras</code> in the complex LAPACK
 1168 
check</code> but failed <code>make test-all-extras</code> in the complex LAPACK
1169 
tests.
 1169 
tests.
1170 
 
 1170 
 
1171 
<a name="Alpha%2fOSF1"></a>
 1171 
<a name="Alpha%2fOSF1"></a>
1172 
 
 1172 
 
1173 
<h3 class="subsection">B.7.6 Alpha/OSF1</h4>
 1173 
<h3 class="subsection">B.7.6 Alpha/OSF1</h4>
1174 
 
 1174 
 
1175 
<p>R has been built successfully on an Alpha running OSF1 V4.0 using
 1175 
<p>R has been built successfully on an Alpha running OSF1 V4.0 using
1176 
<code>gcc</code>/<code>g77</code> and <code>cc</code>/<code>f77</code>.  Mixing
 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
 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
 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
 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
 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
 1181 
<code>SIGFPE</code> on platforms that support <small>IEEE</small> arithmetic, so
1182 
these are fatal.
 1182 
these are fatal.
1183 
 
 1183 
 
1184 
<a name="Alpha%2fFreeBSD"></a>
 1184 
<a name="Alpha%2fFreeBSD"></a>
1185 
 
 1185 
 
1186 
<h3 class="subsection">B.7.7 Alpha/FreeBSD</h4>
 1186 
<h3 class="subsection">B.7.7 Alpha/FreeBSD</h4>
1187 
 
 1187 
 
1188 
<p>Attempts to build R on an Alpha with FreeBSD 4.3 have been only
 1188 
<p>Attempts to build R on an Alpha with FreeBSD 4.3 have been only
1189 
partly successful.  Configuring with <code>-mieee</code> added to both
 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
 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
 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
 1192 
rather than suppressing them entirely.  Advice on how to complete this
1193 
port would be greatly appreciated.
 1193 
port would be greatly appreciated.
1194 
 
 1194 
 
1195 
<a name="AIX"></a>
 1195 
<a name="AIX"></a>
1196 
 
 1196 
 
1197 
<h3 class="subsection">B.7.8 AIX</h4>
 1197 
<h3 class="subsection">B.7.8 AIX</h4>
1198 
 
 1198 
 
1199 
<p>On AIX 4.3.3 and AIX 5.1, it was found that the use of "run time
 1199 
<p>On AIX 4.3.3 and AIX 5.1, it was found that the use of "run time
1200 
linking" (as opposed to normal AIX style linking) was required.  For
 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
 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
 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
 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
 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
 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.
 1206 
dynamically load modules (such as X11) with the <code>dlopen</code> call.
1207 
 
 1207 
 
1208 
   <p>When setting <code>MAIN_LDFLAGS</code> and <code>SHLIB_LDFLAGS</code> accordingly,
 1208 
   <p>When setting <code>MAIN_LDFLAGS</code> and <code>SHLIB_LDFLAGS</code> accordingly,
1209 
note that linker flags must be escaped using <code>-Wl,</code> if
 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>
 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.
 1211 
and <code>SHLIB_LDFLAGS="-Wl,-G"</code> in this case.
1212 
 
 1212 
 
1213 
   <p>Harald Servat Gelabert &lt;harald at cepba dot upc dot es&gt; reported
 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
 1214 
success building R 1.7.0 under AIX 5.1 with
1215 
 
 1215 
 
1216 
<pre class="smallexample">     CC=xlc
 1216 
<pre class="smallexample">     CC=xlc
1217 
     F77=xlf
 1217 
     F77=xlf
1218 
     CXX=xlC
 1218 
     CXX=xlC
1219 
     CFLAGS=-O3 -qstrict -qmaxmem=8192
 1219 
     CFLAGS=-O3 -qstrict -qmaxmem=8192
1220 
     FFLAGS=-O3 -qstrict -qmaxmem=8192
 1220 
     FFLAGS=-O3 -qstrict -qmaxmem=8192
1221 
     CXXFLAGS=-O2 -qmaxmem=8192
 1221 
     CXXFLAGS=-O2 -qmaxmem=8192
1222 
     MAIN_LDFLAGS=-Wl,-brtl
 1222 
     MAIN_LDFLAGS=-Wl,-brtl
1223 
     SHLIB_LDFLAGS=-Wl,-G
 1223 
     SHLIB_LDFLAGS=-Wl,-G
1224 
     </pre>
 1224 
     </pre>
1225 
 
 1225 
 
1226 
<p>but was unable to use the X libraries or the native BLAS (ESSL) and so
 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>.
 1227 
used <code>--without-x --without-blas</code>.
1228 
 
 1228 
 
1229 
<a name="New%20platforms"></a>
 1229 
<a name="New%20platforms"></a>
1230 
 
 1230 
 
1231 
<h2 class="appendix">Appendix C New platforms</h2>
 1231 
<h2 class="appendix">Appendix C New platforms</h2>
1232 
 
 1232 
 
1233 
<p>There are a number of sources of problems when installing R on a new
 1233 
<p>There are a number of sources of problems when installing R on a new
1234 
hardware/OS platform.  These include
 1234 
hardware/OS platform.  These include
1235 
 
 1235 
 
1236 
   <p><strong>Floating Point Arithmetic</strong>: R supports the <small>POSIX</small>,
 1236 
   <p><strong>Floating Point Arithmetic</strong>: R supports the <small>POSIX</small>,
1237 
SVID and <small>IEEE</small> models for floating point arithmetic.  The
 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>
 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
 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
 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)
 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
 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
 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
 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
 1245 
be done via the file <code>config.site</code> which resides in the top level
1246 
directory.
 1246 
directory.
1247 
 
 1247 
 
1248 
   <p>Beware of using high levels of optimization, at least initially.  On
 1248 
   <p>Beware of using high levels of optimization, at least initially.  On
1249 
many compilers these reduce the degree of compliance to the
 1249 
many compilers these reduce the degree of compliance to the
1250 
<small>IEEE</small> model.  For example, using <code>-fast</code> on the Solaris
 1250 
<small>IEEE</small> model.  For example, using <code>-fast</code> on the Solaris
1251 
SunPro compilers causes R's <code>NaN</code> to be set incorrectly.
 1251 
SunPro compilers causes R's <code>NaN</code> to be set incorrectly.
1252 
 
 1252 
 
1253 
   <p><strong>Shared Libraries</strong>: There seems to be very little agreement
 1253 
   <p><strong>Shared Libraries</strong>: There seems to be very little agreement
1254 
across platforms on what needs to be done to build shared libraries.
 1254 
across platforms on what needs to be done to build shared libraries.
1255 
there are many different combinations of flags for the compilers and
 1255 
there are many different combinations of flags for the compilers and
1256 
loaders.  GNU libtool cannot be used (yet), as it currently does not
 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>:
 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
 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
 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
 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
 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
 1262 
know about).  This typically works, but you may have to manually
1263 
override the results.  Scanning the manual entries for <code>cc</code> and
 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
 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
 1265 
recipe you can modify the file <code>config.site</code> (following the
1266 
instructions therein) so that the build will use these options.
 1266 
instructions therein) so that the build will use these options.
1267 
 
 1267 
 
1268 
   <p>If you do manage to get R running on a new platform please let us
 1268 
   <p>If you do manage to get R running on a new platform please let us
1269 
know about it so we can modify the configuration procedures to include
 1269 
know about it so we can modify the configuration procedures to include
1270 
that platform.
 1270 
that platform.
1271 
 
 1271 
 
1272 
   <p>If you are having trouble getting R to work on your platform please
 1272 
   <p>If you are having trouble getting R to work on your platform please
1273 
feel free to get in touch to ask questions.  We have had a fair amount
 1273 
feel free to get in touch to ask questions.  We have had a fair amount
1274 
of practice at porting R to new platforms <small class="enddots">....</small>
 1274 
of practice at porting R to new platforms <small class="enddots">....</small>
1275 
 
 1275 
 
1276 
<a name="Function%20and%20variable%20index"></a>
 1276 
<a name="Function%20and%20variable%20index"></a>
1277 
 
 1277 
 
1278 
<h2 class="unnumbered">Function and variable index</h2>
 1278 
<h2 class="unnumbered">Function and variable index</h2>
1279 
 
 1279 
 
1280 
<ul class="index-vr" compact>
 1280 
<ul class="index-vr" compact>
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>
 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>
1282 
<li><code>install.packages</code>: <a href="#Installing%20packages">Installing packages</a>
 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>
 1283 
<li><code>make</code>: <a href="#Using%20make">Using make</a>
1284 
<li><code>R_HOME</code>: <a href="#Simple%20compilation">Simple compilation</a>
 1284 
<li><code>R_HOME</code>: <a href="#Simple%20compilation">Simple compilation</a>
1285 
<li><code>remove.packages</code>: <a href="#Removing%20packages">Removing packages</a>
 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>
 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>
 1287 
<li><code>update.packages</code>: <a href="#Updating%20packages">Updating packages</a>
1288 
</ul>
 1288 
</ul>
1289 
<a name="Concept%20index"></a>
 1289 
<a name="Concept%20index"></a>
1290 
 
 1290 
 
1291 
<h2 class="unnumbered">Concept index</h2>
 1291 
<h2 class="unnumbered">Concept index</h2>
1292 
 
 1292 
 
1293 
<ul class="index-cp" compact>
 1293 
<ul class="index-cp" compact>
1294 
<li>AIX: <a href="#AIX">AIX</a>
 1294 
<li>AIX: <a href="#AIX">AIX</a>
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>
 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>
1296 
<li>FORTRAN: <a href="#Using%20FORTRAN">Using FORTRAN</a>
 1296 
<li>FORTRAN: <a href="#Using%20FORTRAN">Using FORTRAN</a>
1297 
<li>Help pages: <a href="#Simple%20compilation">Simple compilation</a>
 1297 
<li>Help pages: <a href="#Simple%20compilation">Simple compilation</a>
1298 
<li>HP-UX: <a href="#HP-UX">HP-UX</a>
 1298 
<li>HP-UX: <a href="#HP-UX">HP-UX</a>
1299 
<li>Installation: <a href="#Installation">Installation</a>
 1299 
<li>Installation: <a href="#Installation">Installation</a>
1300 
<li>Installing under Unix: <a href="#Installing%20R%20under%20Unix">Installing R under Unix</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>
 1301 
<li>Installing under Windows: <a href="#Installing%20R%20under%20Windows">Installing R under Windows</a>
1302 
<li>IRIS: <a href="#IRIX">IRIX</a>
 1302 
<li>IRIS: <a href="#IRIX">IRIX</a>
1303 
<li>LAPACK library: <a href="#Solaris">Solaris</a>, <a href="#MacOS%20X">MacOS X</a>, <a href="#Linear%20algebra">Linear algebra</a>
 1303 
<li>LAPACK library: <a href="#Solaris">Solaris</a>, <a href="#MacOS%20X">MacOS X</a>, <a href="#Linear%20algebra">Linear algebra</a>
1304 
<li>Linux: <a href="#Linux">Linux</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
 1304 
<li>Linux: <a href="#Linux">Linux</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
1305 
<li>MacOS X: <a href="#MacOS%20X">MacOS X</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
 1305 
<li>MacOS X: <a href="#MacOS%20X">MacOS X</a>, <a href="#Installing%20R%20under%20Unix">Installing R under Unix</a>
1306 
<li>Manuals: <a href="#Making%20the%20manuals">Making the manuals</a>
 1306 
<li>Manuals: <a href="#Making%20the%20manuals">Making the manuals</a>
1307 
<li>Manuals, installing: <a href="#Installation">Installation</a>
 1307 
<li>Manuals, installing: <a href="#Installation">Installation</a>
1308 
<li>Obtaining R: <a href="#Obtaining%20R">Obtaining R</a>
 1308 
<li>Obtaining R: <a href="#Obtaining%20R">Obtaining R</a>
1309 
<li>Packages: <a href="#Add-on%20packages">Add-on packages</a>
 1309 
<li>Packages: <a href="#Add-on%20packages">Add-on packages</a>
1310 
<li>Packages, installing: <a href="#Installing%20packages">Installing packages</a>
 1310 
<li>Packages, installing: <a href="#Installing%20packages">Installing packages</a>
1311 
<li>Packages, removing: <a href="#Removing%20packages">Removing packages</a>
 1311 
<li>Packages, removing: <a href="#Removing%20packages">Removing packages</a>
1312 
<li>Packages, updating: <a href="#Updating%20packages">Updating packages</a>
 1312 
<li>Packages, updating: <a href="#Updating%20packages">Updating packages</a>
1313 
<li>Solaris: <a href="#Solaris">Solaris</a>
 1313 
<li>Solaris: <a href="#Solaris">Solaris</a>
1314 
<li>Sources for R: <a href="#Getting%20and%20unpacking%20the%20sources">Getting and unpacking the sources</a>
 1314 
<li>Sources for R: <a href="#Getting%20and%20unpacking%20the%20sources">Getting and unpacking the sources</a>
1315 
</ul>
 1315 
</ul>
1316 
 
 1316 
 
1317 
 
 1317 
 
1318 
   <div class="footnote">
 1318 
   <div class="footnote">
1319 
<hr>
 1319 
<hr>
1320 
<h4>Footnotes</h4>
 1320 
<h4>Footnotes</h4>
1321 
<ol type="1">
 1321 
<ol type="1">
1322 
<li><a name="fn-1"></a>
 1322 
<li><a name="fn-1"></a>
1323 
<p>if you have the source-code package
 1323 
<p>if you have the source-code package
1324 
files installed</p>
 1324 
files installed</p>
1325 
 
 1325 
 
1326 
   <li><a name="fn-2"></a>
 1326 
   <li><a name="fn-2"></a>
1327 
<p>Using the SunPro aka Forte aka Sun ONE <code>cc</code> and
 1327 
<p>Using the SunPro aka Forte aka Sun ONE <code>cc</code> and
1328 
<code>f95</code> compilers</p>
 1328 
<code>f95</code> compilers</p>
1329 
 
 1329 
 
1330 
   <li><a name="fn-3"></a>
 1330 
   <li><a name="fn-3"></a>
1331 
<p>On HP-UX <code>fort77</code> is the <small>POSIX</small>
 1331 
<p>On HP-UX <code>fort77</code> is the <small>POSIX</small>
1332 
compliant FORTRAN compiler, and comes second in the search list.</p>
 1332 
compliant FORTRAN compiler, and comes second in the search list.</p>
1333 
 
 1333 
 
1334 
   <li><a name="fn-4"></a>
 1334 
   <li><a name="fn-4"></a>
1335 
<p>as well as its equivalence to the <code>Rcomplex</code>
 1335 
<p>as well as its equivalence to the <code>Rcomplex</code>
1336 
structure defined in <code>R_ext/Complex.h</code>.</p>
 1336 
structure defined in <code>R_ext/Complex.h</code>.</p>
1337 
 
 1337 
 
1338 
   <li><a name="fn-5"></a>
 1338 
   <li><a name="fn-5"></a>
1339 
<p>In particular, avoid <code>g77</code>'s
 1339 
<p>In particular, avoid <code>g77</code>'s
1340 
<code>-pedantic</code>, which gives confusing error messages.</p>
 1340 
<code>-pedantic</code>, which gives confusing error messages.</p>
1341 
 
 1341 
 
1342 
   <li><a name="fn-6"></a>
 1342 
   <li><a name="fn-6"></a>
1343 
<p>e.g., to use an optimized BLAS on
 1343 
<p>e.g., to use an optimized BLAS on
1344 
Sun/Sparc</p>
 1344 
Sun/Sparc</p>
1345 
 
 1345 
 
1346 
   </ol><hr></div>
 1346 
   </ol><hr></div>
1347 
 
 1347 
 
1348 
   </body></html>
 1348 
   </body></html>
1349 
 
 1349