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<title>R for Mac OS X FAQ</title>
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<h1 class="settitle">R for Mac OS X FAQ</h1>
19 
<div class="node">
20 
<p><hr>
21 
Node:&nbsp;<a name="Top">Top</a>,
22 
Next:&nbsp;<a rel="next" accesskey="n" href="#Introduction">Introduction</a>,
23 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#dir">(dir)</a>,
24 
Up:&nbsp;<a rel="up" accesskey="u" href="#dir">(dir)</a>
25 
<br>
26 
</div>
27 
 
28 
<h2 class="unnumbered">R for Mac OS X FAQ</h2>
29 
 
30 
<h2>Frequently Asked Questions on R for Mac OS X</h2>
31 
<h2>Version 2.0-0 2004-10-10</h2>
32 
<address>Stefano M. Iacus</address>
33 
<address>Simon Urbanek</address>
34 
<p><p><hr><p>
35 
 
36 
<ul class="menu">
37 
<li><a accesskey="1" href="#Introduction">Introduction</a>:
38 
<li><a accesskey="2" href="#Building%20R%20from%20sources">Building R from sources</a>:
39 
<li><a accesskey="3" href="#Command%20line%20version%20of%20R">Command line version of R</a>:
40 
<li><a accesskey="4" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>:
41 
<li><a accesskey="5" href="#How%20to%20install%20packages">How to install packages</a>:
42 
<li><a accesskey="6" href="#R%20and%20external%20applications">R and external applications</a>:
43 
<li><a accesskey="7" href="#The%20near%20future%20of%20the%20Aqua%20GUI">The near future of the Aqua GUI</a>:
44 
<li><a accesskey="8" href="#Aqua%20GUI%20Bugs">Aqua GUI Bugs</a>:
45 
<li><a accesskey="9" href="#Quartz%20device">Quartz device</a>:
46 
<li><a href="#TclTk%20issues">TclTk issues</a>:
47 
<li><a href="#Additional%20resources">Additional resources</a>:
48 
<li><a href="#Acknowledgments">Acknowledgments</a>:
49 
<li><a href="#Sparse%20questions">Sparse questions</a>:
50 
</ul>
51 
 
52 
<div class="node">
53 
<p><hr>
54 
Node:&nbsp;<a name="Introduction">Introduction</a>,
55 
Next:&nbsp;<a rel="next" accesskey="n" href="#Building%20R%20from%20sources">Building R from sources</a>,
56 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Top">Top</a>,
57 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
58 
<br>
59 
</div>
60 
 
61 
<h2 class="chapter">Introduction</h2>
62 
 
63 
<p>This R for Mac OS X FAQ is rather incomplete at the moment and requires contributions from users.
64 
Anything specific to the R language can be found in the official R-FAQ (see  <a href="http://cran.r-project.org/doc/FAQ/R-FAQ.html">http://cran.r-project.org/doc/FAQ/R-FAQ.html</a>).
65 
Please send any requests/questions you would like answers on to the maintaniers.
66 
 
67 
   <p>This document contains information on how to build <small>R</small> from sources, how to install and run it.
68 
It also contains a user guide to the Aqua GUI version of <small>R</small>.
69 
 
70 
<ul class="menu">
71 
<li><a accesskey="1" href="#How%20many%20versions%20of%20R%20for%20Mac%20OS%20X%3f">How many versions of R for Mac OS X?</a>:
72 
<li><a accesskey="2" href="#What%20machines%20does%20R%20for%20Mac%20OS%20X%20run%20on%3f">What machines does R for Mac OS X run on?</a>:
73 
<li><a accesskey="3" href="#How%20can%20R%20for%20Mac%20OS%20X%20be%20obtained%20and%20installed%3f">How can R for Mac OS X be obtained and installed?</a>:
74 
</ul>
75 
 
76 
<div class="node">
77 
<p><hr>
78 
Node:&nbsp;<a name="How%20many%20versions%20of%20R%20for%20Mac%20OS%20X%3f">How many versions of R for Mac OS X?</a>,
79 
Next:&nbsp;<a rel="next" accesskey="n" href="#What%20machines%20does%20R%20for%20Mac%20OS%20X%20run%20on%3f">What machines does R for Mac OS X run on?</a>,
80 
Up:&nbsp;<a rel="up" accesskey="u" href="#Introduction">Introduction</a>
81 
<br>
82 
</div>
83 
 
84 
<h3 class="section">How many versions of R for Mac OS X?</h3>
85 
 
86 
<p>There is currently only one version of R for Mac OS X.
87 
But R on Mac OS X can be used as a command-line application (see <a href="#Command%20line%20version%20of%20R">Command line version of R</a>), like on any
88 
other unix-like system, or via the Aqua GUI (see <a href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>). This second approach in using R
89 
for Mac OS X is mostly preferred by "traditional" Macintosh users.
90 
 
91 
<div class="node">
92 
<p><hr>
93 
Node:&nbsp;<a name="What%20machines%20does%20R%20for%20Mac%20OS%20X%20run%20on%3f">What machines does R for Mac OS X run on?</a>,
94 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20can%20R%20for%20Mac%20OS%20X%20be%20obtained%20and%20installed%3f">How can R for Mac OS X be obtained and installed?</a>,
95 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20many%20versions%20of%20R%20for%20Mac%20OS%20X%3f">How many versions of R for Mac OS X?</a>,
96 
Up:&nbsp;<a rel="up" accesskey="u" href="#Introduction">Introduction</a>
97 
<br>
98 
</div>
99 
 
100 
<h3 class="section">What machines does R for Mac OS X run on?</h3>
101 
 
102 
<p>R for Mac OS X requires Mac OS X version 10.2 or higher to run. The latest version of the system is
103 
always preferable though. We do not support Mac OS X version 10.1.
104 
 
105 
<div class="node">
106 
<p><hr>
107 
Node:&nbsp;<a name="How%20can%20R%20for%20Mac%20OS%20X%20be%20obtained%20and%20installed%3f">How can R for Mac OS X be obtained and installed?</a>,
108 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#What%20machines%20does%20R%20for%20Mac%20OS%20X%20run%20on%3f">What machines does R for Mac OS X run on?</a>,
109 
Up:&nbsp;<a rel="up" accesskey="u" href="#Introduction">Introduction</a>
110 
<br>
111 
</div>
112 
 
113 
<h3 class="section">How can R for Mac OS X be obtained and installed?</h3>
114 
 
115 
<div class="node">
116 
<p><hr>
117 
Node:&nbsp;<a name="Building%20R%20from%20sources">Building R from sources</a>,
118 
Next:&nbsp;<a rel="next" accesskey="n" href="#Command%20line%20version%20of%20R">Command line version of R</a>,
119 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Introduction">Introduction</a>,
120 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
121 
<br>
122 
</div>
123 
 
124 
<h2 class="chapter">Building R from sources</h2>
125 
 
126 
<ul class="menu">
127 
<li><a accesskey="1" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>:
128 
<li><a accesskey="2" href="#How%20to%20configure%20and%20build%20R">How to configure and build R</a>:
129 
<li><a accesskey="3" href="#How%20to%20install%20R">How to install R</a>:
130 
<li><a accesskey="4" href="#How%20to%20build%20and%20install%20the%20Aqua%20GUI">How to build and install the Aqua GUI</a>:
131 
</ul>
132 
 
133 
<div class="node">
134 
<p><hr>
135 
Node:&nbsp;<a name="What%20is%20needed%20to%20build%20R">What is needed to build R</a>,
136 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20to%20configure%20and%20build%20R">How to configure and build R</a>,
137 
Up:&nbsp;<a rel="up" accesskey="u" href="#Building%20R%20from%20sources">Building R from sources</a>
138 
<br>
139 
</div>
140 
 
141 
<h3 class="section">What is needed to build R</h3>
142 
 
143 
<ul class="menu">
144 
<li><a accesskey="1" href="#the%20C%2fC++%20compiler%20gcc%203.3">the C/C++ compiler gcc 3.3</a>:
145 
<li><a accesskey="2" href="#the%20Fortran%20compiler%20g77%20for%20gcc%203.3">the Fortran compiler g77 for gcc 3.3</a>:
146 
<li><a accesskey="3" href="#the%20libreadline%204.3%20(optional)">the libreadline 4.3 (optional)</a>:
147 
<li><a accesskey="4" href="#the%20X11%20window%20server%20(optional)">the X11 window server (optional)</a>:
148 
<li><a accesskey="5" href="#the%20X11%20TclTk%20headers%20and%20libraries%20(optional)">the X11 TclTk headers and libraries (optional)</a>:
149 
<li><a accesskey="6" href="#the%20Aqua%20TclTk%20headers%20and%20libraries%20(optional)">the Aqua TclTk headers and libraries (optional)</a>:
150 
<li><a accesskey="7" href="#a%20TeX%20suite%20of%20tools%20for%20documentation%20(optional)">a TeX suite of tools for documentation (optional)</a>:
151 
</ul>
152 
 
153 
<div class="node">
154 
<p><hr>
155 
Node:&nbsp;<a name="the%20C%2fC++%20compiler%20gcc%203.3">the C/C++ compiler gcc 3.3</a>,
156 
Next:&nbsp;<a rel="next" accesskey="n" href="#the%20Fortran%20compiler%20g77%20for%20gcc%203.3">the Fortran compiler g77 for gcc 3.3</a>,
157 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
158 
<br>
159 
</div>
160 
 
161 
<h3 class="subsection">the C/C++ compiler gcc 3.3</h4>
162 
 
163 
<p>If you have Mac OS X 10.3 (aka Panther) you just need to install the software inside the Xcode Tools CD
164 
(which is CD number 4). This is only true if you bought Panther. In most of the cases you have
165 
Panther already installed on your brand new machine, which means that you don't have the forth
166 
Developer CD. You should take it from Apple Developer Connection site (see <a href="#Apple%20Developer%20Connection">Apple Developer Connection</a>): in the
167 
download section, look for Xcode Tools v 1.1 or above.
168 
 
169 
   <p>If you are using Mac OS X 10.2 (aka Jaguar) then you should download and install the
170 
Apple Developers Tools Dec 2002 including the latest updates which dates August 2003. Either it comes
171 
on a separate CD with your Mac, either you can download these  from the Apple Developer Connection site (see <a href="#Apple%20Developer%20Connection">Apple Developer Connection</a>)
172 
In either cases be sure you have gcc version 3.3 just by typing in a Terminal window
173 
<pre class="example">     gcc -vv
174 
     </pre>
175 
 
176 
<div class="node">
177 
<p><hr>
178 
Node:&nbsp;<a name="the%20Fortran%20compiler%20g77%20for%20gcc%203.3">the Fortran compiler g77 for gcc 3.3</a>,
179 
Next:&nbsp;<a rel="next" accesskey="n" href="#the%20libreadline%204.3%20(optional)">the libreadline 4.3 (optional)</a>,
180 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20C%2fC++%20compiler%20gcc%203.3">the C/C++ compiler gcc 3.3</a>,
181 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
182 
<br>
183 
</div>
184 
 
185 
<h3 class="subsection">the Fortran compiler g77 for gcc 3.3</h4>
186 
 
187 
<p>You need to install a version of the g77 Fortran compiler which is built for gcc 3.3.
188 
The following instructions apply to binaries coming from  HPC for Mac OS X page <a href="http://hpc.sourceforge.net">http://hpc.sourceforge.net</a>.
189 
Please take care: there are two versions of the g77 binaries, one for Jaguar and one for Panther.
190 
Use the appropriate one.
191 
 
192 
   <p>Once you have the binaries, please do the following (you'll be asked for a root password):
193 
cd to the download folder and type
194 
<pre class="example">     sudo tar -zxvf g77v3.4-bin.tar.gz -C /
195 
     rehash
196 
     </pre>
197 
   It installs everything in <em>/usr/local</em>. The name of the .tar.gz archive can be different, see the related web page.
198 
 
199 
<div class="node">
200 
<p><hr>
201 
Node:&nbsp;<a name="the%20libreadline%204.3%20(optional)">the libreadline 4.3 (optional)</a>,
202 
Next:&nbsp;<a rel="next" accesskey="n" href="#the%20X11%20window%20server%20(optional)">the X11 window server (optional)</a>,
203 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20Fortran%20compiler%20g77%20for%20gcc%203.3">the Fortran compiler g77 for gcc 3.3</a>,
204 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
205 
<br>
206 
</div>
207 
 
208 
<h3 class="subsection">the libreadline 4.3 (optional)</h4>
209 
 
210 
<p>This library is optional.
211 
You need this library to be able to retrieve history using use arrow keys or for tab completion of filenames
212 
when you run R as a command line tool. The original source archive is located at GNU Org web page <a href="ftp://www.gnu.org">ftp://www.gnu.org</a>.
213 
You need to modify the original file <em>shlib/Makefile.in</em> in order to make it
214 
work under Mac OS X 10.2.x and later (this is because libreadline needs to be linked against
215 
<em>-lncurses -lcc_dynamic</em>). If you can do better at configure time working on the original archive
216 
let me know. I suggest you to download my patched version from <a href="http://www.economia.unimi.it/R">http://www.economia.unimi.it/R</a>.
217 
Once you have done, please do the following (you'll be asked for a root password):
218 
uncompress the archive, cd inside the folder and type the following
219 
<pre class="example">     ./configure
220 
     make
221 
     sudo make install
222 
     </pre>
223 
   It installs everything in <em>/usr/local</em>.
224 
These instructions apply to both Jaguar and Panther.
225 
 
226 
<div class="node">
227 
<p><hr>
228 
Node:&nbsp;<a name="the%20X11%20window%20server%20(optional)">the X11 window server (optional)</a>,
229 
Next:&nbsp;<a rel="next" accesskey="n" href="#the%20X11%20TclTk%20headers%20and%20libraries%20(optional)">the X11 TclTk headers and libraries (optional)</a>,
230 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20libreadline%204.3%20(optional)">the libreadline 4.3 (optional)</a>,
231 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
232 
<br>
233 
</div>
234 
 
235 
<h3 class="subsection">the X11 window server (optional)</h4>
236 
 
237 
<p>If you have Panther, you probably have the X11 Window server already installed on your system.
238 
This is what you need to run a version of R with the capability of using the X11 device, but it isn't sufficient
239 
if you want to build it.
240 
You need to install the additional X11 SDK package from the Xcode Tools CD.
241 
Please note: the installer on the Xcode Tools CD does not install the X11 SDK by default:
242 
you should look inside the Xcode Tools CD and install manually the X11 SDK.
243 
 
244 
   <p>If you have Jaguar, you'll need to install both the X11 Window server and the X11 SDK package from
245 
the XFree86 web page.  Apple site only supports the latest version of his OS (at the moment Panther).
246 
Users report that other version of X11 Window Servers (other than the one distributed by Apple) work as well.
247 
 
248 
<div class="node">
249 
<p><hr>
250 
Node:&nbsp;<a name="the%20X11%20TclTk%20headers%20and%20libraries%20(optional)">the X11 TclTk headers and libraries (optional)</a>,
251 
Next:&nbsp;<a rel="next" accesskey="n" href="#the%20Aqua%20TclTk%20headers%20and%20libraries%20(optional)">the Aqua TclTk headers and libraries (optional)</a>,
252 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20X11%20window%20server%20(optional)">the X11 window server (optional)</a>,
253 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
254 
<br>
255 
</div>
256 
 
257 
<h3 class="subsection">the X11 TclTk headers and libraries (optional)</h4>
258 
 
259 
<p>You need to download the sources of the Tcl and Tk 8.4.x packages to build yourself the sources.
260 
The original sources can be found on the official TclTk web page <a href="http://www.tcl.tk/software/tcltk/8.4.html">http://www.tcl.tk/software/tcltk/8.4.html</a>.
261 
Please do the following respecting the sequence (you'll be asked for a root password). These are examples for version 8.4.4
262 
of the Tcl and Tk sources, you'll probably find new version on the web page, thus only the name of the .tar.gz archives
263 
changes.
264 
 
265 
   <p>For Tcl: download the tlc 8.4 sources, cd inside the folder where you have downloaded the archive and
266 
type:
267 
<pre class="example">     tar zxf tcl8.4.4-src.tar.gz
268 
     cd tcl8.4.4/unix/
269 
     ./configure
270 
     make
271 
     sudo make install
272 
     </pre>
273 
 
274 
   <p>For Tk: download the tk 8.4 sources, cd inside the folder where you have downloaded the archive and type:
275 
<pre class="example">     tar zxf tk8.4.4-src.tar.gz
276 
     cd tk8.4.4/unix/
277 
     ./configure
278 
     make
279 
     sudo make install
280 
     </pre>
281 
 
282 
<div class="node">
283 
<p><hr>
284 
Node:&nbsp;<a name="the%20Aqua%20TclTk%20headers%20and%20libraries%20(optional)">the Aqua TclTk headers and libraries (optional)</a>,
285 
Next:&nbsp;<a rel="next" accesskey="n" href="#a%20TeX%20suite%20of%20tools%20for%20documentation%20(optional)">a TeX suite of tools for documentation (optional)</a>,
286 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20X11%20TclTk%20headers%20and%20libraries%20(optional)">the X11 TclTk headers and libraries (optional)</a>,
287 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
288 
<br>
289 
</div>
290 
 
291 
<h3 class="subsection">the Aqua TclTk headers and libraries (optional)</h4>
292 
 
293 
<p>Once you have installed the AquaTclTk libraries and headers files you should configure <small>R</small> using this additional
294 
arguments
295 
<pre class="example">     --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
296 
     --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
297 
     TCLTK_LIBS='-framework Tcl -framework Tk'
298 
     TCLTK_CPPFLAGS='-I/Library/Frameworks/Tcl.Framework/Headers -I/Library/Frameworks/Tk.Framework/Headers'
299 
     </pre>
300 
 
301 
<div class="node">
302 
<p><hr>
303 
Node:&nbsp;<a name="a%20TeX%20suite%20of%20tools%20for%20documentation%20(optional)">a TeX suite of tools for documentation (optional)</a>,
304 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#the%20Aqua%20TclTk%20headers%20and%20libraries%20(optional)">the Aqua TclTk headers and libraries (optional)</a>,
305 
Up:&nbsp;<a rel="up" accesskey="u" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>
306 
<br>
307 
</div>
308 
 
309 
<h3 class="subsection">a TeX suite of tools for documentation (optional)</h4>
310 
 
311 
<p>There is a nice installer, called the i-installer II, that allows you to install a complete
312 
teTeX distribution. You can find details on the i-installer at <a href="http://www.rna.nl/ii.html">http://www.rna.nl/ii.html</a>.
313 
The teTeX is one of the i-Packages.
314 
 
315 
<div class="node">
316 
<p><hr>
317 
Node:&nbsp;<a name="How%20to%20configure%20and%20build%20R">How to configure and build R</a>,
318 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20to%20install%20R">How to install R</a>,
319 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#What%20is%20needed%20to%20build%20R">What is needed to build R</a>,
320 
Up:&nbsp;<a rel="up" accesskey="u" href="#Building%20R%20from%20sources">Building R from sources</a>
321 
<br>
322 
</div>
323 
 
324 
<h3 class="section">How to configure and build R</h3>
325 
 
326 
<p>Download the latest sources of R from <small>CRAN</small>. Unpack the archive with tar -zxf <em>name_of_R_sources_archive</em> and cd
327 
inside the R sources directory. Then you need to configure R for your system and build R.
328 
Just type
329 
<pre class="example">     ./configure --with-blas='-framework vecLib' --with-lapack --with-aqua
330 
     make
331 
     </pre>
332 
   This will configure R to be built as a Framework to be installed inside your <em>/Library/Frameworks</em> directory with the name
333 
<em>R.framework</em>. You can change the default location of the <em>R.framework</em>
334 
installation at configure time by specifying the flag <em>-enable-R-framework[=DIR]</em>, i.e.
335 
with something like
336 
<pre class="example">     ./configure --with-blas='-framework vecLib' --with-lapack
337 
                 --with-aqua --enable-R-framework=FOO
338 
     </pre>
339 
   and the final destination of the <em>R.framework</em> will be <em>FOO/R.framework</em>, which means that you
340 
don't have to specify the <em>R.framework</em> text in the path.
341 
 
342 
<div class="node">
343 
<p><hr>
344 
Node:&nbsp;<a name="How%20to%20install%20R">How to install R</a>,
345 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20to%20build%20and%20install%20the%20Aqua%20GUI">How to build and install the Aqua GUI</a>,
346 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20to%20configure%20and%20build%20R">How to configure and build R</a>,
347 
Up:&nbsp;<a rel="up" accesskey="u" href="#Building%20R%20from%20sources">Building R from sources</a>
348 
<br>
349 
</div>
350 
 
351 
<h3 class="section">How to install R</h3>
352 
 
353 
<p>A standard installation of R requires you have built it as a Framework. At this point just type (a root
354 
password will be required):
355 
<pre class="example">     sudo make install
356 
     </pre>
357 
   and all will be installed in <em>/Library/Frameworks</em>.
358 
You can decide to change the R.framework destination by using the <em>prefix</em> option specifying the
359 
final destination.
360 
<pre class="smallexample">     sudo make prefix=/where/you/want/R.framework/to/go install
361 
     </pre>
362 
   As in the above, you don't need to specify the name <em>R.framework</em> in the path.
363 
 
364 
<div class="node">
365 
<p><hr>
366 
Node:&nbsp;<a name="How%20to%20build%20and%20install%20the%20Aqua%20GUI">How to build and install the Aqua GUI</a>,
367 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20to%20install%20R">How to install R</a>,
368 
Up:&nbsp;<a rel="up" accesskey="u" href="#Building%20R%20from%20sources">Building R from sources</a>
369 
<br>
370 
</div>
371 
 
372 
<h3 class="section">How to build and install the Aqua GUI</h3>
373 
 
374 
<p>At the moment, there is nothing special to  do to build the Aqua GUI.
375 
You just need to install it using
376 
<pre class="example">     make install-aqua
377 
     </pre>
378 
   and it will install the <em>R.app</em> application in the <em>Applications</em> folder on your system.
379 
The install procedure fails if the <code>R.framework</code> has not been installed first.
380 
 
381 
<div class="node">
382 
<p><hr>
383 
Node:&nbsp;<a name="Command%20line%20version%20of%20R">Command line version of R</a>,
384 
Next:&nbsp;<a rel="next" accesskey="n" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>,
385 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Building%20R%20from%20sources">Building R from sources</a>,
386 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
387 
<br>
388 
</div>
389 
 
390 
<h2 class="chapter">Command line version of R</h2>
391 
 
392 
<p>The command line version of <small>R</small> is nothing but a classic unix-like implementation of <small>R</small>. So general
393 
documentation for <small>R</small> applies to this version as well.
394 
On each release (and patched-release) ready to use binaries are distributed through <small>CRAN</small>.
395 
These binaries come with a common installer used by R with Aqua GUI so please read
396 
the related notes (see <a href="#How%20to%20get%20R%20with%20Aqua%20GUI">How to get R with Aqua GUI</a>).
397 
To use <small>R</small> you probably need to add a symbolic link on your System as the <small>R</small> binary is
398 
located inside the framework.
399 
Suppose you have the <em>/usr/local/bin</em> directory on your System, than you should just
400 
type in your Terminal (a root password is required)
401 
<pre class="smallexample">     sudo ln -s /Library/Frameworks/R.framework/Resources/R /usr/local/bin/R
402 
     </pre>
403 
   Assuming that you have <em>/usr/local/bin</em> in your <em>PATH</em> environment variable, you'll be able to launch R from any location
404 
on your System just by typing <em>R</em>.
405 
In this way, when you install a new version of the <em>R.framework</em> this link will point to the latest R binary.
406 
 
407 
<div class="node">
408 
<p><hr>
409 
Node:&nbsp;<a name="R%20with%20Aqua%20GUI">R with Aqua GUI</a>,
410 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20to%20install%20packages">How to install packages</a>,
411 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Command%20line%20version%20of%20R">Command line version of R</a>,
412 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
413 
<br>
414 
</div>
415 
 
416 
<h2 class="chapter">R with Aqua GUI</h2>
417 
 
418 
<ul class="menu">
419 
<li><a accesskey="1" href="#How%20to%20get%20R%20with%20Aqua%20GUI">How to get R with Aqua GUI</a>:
420 
<li><a accesskey="2" href="#How%20to%20install%20the%20Aqua%20GUI">How to install the Aqua GUI</a>:
421 
<li><a accesskey="3" href="#The%20R%20Console">The R Console</a>:
422 
<li><a accesskey="4" href="#The%20Menus">The Menus</a>:
423 
<li><a accesskey="5" href="#Preferences">Preferences</a>:
424 
<li><a accesskey="6" href="#The%20near%20future%20of%20the%20Aqua%20GUI">The near future of the Aqua GUI</a>:
425 
<li><a accesskey="7" href="#Aqua%20GUI%20Bugs">Aqua GUI Bugs</a>:
426 
</ul>
427 
 
428 
<div class="node">
429 
<p><hr>
430 
Node:&nbsp;<a name="How%20to%20get%20R%20with%20Aqua%20GUI">How to get R with Aqua GUI</a>,
431 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20to%20install%20the%20Aqua%20GUI">How to install the Aqua GUI</a>,
432 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
433 
<br>
434 
</div>
435 
 
436 
<h3 class="section">How to get R with Aqua GUI</h3>
437 
 
438 
<p>The <code>bin/macosx</code> directory of a <small>CRAN</small> site contains a standard
439 
Apple installer package named <code>R.dmg.sit</code> compressed in Aladdin
440 
Stuffit format.  Once downloaded, uncompressed and executed, the
441 
installer will install the current non-developer release of R.  R  is
442 
a native Mac OS X Darwin version of R with an Aqua GUI.
443 
Inside
444 
<code>bin/macosx/</code><var>x</var><code>.</code><var>y</var><code></code> there are prebuilt binary packages to
445 
be used with R corresponding to the "<var>x</var>.<var>y</var>" release of
446 
R. The installation of these packages is available through the
447 
"Package" menu of the Aqua GUI (see <a href="#Packages%20Menu">Packages Menu</a>).
448 
 
449 
<div class="node">
450 
<p><hr>
451 
Node:&nbsp;<a name="How%20to%20install%20the%20Aqua%20GUI">How to install the Aqua GUI</a>,
452 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20R%20Console">The R Console</a>,
453 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20to%20get%20R%20with%20Aqua%20GUI">How to get R with Aqua GUI</a>,
454 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
455 
<br>
456 
</div>
457 
 
458 
<h3 class="section">How to install the Aqua GUI</h3>
459 
 
460 
<div class="node">
461 
<p><hr>
462 
Node:&nbsp;<a name="The%20R%20Console">The R Console</a>,
463 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20Menus">The Menus</a>,
464 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20to%20install%20the%20Aqua%20GUI">How to install the Aqua GUI</a>,
465 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
466 
<br>
467 
</div>
468 
 
469 
<h3 class="section">The R Console</h3>
470 
 
471 
<p>In this section you'll find general informations on the Aqua GUI. For specific <small>R</small> tasks that
472 
can be done via the Aqua GUI using menus you should read below (see <a href="#The%20Menus">The Menus</a>).
473 
 
474 
<ul class="menu">
475 
<li><a accesskey="1" href="#The%20Input%20and%20the%20Output">The Input and the Output</a>:
476 
<li><a accesskey="2" href="#Copy%20and%20Paste">Copy and Paste</a>:
477 
<li><a accesskey="3" href="#The%20current%20and%20startup%20working%20directories">The current and startup working directories</a>:
478 
<li><a accesskey="4" href="#Resizing%20the%20R%20Console">Resizing the R Console</a>:
479 
<li><a accesskey="5" href="#Input%20and%20Output%20text%20colors">Input and Output text colors</a>:
480 
</ul>
481 
 
482 
<div class="node">
483 
<p><hr>
484 
Node:&nbsp;<a name="The%20Input%20and%20the%20Output">The Input and the Output</a>,
485 
Next:&nbsp;<a rel="next" accesskey="n" href="#Copy%20and%20Paste">Copy and Paste</a>,
486 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20R%20Console">The R Console</a>
487 
<br>
488 
</div>
489 
 
490 
<h3 class="subsection">The Input and the Output</h4>
491 
 
492 
<p>The current design of the R Console is to have separate frames for input (user) and output (R).
493 
The user is supposed to type command into the bottom frame of the R Console, this input is echoed
494 
into the upper frame and R will give any related output in the upper frame.
495 
The output frame (the upper one) is a read-only frame.
496 
 
497 
<div class="node">
498 
<p><hr>
499 
Node:&nbsp;<a name="Copy%20and%20Paste">Copy and Paste</a>,
500 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20current%20and%20startup%20working%20directories">The current and startup working directories</a>,
501 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#The%20Input%20and%20the%20Output">The Input and the Output</a>,
502 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20R%20Console">The R Console</a>
503 
<br>
504 
</div>
505 
 
506 
<h3 class="subsection">Copy and Paste</h4>
507 
 
508 
<p>Copy and paste works in R as in any other Macintosh application.
509 
But when two selection are active: one in the output frame and one in the input frame, the output frame takes precedence
510 
when copying to the clipboard.
511 
You can also copy from the <em>quartz()</em> graphic device (see <a href="#Quartz%20device">Quartz device</a>) to the clipboard. In this case a bitmap image is
512 
created. If you want high resolution graphic exports, you should better save the image using the <em>File/Save as</em> menu item (see <a href="#Quartz%20device">Quartz device</a>).
513 
 
514 
<div class="node">
515 
<p><hr>
516 
Node:&nbsp;<a name="The%20current%20and%20startup%20working%20directories">The current and startup working directories</a>,
517 
Next:&nbsp;<a rel="next" accesskey="n" href="#Resizing%20the%20R%20Console">Resizing the R Console</a>,
518 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Copy%20and%20Paste">Copy and Paste</a>,
519 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20R%20Console">The R Console</a>
520 
<br>
521 
</div>
522 
 
523 
<h3 class="subsection">The current and startup working directories</h4>
524 
 
525 
<p>If not otherwise specified in the Preferences (see <a href="#Preferences">Preferences</a>), or if the specified path is no longer available, then
526 
the default working directory at startup is the user home.
527 
The working directory can be changed using the <em>setwd</em> R command or using the <em>Tools</em> menu item <em>Change working directory</em>.
528 
The current working directory is displayed on the main bar of the R Console window.
529 
 
530 
<p>This feature is useful if you want different startup procedures defined by the <code>.Rprofile</code>; you can
531 
edit a <code>.Rprofile</code> (containing you personal initialization <small>R</small> commands) in a particular directory and use
532 
the Preferences to change the startup directory. Next time you launch <code>R.app</code> the <code>.Rprofile</code> is read and executed
533 
by <small>R</small> at startup. This is the equivalent on Unix (or the command line) to launch <small>R</small> from different directories.
534 
 
535 
<div class="node">
536 
<p><hr>
537 
Node:&nbsp;<a name="Resizing%20the%20R%20Console">Resizing the R Console</a>,
538 
Next:&nbsp;<a rel="next" accesskey="n" href="#Input%20and%20Output%20text%20colors">Input and Output text colors</a>,
539 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#The%20current%20and%20startup%20working%20directories">The current and startup working directories</a>,
540 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20R%20Console">The R Console</a>
541 
<br>
542 
</div>
543 
 
544 
<h3 class="subsection">Resizing the R Console</h4>
545 
 
546 
<p>When the R Console Window is resized, the R option <em>width</em> is set appropriately so that any future
547 
output will fit the window size. This behavior can be inhibited using the Preferences settings (see <a href="#Preferences">Preferences</a>).
548 
On closing the R application, the position and the size of the R Console window are saved in the Preferences and reused
549 
next time you launch R. You can inhibit R to do this using the appropriate Preferences settings.
550 
 
551 
<div class="node">
552 
<p><hr>
553 
Node:&nbsp;<a name="Input%20and%20Output%20text%20colors">Input and Output text colors</a>,
554 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Resizing%20the%20R%20Console">Resizing the R Console</a>,
555 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20R%20Console">The R Console</a>
556 
<br>
557 
</div>
558 
 
559 
<h3 class="subsection">Input and Output text colors</h4>
560 
 
561 
<p>Text windows and frames are divided in Read-Only and Read and Write ones. Text colors can be set separately
562 
for the two kinds of windows. This happens as well for their respective backgrounds. Use the Preferences window to set these
563 
colors (see <a href="#Preferences">Preferences</a>).
564 
 
565 
<div class="node">
566 
<p><hr>
567 
Node:&nbsp;<a name="The%20Menus">The Menus</a>,
568 
Next:&nbsp;<a rel="next" accesskey="n" href="#Preferences">Preferences</a>,
569 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#The%20R%20Console">The R Console</a>,
570 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
571 
<br>
572 
</div>
573 
 
574 
<h3 class="section">The Menus</h3>
575 
 
576 
<ul class="menu">
577 
<li><a accesskey="1" href="#Application%20Menu">Application Menu</a>:
578 
<li><a accesskey="2" href="#File%20Menu">File Menu</a>:
579 
<li><a accesskey="3" href="#Edit%20Menu">Edit Menu</a>:
580 
<li><a accesskey="4" href="#Tools%20Menu">Tools Menu</a>:
581 
<li><a accesskey="5" href="#Workspace%20Menu">Workspace Menu</a>:
582 
<li><a accesskey="6" href="#Packages%20Menu">Packages Menu</a>:
583 
<li><a accesskey="7" href="#The%20Help%20Menu">The Help Menu</a>:
584 
</ul>
585 
 
586 
<div class="node">
587 
<p><hr>
588 
Node:&nbsp;<a name="Application%20Menu">Application Menu</a>,
589 
Next:&nbsp;<a rel="next" accesskey="n" href="#File%20Menu">File Menu</a>,
590 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
591 
<br>
592 
</div>
593 
 
594 
<h3 class="subsection">Application Menu</h4>
595 
 
596 
<p>The Application menu is the first one after the main Apple Menu. In Mac OS X 10.3 it reports the name R.bin under Mac OS X 10.2 it is just R (as it should be).
597 
We are not able to fix this behavior at the moment.
598 
 
599 
   <p>With this menu you can access three items: 1. the About box, which tells you which version of R is currently in use, 2. Check for updates, which search on <small>CRAN</small> if a new version
600 
of the binary distribution of <small>R</small> for Mac OS X is available (you need an internet connection), 3. you can access the Preferences (see <a href="#Preferences">Preferences</a>).
601 
 
602 
<div class="node">
603 
<p><hr>
604 
Node:&nbsp;<a name="File%20Menu">File Menu</a>,
605 
Next:&nbsp;<a rel="next" accesskey="n" href="#Edit%20Menu">Edit Menu</a>,
606 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Application%20Menu">Application Menu</a>,
607 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
608 
<br>
609 
</div>
610 
 
611 
<h3 class="subsection">File Menu</h4>
612 
 
613 
<p>This menu provides standard functionalities.
614 
The <em>open</em> command is associated to the action  <em>Source </em><small>R</small><em> code</em>, which means that you can select a file, which is a script, and it will be executed
615 
in <small>R</small>. This is a interface to the <small>R</small> source command <code>source</code>.
616 
 
617 
<div class="node">
618 
<p><hr>
619 
Node:&nbsp;<a name="Edit%20Menu">Edit Menu</a>,
620 
Next:&nbsp;<a rel="next" accesskey="n" href="#Tools%20Menu">Tools Menu</a>,
621 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#File%20Menu">File Menu</a>,
622 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
623 
<br>
624 
</div>
625 
 
626 
<h3 class="subsection">Tools Menu</h4>
627 
 
628 
<p>Apart for standard functionalities, the only relevant item in this menu is the <em>Edito Object</em> which is an interface to
629 
the  <small>R</small> <code>edit</code> function.
630 
 
631 
<div class="node">
632 
<p><hr>
633 
Node:&nbsp;<a name="Tools%20Menu">Tools Menu</a>,
634 
Next:&nbsp;<a rel="next" accesskey="n" href="#Workspace%20Menu">Workspace Menu</a>,
635 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Edit%20Menu">Edit Menu</a>,
636 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
637 
<br>
638 
</div>
639 
 
640 
<h3 class="subsection">Tools Menu</h4>
641 
 
642 
<p>With this menu you can load and save the history of commands typed in the <small>R</small> Console or view what's currently inside.
643 
You can also change the current working directory, let <small>R</small> show you the current working directory or set it back to the
644 
startup directory. From release 1.9.0 of <small>R</small> the current working directory is also shown on the main window bar.
645 
 
646 
<div class="node">
647 
<p><hr>
648 
Node:&nbsp;<a name="Workspace%20Menu">Workspace Menu</a>,
649 
Next:&nbsp;<a rel="next" accesskey="n" href="#Packages%20Menu">Packages Menu</a>,
650 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Tools%20Menu">Tools Menu</a>,
651 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
652 
<br>
653 
</div>
654 
 
655 
<h3 class="subsection">Workspace Menu</h4>
656 
 
657 
<p>Here you find self explanatory menu items for manage your workspace in <small>R</small>. You can either load and save the workspace also
658 
by specifying file name. All of these are interfaces to the <code>load</code> and <code>save</code> <small>R</small> commands.
659 
The only relevant item, which is specific to this GUI, is the <em>Browse workspace</em>. This will open a window with a summary
660 
description of the objects in your workspace. Complex objects (like lists, data.frame etc) can be expanded (one level only though).
661 
 
662 
<div class="node">
663 
<p><hr>
664 
Node:&nbsp;<a name="Packages%20Menu">Packages Menu</a>,
665 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20Help%20Menu">The Help Menu</a>,
666 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Workspace%20Menu">Workspace Menu</a>,
667 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
668 
<br>
669 
</div>
670 
 
671 
<h3 class="subsection">Packages Menu</h4>
672 
 
673 
<p>Using this menu you can have access to the list of packages and data-sets installed on your system and to the ones
674 
on <small>CRAN</small> or on the Bioconductor site.
675 
 
676 
   <p>With the first two menus you can load and detach packages and data-set from the workspace.
677 
Let's start with the <em>Package Manager</em>. This opens a window with several columns displayed.
678 
For each package on your system you can see a check box, the current status of the package (loaded/not loaded), its name
679 
and the package description text. You use the check box to select/de-select the packages you want.
680 
On window closure, the checked packaged will be loaded and the unchecked ones (if loaded) will the detached (not completely as on Mac OS X you cannot
681 
unload completely dynamic libraries).
682 
 
683 
   <p>The same applies to the <em>Dataset Manager</em> menu but for data-sets.
684 
 
685 
   <p>You can than get or update packages <small>CRAN</small> either in binary or source format. Daily build of <small>CRAN</small> packages are available
686 
for Mac OS X. If you don't know how to build <small>R</small> itself from source (see <a href="#Building%20R%20from%20sources">Building R from sources</a>),
687 
you'll probably be unable to build packages from source on your own.
688 
In this case, you should always choose for the binary option. These binary packages work (for sure!) for the release version of <small>R</small> for Mac OS X
689 
you find on <small>CRAN</small> even though it is not excluded that they will work for other prebuilt versions of <small>R</small>.
690 
 
691 
   <p>When you attempt to install packages from <small>CRAN</small>, <small>R</small> first tries to get a connection to the Internet to download
692 
the list of available packages. Than a window will open similar to the one in the package manager with the only difference that
693 
for each package there is also the information concerning the version of the package installed on your system (if any) and
694 
the version of the prebuilt package available on <small>CRAN</small>. When you close the window, the select packages will be downloaded.
695 
 
696 
   <p>The same strategy applies to the Bioconductor menu item, with some more options typical of the Bioconductor way
697 
of managing packages.
698 
 
699 
   <p>For some reason it could happen that you have the package you want to install (either in binary or source form) on one of your
700 
local disks, or even a directory containing a package source. You can use the last menu to do the task of installing the package.
701 
Having a package in a directory form usually applies to people that are developing packages themselves.
702 
 
703 
   <p>For more information on this topic see also <a href="#How%20to%20install%20packages">How to install packages</a>.
704 
 
705 
<div class="node">
706 
<p><hr>
707 
Node:&nbsp;<a name="The%20Help%20Menu">The Help Menu</a>,
708 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Packages%20Menu">Packages Menu</a>,
709 
Up:&nbsp;<a rel="up" accesskey="u" href="#The%20Menus">The Menus</a>
710 
<br>
711 
</div>
712 
 
713 
<h3 class="subsection">The Help Menu</h4>
714 
 
715 
<p>Using this menu you can open the on-line manuals (<em>R Help</em>), read this FAQ and  review the latest changes, bug fixes and new features of R for Mac OS X (<em>What's new in this version</em>).
716 
There are also interfaces to the R <em>help</em> and <em>help.search</em> functions as well as the <em>example</em> function.
717 
 
718 
<div class="node">
719 
<p><hr>
720 
Node:&nbsp;<a name="Preferences">Preferences</a>,
721 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20near%20future%20of%20the%20Aqua%20GUI">The near future of the Aqua GUI</a>,
722 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#The%20Menus">The Menus</a>,
723 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
724 
<br>
725 
</div>
726 
 
727 
<h3 class="section">Preferences</h3>
728 
 
729 
<p>You can set several aspects of the <small>R</small> GUI via preferences. You can access the Preferences window via the Application menu when the
730 
<small>R</small> Console is open.
731 
Preferences are organized in Tabs, more or less grouped for content.
732 
 
733 
<ul class="menu">
734 
<li><a accesskey="1" href="#Text%20Windows%20tab">Text Windows tab</a>:
735 
<li><a accesskey="2" href="#Quartz%20device%20tab">Quartz device tab</a>:
736 
<li><a accesskey="3" href="#Packages%20tab">Packages tab</a>:
737 
<li><a accesskey="4" href="#Misc%20tab">Misc tab</a>:
738 
</ul>
739 
 
740 
<div class="node">
741 
<p><hr>
742 
Node:&nbsp;<a name="Text%20Windows%20tab">Text Windows tab</a>,
743 
Next:&nbsp;<a rel="next" accesskey="n" href="#Quartz%20device%20tab">Quartz device tab</a>,
744 
Up:&nbsp;<a rel="up" accesskey="u" href="#Preferences">Preferences</a>
745 
<br>
746 
</div>
747 
 
748 
<h3 class="subsection">Text Windows tab</h4>
749 
 
750 
<p>You can change the font size, face and the tab size in all the windows including the Console.
751 
If you have help windows opened, the changed only apply to the Console window and to the window
752 
you'll open from now on. This is a misfeature more than a bug.
753 
 
754 
   <p>You can also change the foreground and background colors for the read-only windows (i.e. the <small>R</small> Console
755 
output and the Help windows) and for read-and-write windows (i.e. the <small>R</small> Console input and the Edit windows).
756 
At the moment you cannot change the color of the cursor which always stays black which ever  background you choose.
757 
So, for the time being, it's a bad idea to set the background of the <small>R</small> Console to black.
758 
 
759 
   <p>You have also the possibility to check two options. The first is for adapting the <small>R</small> output when you resize the
760 
<small>R</small> Console to the maximum character displayable, the second one is to let <small>R</small> remember the position of the
761 
<small>R</small> Console on exit.
762 
 
763 
<div class="node">
764 
<p><hr>
765 
Node:&nbsp;<a name="Quartz%20device%20tab">Quartz device tab</a>,
766 
Next:&nbsp;<a rel="next" accesskey="n" href="#Packages%20tab">Packages tab</a>,
767 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Text%20Windows%20tab">Text Windows tab</a>,
768 
Up:&nbsp;<a rel="up" accesskey="u" href="#Preferences">Preferences</a>
769 
<br>
770 
</div>
771 
 
772 
<h3 class="subsection">Quartz device tab</h4>
773 
 
774 
<p>You can set all the parameters of the <code>quartz</code> device for this tab. Please note: your changes only take effect
775 
if you select the final checkbox, namely <em>override the R quartz default settings</em>.
776 
 
777 
   <p>This also apply to the <em>Quartz window position</em> option even if it is not a <code>quartz</code> parameter itself.
778 
 
779 
<div class="node">
780 
<p><hr>
781 
Node:&nbsp;<a name="Packages%20tab">Packages tab</a>,
782 
Next:&nbsp;<a rel="next" accesskey="n" href="#Misc%20tab">Misc tab</a>,
783 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Quartz%20device%20tab">Quartz device tab</a>,
784 
Up:&nbsp;<a rel="up" accesskey="u" href="#Preferences">Preferences</a>
785 
<br>
786 
</div>
787 
 
788 
<h3 class="subsection">Packages tab</h4>
789 
 
790 
<p>From this tab you can set the default repositories for the <small>CRAN</small> and Bioconductor urls. This will affect the
791 
corresponding <small>R</small> <code>options</code>.
792 
 
793 
<div class="node">
794 
<p><hr>
795 
Node:&nbsp;<a name="Misc%20tab">Misc tab</a>,
796 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Packages%20tab">Packages tab</a>,
797 
Up:&nbsp;<a rel="up" accesskey="u" href="#Preferences">Preferences</a>
798 
<br>
799 
</div>
800 
 
801 
<h3 class="subsection">Misc tab</h4>
802 
 
803 
<p>For this tab you can decide to redirect the stderr and stdout of <small>R</small> and the tasks launched by <small>R</small>, to the <small>R</small> Console.
804 
This is useful, for example, during package installation. If you don't check these options, every output will be sent to the <em>Console</em>
805 
application which you can find on every Mac OS X installation inside the directory <code>/Applications/Utilities</code>.
806 
 
807 
   <p>You can also set the startup working directory. This is very useful for having different sessions in different
808 
directories (see <a href="#The%20current%20and%20startup%20working%20directories">The current and startup working directories</a> and <a href="#How%20can%20I%20have%20a%20per%20session%20.Rprofile%3f">How can I have a per session .Rprofile?</a>).
809 
 
810 
<div class="node">
811 
<p><hr>
812 
Node:&nbsp;<a name="The%20near%20future%20of%20the%20Aqua%20GUI">The near future of the Aqua GUI</a>,
813 
Next:&nbsp;<a rel="next" accesskey="n" href="#Aqua%20GUI%20Bugs">Aqua GUI Bugs</a>,
814 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Preferences">Preferences</a>,
815 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
816 
<br>
817 
</div>
818 
 
819 
<h3 class="section">The near future of the Aqua GUI</h3>
820 
 
821 
<p>Jointly with Simon Urbanek we are currently working to replace the current Aqua GUI, which is Carbon-based,
822 
with a pure Cocoa GUI. This will allow for a better integration of R with Mac OS X and
823 
a fully Aqua-compliant GUI.
824 
A preview of the Cocoa GUI for Darwin R can be obtained after the official
825 
release of R 1.9.0 is out from <a href="http://www.economia.unimi.it/R">http://www.economia.unimi.it/R</a>.
826 
 
827 
<div class="node">
828 
<p><hr>
829 
Node:&nbsp;<a name="Aqua%20GUI%20Bugs">Aqua GUI Bugs</a>,
830 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#The%20near%20future%20of%20the%20Aqua%20GUI">The near future of the Aqua GUI</a>,
831 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>
832 
<br>
833 
</div>
834 
 
835 
<h3 class="section">Aqua GUI Bugs</h3>
836 
 
837 
<p>On Unix systems a bug report can be generated using the function
838 
<code>bug.report()</code>.  This automatically includes the version
839 
information and sends the bug to the correct address.  Alternatively the
840 
bug report can be emailed to <a href="mailto:R-bugs@R-project.org">R-bugs@R-project.org</a> or submitted
841 
to the Web page at <a href="http://bugs.R-project.org/">http://bugs.R-project.org/</a>.
842 
 
843 
   <p>You can also send specific Aqua GUI bugs directly to <a href="mailto:stefano.iacus@unimi.it">stefano.iacus@unimi.it</a>
844 
 
845 
   <p>In any circumstances, in case of a crash, please report the
846 
crash.log for the <em>R.bin</em> application. You can get this
847 
crash.log using the <em>Console.app</em> located inside <em>/Applications/Utilities</em>.
848 
 
849 
<div class="node">
850 
<p><hr>
851 
Node:&nbsp;<a name="How%20to%20install%20packages">How to install packages</a>,
852 
Next:&nbsp;<a rel="next" accesskey="n" href="#R%20and%20external%20applications">R and external applications</a>,
853 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#R%20with%20Aqua%20GUI">R with Aqua GUI</a>,
854 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
855 
<br>
856 
</div>
857 
 
858 
<h2 class="chapter">How to install packages</h2>
859 
 
860 
<p>You have several options for installing new packages on your system. We discuss here only the interface to the standard
861 
<small>R</small> functions like <code>install.package</code>. For the <small>R</small> functions see the standard <small>R</small> documentation.
862 
 
863 
<ul class="menu">
864 
<li><a accesskey="1" href="#Which%20kind%20of%20packages%20can%20I%20install%20using%20the%20GUI%3f">Which kind of packages can I install using the GUI?</a>:
865 
<li><a accesskey="2" href="#Installation%20of%20packages%20from%20source">Installation of packages from source</a>:
866 
<li><a accesskey="3" href="#Installation%20of%20pre-built%20binary%20packages">Installation of pre-built binary packages</a>:
867 
<li><a accesskey="4" href="#Can%20I%20install%20packages%20built%20for%20other%20platforms%3f">Can I install packages built for other platforms?</a>:
868 
<li><a accesskey="5" href="#Where%20are%20the%20packages%20I've%20installed%3f">Where are the packages I've installed?</a>:
869 
</ul>
870 
 
871 
<div class="node">
872 
<p><hr>
873 
Node:&nbsp;<a name="Which%20kind%20of%20packages%20can%20I%20install%20using%20the%20GUI%3f">Which kind of packages can I install using the GUI?</a>,
874 
Next:&nbsp;<a rel="next" accesskey="n" href="#Installation%20of%20packages%20from%20source">Installation of packages from source</a>,
875 
Up:&nbsp;<a rel="up" accesskey="u" href="#How%20to%20install%20packages">How to install packages</a>
876 
<br>
877 
</div>
878 
 
879 
<h3 class="section">Which kind of packages can I install using the GUI?</h3>
880 
 
881 
<p>At the moment the GUI menus only provide direct access/download/installation of packages located on <small>CRAN</small> or in the
882 
Bioconductor repository. You can also install packages from local files, either binary of source packages, as explained
883 
below. Otherwise you can use the appropriate <small>R</small> commands to install packages from a specific location other than the above mentioned ones.
884 
 
885 
<div class="node">
886 
<p><hr>
887 
Node:&nbsp;<a name="Installation%20of%20packages%20from%20source">Installation of packages from source</a>,
888 
Next:&nbsp;<a rel="next" accesskey="n" href="#Installation%20of%20pre-built%20binary%20packages">Installation of pre-built binary packages</a>,
889 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Which%20kind%20of%20packages%20can%20I%20install%20using%20the%20GUI%3f">Which kind of packages can I install using the GUI?</a>,
890 
Up:&nbsp;<a rel="up" accesskey="u" href="#How%20to%20install%20packages">How to install packages</a>
891 
<br>
892 
</div>
893 
 
894 
<h3 class="section">Installation of packages from source</h3>
895 
 
896 
<p>You can choose to install packages from source if they are located on <small>CRAN</small>, on the BioConductor repository and
897 
on your local disk. In any case, in order to be able to build packages from source, you need to have the same working
898 
setup for building <small>R</small> itself (see <a href="#Building%20R%20from%20sources">Building R from sources</a>). In same cases you can still build packages without all
899 
the tools installed, but surely not for all the packages containing C/C++ or Fortran source code.
900 
 
901 
<p>If you decide to install packages from <small>CRAN</small> you should use the <em>Packages</em> menu of the GUI. In particular the sub-item <em>Get CRAN packages.../Source</em>.
902 
This will connect to <small>CRAN</small> through the Internet and a list of available packages will be shown.
903 
This is list tells you if a package is already installed on your system, the version of the package available on <small>CRAN</small> and the version
904 
of the same package if already installed.
905 
You can make multiple selection of packages you intend to install using the checkboxes (one per package).
906 
When you close this window, you'll be asked if you really want to download the selected packages and the process of installation
907 
begins. If you don't select any package, nothing happens.
908 
<small>R</small> will not respond on the Console until you  close this window.
909 
The same applies for packages in the BioConductor repository. You have also several other options specific to the
910 
BioConductor way of managing repositories of packages.
911 
 
912 
<p>You can also download any other package from the Internet yourself and decide to install it from source.
913 
You have to use <em>Packages/-&gt;Install form local file</em> submenus. Where you can choose a standard <code>package.tar.gz</code>
914 
tarball or the directory containing your package if you have the package in expanded form.
915 
 
916 
<div class="node">
917 
<p><hr>
918 
Node:&nbsp;<a name="Installation%20of%20pre-built%20binary%20packages">Installation of pre-built binary packages</a>,
919 
Next:&nbsp;<a rel="next" accesskey="n" href="#Can%20I%20install%20packages%20built%20for%20other%20platforms%3f">Can I install packages built for other platforms?</a>,
920 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Installation%20of%20packages%20from%20source">Installation of packages from source</a>,
921 
Up:&nbsp;<a rel="up" accesskey="u" href="#How%20to%20install%20packages">How to install packages</a>
922 
<br>
923 
</div>
924 
 
925 
<h3 class="section">Installation of pre-built binary packages</h3>
926 
 
927 
<p>Same considerations of above apply with two minor differences. The first one is that se only distribute pre-built
928 
version of packages which pass all the test/checks on Mac OS X. So you'll see that some of the packages are missing with respect to the huge list
929 
of source packages available on <small>CRAN</small>.
930 
 
931 
<p>The second difference is that, when you install packages from local file, it is assumed that the binary package is named
932 
as <code>package.tgz</code>. This is to distinguish among source and binary archives.
933 
 
934 
<div class="node">
935 
<p><hr>
936 
Node:&nbsp;<a name="Can%20I%20install%20packages%20built%20for%20other%20platforms%3f">Can I install packages built for other platforms?</a>,
937 
Next:&nbsp;<a rel="next" accesskey="n" href="#Where%20are%20the%20packages%20I've%20installed%3f">Where are the packages I've installed?</a>,
938 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Installation%20of%20pre-built%20binary%20packages">Installation of pre-built binary packages</a>,
939 
Up:&nbsp;<a rel="up" accesskey="u" href="#How%20to%20install%20packages">How to install packages</a>
940 
<br>
941 
</div>
942 
 
943 
<h3 class="section">Can I install packages built for other platforms?</h3>
944 
 
945 
<p>As a general rule the answer is <em>yes</em> if the package does not contain any C/C++/Fortran code in the sources, otherwise
946 
the answer is negative. Another caution should be taken, that is, the package and the installed version of <small>R</small> should be
947 
the same major release, i.e. you can install a package built for <small>R</small> 1.8.0 on <small>R</small> 1.8.1, but usually not the same
948 
package on <small>R</small> 1.9.0.
949 
 
950 
<p>A Mac OS X specific requirements, is that a prebuilt package is assumed to be named (and accordingly archived and
951 
compressed) as <code>package_name.tgz</code>.
952 
On Windows, for example, packages come in a zipped format.
953 
 
954 
<div class="node">
955 
<p><hr>
956 
Node:&nbsp;<a name="Where%20are%20the%20packages%20I've%20installed%3f">Where are the packages I've installed?</a>,
957 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Can%20I%20install%20packages%20built%20for%20other%20platforms%3f">Can I install packages built for other platforms?</a>,
958 
Up:&nbsp;<a rel="up" accesskey="u" href="#How%20to%20install%20packages">How to install packages</a>
959 
<br>
960 
</div>
961 
 
962 
<h3 class="section">Where are the packages I've installed?</h3>
963 
 
964 
<p>The main library of packages is the one located inside the R.framework. This library contains the packages (base and
965 
recommended ones) distributed along with <small>R</small>. At the moment you cannot use the GUI Console to install packages
966 
in this location because of authentication problems, you can surely do this from the command line with an admin
967 
password, with something like
968 
<pre class="example">     sudo R CMD INSTALL pkg_ver.tar.gz
969 
     </pre>
970 
 
971 
<p>By default, the user of <code>R.app</code> installs packages inside the <code>Library/R/library</code> directory
972 
in his home directory, i.e. <code>~/Library/R/library</code>.
973 
If you install a package using the <code>R.app</code> interfaces and you then use <small>R</small> from the command line,
974 
you won't see or have access to these packages unless you add the <code>~/Library/R/library</code> to the
975 
list of libraries locations. You can do the following from inside <small>R</small>
976 
<pre class="example">     .libPaths("~/Library/R/library")
977 
     </pre>
978 
   or write this command in the <code>.Rprofile</code> file in your startup directory.
979 
On some version of OS X the <code>~</code> symbol is not correctly expanded. You should preferably use this
980 
version of the above command
981 
<pre class="example">     .libPaths(path.expand("~/Library/R/library"))
982 
     </pre>
983 
 
984 
<p>If you have a version of <code>RAqua.app</code> installed on your system, it is likely that you have all the
985 
packages installed in <code>~/Library/RAqua/library</code>. You can add this library of packages in the <code>.libPaths()</code>
986 
but most of them will probably not work as they were built for release 1.8.x of <small>R</small>.
987 
 
988 
<div class="node">
989 
<p><hr>
990 
Node:&nbsp;<a name="R%20and%20external%20applications">R and external applications</a>,
991 
Next:&nbsp;<a rel="next" accesskey="n" href="#Quartz%20device">Quartz device</a>,
992 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20to%20install%20packages">How to install packages</a>,
993 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
994 
<br>
995 
</div>
996 
 
997 
<h2 class="chapter">R and external applications</h2>
998 
 
999 
<ul class="menu">
1000 
<li><a accesskey="1" href="#AppleScript%20support">AppleScript support</a>:
1001 
<li><a accesskey="2" href="#External%20editors">External editors</a>:
1002 
<li><a accesskey="3" href="#Finder%20actions">Finder actions</a>:
1003 
</ul>
1004 
 
1005 
<div class="node">
1006 
<p><hr>
1007 
Node:&nbsp;<a name="AppleScript%20support">AppleScript support</a>,
1008 
Next:&nbsp;<a rel="next" accesskey="n" href="#External%20editors">External editors</a>,
1009 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20and%20external%20applications">R and external applications</a>
1010 
<br>
1011 
</div>
1012 
 
1013 
<h3 class="section">AppleScript support</h3>
1014 
 
1015 
<p><small>R</small> has partial support for Apple-Scripts.
1016 
At the moment R can be invoked and asked to run commands from an AppleScript script.
1017 
What follows is an example of script that interacts with <small>R</small>. It firstly  invokes <small>R</small> and then
1018 
sends commands to <small>R</small> with the <code>cmd</code> applescript command.
1019 
 
1020 
<pre class="example">     set CommandLine to "R.Version()"
1021 
     try
1022 
     	tell application "R"
1023 
     		activate
1024 
     		with timeout of 90000 seconds
1025 
     			cmd CommandLine
1026 
     			cmd "Sys.getenv()"
1027 
     			cmd "print(\"HelloWorld!\")"
1028 
     		end timeout
1029 
     	end tell
1030 
     end try
1031 
     </pre>
1032 
 
1033 
<p>In the above, <code>cmd</code> is the (only) applescript command in the <small>R</small> dictionary that is
1034 
used to tell <small>R</small> to execute an <small>R</small> command in the R Console. The syntax is
1035 
<pre class="example">     cmd &lt;command string&gt;
1036 
     </pre>
1037 
   where command string have to be in quotes. Actually, the output of the command
1038 
is not sent back to the application that is calling <small>R</small> but to the <small>R</small> Console directly.
1039 
 
1040 
<p>There are some issues. The first is that if <small>R</small> is still not running, it will take a while (depending on
1041 
how fast your machine is) to startup. In the meanwhile the script sends commands without waiting and it
1042 
could happen that some commands are missed by <small>R</small>, i.e. they arrive before <small>R</small> is ready to
1043 
receive applescript commands. The second issue, is that it could be that the applescript calls a bad version
1044 
of <small>R</small>. This could happen if you have an old version of <small>R</small> (for example the old Carbon <small>R</small>) installed on your
1045 
System.
1046 
 
1047 
<p>As an example, we report here a small script that asks <small>R</small> to <code>source</code> a file using a file dialog.
1048 
<pre class="smallexample">     set file_to_source to (choose file with prompt "Choose file to source") as alias
1049 
 
1050 
     try
1051 
     	tell application "R"
1052 
     		activate
1053 
     		with timeout of 90000 seconds
1054 
     			cmd "source(\"" &amp; file_to_source &amp; "\")"
1055 
     		end timeout
1056 
     	end tell
1057 
     end try
1058 
     </pre>
1059 
 
1060 
<div class="node">
1061 
<p><hr>
1062 
Node:&nbsp;<a name="External%20editors">External editors</a>,
1063 
Next:&nbsp;<a rel="next" accesskey="n" href="#Finder%20actions">Finder actions</a>,
1064 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#AppleScript%20support">AppleScript support</a>,
1065 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20and%20external%20applications">R and external applications</a>
1066 
<br>
1067 
</div>
1068 
 
1069 
<h3 class="section">External editors</h3>
1070 
 
1071 
<p><small>R</small> accepts the Apple Event command <em>open</em>. This means than an external editor can communicate with <small>R</small> sending
1072 
portions of <small>R</small> code to execute via files. This is the approach used by the <small>R</small>-Tcl Mode in Alpha X
1073 
(see <a href="http://www.kelehers.org/alpha/">http://www.kelehers.org/alpha/</a>).
1074 
 
1075 
<div class="node">
1076 
<p><hr>
1077 
Node:&nbsp;<a name="Finder%20actions">Finder actions</a>,
1078 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#External%20editors">External editors</a>,
1079 
Up:&nbsp;<a rel="up" accesskey="u" href="#R%20and%20external%20applications">R and external applications</a>
1080 
<br>
1081 
</div>
1082 
 
1083 
<h3 class="section">Finder actions</h3>
1084 
 
1085 
<p>Dragging a file on the <small>R</small> icon, causes <small>R</small> to source this file via the <code>source</code> <small>R</small> command or,
1086 
if the file is an <small>R</small> image data file RDX1 or RDX2 (normally files with extension <code>.rda</code> or <code>.Rdata</code>), the data is loaded in the workspace and every object
1087 
with the same name in the workspace is overwritten without notice. Loading a data file is equivalent to
1088 
the <small>R</small> command <code>load</code>.
1089 
At the moment there is no control over the file types, i.e. dragging wrong files (i.e. files that are
1090 
not <small>R</small> scripts or image data) simply gives an error. It's up to the user to <em>do the right thing</em>.
1091 
 
1092 
<p>If <small>R</small> is not yet running this action causes <small>R</small> to startup.
1093 
 
1094 
<div class="node">
1095 
<p><hr>
1096 
Node:&nbsp;<a name="Quartz%20device">Quartz device</a>,
1097 
Next:&nbsp;<a rel="next" accesskey="n" href="#TclTk%20issues">TclTk issues</a>,
1098 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#R%20and%20external%20applications">R and external applications</a>,
1099 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
1100 
<br>
1101 
</div>
1102 
 
1103 
<h2 class="chapter">Quartz device</h2>
1104 
 
1105 
<p>The quartz device is the native graphic device in R for Mac OS X. It's name derives from Apple's Quartz Technology
1106 
which is essentially similar to PDF rendering. One of the most amazing features of Quartz is antialiasing which gives you
1107 
<em>very nice</em> plots and images. Try to compare  a quartz plot  with the same plot generated on
1108 
any other interactive device. For its PDF nature it is also resolution independent.
1109 
 
1110 
<ul class="menu">
1111 
<li><a accesskey="1" href="#Interactive%20mode">Interactive mode</a>:
1112 
<li><a accesskey="2" href="#Saving%20the%20image">Saving the image</a>:
1113 
<li><a accesskey="3" href="#Copying%20the%20image%20into%20the%20clipboard">Copying the image into the clipboard</a>:
1114 
<li><a accesskey="4" href="#Known%20bugs%20and%20missing%20features">Known bugs and missing features</a>:
1115 
</ul>
1116 
 
1117 
<div class="node">
1118 
<p><hr>
1119 
Node:&nbsp;<a name="Interactive%20mode">Interactive mode</a>,
1120 
Next:&nbsp;<a rel="next" accesskey="n" href="#Saving%20the%20image">Saving the image</a>,
1121 
Up:&nbsp;<a rel="up" accesskey="u" href="#Quartz%20device">Quartz device</a>
1122 
<br>
1123 
</div>
1124 
 
1125 
<h3 class="section">Interactive mode</h3>
1126 
 
1127 
<p>The quartz device allows for interaction. You can use both <code>identify</code> and <code>locator</code> functions.
1128 
To break the sequence you should press the ESC key on your keyboard as Apple's mouse have ever had only one
1129 
button.
1130 
 
1131 
<div class="node">
1132 
<p><hr>
1133 
Node:&nbsp;<a name="Saving%20the%20image">Saving the image</a>,
1134 
Next:&nbsp;<a rel="next" accesskey="n" href="#Copying%20the%20image%20into%20the%20clipboard">Copying the image into the clipboard</a>,
1135 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Interactive%20mode">Interactive mode</a>,
1136 
Up:&nbsp;<a rel="up" accesskey="u" href="#Quartz%20device">Quartz device</a>
1137 
<br>
1138 
</div>
1139 
 
1140 
<h3 class="section">Saving the image</h3>
1141 
 
1142 
<p>You can can the content of the quartz device window into a PDF file. This is a very simple way to
1143 
export high quality graphics from <small>R</small> into other applications on Mac OS X graphics is PDF based (so are almost all
1144 
applications available). If you want bitmap copies of you quartz device window just use copy, to copy the image into the clipboard and
1145 
paste the result in a graphic application (see <a href="#Copying%20the%20image%20into%20the%20clipboard">Copying the image into the clipboard</a>).
1146 
 
1147 
<div class="node">
1148 
<p><hr>
1149 
Node:&nbsp;<a name="Copying%20the%20image%20into%20the%20clipboard">Copying the image into the clipboard</a>,
1150 
Next:&nbsp;<a rel="next" accesskey="n" href="#Known%20bugs%20and%20missing%20features">Known bugs and missing features</a>,
1151 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Saving%20the%20image">Saving the image</a>,
1152 
Up:&nbsp;<a rel="up" accesskey="u" href="#Quartz%20device">Quartz device</a>
1153 
<br>
1154 
</div>
1155 
 
1156 
<h3 class="section">Copying the image into the clipboard</h3>
1157 
 
1158 
<p>You can copy the content of the quartz device window in the clipboard to make the resulting image available for
1159 
pasting into other applications. The clipboard will contain a bitmap copy of the quartz device window. If you
1160 
want to work with high resolution images, you should save the content of the quartz device as a PDF file (see <a href="#Saving%20the%20image">Saving the image</a>).
1161 
Pay attention to the following fact: the bitmap image produced has exactly the same dimensions of the quartz device window. This
1162 
means that if you resize the window, the resulting image you obtain in the clipboard will have the same
1163 
dimensions and you cannot resize the image from the inside another applications (say MS-Word) without loosing quality.
1164 
 
1165 
<div class="node">
1166 
<p><hr>
1167 
Node:&nbsp;<a name="Known%20bugs%20and%20missing%20features">Known bugs and missing features</a>,
1168 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Copying%20the%20image%20into%20the%20clipboard">Copying the image into the clipboard</a>,
1169 
Up:&nbsp;<a rel="up" accesskey="u" href="#Quartz%20device">Quartz device</a>
1170 
<br>
1171 
</div>
1172 
 
1173 
<h3 class="section">Known bugs and missing features</h3>
1174 
 
1175 
<p>When rendering text and/or mathematical symbols the style is ignored, i.e. only plain style is drawn.
1176 
The printing function is not yet implemented.
1177 
 
1178 
<div class="node">
1179 
<p><hr>
1180 
Node:&nbsp;<a name="TclTk%20issues">TclTk issues</a>,
1181 
Next:&nbsp;<a rel="next" accesskey="n" href="#Additional%20resources">Additional resources</a>,
1182 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Quartz%20device">Quartz device</a>,
1183 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
1184 
<br>
1185 
</div>
1186 
 
1187 
<h2 class="chapter">TclTk issues</h2>
1188 
 
1189 
<p>Each binary distribution of <small>R</small> available through <small>CRAN</small> is built to use the X11 implementation of TclTk.
1190 
Of course a X windows server has to be started first. If you are not using the Aqua GUI you need to also
1191 
define the environment variable DISPLAY before attempting to use X11 from inside <small>R</small>. You can do this as follows
1192 
<pre class="example">     Sys.putenv("DISPLAY"=":0")
1193 
     </pre>
1194 
   If you don't like the X11 GUI you would probably want to build R using the Aqua version of TclTk (see <a href="#the%20Aqua%20TclTk%20headers%20and%20libraries%20(optional)">the Aqua TclTk headers and libraries (optional)</a>).
1195 
After installing the R.framework you should do the following to have the quartz device working under Aqua TclTk. Open a
1196 
Terminal window and move inside the <code>Resources/bin</code> directory of the <code>R.framework</code>
1197 
(usually <code>/Library/Frameworks/R.framework</code>), then type the following
1198 
<pre class="example">     sudo /Developer/Tools/Rez -t APPL Carbon.r -o R.bin
1199 
     </pre>
1200 
 
1201 
<div class="node">
1202 
<p><hr>
1203 
Node:&nbsp;<a name="Additional%20resources">Additional resources</a>,
1204 
Next:&nbsp;<a rel="next" accesskey="n" href="#Acknowledgments">Acknowledgments</a>,
1205 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#TclTk%20issues">TclTk issues</a>,
1206 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
1207 
<br>
1208 
</div>
1209 
 
1210 
<h2 class="chapter">Additional resources</h2>
1211 
 
1212 
<p>Here are few references that can be of interest for Mac OS X and/or developers.
1213 
 
1214 
<ul class="menu">
1215 
<li><a accesskey="1" href="#Apple%20Developer%20Connection">Apple Developer Connection</a>:
1216 
<li><a accesskey="2" href="#The%20R%20for%20Mac%20OS%20X%20Developer%20page">The R for Mac OS X Developer page</a>:
1217 
</ul>
1218 
 
1219 
<div class="node">
1220 
<p><hr>
1221 
Node:&nbsp;<a name="Apple%20Developer%20Connection">Apple Developer Connection</a>,
1222 
Next:&nbsp;<a rel="next" accesskey="n" href="#The%20R%20for%20Mac%20OS%20X%20Developer%20page">The R for Mac OS X Developer page</a>,
1223 
Up:&nbsp;<a rel="up" accesskey="u" href="#Additional%20resources">Additional resources</a>
1224 
<br>
1225 
</div>
1226 
 
1227 
<h3 class="section">Apple Developer Connection</h3>
1228 
 
1229 
<p>The Apple Developer Connection (can be reached at <a href="http://developer.apple.com">http://developer.apple.com</a>) is the main source
1230 
of information for Apple products (OS, hardware, software) for developers. You can subscribe for free to
1231 
ADC and get the latest up-to-date tools from Apple (compilers for example).
1232 
 
1233 
<div class="node">
1234 
<p><hr>
1235 
Node:&nbsp;<a name="The%20R%20for%20Mac%20OS%20X%20Developer%20page">The R for Mac OS X Developer page</a>,
1236 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Apple%20Developer%20Connection">Apple Developer Connection</a>,
1237 
Up:&nbsp;<a rel="up" accesskey="u" href="#Additional%20resources">Additional resources</a>
1238 
<br>
1239 
</div>
1240 
 
1241 
<h3 class="section">The R for Mac OS X Developer page</h3>
1242 
 
1243 
<p>There is a page dedicated to the latest R-devel version of R. This page is located at
1244 
<a href="http://www.economia.unimi.it/R">http://www.economia.unimi.it/R</a> and is maintained by Stefano M. Iacus.
1245 
This page is intended to give additional documentation for building  the latest R-devel
1246 
version of R. From time to time, snapshots of R-devel binaries are available for testing purposes.
1247 
 
1248 
<div class="node">
1249 
<p><hr>
1250 
Node:&nbsp;<a name="Acknowledgments">Acknowledgments</a>,
1251 
Next:&nbsp;<a rel="next" accesskey="n" href="#Sparse%20questions">Sparse questions</a>,
1252 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Additional%20resources">Additional resources</a>,
1253 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
1254 
<br>
1255 
</div>
1256 
 
1257 
<h2 class="chapter">Acknowledgments</h2>
1258 
 
1259 
<p>Special thanks go to Simon Urbanek, Jan de Leeuw, Byron Ellis and Thomas Lumley
1260 
in random order. Last but not least Apple for amazing OS and GUI.
1261 
 
1262 
<div class="node">
1263 
<p><hr>
1264 
Node:&nbsp;<a name="Sparse%20questions">Sparse questions</a>,
1265 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#Acknowledgments">Acknowledgments</a>,
1266 
Up:&nbsp;<a rel="up" accesskey="u" href="#Top">Top</a>
1267 
<br>
1268 
</div>
1269 
 
1270 
<h2 class="chapter">Sparse questions</h2>
1271 
 
1272 
<ul class="menu">
1273 
<li><a accesskey="1" href="#How%20can%20I%20have%20a%20per%20session%20.Rprofile%3f">How can I have a per session .Rprofile?</a>:
1274 
<li><a accesskey="2" href="#What%20happens%20if%20I%20drag%20a%20file%20on%20the%20R%20icon%3f">What happens if I drag a file on the R icon?</a>:
1275 
<li><a accesskey="3" href="#How%20can%20I%20interrupt%20lengthy%20operations%20or%20output%3f">How can I interrupt lengthy operations or output?</a>:
1276 
<li><a accesskey="4" href="#I%20don't%20see%20a%20thing%20when%20installing%20packages!">I don't see a thing when installing packages!</a>:
1277 
</ul>
1278 
 
1279 
<div class="node">
1280 
<p><hr>
1281 
Node:&nbsp;<a name="How%20can%20I%20have%20a%20per%20session%20.Rprofile%3f">How can I have a per session .Rprofile?</a>,
1282 
Next:&nbsp;<a rel="next" accesskey="n" href="#What%20happens%20if%20I%20drag%20a%20file%20on%20the%20R%20icon%3f">What happens if I drag a file on the R icon?</a>,
1283 
Up:&nbsp;<a rel="up" accesskey="u" href="#Sparse%20questions">Sparse questions</a>
1284 
<br>
1285 
</div>
1286 
 
1287 
<h3 class="section">How can I have a per session .Rprofile?</h3>
1288 
 
1289 
<p>You can by writing a <code>.Rprofile</code> file in your favorite
1290 
session directory and change accordingly the startup working directory using the Preferences (see <a href="#The%20current%20and%20startup%20working%20directories">The current and startup working directories</a>).
1291 
 
1292 
<div class="node">
1293 
<p><hr>
1294 
Node:&nbsp;<a name="What%20happens%20if%20I%20drag%20a%20file%20on%20the%20R%20icon%3f">What happens if I drag a file on the R icon?</a>,
1295 
Next:&nbsp;<a rel="next" accesskey="n" href="#How%20can%20I%20interrupt%20lengthy%20operations%20or%20output%3f">How can I interrupt lengthy operations or output?</a>,
1296 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20can%20I%20have%20a%20per%20session%20.Rprofile%3f">How can I have a per session .Rprofile?</a>,
1297 
Up:&nbsp;<a rel="up" accesskey="u" href="#Sparse%20questions">Sparse questions</a>
1298 
<br>
1299 
</div>
1300 
 
1301 
<h3 class="section">What happens if I drag a file on the R icon?</h3>
1302 
 
1303 
<p>In this case <small>R</small> will try to source this file or load the image data file (see <a href="#Finder%20actions">Finder actions</a>). If <small>R</small> is not
1304 
yet running it will be launched.
1305 
 
1306 
<div class="node">
1307 
<p><hr>
1308 
Node:&nbsp;<a name="How%20can%20I%20interrupt%20lengthy%20operations%20or%20output%3f">How can I interrupt lengthy operations or output?</a>,
1309 
Next:&nbsp;<a rel="next" accesskey="n" href="#I%20don't%20see%20a%20thing%20when%20installing%20packages!">I don't see a thing when installing packages!</a>,
1310 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#What%20happens%20if%20I%20drag%20a%20file%20on%20the%20R%20icon%3f">What happens if I drag a file on the R icon?</a>,
1311 
Up:&nbsp;<a rel="up" accesskey="u" href="#Sparse%20questions">Sparse questions</a>
1312 
<br>
1313 
</div>
1314 
 
1315 
<h3 class="section">How can I interrupt lengthy operations or output?</h3>
1316 
 
1317 
<p>You can now use the standard Macintosh control break sequence, that is you should press
1318 
"Cmd option" and "." (dot). This will interrupt any <small>R</small> loops. The "Esc" key gives you the same result.
1319 
 
1320 
<div class="node">
1321 
<p><hr>
1322 
Node:&nbsp;<a name="I%20don't%20see%20a%20thing%20when%20installing%20packages!">I don't see a thing when installing packages!</a>,
1323 
Previous:&nbsp;<a rel="previous" accesskey="p" href="#How%20can%20I%20interrupt%20lengthy%20operations%20or%20output%3f">How can I interrupt lengthy operations or output?</a>,
1324 
Up:&nbsp;<a rel="up" accesskey="u" href="#Sparse%20questions">Sparse questions</a>
1325 
<br>
1326 
</div>
1327 
 
1328 
<h3 class="section">I don't see a thing when installing packages!</h3>
1329 
 
1330 
<p>Well, this is not a question but the answer is that you are not looking at the right place.
1331 
Every input and output which is not <small>R</small> specific (i.e. the output of standard commands) is generally sent to
1332 
the standard output (stdout) or standard error (stderr) depending on its nature. In particular every call to the
1333 
<code>system</code> function, executes outside <small>R</small> in a Mac OS X shell. The package installation is done via
1334 
the <code>system</code> facility.
1335 
You have to use the Preferences to redirect the stderr and/or the stdout to the <small>R</small> Console (see <a href="#Misc%20tab">Misc tab</a>)
1336 
or you can look at the <em>Console</em> application inside <code>/Applications/Utilities</code> on your system.
1337 
This applies to every GUI application on Mac OS X so, as a general rule, if an application behaves strangely or quits,
1338 
please have a look to the <em>Console</em> application.
1339 
 
1340 
   </body></html>
1341