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<h1 class="settitle">R Installation and Administration</h1>
<div class="contents">
<h2>Table of Contents</h2>
<ul>
<li><a name="toc_Top" href="#Top">R Installation and Administration</a>
<li><a name="toc_Obtaining-R" href="#Obtaining-R">1 Obtaining R</a>
<ul>
<li><a href="#Getting-and-unpacking-the-sources">1.1 Getting and unpacking the sources</a>
<li><a href="#Getting-patched-and-development-versions">1.2 Getting patched and development versions</a>
<ul>
<li><a href="#Using-Subversion-and-rsync">1.2.1 Using Subversion and rsync</a>
</li></ul>
</li></ul>
<li><a name="toc_Installing-R-under-Unix_002dalikes" href="#Installing-R-under-Unix_002dalikes">2 Installing R under Unix-alikes</a>
<ul>
<li><a href="#Simple-compilation">2.1 Simple compilation</a>
<li><a href="#Help-options">2.2 Help options</a>
<li><a href="#Making-the-manuals">2.3 Making the manuals</a>
<li><a href="#Installation">2.4 Installation</a>
<li><a href="#Uninstallation">2.5 Uninstallation</a>
<li><a href="#Sub_002darchitectures">2.6 Sub-architectures</a>
<ul>
<li><a href="#Multilib">2.6.1 Multilib</a>
</li></ul>
<li><a href="#Other-Options">2.7 Other Options</a>
<li><a href="#Testing-a-Unix_002dalike-Installation">2.8 Testing an Installation</a>
</li></ul>
<li><a name="toc_Installing-R-under-Windows" href="#Installing-R-under-Windows">3 Installing R under Windows</a>
<ul>
<li><a href="#Building-from-source">3.1 Building from source</a>
<ul>
<li><a href="#Getting-the-tools">3.1.1 Getting the tools</a>
<li><a href="#Getting-the-source-files">3.1.2 Getting the source files</a>
<li><a href="#Building-the-core-files">3.1.3 Building the core files</a>
<li><a href="#Building-the-bitmap-files">3.1.4 Building the bitmap files</a>
<li><a href="#Building-the-cairo-devices-files">3.1.5 Building the cairo devices</a>
<li><a href="#Checking-the-build">3.1.6 Checking the build</a>
<li><a href="#Building-the-manuals">3.1.7 Building the manuals</a>
<li><a href="#Building-the-Inno-Setup-installer">3.1.8 Building the Inno Setup installer</a>
<li><a href="#Building-the-MSI-installer">3.1.9 Building the MSI installer</a>
<li><a href="#64_002dbit-Windows-builds">3.1.10 64-bit Windows builds</a>
</li></ul>
<li><a href="#Testing-a-Windows-Installation">3.2 Testing an Installation</a>
</li></ul>
<li><a name="toc_Installing-R-under-OS-X" href="#Installing-R-under-OS-X">4 Installing R under OS X</a>
<ul>
<li><a href="#Running-R-under-OS-X">4.1 Running R under OS X</a>
<li><a href="#Uninstalling-under-OS-X">4.2 Uninstalling under OS X</a>
<li><a href="#Multiple-versions">4.3 Multiple versions</a>
</li></ul>
<li><a name="toc_Running-R" href="#Running-R">5 Running R</a>
<li><a name="toc_Add_002don-packages" href="#Add_002don-packages">6 Add-on packages</a>
<ul>
<li><a href="#Default-packages">6.1 Default packages</a>
<li><a href="#Managing-libraries">6.2 Managing libraries</a>
<li><a href="#Installing-packages">6.3 Installing packages</a>
<ul>
<li><a href="#Windows-packages">6.3.1 Windows</a>
<li><a href="#OS-X-packages">6.3.2 OS X</a>
<li><a href="#Customizing-package-compilation">6.3.3 Customizing package compilation</a>
<li><a href="#Multiple-sub_002darchitectures">6.3.4 Multiple sub-architectures</a>
<li><a href="#Byte_002dcompilation">6.3.5 Byte-compilation</a>
</li></ul>
<li><a href="#Updating-packages">6.4 Updating packages</a>
<li><a href="#Removing-packages">6.5 Removing packages</a>
<li><a href="#Setting-up-a-package-repository">6.6 Setting up a package repository</a>
<li><a href="#Checking-installed-source-packages">6.7 Checking installed source packages</a>
</li></ul>
<li><a name="toc_Internationalization" href="#Internationalization">7 Internationalization and Localization</a>
<ul>
<li><a href="#Locales">7.1 Locales</a>
<ul>
<li><a href="#Locales-under-Unix_002dalikes">7.1.1 Locales under Unix-alikes</a>
<li><a href="#Locales-under-Windows">7.1.2 Locales under Windows</a>
<li><a href="#Locales-under-OS-X">7.1.3 Locales under OS X</a>
</li></ul>
<li><a href="#Localization-of-messages">7.2 Localization of messages</a>
</li></ul>
<li><a name="toc_Choosing-between-32_002d-and-64_002dbit-builds" href="#Choosing-between-32_002d-and-64_002dbit-builds">8 Choosing between 32- and 64-bit builds</a>
<li><a name="toc_The-standalone-Rmath-library" href="#The-standalone-Rmath-library">9 The standalone Rmath library</a>
<ul>
<li><a href="#Unix_002dalike-standalone">9.1 Unix-alikes</a>
<li><a href="#Windows-standalone">9.2 Windows</a>
</li></ul>
<li><a name="toc_Essential-and-useful-other-programs-under-a-Unix_002dalike" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Appendix A Essential and useful other programs under a Unix-alike</a>
<ul>
<li><a href="#Essential-programs-and-libraries">A.1 Essential programs and libraries</a>
<li><a href="#Useful-libraries-and-programs">A.2 Useful libraries and programs</a>
<ul>
<li><a href="#Tcl_002fTk">A.2.1 Tcl/Tk</a>
<li><a href="#Java-support">A.2.2 Java support</a>
</li></ul>
<li><a href="#Linear-algebra">A.3 Linear algebra</a>
<ul>
<li><a href="#BLAS">A.3.1 BLAS</a>
<ul>
<li><a href="#ATLAS">A.3.1.1 ATLAS</a>
<li><a href="#ACML">A.3.1.2 ACML</a>
<li><a href="#Goto-and-OpenBLAS">A.3.1.3 Goto and OpenBLAS</a>
<li><a href="#MKL">A.3.1.4 Intel MKL</a>
<li><a href="#Shared-BLAS">A.3.1.5 Shared BLAS</a>
</li></ul>
<li><a href="#LAPACK">A.3.2 LAPACK</a>
<li><a href="#Caveats">A.3.3 Caveats</a>
</li></ul>
</li></ul>
<li><a name="toc_Configuration-on-a-Unix_002dalike" href="#Configuration-on-a-Unix_002dalike">Appendix B Configuration on a Unix-alike</a>
<ul>
<li><a href="#Configuration-options">B.1 Configuration options</a>
<li><a href="#Internationalization-support">B.2 Internationalization support</a>
<li><a href="#Configuration-variables">B.3 Configuration variables</a>
<ul>
<li><a href="#Setting-paper-size">B.3.1 Setting paper size</a>
<li><a href="#Setting-the-browsers">B.3.2 Setting the browsers</a>
<li><a href="#Compilation-flags">B.3.3 Compilation flags</a>
<li><a href="#Making-manuals">B.3.4 Making manuals</a>
</li></ul>
<li><a href="#Setting-the-shell">B.4 Setting the shell</a>
<li><a href="#Using-make">B.5 Using make</a>
<li><a href="#Using-FORTRAN">B.6 Using FORTRAN</a>
<ul>
<li><a href="#Using-gfortran">B.6.1 Using gfortran</a>
</li></ul>
<li><a href="#Compile-and-load-flags">B.7 Compile and load flags</a>
</li></ul>
<li><a name="toc_Platform-notes" href="#Platform-notes">Appendix C Platform notes</a>
<ul>
<li><a href="#X11-issues">C.1 X11 issues</a>
<li><a href="#Linux">C.2 Linux</a>
<ul>
<li><a href="#Clang">C.2.1 Clang</a>
<li><a href="#Intel-compilers">C.2.2 Intel compilers</a>
<li><a href="#Oracle-Solaris-Studio-compilers">C.2.3 Oracle Solaris Studio compilers</a>
</li></ul>
<li><a href="#OS-X">C.3 OS X</a>
<ul>
<li><a href="#Snow-Leopard">C.3.1 Snow Leopard</a>
<li><a href="#Lion">C.3.2 Lion</a>
<li><a href="#Mountain-Lion">C.3.3 Mountain Lion</a>
<li><a href="#Mavericks">C.3.4 Mavericks</a>
<li><a href="#Tcl_002fTk-headers-and-libraries">C.3.5 Tcl/Tk headers and libraries</a>
<li><a href="#Java-_0028OS-X_0029">C.3.6 Java</a>
<li><a href="#Frameworks">C.3.7 Frameworks</a>
<li><a href="#Building-R_002eapp">C.3.8 Building R.app</a>
</li></ul>
<li><a href="#Solaris">C.4 Solaris</a>
<ul>
<li><a href="#Using-gcc">C.4.1 Using gcc</a>
</li></ul>
<li><a href="#AIX">C.5 AIX</a>
<li><a href="#FreeBSD">C.6 FreeBSD</a>
<li><a href="#Cygwin">C.7 Cygwin</a>
<li><a href="#New-platforms">C.8 New platforms</a>
</li></ul>
<li><a name="toc_The-Windows-toolset" href="#The-Windows-toolset">Appendix D The Windows toolset</a>
<ul>
<li><a href="#LaTeX">D.1 LaTeX</a>
<li><a href="#The-Inno-Setup-installer">D.2 The Inno Setup installer</a>
<li><a href="#The-command-line-tools">D.3 The command line tools</a>
<li><a href="#The-MinGW_002dw64-toolchain">D.4 The MinGW-w64 toolchain</a>
<li><a href="#Useful-additional-programs">D.5 Useful additional programs</a>
</li></ul>
<li><a name="toc_Function-and-variable-index" href="#Function-and-variable-index">Function and variable index</a>
<li><a name="toc_Concept-index" href="#Concept-index">Concept index</a>
<li><a name="toc_Environment-variable-index" href="#Environment-variable-index">Environment variable index</a>
</li></ul>
</div>
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<a name="Top"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Obtaining-R">Obtaining R</a>,
Previous: <a rel="previous" accesskey="p" href="#dir">(dir)</a>,
Up: <a rel="up" accesskey="u" href="#dir">(dir)</a>
</div>
<h2 class="unnumbered">R Installation and Administration</h2>
<p>This is a guide to installation and administration for R.
<p>This manual is for R, version 3.0.2 (2013-09-25).
<p>Copyright © 2001–2013 R Core Team
<blockquote>
Permission is granted to make and distribute verbatim copies of this
manual provided the copyright notice and this permission notice are
preserved on all copies.
<p>Permission is granted to copy and distribute modified versions of this
manual under the conditions for verbatim copying, provided that the
entire resulting derived work is distributed under the terms of a
permission notice identical to this one.
<p>Permission is granted to copy and distribute translations of this manual
into another language, under the above conditions for modified versions,
except that this permission notice may be stated in a translation
approved by the R Core Team.
</blockquote>
<ul class="menu">
<li><a accesskey="1" href="#Obtaining-R">Obtaining R</a>
<li><a accesskey="2" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
<li><a accesskey="3" href="#Installing-R-under-Windows">Installing R under Windows</a>
<li><a accesskey="4" href="#Installing-R-under-OS-X">Installing R under OS X</a>
<li><a accesskey="5" href="#Running-R">Running R</a>
<li><a accesskey="6" href="#Add_002don-packages">Add-on packages</a>
<li><a accesskey="7" href="#Internationalization">Internationalization</a>
<li><a accesskey="8" href="#Choosing-between-32_002d-and-64_002dbit-builds">Choosing between 32- and 64-bit builds</a>
<li><a accesskey="9" href="#The-standalone-Rmath-library">The standalone Rmath library</a>
<li><a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>
<li><a href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
<li><a href="#Platform-notes">Platform notes</a>
<li><a href="#The-Windows-toolset">The Windows toolset</a>
<li><a href="#Function-and-variable-index">Function and variable index</a>
<li><a href="#Concept-index">Concept index</a>
<li><a href="#Environment-variable-index">Environment variable index</a>
</ul>
<div class="node">
<a name="Obtaining-R"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>,
Previous: <a rel="previous" accesskey="p" href="#Top">Top</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">1 Obtaining R</h2>
<p><a name="index-Obtaining-R-1"></a>
Sources, binaries and documentation for R can be obtained via
<acronym>CRAN</acronym>, the “Comprehensive R Archive Network” whose current
members are listed at <a href="http://CRAN.R-project.org/mirrors.html">http://CRAN.R-project.org/mirrors.html</a>.
<ul class="menu">
<li><a accesskey="1" href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a>
<li><a accesskey="2" href="#Getting-patched-and-development-versions">Getting patched and development versions</a>
</ul>
<div class="node">
<a name="Getting-and-unpacking-the-sources"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Getting-patched-and-development-versions">Getting patched and development versions</a>,
Previous: <a rel="previous" accesskey="p" href="#Obtaining-R">Obtaining R</a>,
Up: <a rel="up" accesskey="u" href="#Obtaining-R">Obtaining R</a>
</div>
<h3 class="section">1.1 Getting and unpacking the sources</h3>
<p><a name="index-Sources-for-R-2"></a>
The simplest way is to download the most recent
<samp><span class="file">R-</span><var>x</var><span class="file">.</span><var>y</var><span class="file">.</span><var>z</var><span class="file">.tar.gz</span></samp> file, and unpack it with
<pre class="example"> tar -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz
</pre>
<p class="noindent">on systems that have a suitable<a rel="footnote" href="#fn-1" name="fnd-1"><sup>1</sup></a>
<samp><span class="command">tar</span></samp> installed. On other systems you need to have the
<samp><span class="command">gzip</span></samp> program installed, when you can use
<pre class="example"> gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz | tar -xf -
</pre>
<p>The pathname of the directory into which the sources are unpacked should
not contain spaces, as most <samp><span class="command">make</span></samp> programs (and specifically
<acronym>GNU</acronym> <samp><span class="command">make</span></samp>) do not expect spaces.
<p>If you want the build to be usable by a group of users, set <code>umask</code>
before unpacking so that the files will be readable by the target group
(e.g., <code>umask 022</code> to be usable by all users). Keep this
setting of <code>umask</code> whilst building and installing.
<p>If you use a recent GNU version of <samp><span class="command">tar</span></samp> and do this as a root
account (which on Windows includes accounts with administrator
privileges) you may see many warnings about changing ownership. In
which case you can use
<pre class="example"> tar --no-same-owner -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz
</pre>
<p class="noindent">and perhaps also include the option <samp><span class="option">--no-same-permissions</span></samp>.
<a name="index-TAR_005fOPTIONS-3"></a>(These options can also be set in the <samp><span class="env">TAR_OPTIONS</span></samp> environment
variable: if more than one option is included they should be separated
by spaces.)
<div class="node">
<a name="Getting-patched-and-development-versions"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a>,
Up: <a rel="up" accesskey="u" href="#Obtaining-R">Obtaining R</a>
</div>
<h3 class="section">1.2 Getting patched and development versions</h3>
<p>A patched version of the current release, ‘<samp><span class="samp">r-patched</span></samp>’, and the
current development version, ‘<samp><span class="samp">r-devel</span></samp>’, are available as daily
tarballs and via access to the R Subversion repository. (For the two
weeks prior to the release of a minor (3.x.0) version, ‘<samp><span class="samp">r-patched</span></samp>’
tarballs may refer to beta/release candidates of the upcoming release,
the patched version of the current release being available via
Subversion.)
<p>The tarballs are available from
<a href="ftp://ftp.stat.math.ethz.ch/pub/Software/R/">ftp://ftp.stat.math.ethz.ch/pub/Software/R/</a>. Download
<samp><span class="file">R-patched.tar.gz</span></samp> or <samp><span class="file">R-devel.tar.gz</span></samp> (or the <samp><span class="file">.tar.bz2</span></samp>
versions) and unpack as described in the previous section. They are
built in exactly the same way as distributions of R releases.
<ul class="menu">
<li><a accesskey="1" href="#Using-Subversion-and-rsync">Using Subversion and rsync</a>
</ul>
<div class="node">
<a name="Using-Subversion-and-rsync"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Getting-patched-and-development-versions">Getting patched and development versions</a>,
Up: <a rel="up" accesskey="u" href="#Getting-patched-and-development-versions">Getting patched and development versions</a>
</div>
<h4 class="subsection">1.2.1 Using Subversion and rsync</h4>
<p><a name="index-Subversion-4"></a>
Sources are also available via <a href="https://svn.R-project.org/R/">https://svn.R-project.org/R/</a>, the
R Subversion repository. If you have a Subversion client (see
<a href="http://subversion.apache.org/">http://subversion.apache.org/</a>), you can check out and update the
current ‘<samp><span class="samp">r-devel</span></samp>’ from
<a href="https://svn.r-project.org/R/trunk/">https://svn.r-project.org/R/trunk/</a> and the current
‘<samp><span class="samp">r-patched</span></samp>’ from
‘<samp><span class="samp">https://svn.r-project.org/R/branches/R-</span><var>x</var><span class="samp">-</span><var>y</var><span class="samp">-branch/</span></samp>’
(where <var>x</var> and <var>y</var> are the major and minor number of the current
released version of R). E.g., use
<pre class="example"> svn checkout https://svn.r-project.org/R/trunk/ <var>path</var>
</pre>
<p class="noindent">to check out ‘<samp><span class="samp">r-devel</span></samp>’ into directory <var>path</var> (which will be
created if necessary). The alpha, beta and RC versions of an upcoming
<var>x.y.0</var> release are available from
‘<samp><span class="samp">https://svn.r-project.org/R/branches/R-</span><var>x</var><span class="samp">-</span><var>y</var><span class="samp">-branch/</span></samp>’ in
the four-week period prior to the release.
<p>Note that ‘<samp><span class="samp">https:</span></samp>’ is required<a rel="footnote" href="#fn-2" name="fnd-2"><sup>2</sup></a>,
and that the SSL certificate for the Subversion server of the R project
should be recognized as from a trusted source.
<p>Note that retrieving the sources by e.g. <samp><span class="command">wget -r</span></samp> or
<samp><span class="command">svn export</span></samp> from that URL will not work (and will give a error
early in the <samp><span class="command">make</span></samp> process): the Subversion information is
needed to build R.
<p>The Subversion repository does not contain the current sources for the
recommended packages, which can be obtained by <samp><span class="command">rsync</span></samp> or
downloaded from <acronym>CRAN</acronym>. To use <code>rsync</code> to install the
appropriate sources for the recommended packages, run
<code>./tools/rsync-recommended</code> from the top-level directory of the
R sources.
<p>If downloading manually from <acronym>CRAN</acronym>, do ensure that you have the
correct versions of the recommended packages: if the number in the file
<samp><span class="file">VERSION</span></samp> is ‘<samp><var>x</var><span class="samp">.</span><var>y</var><span class="samp">.</span><var>z</var></samp>’ you need to download
the contents of ‘<samp><span class="samp">http://CRAN.R-project.org/src/contrib/</span><var>dir</var></samp>’,
where <var>dir</var> is ‘<samp><var>x</var><span class="samp">.</span><var>y</var><span class="samp">.</span><var>z</var><span class="samp">/Recommended</span></samp>’ for
r-devel or <samp><var>x</var><span class="file">.</span><var>y</var><span class="file">-patched/Recommended</span></samp> for r-patched,
respectively, to directory <samp><span class="file">src/library/Recommended</span></samp> in the sources
you have unpacked. After downloading manually you need to execute
<samp><span class="command">tools/link-recommended</span></samp> from the top level of the sources to
make the requisite links in <samp><span class="file">src/library/Recommended</span></samp>. A suitable
incantation from the top level of the R sources using <samp><span class="command">wget</span></samp>
might be (for the correct value of <samp><var>dir</var></samp>)
<pre class="example"> wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \
http://CRAN.R-project.org/src/contrib/<var>dir</var>
./tools/link-recommended
</pre>
<div class="node">
<a name="Installing-R-under-Unix-alikes"></a>
<a name="Installing-R-under-Unix_002dalikes"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Installing-R-under-Windows">Installing R under Windows</a>,
Previous: <a rel="previous" accesskey="p" href="#Obtaining-R">Obtaining R</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">2 Installing R under Unix-alikes</h2>
<p><a name="index-Installing-under-Unix_002dalikes-5"></a>
R will configure and build under most common Unix and Unix-alike
platforms including ‘<samp><var>cpu</var><span class="samp">-*-linux-gnu</span></samp>’ for the
‘<samp><span class="samp">alpha</span></samp>’, ‘<samp><span class="samp">arm</span></samp>’, ‘<samp><span class="samp">hppa</span></samp>’, ‘<samp><span class="samp">ix86</span></samp>’,
‘<samp><span class="samp">ia64</span></samp>’, ‘<samp><span class="samp">m68k</span></samp>’, ‘<samp><span class="samp">mips</span></samp>’, ‘<samp><span class="samp">mipsel</span></samp>’,
‘<samp><span class="samp">powerpc</span></samp>’, ‘<samp><span class="samp">s390</span></samp>’, ‘<samp><span class="samp">sparc</span></samp>’, and ‘<samp><span class="samp">x86_64</span></samp>’
<acronym>CPU</acronym>s,
<!-- (see e.g.@: @uref{http://buildd.debian.org/build.php?&pkg=r-base}), -->
<!-- Actually, see http://packages.debian.org/unstable/math/r-base-core as -->
<!-- the build daemon is not used for all platforms; note also that Debian -->
<!-- has x86_64 <=> amd, ix86 <=> i386. -->
‘<samp><span class="samp">x86_64-apple-darwin</span></samp>’, ‘<samp><span class="samp">i386-sun-solaris</span></samp>’ and
‘<samp><span class="samp">sparc-sun-solaris</span></samp>’ as well as
perhaps (it is tested less frequently on these platforms)
‘<samp><span class="samp">i386-apple-darwin</span></samp>’, ‘<samp><span class="samp">i386-*-freebsd</span></samp>’, ‘<samp><span class="samp">x86_64-*-freebsd</span></samp>’,
‘<samp><span class="samp">i386-*-netbsd</span></samp>’, ‘<samp><span class="samp">i386-*-openbsd</span></samp>’ and
‘<samp><span class="samp">powerpc-ibm-aix6*</span></samp>’
<p><a name="index-Linux-6"></a><a name="index-OS-X-7"></a>In addition, binary distributions are available for some common Linux
distributions and for OS X (formerly Mac OS). See the <acronym>FAQ</acronym> for
current details. These are installed in platform-specific ways, so for
the rest of this chapter we consider only building from the sources.
<ul class="menu">
<li><a accesskey="1" href="#Simple-compilation">Simple compilation</a>
<li><a accesskey="2" href="#Help-options">Help options</a>
<li><a accesskey="3" href="#Making-the-manuals">Making the manuals</a>
<li><a accesskey="4" href="#Installation">Installation</a>
<li><a accesskey="5" href="#Uninstallation">Uninstallation</a>
<li><a accesskey="6" href="#Sub_002darchitectures">Sub-architectures</a>
<li><a accesskey="7" href="#Other-Options">Other Options</a>
<li><a accesskey="8" href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a>
</ul>
<div class="node">
<a name="Simple-compilation"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Help-options">Help options</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.1 Simple compilation</h3>
<p>First review the essential and useful tools and libraries in
<a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>, and install
those you
<a name="index-TMPDIR-8"></a>want or need. Ensure that the environment variable <samp><span class="env">TMPDIR</span></samp> is
either unset (and <samp><span class="file">/tmp</span></samp> exists and can be written in and scripts
can be executed from) or points to a valid temporary directory (one from
which execution of scripts is allowed) whose path does not contain
spaces.<a rel="footnote" href="#fn-3" name="fnd-3"><sup>3</sup></a>
<p><a name="index-R_005fHOME-9"></a>Choose a directory to install the R tree (R is not just a binary, but
has additional data sets, help files, font metrics etc). Let us call
this place <var>R_HOME</var>. Untar the source code. This should create
directories <samp><span class="file">src</span></samp>, <samp><span class="file">doc</span></samp>, and several more under a top-level
directory: change to that top-level directory (At this point North
American readers should consult <a href="#Setting-paper-size">Setting paper size</a>.) Issue the
following commands:
<p><a name="index-configure-10"></a>
<pre class="example"> ./configure
make
</pre>
<p class="noindent">(See <a href="#Using-make">Using make</a> if your make is not called ‘<samp><span class="samp">make</span></samp>’.) Users of
Debian-based 64-bit systems<a rel="footnote" href="#fn-4" name="fnd-4"><sup>4</sup></a> may need
<pre class="example"> ./configure LIBnn=lib
make
</pre>
<p>Then check the built system works correctly by
<pre class="example"> make check
</pre>
<p class="noindent">Failures are not necessarily problems as they might be caused by missing
functionality,<a rel="footnote" href="#fn-5" name="fnd-5"><sup>5</sup></a> but you should look carefully at any
reported discrepancies. (Some non-fatal errors are expected in locales
that do not support Latin-1, in particular in true <code>C</code> locales and
non-UTF-8 non-Western-European locales.) A failure in
<samp><span class="file">tests/ok-errors.R</span></samp> may indicate inadequate resource limits
(see <a href="#Running-R">Running R</a>).
<p>More comprehensive testing can be done by
<pre class="example"> make check-devel
</pre>
<p class="noindent">or
<pre class="example"> make check-all
</pre>
<p class="noindent">see file <samp><span class="file">tests/README</span></samp>.
<p>If the command <samp><span class="command">configure</span></samp> and <samp><span class="command">make</span></samp> commands execute
successfully, a shell-script front-end called <samp><span class="file">R</span></samp> will be created
and copied to <samp><var>R_HOME</var><span class="file">/bin</span></samp>. You can link or copy this script
to a place where users can invoke it, for example to
<samp><span class="file">/usr/local/bin/R</span></samp>. You could also copy the man page <samp><span class="file">R.1</span></samp> to
a place where your <samp><span class="command">man</span></samp> reader finds it, such as
<samp><span class="file">/usr/local/man/man1</span></samp>. If you want to install the complete R
tree to, e.g., <samp><span class="file">/usr/local/lib/R</span></samp>, see <a href="#Installation">Installation</a>. Note:
you do not <em>need</em> to install R: you can run it from where it was
built.
<p>You do not necessarily have to build R in the top-level source
directory (say, <samp><var>TOP_SRCDIR</var></samp>). To build in
<samp><var>BUILDDIR</var></samp>, run
<p><a name="index-configure-11"></a>
<pre class="example"> cd <var>BUILDDIR</var>
<var>TOP_SRCDIR</var>/configure
make
</pre>
<p class="noindent">and so on, as described further below. This has the advantage of always
keeping your source tree clean and is particularly recommended when you
work with a version of R from Subversion. (You may need
<acronym>GNU</acronym> <samp><span class="command">make</span></samp> to allow this, and you will need no spaces
in the path to the build directory.)
<!-- For those obtaining @R{} @emph{via} Subversion, one additional step is -->
<!-- necessary: -->
<!-- @cindex Vignettes -->
<!-- @cindex Subversion -->
<!-- @example -->
<!-- make vignettes -->
<!-- @end example -->
<!-- @noindent -->
<!-- which makes the @pkg{grid} vignettes (which are contained in the -->
<!-- tarballs): it make take several minutes. -->
<p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals
and the R <acronym>FAQ</acronym> (files <samp><span class="file">FAQ</span></samp> or
<samp><span class="file">doc/manual/R-FAQ.html</span></samp>, or
<a href="http://CRAN.R-project.org/doc/FAQ/R-FAQ.html">http://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a> which always
has the version for the latest release of R).
<div class="node">
<a name="Help-options"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Making-the-manuals">Making the manuals</a>,
Previous: <a rel="previous" accesskey="p" href="#Simple-compilation">Simple compilation</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.2 Help options</h3>
<p>By default <acronym>HTML</acronym> help pages are created when needed rather than being
built at install time.
<p>If you need to disable the server and want <acronym>HTML</acronym> help, there is the
option to build <acronym>HTML</acronym> pages when packages are installed
(including those installed with R). This is enabled by the
<samp><span class="command">configure</span></samp> option <samp><span class="option">--enable-prebuilt-html</span></samp>. Whether
<samp><span class="command">R CMD INSTALL</span></samp> (and hence <code>install.packages</code>) pre-builds
<acronym>HTML</acronym> pages is determined by looking at the R installation and is
reported by <samp><span class="command">R CMD INSTALL --help</span></samp>: it can be overridden by
specifying one of the <samp><span class="command">INSTALL</span></samp> options <samp><span class="option">--html</span></samp> or
<samp><span class="option">--no-html</span></samp>.
<p>The server is disabled by setting the environment variable
<a name="index-R_005fDISABLE_005fHTTPD-12"></a><samp><span class="env">R_DISABLE_HTTPD</span></samp> to a non-empty value, either before R is
started or within the R session before <acronym>HTML</acronym> help (including
<code>help.start</code>) is used. It is also possible that system security
measures will prevent the server from being started, for example if the
loopback interface has been disabled. See
<code>?tools::startDynamicHelp</code> for more details.
<div class="node">
<a name="Making-the-manuals"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Installation">Installation</a>,
Previous: <a rel="previous" accesskey="p" href="#Help-options">Help options</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.3 Making the manuals</h3>
<p><a name="index-Manuals-13"></a>
There is a set of manuals that can be built from the sources,
<dl>
<dt>‘<samp><span class="samp">fullrefman</span></samp>’<dd>Printed versions of all the help pages for base and recommended packages
(over 3300 pages).
<br><dt>‘<samp><span class="samp">refman</span></samp>’<dd>Printed versions of the help pages for selected base packages (over 1900 pages)
<br><dt>‘<samp><span class="samp">R-FAQ</span></samp>’<dd>R <acronym>FAQ</acronym>
<br><dt>‘<samp><span class="samp">R-intro</span></samp>’<dd>“An Introduction to R”.
<br><dt>‘<samp><span class="samp">R-data</span></samp>’<dd>“R Data Import/Export”.
<br><dt>‘<samp><span class="samp">R-admin</span></samp>’<dd>“R Installation and Administration”, this manual.
<br><dt>‘<samp><span class="samp">R-exts</span></samp>’<dd>“Writing R Extensions”.
<br><dt>‘<samp><span class="samp">R-lang</span></samp>’<dd>“The R Language Definition”.
</dl>
<p class="noindent">To make these (with ‘<samp><span class="samp">fullrefman</span></samp>’ rather than ‘<samp><span class="samp">refman</span></samp>’), use
<pre class="example"> make pdf <span class="roman">to create PDF versions</span>
make info <span class="roman">to create info files (not ‘</span><samp><span class="samp">refman</span></samp><span class="roman">’ nor ‘</span><samp><span class="samp">fullrefman</span></samp><span class="roman">’).</span>
</pre>
<p>You will not be able to build any of these unless you have
<samp><span class="command">makeinfo</span></samp> version 4.7 or later installed, and for PDF you must
have <samp><span class="command">texi2dvi</span></samp> and <samp><span class="file">texinfo.tex</span></samp> installed (which are part
of the <acronym>GNU</acronym> <strong>texinfo</strong> distribution but are, especially
<samp><span class="file">texinfo.tex</span></samp>, often made part of the TeX package in
re-distributions).
<p>The PDF versions can be viewed using any recent PDF viewer: they have
hyperlinks that can be followed. The info files are suitable for
reading online with Emacs or the standalone <acronym>GNU</acronym> <samp><span class="command">info</span></samp>
program. The PDF versions will be created using the paper size selected
at configuration (default ISO a4): this can be overridden by setting
<samp><span class="env">R_PAPERSIZE</span></samp>
<a name="index-R_005fPAPERSIZE-14"></a>on the <samp><span class="command">make</span></samp> command line, or setting <samp><span class="env">R_PAPERSIZE</span></samp> in the
environment and using <samp><span class="command">make -e</span></samp>. (If re-making the manuals for
a different paper size, you should first delete the file
<samp><span class="file">doc/manual/version.texi</span></samp>. The usual value for North America would
be ‘<samp><span class="samp">letter</span></samp>’.)
<p>There are some issues with making the PDF reference manual,
<samp><span class="file">fullrefman.pdf</span></samp> or <samp><span class="file">refman.pdf</span></samp>. The help files contain both
ISO Latin1 characters (e.g. in <samp><span class="file">text.Rd</span></samp>) and upright quotes,
neither of which are contained in the standard LaTeX Computer Modern
fonts. We have provided four alternatives:
<dl>
<dt><code>times</code><dd>(The default.) Using standard PostScript fonts, Times Roman, Helvetica
and Courier. This works well both for on-screen viewing and for
printing. One disadvantage is that the Usage and Examples sections may
come out rather wide: this can be overcome by using <em>in addition</em>
either of the options <code>inconsolata</code>, on a Unix-alike only if found
by <samp><span class="command">configure</span></samp>) or <code>beramono</code>, which replace the Courier
monospaced font by Inconsolata or Bera Sans mono respectively. (You
will need a recent version of the appropriate LaTeX package
<strong>inconsolata</strong> or <strong>bera</strong> installed.)
<p>Note that in most LaTeX installations this will not actually use the
standard fonts for PDF, but rather embed the URW clones NimbusRom,
NimbusSans and (for Courier, if used) NimbusMon.
<br><dt><code>lm</code><dd>Using the <em>Latin Modern</em> fonts. These are not often installed as
part of a TeX distribution, but can obtained from
<a href="http://www.ctan.org/tex-archive/fonts/ps-type1/lm/">http://www.ctan.org/tex-archive/fonts/ps-type1/lm/</a> and
mirrors. This uses fonts rather similar to Computer Modern, but is not
so good on-screen as <code>times</code>.
<br><dt><code>cm-super</code><dd>Using type-1 versions of the Computer Modern fonts by Vladimir Volovich.
This is a large installation, obtainable from
<a href="http://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/">http://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/</a>
and its mirrors. These type-1 fonts have poor hinting and so are
nowhere near as readable on-screen as the other three options.
<br><dt><code>ae</code><dd>A package to use composites of Computer Modern fonts. This works well
most of the time, and its PDF is more readable on-screen than the
previous two options. There are three fonts for which it will need to
use bitmapped fonts, <samp><span class="file">tctt0900.600pk</span></samp>, <samp><span class="file">tctt1000.600pk</span></samp> and
<samp><span class="file">tcrm1000.600pk</span></samp>. Unfortunately, if those files are not available,
Acrobat Reader will substitute completely incorrect glyphs so you need
to examine the logs carefully.
</dl>
<p>The default can be overridden by setting the environment variable
<a name="index-R_005fRD4PDF-15"></a><samp><span class="env">R_RD4PDF</span></samp>. (On Unix-alikes, this will be picked up at install time
and stored in <samp><span class="file">etc/Renviron</span></samp>, but can still be overridden when the
manuals are built, using <samp><span class="command">make -e</span></samp>.) The usual <a rel="footnote" href="#fn-6" name="fnd-6"><sup>6</sup></a> default value for <samp><span class="env">R_RD4PDF</span></samp> is
‘<samp><span class="samp">times,inconsolata,hyper</span></samp>’: omit ‘<samp><span class="samp">hyper</span></samp>’ if you do not want
hyperlinks (e.g. for printing the manual) or do not have LaTeX
package <strong>hyperref</strong>, and omit ‘<samp><span class="samp">inconsolata</span></samp>’ if you do not have
LaTeX package <strong>inconsolata</strong> installed.
<div class="node">
<a name="Installation"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Uninstallation">Uninstallation</a>,
Previous: <a rel="previous" accesskey="p" href="#Making-the-manuals">Making the manuals</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.4 Installation</h3>
<p><a name="index-Installation-16"></a>
To ensure that the installed tree is usable by the right group of users,
set <code>umask</code> appropriately (perhaps to ‘<samp><span class="samp">022</span></samp>’) before unpacking
the sources and throughout the build process.
<p>After
<p><a name="index-configure-17"></a>
<pre class="example"> ./configure
make
make check
</pre>
<p class="noindent">(or, when building outside the source,
<var>TOP_SRCDIR</var><code>/configure</code>, etc) have been completed
successfully, you can install the complete R tree to your system by
typing
<pre class="example"> make install
</pre>
<p class="noindent">A parallel make can be used (but run <samp><span class="command">make</span></samp> before <samp><span class="command">make
install</span></samp>): however it is not recommended for <samp><span class="command">make check</span></samp> as the
output from different checks will interleaved and hard to decipher.
<p>This will install to the following directories:
<dl>
<dt><samp><var>prefix</var><span class="file">/bin</span></samp> or <samp><var>bindir</var></samp><dd>the front-end shell script and other scripts and executables
<br><dt><samp><var>prefix</var><span class="file">/man/man1</span></samp> or <samp><var>mandir</var><span class="file">/man1</span></samp><dd>the man page
<br><dt><samp><var>prefix</var><span class="file">/</span><var>LIBnn</var><span class="file">/R</span></samp> or <samp><var>libdir</var><span class="file">/R</span></samp><dd>all the rest (libraries, on-line help system, <small class="dots">...</small>). Here
<var>LIBnn</var> is usually ‘<samp><span class="samp">lib</span></samp>’, but may be ‘<samp><span class="samp">lib64</span></samp>’ on some
64-bit Linux systems. This is known as the R home directory.
</dl>
<p class="noindent">where <var>prefix</var> is determined during configuration (typically
<samp><span class="file">/usr/local</span></samp>) and can be set by running <samp><span class="command">configure</span></samp> with
the option <samp><span class="option">--prefix</span></samp>, as in
<p><a name="index-configure-18"></a>
<pre class="example"> ./configure --prefix=/where/you/want/R/to/go
</pre>
<p class="noindent">This causes <samp><span class="command">make install</span></samp> to install the R script to
<samp><span class="file">/where/you/want/R/to/go/bin</span></samp>, and so on. The prefix of the
installation directories can be seen in the status message that is
displayed at the end of <samp><span class="command">configure</span></samp>. You can install into
another directory tree by using
<pre class="example"> make prefix=/path/to/here install
</pre>
<p class="noindent">at least with <acronym>GNU</acronym> <samp><span class="command">make</span></samp> (and current Solaris and
FreeBSD <samp><span class="command">make</span></samp>, but not some older Unix makes).
<p>More precise control is available at configure time via options: see
<samp><span class="command">configure --help</span></samp> for details. (However, most of the `Fine
tuning of the installation directories' options are not used by R.)
<p>Configure options <samp><span class="option">--bindir</span></samp> and <samp><span class="option">--mandir</span></samp> are supported
and govern where a copy of the <samp><span class="command">R</span></samp> script and the <samp><span class="command">man</span></samp>
page are installed.
<p>The configure option <samp><span class="option">--libdir</span></samp> controls where the main R
files are installed: the default is ‘<samp><var>eprefix</var><span class="samp">/</span><var>LIBnn</var></samp>’,
where <var>eprefix</var> is the prefix used for installing
architecture-dependent files, defaults to <var>prefix</var>, and can be set
via the configure option <samp><span class="option">--exec-prefix</span></samp>.
<p>Each of <code>bindir</code>, <code>mandir</code> and <code>libdir</code> can also be
specified on the <samp><span class="command">make install</span></samp> command line (at least for
<acronym>GNU</acronym> <samp><span class="command">make</span></samp>).
<p>The <samp><span class="command">configure</span></samp> or <samp><span class="command">make</span></samp> variables <code>rdocdir</code> and
<code>rsharedir</code> can be used to install the system-independent
<samp><span class="file">doc</span></samp> and <samp><span class="file">share</span></samp> directories to somewhere other than
<code>libdir</code>. The C header files can be installed to the value of
<code>rincludedir</code>: note that as the headers are not installed into a
subdirectory you probably want something like
<code>rincludedir=/usr/local/include/R-3.0.2</code>.
<p>If you want the R home to be something other than
<samp><var>libdir</var><span class="file">/R</span></samp>, use <samp><span class="option">rhome</span></samp>: for example
<pre class="example"> make install rhome=/usr/local/lib64/R-3.0.2
</pre>
<p class="noindent">will use a version-specific R home on a non-Debian Linux 64-bit
system.
<p>If you have made R as a shared/dynamic library you can install it in
your system's library directory by
<pre class="example"> make prefix=/path/to/here install-libR
</pre>
<p class="noindent">where <code>prefix</code> is optional, and <code>libdir</code> will give more
precise control.
<pre class="example"> make install-strip
</pre>
<p class="noindent">will install stripped executables, and on platforms where this is
supported, stripped libraries in directories <samp><span class="file">lib</span></samp> and
<samp><span class="file">modules</span></samp> and in the standard packages.
<p>Note that installing R into a directory whose path contains spaces is
not supported, and at least some aspects (such as installing source
packages) will not work.
<!-- The main problem is the Makefile include in etc/Makeconf -->
<p><a name="index-Manuals_002c-installing-19"></a>
To install info and PDF versions of the manuals, use one or both of
<pre class="example"> make install-info
make install-pdf
</pre>
<p class="noindent">Once again, it is optional to specify <code>prefix</code>, <code>libdir</code> or
<code>rhome</code> (the PDF manuals are installed under the R home
directory). (<samp><span class="command">make install-info</span></samp> needs Perl installed if there
is no command <samp><span class="command">install-info</span></samp> on the system.)
<p>More precise control is possible. For info, the setting used is that of
<code>infodir</code> (default <samp><var>prefix</var><span class="file">/info</span></samp>, set by configure
option <samp><span class="option">--infodir</span></samp>). The PDF files are installed into the R
<samp><span class="file">doc</span></samp> tree, set by the <samp><span class="command">make</span></samp> variable <code>rdocdir</code>.
<p>A staged installation is possible, that it is installing R into a
temporary directory in order to move the installed tree to its final
destination. In this case <code>prefix</code> (and so on) should reflect the
<a name="index-DESTDIR-20"></a>final destination, and <samp><span class="env">DESTDIR</span></samp> should be used: see
<a href="http://www.gnu.org/prep/standards/html_node/DESTDIR.html">http://www.gnu.org/prep/standards/html_node/DESTDIR.html</a>.
<p>You can optionally install the run-time tests that are part of
<samp><span class="command">make check-all</span></samp> by
<pre class="example"> make install-tests
</pre>
<p class="noindent">which populates a <samp><span class="file">tests</span></samp> directory in the installation.
<div class="node">
<a name="Uninstallation"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Sub_002darchitectures">Sub-architectures</a>,
Previous: <a rel="previous" accesskey="p" href="#Installation">Installation</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.5 Uninstallation</h3>
<p>You can uninstall R by
<pre class="example"> make uninstall
</pre>
<p class="noindent">optionally specifying <code>prefix</code> etc in the same way as specified for
installation.
<p>This will also uninstall any installed manuals. There are specific
targets to uninstall info and PDF manuals in file
<samp><span class="file">doc/manual/Makefile</span></samp>.
<p>Target <code>uninstall-tests</code> will uninstall any installed tests, as
well as removing the directory <samp><span class="file">tests</span></samp> containing the test results.
<div class="node">
<a name="Sub-architectures"></a>
<a name="Sub_002darchitectures"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Other-Options">Other Options</a>,
Previous: <a rel="previous" accesskey="p" href="#Uninstallation">Uninstallation</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.6 Sub-architectures</h3>
<p>Some platforms can support closely related builds of R which can
share all but the executables and dynamic objects. Examples include
builds under Linux and Solaris for different <acronym>CPU</acronym>s or 32- and
64-bit builds.
<p>R supports the idea of architecture-specific builds, specified by
adding ‘<samp><span class="samp">r_arch=</span><var>name</var></samp>’ to the <samp><span class="command">configure</span></samp> line. Here
<var>name</var> can be anything non-empty, and is used to name subdirectories
of <samp><span class="file">lib</span></samp>, <samp><span class="file">etc</span></samp>, <samp><span class="file">include</span></samp> and the package <samp><span class="file">libs</span></samp>
subdirectories. Example names from other software are the use of
<samp><span class="file">sparcv9</span></samp> on Sparc Solaris and <samp><span class="file">32</span></samp> by <samp><span class="command">gcc</span></samp> on
‘<samp><span class="samp">x86_64</span></samp>’ Linux.
<p>If you have two or more such builds you can install them over each other
(and for 32/64-bit builds on one architecture, one build can be done
without ‘<samp><span class="samp">r_arch</span></samp>’). The space savings can be considerable: on
‘<samp><span class="samp">x86_64</span></samp>’ Linux a basic install (without debugging symbols) took
63Mb, and adding a 32-bit build added 6Mb. If you have installed
multiple builds you can select which build to run by
<pre class="example"> R --arch=<var>name</var>
</pre>
<p class="noindent">and just running ‘<samp><span class="samp">R</span></samp>’ will run the last build that was installed.
<p><code>R CMD INSTALL</code> will detect if more than one build is installed and
try to install packages with the appropriate library objects for each.
This will not be done if the package has an executable <code>configure</code>
script or a <samp><span class="file">src/Makefile</span></samp> file. In such cases you can install for
extra builds by
<pre class="example"> R --arch=<var>name</var> CMD INSTALL --libs-only <var>pkg1</var> <var>pkg2</var> ...
</pre>
<p>If you want to mix sub-architectures compiled on different platforms
(for example ‘<samp><span class="samp">x86_64</span></samp>’ Linux and ‘<samp><span class="samp">i686</span></samp>’ Linux), it is
wise to use explicit names for each, and you may also need to set
<samp><span class="option">libdir</span></samp> to ensure that they install into the same place.
<p>When sub-architectures are used the version of <samp><span class="command">Rscript</span></samp> in
e.g. <samp><span class="file">/usr/bin</span></samp> will be the last installed, but
architecture-specific versions will be available in e.g.
<samp><span class="file">/usr/lib64/R/bin/exec${</span><var>R_ARCH</var><span class="file">}</span></samp>. Normally all installed
architectures will run on the platform so the architecture of
<samp><span class="command">Rscript</span></samp> itself does not matter. The executable
<samp><span class="command">Rscript</span></samp> will run the <samp><span class="command">R</span></samp> script, and at that time the
<a name="index-R_005fARCH-21"></a>setting of the <samp><span class="env">R_ARCH</span></samp> environment variable determines the
architecture which is run.
<p>When running post-install tests with sub-architectures, use
<pre class="example"> R --arch=<var>name</var> CMD make check[-devel|all]
</pre>
<p class="noindent">to select a sub-architecture to check.
<p>Sub-architectures are also used on Windows, but by selecting executables
within the appropriate <samp><span class="file">bin</span></samp> directory,
<samp><var>R_HOME</var><span class="file">/bin/i386</span></samp> or <samp><var>R_HOME</var><span class="file">/bin/x64</span></samp>. For
backwards compatibility with R < 2.12.0, there are executables
<samp><var>R_HOME</var><span class="file">/bin/R.exe</span></samp> or <samp><var>R_HOME</var><span class="file">/bin/Rscript.exe</span></samp>:
these will run an executable from one of the subdirectories, which one
being taken first from the
<a name="index-R_005fARCH-22"></a><samp><span class="env">R_ARCH</span></samp> environment variable, then from the
<samp><span class="option">--arch</span></samp> command-line option<a rel="footnote" href="#fn-7" name="fnd-7"><sup>7</sup></a> and finally from the
installation default (which is 32-bit for a combined 32/64 bit R
installation).
<ul class="menu">
<li><a accesskey="1" href="#Multilib">Multilib</a>
</ul>
<div class="node">
<a name="Multilib"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Sub_002darchitectures">Sub-architectures</a>,
Up: <a rel="up" accesskey="u" href="#Sub_002darchitectures">Sub-architectures</a>
</div>
<h4 class="subsection">2.6.1 Multilib</h4>
<p>On Linux<a rel="footnote" href="#fn-8" name="fnd-8"><sup>8</sup></a>, there is an alternative mechanism for mixing 32-bit and 64-bit
libraries known as <em>multilib</em>. If a Linux distribution supports
multilib, then parallel builds of R may be installed in the
sub-directories <samp><span class="file">lib</span></samp> (32-bit) and <samp><span class="file">lib64</span></samp> (64-bit). The
build to be run may then be selected using the <samp><span class="command">setarch</span></samp>
command. For example, a 32-bit build may be run by
<pre class="example"> setarch i686 R
</pre>
<p>The <samp><span class="command">setarch</span></samp> command is only operational if both 32-bit and
64-bit builds are installed. If there is only one installation of R,
then this will always be run regardless of the architecture specified
by the <samp><span class="command">setarch</span></samp> command.
<p>There can be problems with installing packages on the non-native
architecture. It is a good idea to run e.g. <code>setarch i686 R</code> for
sessions in which packages are to be installed, even if that is the only
version of R installed (since this tells the package installation
code the architecture needed).
<p>At present there is a potential problem with packages using Java, as
the post-install for a ‘<samp><span class="samp">i386</span></samp>’ RPM on ‘<samp><span class="samp">x86_64</span></samp>’ Linux
reconfigures Java and will find the ‘<samp><span class="samp">x86_64</span></samp>’ Java. If you know
where a 32-bit Java is installed you may be able to run (as root)
<pre class="example"> export JAVA_HOME=<path to jre directory of 32-bit Java>
setarch i686 R CMD javareconf
</pre>
<p class="noindent">to get a suitable setting.
<p>When this mechanism is used, the version of <samp><span class="command">Rscript</span></samp> in
e.g. <samp><span class="file">/usr/bin</span></samp> will be the last installed, but an
architecture-specific version will be available in
e.g. <samp><span class="file">/usr/lib64/R/bin</span></samp>. Normally all installed architectures
will run on the platform so the architecture of <samp><span class="command">Rscript</span></samp> does
not matter.
<div class="node">
<a name="Other-Options"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a>,
Previous: <a rel="previous" accesskey="p" href="#Sub_002darchitectures">Sub-architectures</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.7 Other Options</h3>
<p>There are many other installation options, most of which are listed by
<samp><span class="command">configure --help</span></samp>. Almost all of those not listed elsewhere in
this manual are either standard <samp><span class="command">autoconf</span></samp> options not relevant
to R or intended for specialist uses by the R developers.
<p>One that may be useful when working on R itself is the option
<samp><span class="option">--disable-byte-compiled-packages</span></samp>, which ensures that the base
and recommended packages are lazyloaded but not byte-compiled.
(Alternatively the (make or environment) variable
<samp><span class="env">R_NO_BASE_COMPILE</span></samp> can be set to a non-empty value for the duration
of the build.)
<div class="node">
<a name="Testing-a-Unix-alike-Installation"></a>
<a name="Testing-a-Unix_002dalike-Installation"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Other-Options">Other Options</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>
</div>
<h3 class="section">2.8 Testing an Installation</h3>
<p>Full testing is possible only if the test files have been installed with
<pre class="example"> make install-tests
</pre>
<p class="noindent">which populates a <samp><span class="file">tests</span></samp> directory in the installation.
<p>If this has been done, two testing routes are available.
The first is to move to the home directory of the R installation
(as given by <code>R.home()</code>) and run
<pre class="example"> cd tests
## followed by one of
../bin/R CMD make check
../bin/R CMD make check-devel
../bin/R CMD make check-all
</pre>
<p class="noindent">and other useful targets are <code>test-BasePackages</code> and
<code>test-Recommended</code> to the run tests of the standard and
recommended packages (if installed) respectively.
<p>This re-runs all the tests relevant to the installed R (including for
example code in the package vignettes), but not for example the ones
checking the example code in the manuals nor making the standalone Rmath
library. This can occasionally be useful when the operating environment
has been changed, for example by OS updates or by substituting the
<acronym>BLAS</acronym> (see <a href="#Shared-BLAS">Shared BLAS</a>).
<p>Alternatively, the installed R can be run, preferably with
<samp><span class="option">--vanilla</span></samp>. Then
<a name="index-LC_005fCOLLATE-23"></a>
<pre class="example"> Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base")
testInstalledPackages(scope = "recommended")
</pre>
<p class="noindent">runs the basic tests and then all the tests on the standard and
recommended packages. These tests can be run from anywhere: the basic
tests write their results in the <samp><span class="file">tests</span></samp> folder of the R home
directory and run slightly fewer tests than the first approach: in
particular they do not test Internet access.
<p>These tests work best if <samp><span class="command">diff</span></samp> (in <samp><span class="file">Rtools*.exe</span></samp> for
Windows users) is in the path.
<p>It is possible to test the installed packages (but not the
package-specific tests) by <code>testInstalledPackages</code> even if
<samp><span class="command">make install-tests</span></samp> was not run.
<p>Note that the results may depend on the language set for times and
messages: for maximal similarity to reference results you may want to
try setting
<pre class="example"> LANGUAGE=en LC_TIME=C LC_COLLATE=C
</pre>
<p class="noindent">but use a UTF-8 or Latin-1 locale.
<div class="node">
<a name="Installing-R-under-Windows"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Installing-R-under-OS-X">Installing R under OS X</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">3 Installing R under Windows</h2>
<p><a name="index-Installing-under-Windows-24"></a>
The <samp><span class="file">bin/windows</span></samp> directory of a <acronym>CRAN</acronym> site contains
binaries for a base distribution and a large number of add-on packages
from <acronym>CRAN</acronym> to run on Windows XP or later on ix86 <acronym>CPU</acronym>s
(including AMD64/Intel64 cpus and Windows x64).
<p>Your file system must allow long file names (as is likely except
perhaps for some network-mounted systems).
<p>Installation is <em>via</em> the installer
<samp><span class="file">R-3.0.2-win.exe</span></samp>. Just double-click on the icon and
follow the instructions. When installing on a 64-bit version of Windows
the options will include 32- or 64-bit versions of R (and the default is
to install both). You can uninstall R from the Control Panel.
<p>Note that you will be asked to choose a language for installation, and
that choice applies to both installation and un-installation but not to
running R itself.
<p>See the <a href="http://CRAN.R-project.org/bin/windows/base/rw-FAQ.html">R Windows <acronym>FAQ</acronym></a> for more details on the binary installer.
<ul class="menu">
<li><a accesskey="1" href="#Building-from-source">Building from source</a>
<li><a accesskey="2" href="#Testing-a-Windows-Installation">Testing a Windows Installation</a>
</ul>
<div class="node">
<a name="Building-from-source"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Testing-a-Windows-Installation">Testing a Windows Installation</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-Windows">Installing R under Windows</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Windows">Installing R under Windows</a>
</div>
<h3 class="section">3.1 Building from source</h3>
<p>R can be built as either a 32-bit or 64-bit application on Windows:
to build the 64-bit application you need a 64-bit edition of Windows:
such an OS can also be used to build 32-bit R.
<p>The standard installer combines 32-bit and 64-bit builds into a single
executable which can then be installed into the same location and share
all the files except the <samp><span class="file">.exe</span></samp> and <samp><span class="file">.dll</span></samp> files and some
configuration files in the <samp><span class="file">etc</span></samp> directory.
<ul class="menu">
<li><a accesskey="1" href="#Getting-the-tools">Getting the tools</a>
<li><a accesskey="2" href="#Getting-the-source-files">Getting the source files</a>
<li><a accesskey="3" href="#Building-the-core-files">Building the core files</a>
<li><a accesskey="4" href="#Building-the-bitmap-files">Building the bitmap files</a>
<li><a accesskey="5" href="#Building-the-cairo-devices-files">Building the cairo devices files</a>
<li><a accesskey="6" href="#Checking-the-build">Checking the build</a>
<li><a accesskey="7" href="#Building-the-manuals">Building the manuals</a>
<li><a accesskey="8" href="#Building-the-Inno-Setup-installer">Building the Inno Setup installer</a>
<li><a accesskey="9" href="#Building-the-MSI-installer">Building the MSI installer</a>
<li><a href="#g_t64_002dbit-Windows-builds">64-bit Windows builds</a>
</ul>
<div class="node">
<a name="Getting-the-tools"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Getting-the-source-files">Getting the source files</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-from-source">Building from source</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.1 Getting the tools</h4>
<p>If you want to build R from the sources, you will first need to
collect, install and test an extensive set of tools. See <a href="#The-Windows-toolset">The Windows toolset</a> (and perhaps updates in
<a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a>) for details.
<p>The <samp><span class="file">Rtools*.exe</span></samp> executable installer described in <a href="#The-Windows-toolset">The Windows toolset</a> also includes some source files in addition to the R
source as noted below. You should run it first, to obtain a working
<code>tar</code> and other necessities. Choose a “Full installation”, and
install the extra files into your intended R source directory, e.g.
<samp><span class="file">C:/R</span></samp>. The directory name <em>should not contain spaces</em>. We
will call this directory <samp><var>R_HOME</var></samp> below.
<div class="node">
<a name="Getting-the-source-files"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-core-files">Building the core files</a>,
Previous: <a rel="previous" accesskey="p" href="#Getting-the-tools">Getting the tools</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.2 Getting the source files</h4>
<p>You need to collect the following sets of files:
<ul>
<li>Get the R source code tarball <samp><span class="file">R-3.0.2.tar.gz</span></samp> from
<acronym>CRAN</acronym>. Open a command window (or another shell) at directory
<var>R_HOME</var>, and run
<pre class="example"> tar -xf R-3.0.2.tar.gz
</pre>
<p class="noindent">to create the source tree in <var>R_HOME</var>. <strong>Beware</strong>: do use
<samp><span class="command">tar</span></samp> to extract the sources rather than tools such as WinZip.
If you are using an account with administrative privileges you may get a
lot of messages which can be suppressed by
<pre class="example"> tar --no-same-owner -xf R-3.0.2.tar.gz
</pre>
<p class="noindent"><a name="index-TAR_005fOPTIONS-25"></a>or perhaps better, set the environment variable <samp><span class="env">TAR_OPTIONS</span></samp> to the
value ‘<samp><span class="samp">--no-same-owner --no-same-permissions</span></samp>’.
<p>It is also possible to obtain the source code using Subversion; see
<a href="#Obtaining-R">Obtaining R</a> for details.
<li>If you are not using a tarball you need to obtain copies of the
recommended packages from <acronym>CRAN</acronym>. Put the <samp><span class="file">.tar.gz</span></samp> files
in <samp><var>R_HOME</var><span class="file">/src/library/Recommended</span></samp> and run <code>make
link-recommended</code>. If you have an Internet connection, you can do this
automatically by running in <samp><var>R_HOME</var><span class="file">/src/gnuwin32</span></samp>
<pre class="example"> make rsync-recommended
</pre>
</ul>
<p>The following additional items are normally installed by
<samp><span class="file">Rtools30.exe</span></samp>. If instead you choose to do a completely manual
build you will also need
<ul>
<li>The Tcl/Tk support files are contained in <samp><span class="file">Rtools30.exe</span></samp> and
available as <samp><span class="file">.zip</span></samp> files from
<a href="http://www.stats.ox.ac.uk/pub/Rtools">http://www.stats.ox.ac.uk/pub/Rtools</a>. Please make sure you
install the right version: there is a 32-bit version and a 64-bit
version. They should be installed to <samp><var>R_HOME</var></samp>, creating
directory <samp><span class="file">Tcl</span></samp> there.
<li>You need <code>libpng</code>, <code>jpeg</code> and <code>libtiff</code> sources
(available, e.g., from <a href="http://www.libpng.org/">http://www.libpng.org/</a>,
<a href="http://www.ijg.org">http://www.ijg.org</a> and
<a href="http://download.osgeo.org/libtiff/">http://download.osgeo.org/libtiff/</a>); current versions are
recommended and 7 or later is required. It is also possible to use
‘<samp><span class="samp">libjpeg-turbo</span></samp>’ from
<a href="http://sourceforge.net/projects/libjpeg-turbo/files/">http://sourceforge.net/projects/libjpeg-turbo/files/</a>.
<p>Working in the directory <samp><var>R_HOME</var><span class="file">/src/gnuwin32/bitmap</span></samp>,
install the <code>libpng</code> and <code>jpeg</code> sources in sub-directories.
The <code>jpeg</code> sub-directory for version 9 is named <samp><span class="file">jpeg-9</span></samp>; if
you use a different version (e.g. <samp><span class="file">jpeg-8d</span></samp> or
<samp><span class="file">libjpeg-turbo</span></samp>), copy file <samp><span class="file">src/gnuwin32/MkRules.dist</span></samp> to
<samp><span class="file">src/gnuwin32/MkRules.local</span></samp> and edit the definition of
<code>JPEGDIR</code>: the names of the <samp><span class="file">libpng</span></samp> and <samp><span class="file">libtiff</span></samp>
directories can also be set there.
<p>Example:
<pre class="example"> > tar -zxf libpng-1.6.2.tar.gz
> mv libpng-1.6.2 libpng
> tar -zxf jpegsrc.v9.tar.gz
> tar -zxf tiff-4.0.3.tar.gz
> mv tiff-4.0.3/libtiff .
> rm -rf tiff-4.0.3
</pre>
<p class="noindent">(and see the comment above about <samp><span class="option">--no-same-owner</span></samp>).
</ul>
<div class="node">
<a name="Building-the-core-files"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-bitmap-files">Building the bitmap files</a>,
Previous: <a rel="previous" accesskey="p" href="#Getting-the-source-files">Getting the source files</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.3 Building the core files</h4>
<p><a name="index-TMPDIR-26"></a>Set the environment variable <samp><span class="env">TMPDIR</span></samp> to point to a writable
directory, with a path specified with forward slashes and no spaces.
(The default is <samp><span class="file">/tmp</span></samp>, which may not be useful on Windows.)
<p>You may need to compile under a case-honouring file system: we found
that a <samp><span class="command">samba</span></samp>-mounted file system (which maps all file names to
lower case) did not work.
<p>Open a command window at <samp><var>R_HOME</var><span class="file">/src/gnuwin32</span></samp>. Look at
<samp><span class="file">MkRules.dist</span></samp> and if settings need to be altered, copy it to
<samp><span class="file">MkRules.local</span></samp> and edit the settings there. In particular, this
is where a 64-bit build is selected. Then run
<pre class="example"> make all recommended
</pre>
<p class="noindent">and sit back and wait while the basic compile takes place.
<p>Notes:
<ul>
<li>We have had reports that earlier versions of anti-virus software locking
up the machine, but not for several years. However, aggressive
anti-virus checking such as the on-access scanning of Sophos can slow
the build down several-fold.
<li>By default Doug Lea's <code>malloc</code> in the file
<samp><var>R_HOME</var><span class="file">/src/gnuwin32/malloc.c</span></samp> is used for R's internal
memory allocations. You can opt out of this by setting
<code>LEA_MALLOC=NO</code> in <samp><span class="file">MkRules.dist</span></samp>, in which case the <code>malloc</code>
in <samp><span class="file">msvcrt.dll</span></samp> is used. This does impose a considerable
performance penalty and has not been tested recently.
<li>You can run a parallel make by e.g.
<pre class="example"> make -j4 all
make -j4 recommended
</pre>
<p class="noindent">but this is only likely to be worthwhile on a multi-core machine with
ample memory, and is not 100% reliable.
<li>It is possible (mainly for those working on R itself) to set the
(make or environment) variable <samp><span class="env">R_NO_BASE_COMPILE</span></samp> to a non-empty
value, which inhibits the byte-compilation of the base and recommended
packages.
</ul>
<div class="node">
<a name="Building-the-bitmap-files"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-cairo-devices-files">Building the cairo devices files</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-the-core-files">Building the core files</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.4 Building the bitmap files</h4>
<p><a name="index-Rbitmap_002edll-27"></a>
The file
<samp><var>R_HOME</var><span class="file">/library/grDevices/libs/{i386,x64}Rbitmap.dll</span></samp> is
not built automatically.
<p>Running <code>make</code> in <samp><var>R_HOME</var><span class="file">/src/gnuwin32/bitmap</span></samp> or
<code>make bitmapdll</code> in <samp><var>R_HOME</var><span class="file">/src/gnuwin32</span></samp> should build
<samp><span class="file">Rbitmap.dll</span></samp> and install it under
<samp><var>R_HOME</var><span class="file">/library/grDevices/libs</span></samp>.
<div class="node">
<a name="Building-the-cairo-devices-files"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Checking-the-build">Checking the build</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-the-bitmap-files">Building the bitmap files</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.5 Building the cairo devices</h4>
<p><a name="index-winCairo_002edll-28"></a>
The devices based on cairographics (<code>svg</code>, <code>cairo_pdf</code>,
<code>cairo_ps</code> and the <code>type = "cairo"</code> versions of <code>png</code>,
<code>jpeg</code>, <code>tiff</code> and <code>bmp</code>) are implemented in a separate
DLL <samp><span class="file">winCairo.dll</span></samp> which is loaded when one of these devices is
first used. It is not built by default, and needs to be built after
<samp><span class="file">Rbitmap.dll</span></samp>, by <samp><span class="command">make cairodevices</span></samp>.
<p>To enable the building of these devices you need to install the static
cairographics libraries built by Simon Urbanek at
<a href="http://www.rforge.net/Cairo/files/cairo-current-win.tar.gz">http://www.rforge.net/Cairo/files/cairo-current-win.tar.gz</a>. Set
the macro ‘<samp><span class="samp">CAIRO_HOME</span></samp>’ in <samp><span class="file">MkRules.local</span></samp>. (Note that this
tarball unpacks with a top-level directory <samp><span class="file">src/</span></samp>:
‘<samp><span class="samp">CAIRO_HOME</span></samp>’ needs to include that directory in its path.)
<div class="node">
<a name="Checking-the-build"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-manuals">Building the manuals</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-the-cairo-devices-files">Building the cairo devices files</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.6 Checking the build</h4>
<p>You can test a build by running
<pre class="example"> make check
</pre>
<p class="noindent">The recommended packages can be checked by
<pre class="example"> make check-recommended
</pre>
<p class="noindent">Other levels of checking are
<pre class="example"> make check-devel
</pre>
<p class="noindent">for a more thorough check of the R functionality, and
<pre class="example"> make check-all
</pre>
<p class="noindent">for <code>check-devel</code> and <code>check-recommended</code>.
<p>If a test fails, there will almost always be a <samp><span class="file">.Rout.fail</span></samp> file in
the directory being checked (often <samp><span class="file">tests/Examples</span></samp> or
<samp><span class="file">tests</span></samp>): examine the file to help pinpoint the problem.
<div class="node">
<a name="Building-the-manuals"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-Inno-Setup-installer">Building the Inno Setup installer</a>,
Previous: <a rel="previous" accesskey="p" href="#Checking-the-build">Checking the build</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.7 Building the manuals</h4>
<p>The PDF manuals can be made by
<pre class="example"> make manuals
</pre>
<p class="noindent">If you want to make the info versions (not including the Reference
Manual), use
<pre class="example"> cd ../../doc/manual
make -f Makefile.win info
</pre>
<p class="noindent">(all assuming you have <samp><span class="command">pdftex</span></samp>/<samp><span class="command">pdflatex</span></samp> installed and
in your path).
<p>See the <a href="#Making-the-manuals">Making the manuals</a> section in the Unix-alike section for setting
options such as the paper size and the fonts used.
<div class="node">
<a name="Building-the-Inno-Setup-installer"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-the-MSI-installer">Building the MSI installer</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-the-manuals">Building the manuals</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.8 Building the Inno Setup installer</h4>
<p>You need to have the files for a complete R build, including bitmap and
Tcl/Tk support and the manuals, as well as the recommended packages and
Inno Setup (see <a href="#The-Inno-Setup-installer">The Inno Setup installer</a>).
<p>Once everything is set up
<pre class="example"> make distribution
make check-all
</pre>
<p class="noindent">will make all the pieces and the installers and put them in the
<samp><span class="file">gnuwin32/cran</span></samp> subdirectory, then check the build. This works by
building all the parts in the sequence:
<pre class="example"> rbuild <span class="roman">(the executables, the <acronym>FAQ</acronym> docs etc.)</span>
rpackages <span class="roman">(the base packages)</span>
htmldocs <span class="roman">(the HTML documentation)</span>
bitmapdll <span class="roman">(the bitmap support files)</span>
cairodevices <span class="roman">(the cairo-based graphics devices)</span>
recommended <span class="roman">(the recommended packages)</span>
vignettes <span class="roman">(the vignettes in base packages:</span>
<span class="roman"> only needed if building from an svn checkout)</span>
manuals <span class="roman">(the PDF manuals)</span>
rinstaller <span class="roman">(the install program)</span>
crandir <span class="roman">(the <acronym>CRAN</acronym> distribution directory, only for 64-bit builds)</span>
</pre>
<p>The parts can be made individually if a full build is not needed, but
earlier parts must be built before later ones. (The <samp><span class="file">Makefile</span></samp>
doesn't enforce this dependency—some build targets force a lot of
computation even if all files are up to date.) The first four targets
are the default build if just <samp><span class="command">make</span></samp> (or <samp><span class="command">make all</span></samp>) is
run.
<p>Parallel make is not supported and likely to fail.
<p>If you want to customize the installation by adding extra packages,
replace <code>make rinstaller</code> by something like
<pre class="example"> make rinstaller EXTRA_PKGS='pkg1 pkg2 pkg3'
</pre>
<p>An alternative way to customize the installer starting with a binary
distribution is to first make an installation of R from the standard
installer, then add packages and make other customizations to that
installation. Then (after having customized file <samp><span class="file">MkRules</span></samp>,
possibly <em>via</em> <samp><span class="file">MkRules.local</span></samp>, and having made R in the
source tree) in <samp><span class="file">src/gnuwin32/installer</span></samp> run
<pre class="example"> make myR IMAGEDIR=rootdir
</pre>
<p class="noindent">where <samp><span class="file">rootdir</span></samp> is the path to the root of the customized
installation (in double quotes if it contains spaces or backslashes).
<p>Both methods create an executable with a standard name such as
<samp><span class="file">R-3.0.2-win.exe</span></samp>, so please rename it to indicate that
it is customized. If you intend to <em>distribute</em> a customized
installer please do check that license requirements are met – note that
the installer will state that the contents are distributed under GPL-2
and this has a requirement for <em>you</em> to supply the complete sources
(including the R sources even if you started with a binary distribution
of R, and also the sources of any extra packages (including their
external software) which are included).
<p>The defaults for the startup parameters may also be customized. For example
<pre class="example"> make myR IMAGEDIR=rootdir MDISDI=1
</pre>
<p class="noindent">will create an installer that defaults to installing R to run in SDI
mode. See <samp><span class="file">src/gnuwin32/installer/Makefile</span></samp> for the names and
values that can be set.
<p>The standard <acronym>CRAN</acronym> distribution of a 32/64-bit installer is
made by first building 32-bit R (just
<pre class="example"> make 32-bit
</pre>
<p class="noindent">is needed), and then building 64-bit R with the macro <code>HOME32</code> set
in file <samp><span class="file">MkRules.local</span></samp> to the top-level directory of the 32-bit
build. Then the <samp><span class="command">make rinstaller</span></samp> step copies the files that
differ between architectures from the 32-bit build as it builds the
installer image.
<div class="node">
<a name="Building-the-MSI-installer"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#g_t64_002dbit-Windows-builds">64-bit Windows builds</a>,
Previous: <a rel="previous" accesskey="p" href="#Building-the-Inno-Setup-installer">Building the Inno Setup installer</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.9 Building the MSI installer</h4>
<p>It is also possible to build an installer for use with Microsoft
Installer. This is intended for use by sysadmins doing automated
installs, and is not recommended for casual use.
<p>It makes use of the Windows Installer XML (WiX) toolkit <em>version
3.5</em> (or perhaps later, untested) available from
<a href="http://wix.sourceforge.net/">http://wix.sourceforge.net/</a> or <a href="http://wixtoolset.org/">http://wixtoolset.org/</a>.
Once WiX is installed, set the path to its home directory in
<samp><span class="file">MkRules.local</span></samp>.
<p>You need to have the files for a complete R build, including bitmap and
Tcl/Tk support and the manuals, as well as the recommended packages.
There is no option in the installer to customize startup options, so
edit <samp><span class="file">etc/Rconsole</span></samp> and <samp><span class="file">etc/Rprofile.site</span></samp> to set these as
required. Then
<pre class="example"> cd installer
make msi
</pre>
<p class="noindent">which will result in a file with a name like
<samp><span class="file">R-3.0.2-win32.msi</span></samp>. This can be double-clicked to be
installed, but those who need it will know what to do with it (usually
by running <samp><span class="command">msiexec /i</span></samp> with additional options). Properties
that users might want to set from the <samp><span class="command">msiexec</span></samp> command line
include ‘<samp><span class="samp">ALLUSERS</span></samp>’, ‘<samp><span class="samp">INSTALLDIR</span></samp>’ (something like
<samp><span class="file">c:\Program Files\R\R-3.0.2</span></samp>) and ‘<samp><span class="samp">RMENU</span></samp>’ (the path
to the ‘<samp><span class="samp">R</span></samp>’ folder on the start menu) and ‘<samp><span class="samp">STARTDIR</span></samp>’ (the
starting directory for R shortcuts, defaulting to something like
<samp><span class="file">c:\Users\name\Documents\R</span></samp>).
<p>The MSI installer can be built both from a 32-bit build of R
(<samp><span class="file">R-3.0.2-win32.msi</span></samp>) and from a 64-bit build of R
(<samp><span class="file">R-3.0.2-win64.msi</span></samp>, optionally including 32-bit files
by setting the macro <code>HOME32</code>, when the name is
<samp><span class="file">R-3.0.2-win.msi</span></samp>). Unlike the main installer, a 64-bit
MSI installer can only be run on 64-bit Windows.
<p>Thanks to David del Campo (Dept of Statistics, University of Oxford)
for suggesting WiX and building a prototype installer.
<div class="node">
<a name="64-bit-Windows-builds"></a>
<a name="g_t64_002dbit-Windows-builds"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Building-the-MSI-installer">Building the MSI installer</a>,
Up: <a rel="up" accesskey="u" href="#Building-from-source">Building from source</a>
</div>
<h4 class="subsection">3.1.10 64-bit Windows builds</h4>
<p>To build a 64-bit version of R you need a 64-bit toolchain: the only one
discussed here is based on the work of the MinGW-w64 project
(<a href="http://sourceforge.net/projects/mingw-w64/">http://sourceforge.net/projects/mingw-w64/</a>, but commercial
compilers such as those from Intel and PGI could be used (and have been
by R redistributors).
<p>Support for MinGW-w64 was developed in the R sources over the period
2008–10 and was first released as part of R 2.11.0. The assistance
of Yu Gong at a crucial step in porting R to MinGW-w64 is gratefully
acknowledged, as well as help from Kai Tietz, the lead developer of the
MinGW-w64 project.
<p>Windows 64-bit is now completely integrated into the R and package
build systems.
<div class="node">
<a name="Testing-a-Windows-Installation"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Building-from-source">Building from source</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-Windows">Installing R under Windows</a>
</div>
<h3 class="section">3.2 Testing an Installation</h3>
<p>The Windows installer contains a set of test files used when building
R.
<p>The <code>Rtools</code> are not needed to run these tests. but more
comprehensive analysis of errors will be given if <samp><span class="command">diff</span></samp> is in
the path (and <code>errorsAreFatal = FALSE</code> is then not needed below).
<p>Launch either <code>Rgui</code> or <code>Rterm</code>, preferably with
<samp><span class="option">--vanilla</span></samp>. Then run
<pre class="example"> Sys.setenv(LC_COLLATE = "C", LANGUAGE = "en")
library("tools")
testInstalledBasic("both")
testInstalledPackages(scope = "base", errorsAreFatal = FALSE)
testInstalledPackages(scope = "recommended", errorsAreFatal = FALSE)
</pre>
<p class="noindent">runs the basic tests and then all the tests on the standard and
recommended packages. These tests can be run from anywhere: they write
some of their results in the <samp><span class="file">tests</span></samp> folder of the R home
directory (as given by <code>R.home()</code>), and hence may need to be run
under the account used to install R.
<p>The results of <code>example(md5sums)</code> when testing <strong>tools</strong> will
differ from the reference output as some files are installed with
Windows' CRLF line endings.
<div class="node">
<a name="Installing-R-under-OS-X"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Running-R">Running R</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-Windows">Installing R under Windows</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">4 Installing R under OS X</h2>
<p><a name="index-OS-X-29"></a>
<p>The front page of a <acronym>CRAN</acronym> site has a link `Download R for OS
X'. Click on that, then download the file <samp><span class="file">R-3.0.2.pkg</span></samp>
and install it. This runs on OS X 10.6 and later (Snow Leopard, Lion,
Mountain Lion, Mavericks, <small class="dots">...</small>); it is a 64-bit (‘<samp><span class="samp">x86_64</span></samp>’)
build which should run on all Macs from mid-2008 on. For older Intel
Macs and some older versions of the OS you can install R from the
sources.
<p>It is important that is you use the binary package that your OS is fully
updated: run ‘Software Update’ from the Apple menu to be sure.
<p>To install, just double-click on the icon of the file you downloaded.
At the ‘Installation Type’ stage, note the option to ‘Customize’. This
currently shows three components (‘Package Name’). Everyone will need
the ‘R Framework’ component: the ‘R GUI’ and ‘Tcl/Tk’ components are
optional (the latter being needed to use package <strong>tcltk</strong>).
<p>This is an Apple Installer package. If you encounter any problem during
the installation, please check the Installer log by clicking on the
“Window” menu and item “Installer Log”. The full output (select
“Show All Log”) is useful for tracking down problems.
<p>On Mountain Lion and later with ‘GateKeeper’ active you will need to
right/control-click on any unsigned packages and select ‘<samp><span class="samp">Open</span></samp>’:
recent <acronym>CRAN</acronym> packages are signed.
<p>For building R from source, see <a href="#OS-X">OS X</a>.
<ul class="menu">
<li><a accesskey="1" href="#Running-R-under-OS-X">Running R under OS X</a>
<li><a accesskey="2" href="#Uninstalling-under-OS-X">Uninstalling under OS X</a>
<li><a accesskey="3" href="#Multiple-versions">Multiple versions</a>
</ul>
<div class="node">
<a name="Running-R-under-OS-X"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Uninstalling-under-OS-X">Uninstalling under OS X</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-OS-X">Installing R under OS X</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-OS-X">Installing R under OS X</a>
</div>
<h3 class="section">4.1 Running R under OS X</h3>
<p>There are two ways to run R on OS X from the <acronym>CRAN</acronym> binary
distribution.
<p>There is a GUI console normally installed with the R icon in
<samp><span class="file">/Applications</span></samp> which you can run by double-clicking (e.g. from
Launchpad or Finder). This is usually referred to as <span class="sc">R.app</span> to
distinguish it from command-line R: its user manual is currently part
of the OS X FAQ at
<a href="http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html">http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html</a>
<p>You can run command-line R from a Terminal like any other Unix-alike:
see the next chapter of this manual. There are some small differences
which may surprise users of R on other platforms, notably the default
personal library directory (under <samp><span class="file">~/Library/R</span></samp>,
e.g. <samp><span class="file">~/Library/R/3.0/library</span></samp>), and that warnings, messages and
other output to <samp><span class="file">stderr</span></samp> are highlighted in bold.
<div class="node">
<a name="Uninstalling-under-OS-X"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Multiple-versions">Multiple versions</a>,
Previous: <a rel="previous" accesskey="p" href="#Running-R-under-OS-X">Running R under OS X</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-OS-X">Installing R under OS X</a>
</div>
<h3 class="section">4.2 Uninstalling under OS X</h3>
<p>R for OS X consists of two parts: the GUI (<span class="sc">R.app</span>) and the R
framework. The un-installation is as simple as removing those folders
(e.g. by dragging them into the Trash). The typical installation will
install the GUI into the <samp><span class="file">/Applications/R.app</span></samp> folder and the R
framework into the <samp><span class="file">/Library/Frameworks/R.frameweork</span></samp> folder. This
does leave some links in <samp><span class="file">/usr/bin</span></samp>.
<p>If you want to get rid of R more completely using a Terminal, simply
run (prepend <code>sudo</code> if needed):
<pre class="example"> rm -rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/bin/R /usr/bin/Rscript
</pre>
<p>The installation consisted of three Apple packages:
<code>org.r-project.R.Leopard.fw.pkg</code>,
<code>org.r-project.R.Leopard.GUI.pkg</code> and
<code>org.r-project.x86_64.tcltk.x11</code> (not all of which need be
installed). You can use <code>pkgutil --unlink</code> (not supported by Lion
or later) to remove their files or <code>pkgutil --forget</code> if you want
the Apple Installer to forget about the package without deleting its
files (useful for the R framework when installing multiple R versions
in parallel), or after you have deleted the files.
<p>Uninstalling the Tcl/Tk component (which is installed under
<samp><span class="file">/usr/local</span></samp>) is not simple. You can list the files it installed
in a Terminal by
<pre class="example"> pkgutil --files org.r-project.x86_64.tcltk.x11
</pre>
<p class="noindent">Note that some but not all of these files replace those in the Tcl/Tk 8.5.5
installation used for R 2.x, so care is needed if removing either.
<div class="node">
<a name="Multiple-versions"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Uninstalling-under-OS-X">Uninstalling under OS X</a>,
Up: <a rel="up" accesskey="u" href="#Installing-R-under-OS-X">Installing R under OS X</a>
</div>
<h3 class="section">4.3 Multiple versions</h3>
<p>The installer will remove any previous version of the R framework
which it finds installed. This can be avoided by using <samp><span class="command">pkgutil
--forget</span></samp> (see the previous section). However, note that different
versions are installed under
<samp><span class="file">/Library/Frameworks/R.framework/Versions</span></samp> as <samp><span class="file">2.15</span></samp>,
<samp><span class="file">3.0</span></samp> and so on, so it is not possible to have different
‘<samp><span class="samp">3.x.y</span></samp>’ versions installed for the same ‘<samp><span class="samp">x</span></samp>’.
<p>A version of R can be run directly from the command-line as e.g.
<pre class="example"> /Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R
</pre>
<p class="noindent">However, <span class="sc">R.app</span> will always run the ‘current’ version, that is the last
installed version. A small utility, <samp><span class="command">Rswitch.app</span></samp> (available at
<a href="http://r.research.att.com/#other">http://r.research.att.com/#other</a>), can be used to change the
‘current’ version. However, this is of limited use as <span class="sc">R.app</span> is
compiled against a particular version of R and will likely crash if
switched to an earlier version. This may allow you to install a
development version of R (de-selecting <span class="sc">R.app</span>) and then switch back
to the release version.
<div class="node">
<a name="Running-R"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Add_002don-packages">Add-on packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-R-under-OS-X">Installing R under OS X</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">5 Running R</h2>
<p>How to start R and what command-line options are available is discussed
in <a href="R-intro.html#Invoking-R">Invoking R</a>.
<p>You should ensure that the shell has set adequate resource limits: R
expects a stack size of at least 8MB and to be able to open at least 256
file descriptors. (Any modern OS will have default limits at least as
large as these, but apparently NetBSD does not. Use the shell command
<samp><span class="command">ulimit</span></samp> (<samp><span class="command">sh</span></samp>/<samp><span class="command">bash</span></samp>) or <samp><span class="command">limit</span></samp>
(<samp><span class="command">csh</span></samp>/<samp><span class="command">tcsh</span></samp>) to check.)
<p>R makes use of a number of environment variables, the default values
of many of which are set in file <samp><var>R_HOME</var><span class="file">/etc/Renviron</span></samp> (there
are none set by default on Windows and hence no such file). These are
set at <samp><span class="command">configure</span></samp> time, and you would not normally want to
<a name="index-R_005fPAPERSIZE-30"></a>change them – a possible exception is <samp><span class="env">R_PAPERSIZE</span></samp> (see <a href="#Setting-paper-size">Setting paper size</a>). The paper size will be deduced from the ‘<samp><span class="samp">LC_PAPER</span></samp>’
locale category if it exists and <samp><span class="env">R_PAPERSIZE</span></samp> is unset, and this
will normally produce the right choice from ‘<samp><span class="samp">a4</span></samp>’ and ‘<samp><span class="samp">letter</span></samp>’
on modern Unix-alikes (but can always be overridden by setting
<samp><span class="env">R_PAPERSIZE</span></samp>).
<p>Various environment variables can be set to determine where R creates
its per-session temporary directory. The environment variables
<a name="index-TMPDIR-31"></a><a name="index-TMP-32"></a><a name="index-TEMP-33"></a><samp><span class="env">TMPDIR</span></samp>, <samp><span class="env">TMP</span></samp> and <samp><span class="env">TEMP</span></samp> are searched in turn and the
first one which is set and points to a writable area is used. If none
do, the final default is <samp><span class="file">/tmp</span></samp> on Unix-alikes and the value of
<a name="index-R_005fUSER-34"></a><samp><span class="env">R_USER</span></samp> on Windows. The path should not contain spaces.
<p>Some Unix-alike systems are set up to remove files and directories
periodically from <samp><span class="file">/tmp</span></samp>, for example by a <samp><span class="command">cron</span></samp> job
<a name="index-TMPDIR-35"></a>running <samp><span class="command">tmpwatch</span></samp>. Set <samp><span class="env">TMPDIR</span></samp> to another directory
before starting long-running jobs on such a system.
<p>Note that <samp><span class="env">TMPDIR</span></samp> will be used to execute <samp><span class="command">configure</span></samp>
scripts when installing packages, so if <samp><span class="file">/tmp</span></samp> has been mounted as
‘<samp><span class="samp">noexec</span></samp>’, <samp><span class="env">TMPDIR</span></samp> needs to be set to a directory from which
execution is allowed.
<div class="node">
<a name="Add-on-packages"></a>
<a name="Add_002don-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Internationalization">Internationalization</a>,
Previous: <a rel="previous" accesskey="p" href="#Running-R">Running R</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">6 Add-on packages</h2>
<p><a name="index-Packages-36"></a><a name="index-Libraries-37"></a>
<ul class="menu">
<li><a accesskey="1" href="#Default-packages">Default packages</a>
<li><a accesskey="2" href="#Managing-libraries">Managing libraries</a>
<li><a accesskey="3" href="#Installing-packages">Installing packages</a>
<li><a accesskey="4" href="#Updating-packages">Updating packages</a>
<li><a accesskey="5" href="#Removing-packages">Removing packages</a>
<li><a accesskey="6" href="#Setting-up-a-package-repository">Setting up a package repository</a>
<li><a accesskey="7" href="#Checking-installed-source-packages">Checking installed source packages</a>
</ul>
<p>It is helpful to use the correct terminology. A <em>package</em> is
loaded from a <em>library</em> by the function <code>library()</code>. Thus a
library is a directory containing installed packages; the main library
is <samp><var>R_HOME</var><span class="file">/library</span></samp>, but others can be used, for example by
<a name="index-R_005fLIBS-38"></a>setting the environment variable <samp><span class="env">R_LIBS</span></samp> or using the R function
<code>.libPaths()</code>.
<div class="node">
<a name="Default-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Managing-libraries">Managing libraries</a>,
Previous: <a rel="previous" accesskey="p" href="#Add_002don-packages">Add-on packages</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.1 Default packages</h3>
<p><a name="index-Packages_002c-default-39"></a>
The set of packages loaded on startup is by default
<pre class="example"> > getOption("defaultPackages")
[1] "datasets" "utils" "grDevices" "graphics" "stats" "methods"
</pre>
<p class="noindent">(plus, of course, <strong>base</strong>) and this can be changed by setting the
option in startup code (e.g. in <samp><span class="file">~/.Rprofile</span></samp>). It is initially
<a name="index-R_005fDEFAULT_005fPACKAGES-40"></a>set to the value of the environment variable <samp><span class="env">R_DEFAULT_PACKAGES</span></samp> if
set (as a comma-separated list). Setting <samp><span class="env">R_DEFAULT_PACKAGES=NULL</span></samp>
ensures that only package <strong>base</strong> is loaded.
<p>Changing the set of default packages is normally used to reduce the set
for speed when scripting: in particular not using <strong>methods</strong> will
reduce the start-up time by a factor of up to two (and this is done by
<samp><span class="command">Rscript</span></samp>). But it can also be used to customize R, e.g.
for class use.
<div class="node">
<a name="Managing-libraries"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Installing-packages">Installing packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Default-packages">Default packages</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.2 Managing libraries</h3>
<p><a name="index-Libraries_002c-managing-41"></a>
R packages are installed into <em>libraries</em>, which are
directories in the file system containing a subdirectory for each
package installed there.
<p>R comes with a single library, <samp><var>R_HOME</var><span class="file">/library</span></samp> which is
the value of the R object ‘<samp><span class="samp">.Library</span></samp>’ containing the standard and
recommended<a rel="footnote" href="#fn-9" name="fnd-9"><sup>9</sup></a> packages.
Both sites and users can create others and make use of them (or not) in
an R session. At the lowest level ‘<samp><span class="samp">.libPaths()</span></samp>’ can be used to
add paths to the collection of libraries or to report the current
collection.
<p><a name="index-Libraries_002c-site-42"></a><a name="index-Site-libraries-43"></a>R will automatically make use of a site-specific library
<samp><var>R_HOME</var><span class="file">/site-library</span></samp> if this exists (it does not in a
vanilla R installation). This location can be overridden by
setting<a rel="footnote" href="#fn-10" name="fnd-10"><sup>10</sup></a> ‘<samp><span class="samp">.Library.site</span></samp>’ in
<samp><var>R_HOME</var><span class="file">/etc/Rprofile.site</span></samp>, or (not recommended) by setting
the
<a name="index-R_005fLIBS_005fSITE-44"></a>environment variable <samp><span class="env">R_LIBS_SITE</span></samp>. Like ‘<samp><span class="samp">.Library</span></samp>’, the
site libraries are always included by ‘<samp><span class="samp">.libPaths()</span></samp>’.
<p><a name="index-Libraries_002c-user-45"></a><a name="index-User-libraries-46"></a><a name="index-R_005fLIBS_005fUSER-47"></a>Users can have one or more libraries, normally specified by the
environment variable <samp><span class="env">R_LIBS_USER</span></samp>. This has a default value (to
see it, use ‘<samp><span class="samp">Sys.getenv("R_LIBS_USER")</span></samp>’ within an R session),
but that is only used if the corresponding directory actually exists
(which by default it will not).
<p>Both <samp><span class="env">R_LIBS_USER</span></samp> and <samp><span class="env">R_LIBS_SITE</span></samp> can specify multiple
library paths, separated by colons (semicolons on Windows).
<div class="node">
<a name="Installing-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Updating-packages">Updating packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Managing-libraries">Managing libraries</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.3 Installing packages</h3>
<p><a name="index-Packages_002c-installing-48"></a>
<ul class="menu">
<li><a accesskey="1" href="#Windows-packages">Windows packages</a>
<li><a accesskey="2" href="#OS-X-packages">OS X packages</a>
<li><a accesskey="3" href="#Customizing-package-compilation">Customizing package compilation</a>
<li><a accesskey="4" href="#Multiple-sub_002darchitectures">Multiple sub-architectures</a>
<li><a accesskey="5" href="#Byte_002dcompilation">Byte-compilation</a>
</ul>
<p>Packages may be distributed in source form or compiled binary form.
Installing source packages which contain C/C++/Fortran code requires
that compilers and related tools be installed. Binary packages are
platform-specific and generally need no special tools to install, but
see the documentation for your platform for details.
<p>Note that you may need to specify implicitly or explicitly the library to
which the package is to be installed. This is only an issue if you have
more than one library, of course.
<!-- If installing packages on a Unix-alike to be used by other users, ensure -->
<!-- that the system @code{umask} is set to give sufficient permissions (see -->
<!-- also @code{Sys.umask} in @R{}). (To a large extent this is unnecessary -->
<!-- in recent versions of @R{}, which install packages as if @code{umask = 022}.) -->
<p><a name="index-TMPDIR-49"></a>Ensure that the environment variable <samp><span class="env">TMPDIR</span></samp> is either unset (and
<samp><span class="file">/tmp</span></samp> exists and can be written in and executed from) or points to
a valid temporary directory with a path not containing spaces.
<p>For most users it suffices to call
‘<samp><span class="samp">install.packages(</span><var>pkgname</var><span class="samp">)</span></samp>’ or its GUI equivalent if the
intention is to install a <acronym>CRAN</acronym> package and internet access is
available.<a rel="footnote" href="#fn-11" name="fnd-11"><sup>11</sup></a> On most systems ‘<samp><span class="samp">install.packages()</span></samp>’
will allow packages to be selected from a list box (typically with
several thousand items).
<p>To install packages from source on a Unix-alike use
<pre class="example"> R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
</pre>
<p class="noindent">The part ‘<samp><span class="samp">-l /path/to/library</span></samp>’ can be omitted, in which case the
first library of a normal R session is used (that shown by
<code>.libPaths()[1]</code>).
<p>There are a number of options available: use <code>R CMD INSTALL --help</code>
to see the current list.
<p><a name="index-install_002epackages-50"></a>Alternatively, packages can be downloaded and installed from within
R. First set the option <code>CRAN</code> to your nearest <acronym>CRAN</acronym>
mirror using <samp><span class="command">chooseCRANmirror()</span></samp>. Then download
and install packages <strong>pkg1</strong> and <strong>pkg2</strong> by
<pre class="example"> > install.packages(c("pkg1", "pkg2"))
</pre>
<p class="noindent">The essential dependencies of the specified packages will also be fetched.
Unless the library is specified (argument <code>lib</code>) the first library
in the library search path is used: if this is not writable, R will
ask the user (in an interactive session) if the default personal library
should be created, and if allowed to will install the packages there.
<p>If you want to fetch a package and all those it depends on (in any way)
that are not already installed, use e.g.
<pre class="example"> > install.packages("Rcmdr", dependencies = TRUE)
</pre>
<p><code>install.packages</code> can install a source package from a local
<samp><span class="file">.tar.gz</span></samp> file by setting argument <code>repos</code> to <code>NULL</code>:
this will be selected automatically if the name given is a single
<samp><span class="file">.tar.gz</span></samp> file.
<p><code>install.packages</code> can look in several repositories, specified as a
character vector by the argument <code>repos</code>: these can include a
<acronym>CRAN</acronym> mirror, Bioconductor, Omegahat, R-forge, rforge.net,
local archives, local files, <small class="dots">...</small>). Function
<code>setRepositories()</code> can select amongst those repositories that the
R installation is aware of.
<p>Naive users sometimes forget that as well as installing a package, they
have to use <code>library</code> to make its functionality available.
<div class="node">
<a name="Windows-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#OS-X-packages">OS X packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-packages">Installing packages</a>,
Up: <a rel="up" accesskey="u" href="#Installing-packages">Installing packages</a>
</div>
<h4 class="subsection">6.3.1 Windows</h4>
<p>What <code>install.packages</code> does by default is different on Unix-alikes
(except OS X) and Windows. On Unix-alikes it consults the list of
available <em>source</em> packages on <acronym>CRAN</acronym> (or other
repository/ies), downloads the latest version of the package sources,
and installs them (via <code>R CMD INSTALL</code>). On Windows it looks (by
default) at the list of <em>binary</em> versions of packages available for
your version of R and downloads the latest versions (if any),
although optionally it will also download and install a source package
by setting the <code>type</code> argument.
<p>On Windows <code>install.packages</code> can also install a binary package
from a local <samp><span class="file">zip</span></samp> file by setting argument <code>repos</code> to
<code>NULL</code>. <code>Rgui.exe</code> has a menu <code>Packages</code> with a GUI
interface to <code>install.packages</code>, <code>update.packages</code> and
<code>library</code>.
<p>Windows binary packages for R are distributed as a single binary
containing either or both architectures.
<p>A few of the binary packages need other software to be installed on your
system: see for example
<a href="http://CRAN.R-project.org/bin/windows/contrib/3.0/@ReadMe">http://CRAN.R-project.org/bin/windows/contrib/3.0/@ReadMe</a>.
For 64-bit builds, packages using Gtk+ (<a href="http://CRAN.R-project.org/package=Cairo"><strong>Cairo</strong></a>,
<a href="http://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>, <a href="http://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them)
need the <samp><span class="file">bin</span></samp> directory of a bundled distribution from
<a href="http://www.gtk.org/download-windows-64bit.html">http://www.gtk.org/download-windows-64bit.html</a> in the path: it
should work to have both 32- and 64-bit Gtk+ <samp><span class="file">bin</span></samp> directories in
the path on a 64-bit version of R.
<p><samp><span class="command">R CMD INSTALL</span></samp> works in Windows to install source packages. No
additional tools are needed if the package does not contain compiled
code, and <code>install.packages(type="source")</code> will work for such
packages (and for those with compiled code if the tools (see <a href="#The-Windows-toolset">The Windows toolset</a>) are in the path). We have seen occasional permission
problems after unpacking source packages on some Vista/Windows 7/Server
2008 systems: these have been circumvented by setting the environment
variable <samp><span class="env">R_INSTALL_TAR</span></samp> to ‘<samp><span class="samp">tar.exe</span></samp>’.
<a name="index-R_005fINSTALL_005fTAR-51"></a>
If you have only a source package that is known to work with current
R and just want a binary Windows build of it, you could make use of
the building service offered at
<a href="http://win-builder.r-project.org/">http://win-builder.r-project.org/</a>.
<p>For almost all packages <samp><span class="command">R CMD INSTALL</span></samp> will attempt to install
both 32- and 64-bit builds of a package if run from a 32/64-bit install
of R. It will report success if the installation of the architecture
of the running <samp><span class="command">R</span></samp> succeeded, whether or not the other
architecture was successfully installed. The exceptions are packages
with a non-empty <samp><span class="file">configure.win</span></samp> script or which make use of
<samp><span class="file">src/Makefile.win</span></samp>. If <samp><span class="file">configure.win</span></samp> does something
appropriate to both architectures use<a rel="footnote" href="#fn-12" name="fnd-12"><sup>12</sup></a> option
<samp><span class="option">--force-biarch</span></samp>: otherwise <samp><span class="command">R CMD INSTALL
--merge-multiarch</span></samp> can be applied to a source tarball to merge separate
32- and 64-bit installs. (This can only be applied to a tarball, and
will only succeed if both installs succeed.)
<p>If you have a package without compiled code and no Windows-specific
help, you can zip up an installation on another OS and install from the
that zip file on Windows. However, such a package can be installed from
the sources on Windows without any additional tools.
<p><a name="index-LOCAL_005fSOFT-52"></a>There is provision to make use of a system-wide library of installed
external software by setting the <samp><span class="command">make</span></samp> variable
<code>LOCAL_SOFT</code>, to give an equivalent of <samp><span class="file">/usr/local</span></samp> on a
Unix-alike. This can be set in <samp><span class="file">src/gnuwin/MkRules.local</span></samp> when
R is built from sources (see the comments in
<samp><span class="file">src/gnuwin/MkRules.dist</span></samp>), or in file<a rel="footnote" href="#fn-13" name="fnd-13"><sup>13</sup></a> <samp><span class="file">etc/i386/Makeconf</span></samp> or <samp><span class="file">etc/x64/Makeconf</span></samp> for an
installed version of R. The version used by <acronym>CRAN</acronym> can be
downloaded from <a href="http://www.stats.ox.ac.uk/pub/Rtools/libs.html">http://www.stats.ox.ac.uk/pub/Rtools/libs.html</a>.
<div class="node">
<a name="OS-X-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Customizing-package-compilation">Customizing package compilation</a>,
Previous: <a rel="previous" accesskey="p" href="#Windows-packages">Windows packages</a>,
Up: <a rel="up" accesskey="u" href="#Installing-packages">Installing packages</a>
</div>
<h4 class="subsection">6.3.2 OS X</h4>
<p>On OS X <code>install.packages</code> works as it does on other Unix-alike
systems, but there is an additional type <code>mac.binary</code> (the default
in the <acronym>CRAN</acronym> distribution but not when compiling from source)
that can be passed to <code>install.packages</code> in order to download and
install binary packages from a suitable repository. These OS X binary
package files have the extension ‘<samp><span class="samp">tgz</span></samp>’. The <span class="sc">R.app</span> GUI provides
menus for installation of either binary or source packages, from
<acronym>CRAN</acronym> or local files.
<p>Note that many binary packages including compiled code are tied to a
particular series (e.g. R 3.0.x or 3.1.x) of R.
<p>Installing source packages which do not contain compiled code should
work with no additional tools. For others you will need the `Command
Line Tools' for <samp><span class="command">Xcode</span></samp> and compilers which match those used to
build R: see <a href="#OS-X">OS X</a>.
<p>Package <a href="http://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and those which depend on it need a Java runtime
installed and several packages need X11 installed, including those using
Tk. For Mountain Lion and Mavericks see <a href="#OS-X">OS X</a> and <a href="#Java-_0028OS-X_0029">Java (OS X)</a>.
<p>Tcl/Tk extensions <code>BWidget</code> and <code>Tktable</code> are part of the
Tcl/Tk contained in the R installer. These are required by a number
of <acronym>CRAN</acronym> and Bioconductor packages.
<p>A few of the binary packages need other software to be installed on your
system. In particular packages using Gtk+ (<a href="http://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>,
<a href="http://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them) need the GTK
framework installed from <a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a>: the
appropriate version at the time of writing was
<a href="http://r.research.att.com/libs/GTK_2.24.17-X11.pkg">http://r.research.att.com/libs/GTK_2.24.17-X11.pkg</a>
<p>It is often possible to use other compilers with the <acronym>CRAN</acronym>
distribution of R, but the settings in the file
<samp><span class="file">/Library/Frameworks/R.framework/Resources/etc/Makeconf</span></samp> will need
to be changed, either by editing that file or in a file such as
<samp><span class="file">~/.R/Makevars</span></samp> (see the next section). Entries which may need to
be changed include ‘<samp><span class="samp">CC</span></samp>’, ‘<samp><span class="samp">CXX</span></samp>’, ‘<samp><span class="samp">FC</span></samp>’, ‘<samp><span class="samp">F77</span></samp>’,
‘<samp><span class="samp">FLIBS</span></samp>’ and the corresponding flags, and perhaps ‘<samp><span class="samp">CXXCPP</span></samp>’,
‘<samp><span class="samp">DYLIB_LD</span></samp>’, ‘<samp><span class="samp">MAIN_LD</span></samp>’, ‘<samp><span class="samp">SHLIB_CXXLD</span></samp>’, ‘<samp><span class="samp">SHLIB_FCLD</span></samp>’
and ‘<samp><span class="samp">SHLIB_LD</span></samp>’.
<p>So for example you could select <samp><span class="command">clang</span></samp> for both C and C++ with
extensive checking by having in <samp><span class="file">~/.R/Makevars</span></samp>
<pre class="example"> CC=clang
CXX=clang++
CFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
CXXFLAGS="-mtune=native -g -O2 -Wall -pedantic -Wconversion"
</pre>
<p class="noindent">(this is expected to become necessary once Xcode 5 is released) and
for another version of <samp><span class="command">gfortran-4.2</span></samp> we needed
<pre class="example"> FLIBS=-lgfortran
</pre>
<div class="node">
<a name="Customizing-package-compilation"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Multiple-sub_002darchitectures">Multiple sub-architectures</a>,
Previous: <a rel="previous" accesskey="p" href="#OS-X-packages">OS X packages</a>,
Up: <a rel="up" accesskey="u" href="#Installing-packages">Installing packages</a>
</div>
<h4 class="subsection">6.3.3 Customizing package compilation</h4>
<p>The R system and package-specific compilation flags can be overridden or
added to by setting the appropriate Make variables in the personal file
<samp><var>HOME</var><span class="file">/.R/Makevars-</span><var>R_PLATFORM</var></samp> (but
<samp><var>HOME</var><span class="file">/.R/Makevars.win</span></samp> or <samp><var>HOME</var><span class="file">/.R/Makevars.win64</span></samp>
on Windows), or if that does not exist, <samp><var>HOME</var><span class="file">/.R/Makevars</span></samp>,
where ‘<samp><span class="samp">R_PLATFORM</span></samp>’ is the platform for which R was built, as
available in the <code>platform</code> component of the R variable
<code>R.version</code>. An alternative personal file can be specified
<em>via</em> the environment variable <samp><span class="env">R_MAKEVARS_USER</span></samp>.
<p>Package developers are encouraged to use this mechanism to enable a
reasonable amount of diagnostic messaging (“warnings”) when compiling,
such as e.g. <samp><span class="option">-Wall -pedantic</span></samp> for tools from GCC, the Gnu
Compiler Collection.
<p>Note that this mechanism can also be used when it necessary to change
the optimization level for a particular package. For example
<pre class="example"> ## <span class="roman">for C code</span>
CFLAGS=-g -O -mtune=native
## <span class="roman">for C++ code</span>
CXXFLAGS=-g -O -mtune=native
## <span class="roman">for Fortran code</span>
FFLAGS=-g -O -mtune=native
## <span class="roman">for Fortran 95 code</span>
FCFLAGS=-g -O -mtune=native
</pre>
<p>There is also provision for a site-wide <samp><span class="file">Makevars.site</span></samp> file under
<samp><var>R_HOME</var><span class="file">/etc</span></samp> (in a sub-architecture-specific directory if
appropriate). This is read immediately after <samp><span class="file">Makeconf</span></samp>, and an
alternative file can be specified by environment variable
<samp><span class="env">R_MAKEVARS_SITE</span></samp>.
<div class="node">
<a name="Multiple-sub-architectures"></a>
<a name="Multiple-sub_002darchitectures"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Byte_002dcompilation">Byte-compilation</a>,
Previous: <a rel="previous" accesskey="p" href="#Customizing-package-compilation">Customizing package compilation</a>,
Up: <a rel="up" accesskey="u" href="#Installing-packages">Installing packages</a>
</div>
<h4 class="subsection">6.3.4 Multiple sub-architectures</h4>
<p>When installing packages from their sources, there are some extra
considerations on installations which use sub-architectures. These are
commonly used on Windows but can in principle be used on other
platforms.
<p>When a source package is installed by a build of R which supports
multiple sub-architectures, the normal installation process installs the
packages for all sub-architectures. The exceptions are
<dl>
<dt><em>Unix-alikes</em><dd>
where there is an <samp><span class="file">configure</span></samp> script, or a file <samp><span class="file">src/Makefile</span></samp>.
<br><dt><em>Windows</em><dd>
where there is a non-empty <samp><span class="file">configure.win</span></samp> script, or a file
<samp><span class="file">src/Makefile.win</span></samp> (with some exceptions where the package is known
to have an architecture-independent <samp><span class="file">configure.win</span></samp>, or if
<samp><span class="option">--force-biarch</span></samp> or a field in the <samp><span class="file">DESCRIPTION</span></samp> file is
used to assert so).
</dl>
<p class="noindent">In those cases only the current architecture is installed. Further
sub-architectures can be installed by
<pre class="example"> R CMD INSTALL --libs-only <var>pkg</var>
</pre>
<p class="noindent">using the path to <samp><span class="command">R</span></samp> or <samp><span class="command">R --arch</span></samp> to select the
additional sub-architecture. There is also <samp><span class="command">R CMD INSTALL
--merge-multiarch</span></samp> to build and merge the two architectures, starting
with a source tarball.
<div class="node">
<a name="Byte-compilation"></a>
<a name="Byte_002dcompilation"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Multiple-sub_002darchitectures">Multiple sub-architectures</a>,
Up: <a rel="up" accesskey="u" href="#Installing-packages">Installing packages</a>
</div>
<h4 class="subsection">6.3.5 Byte-compilation</h4>
<p>The base and recommended packages are byte-compiled by default. Other
packages can be byte-compiled on installation by using the option
<samp><span class="option">--byte-compile</span></samp> with <samp><span class="command">R CMD INSTALL</span></samp> or with
<code>install.packages(type = "source")</code>.
<p>Not all contributed packages work correctly when byte-compiled (for
example because they interfere with the sealing of namespaces). For
most packages (especially those which make extensive use of compiled
code) the speed-up is small. Unless a package is used frequently the
time spent in byte-compilation can outweigh the time saved in execution:
also byte-compilation can add substantially to the installed size of the
package.
<p>Byte-compilation can be controlled on a per-package basis by the
‘<samp><span class="samp">ByteCompile</span></samp>’ field in the <samp><span class="file">DESCRIPTION</span></samp> file.
<div class="node">
<a name="Updating-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Removing-packages">Removing packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Installing-packages">Installing packages</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.4 Updating packages</h3>
<p><a name="index-update_002epackages-53"></a><a name="index-Packages_002c-updating-54"></a>
The command <code>update.packages()</code> is the simplest way to ensure that
all the packages on your system are up to date. It downloads the list
of available packages and their current versions, compares it with those
installed and offers to fetch and install any that have later versions
on the repositories.
<p>An alternative interface to keeping packages up-to-date is provided by
the command <code>packageStatus()</code>, which returns an object with
information on all installed packages and packages available at multiple
repositories. The <code>print</code> and <code>summary</code> methods give an
overview of installed and available packages, the <code>upgrade</code> method
offers to fetch and install the latest versions of outdated packages.
<p>One sometimes-useful additional piece of information that
<code>packageStatus()</code> returns is the status of a package, as
<code>"ok"</code>, <code>"upgrade"</code> or <code>"unavailable"</code> (in the currently
selected repositories). For example
<pre class="example"> > inst <- packageStatus()$inst
> inst[inst$Status != "ok", c("Package", "Version", "Status")]
Package Version Status
Biobase Biobase 2.8.0 unavailable
RCurl RCurl 1.4-2 upgrade
Rgraphviz Rgraphviz 1.26.0 unavailable
rgdal rgdal 0.6-27 upgrade
</pre>
<div class="node">
<a name="Removing-packages"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Setting-up-a-package-repository">Setting up a package repository</a>,
Previous: <a rel="previous" accesskey="p" href="#Updating-packages">Updating packages</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.5 Removing packages</h3>
<p><a name="index-remove_002epackages-55"></a><a name="index-Packages_002c-removing-56"></a>
Packages can be removed in a number of ways. From a command prompt they
can be removed by
<pre class="example"> R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> ...
</pre>
<p>From a running R process they can be removed by
<pre class="example"> > remove.packages(c("pkg1", "pkg2"),
lib = file.path("path", "to", "library"))
</pre>
<p>Finally, in most installations one can just remove the package directory
from the library.
<div class="node">
<a name="Setting-up-a-package-repository"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Checking-installed-source-packages">Checking installed source packages</a>,
Previous: <a rel="previous" accesskey="p" href="#Removing-packages">Removing packages</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.6 Setting up a package repository</h3>
<p><a name="index-Repositories-57"></a>
Utilities such as <code>install.packages</code> can be pointed at any
<acronym>CRAN</acronym>-style repository, and R users may want to set up their
own. The ‘base’ of a repository is a URL such as
<a href="http://www.omegahat.org/R/">http://www.omegahat.org/R/</a>: this must be an URL scheme that
<code>download.packages</code> supports (which also includes ‘<samp><span class="samp">ftp://</span></samp>’ and
‘<samp><span class="samp">file://</span></samp>’, but not on most systems ‘<samp><span class="samp">https://</span></samp>’). Under that
base URL there should be directory trees for one or more of the
following types of package distributions:
<ul>
<li><code>"source"</code>: located at <samp><span class="file">src/contrib</span></samp> and containing
<samp><span class="file">.tar.gz</span></samp> files. Other forms of compression can be used, e.g.
<samp><span class="file">.tar.bz2</span></samp> or <samp><span class="file">.tar.xz</span></samp> files. Complete repositories contain
the sources corresponding to any binary packages, and in any case it is
wise to have a <samp><span class="file">src/contrib</span></samp> area with a possibly empty
<samp><span class="file">PACKAGES</span></samp> file.
<li><code>"win.binary"</code>: located at <samp><span class="file">bin/windows/contrib/</span><var>x.y</var></samp> for
R versions <var>x.y.z</var> and containing <samp><span class="file">.zip</span></samp> files for Windows.
<li><code>"mac.binary"</code>: located at
<samp><span class="file">bin/macosx/contrib/</span><var>3.y</var></samp> for R versions
<var>3.y.z</var> and containing <samp><span class="file">.tgz</span></samp> files.
<li><code>"mac.binary.leopard"</code>: located at
<samp><span class="file">bin/macosx/leopard/contrib/</span><var>2.y</var></samp> for R versions
<var>2.y.z</var> and containing <samp><span class="file">.tgz</span></samp> files.
</ul>
<p>Each terminal directory must also contain a <samp><span class="file">PACKAGES</span></samp> file. This
can be a concatenation of the <samp><span class="file">DESCRIPTION</span></samp> files of the packages
separated by blank lines, but only a few of the fields are needed. The
simplest way to set up such a file is to use function
<code>write_PACKAGES</code> in the <strong>tools</strong> package, and its help explains
which fields are needed. Optionally there can also be a
<samp><span class="file">PACKAGES.gz</span></samp> file, a <samp><span class="command">gzip</span></samp>-compressed version of
<samp><span class="file">PACKAGES</span></samp>—as this will be downloaded in preference to
<samp><span class="file">PACKAGES</span></samp> it should be included for large repositories. (If you
have a mis-configured server that does not report correctly non-existent
files you may need <samp><span class="file">PACKAGES.gz</span></samp>.)
<p>To add your repository to the list offered by <code>setRepositories()</code>,
see the help file for that function.
<p>Incomplete repositories are better specified <em>via</em> a
<code>contriburl</code> argument than <em>via</em> being set as a repository.
<p>A repository can contain subdirectories, when the descriptions in the
<samp><span class="file">PACKAGES</span></samp> file of packages in subdirectories must include a line
of the form
<pre class="example"> Path: <var>path/to/subdirectory</var>
</pre>
<p class="noindent">—once again <code>write_PACKAGES</code> is the simplest way to set this up.
<div class="node">
<a name="Checking-installed-source-packages"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Setting-up-a-package-repository">Setting up a package repository</a>,
Up: <a rel="up" accesskey="u" href="#Add_002don-packages">Add-on packages</a>
</div>
<h3 class="section">6.7 Checking installed source packages</h3>
<p>It can be convenient to run <samp><span class="command">R CMD check</span></samp> on an installed
package, particularly on a platform which uses sub-architectures. The
outline of how to do this is, with the source package in directory
<samp><var>pkg</var></samp> (or a tarball filename):
<pre class="example"> R CMD INSTALL -l <var>libdir</var> <var>pkg</var> > <var>pkg</var>.log 2>&1
R CMD check -l <var>libdir</var> --install=check:<var>pkg</var>.log <var>pkg</var>
</pre>
<p class="noindent">Where sub-architectures are in use the <samp><span class="command">R CMD check</span></samp> line can be
repeated with additional architectures by
<pre class="example"> R --arch <var>arch</var> CMD check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
</pre>
<p class="noindent">where <samp><span class="option">--extra-arch</span></samp> selects only those checks which depend on
the installed code and not those which analyse the sources. (If
multiple sub-architectures fail only because they need different
settings, e.g. environment variables, <samp><span class="option">--no-multiarch</span></samp> may need
to be added to the <code>INSTALL</code> lines.) On Unix-alikes the
architecture to run is selected by <samp><span class="option">--arch</span></samp>: this can also be
used on Windows with <samp><var>R_HOME</var><span class="file">/bin/R.exe</span></samp>, but it is more usual
to select the path to the <samp><span class="command">Rcmd.exe</span></samp> of the desired
architecture.
<p>So on Windows to install, check and package for distribution a source
package from a tarball which has been tested on another platform one
might use
<pre class="example"> .../bin/i386/Rcmd INSTALL -l <var>libdir</var> <var>tarball</var> --build > <var>pkg</var>.log 2>&1
.../bin/i386/Rcmd check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
.../bin/x64/Rcmd check -l <var>libdir</var> --extra-arch --install=check:<var>pkg</var>.log <var>pkg</var>
</pre>
<p class="noindent">where one might want to run the second and third lines in a different
shell with different settings for environment variables and the path (to
find external software, notably for Gtk+).
<p><samp><span class="command">R CMD INSTALL</span></samp> can do a <code>i386</code> install and then add the
<code>x64</code> DLL from a single command by
<pre class="example"> R CMD INSTALL --merge-multiarch -l <var>libdir</var> <var>tarball</var>
</pre>
<p class="noindent">and <samp><span class="option">--build</span></samp> can be added to zip up the installation.
<div class="node">
<a name="Internationalization"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Choosing-between-32_002d-and-64_002dbit-builds">Choosing between 32- and 64-bit builds</a>,
Previous: <a rel="previous" accesskey="p" href="#Add_002don-packages">Add-on packages</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">7 Internationalization and Localization</h2>
<p><a name="index-Internationalization-58"></a><a name="index-Localization-59"></a>
<em>Internationalization</em> refers to the process of enabling support
for many human languages, and <em>localization</em> to adapting to a
specific country and language.
<!-- Prior to 2005 @R{} worked in the ISO Latin-1 8-bit character set and so -->
<!-- covered English and most Western European languages (if not necessarily -->
<!-- their currency symbols). Since @R{} 2.1.0 it has supported Eastern -->
<!-- European 8-bit character sets, and multi-byte character sets such as -->
<!-- UTF-8 and others used for Chinese, Japanese and Korean. -->
<p>Current builds of R support all the character sets that the
underlying OS can handle. These are interpreted according to the
<a name="index-Locale-60"></a>current <code>locale</code>, a sufficiently complicated topic to merit a
separate section. Note though that R has no built-in support for
right-to-left languages and bidirectional output, relying on the OS
services. For example, how character vectors in UTF-8 containing both
English digits and Hebrew characters are printed is OS-dependent (and
perhaps locale-dependent).
<p>The other aspect of the internationalization is support for the
translation of messages. This is enabled in almost all builds of R.
<ul class="menu">
<li><a accesskey="1" href="#Locales">Locales</a>
<li><a accesskey="2" href="#Localization-of-messages">Localization of messages</a>
</ul>
<div class="node">
<a name="Locales"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Localization-of-messages">Localization of messages</a>,
Previous: <a rel="previous" accesskey="p" href="#Internationalization">Internationalization</a>,
Up: <a rel="up" accesskey="u" href="#Internationalization">Internationalization</a>
</div>
<h3 class="section">7.1 Locales</h3>
<p><a name="index-Locale-61"></a>
A <em>locale</em> is a description of the local environment of the user,
including the preferred language, the encoding of characters, the
currency used and its conventions, and so on. Aspects of the locale are
accessed by the R functions <code>Sys.getlocale</code> and
<code>Sys.localeconv</code>.
<p>The system of naming locales is OS-specific. There is quite wide
agreement on schemes, but not on the details of their implementation. A
locale needs to specify
<ul>
<li>A human language. These are generally specified by a lower-case
two-character abbreviation following ISO 639 (see e.g.
<a href="http://en.wikipedia.org/wiki/ISO_639-1">http://en.wikipedia.org/wiki/ISO_639-1</a>).
<li>A ‘territory’, used mainly to specify the currency. These are generally
specified by an upper-case two-character abbreviation following ISO 3166
(see e.g. <a href="http://en.wikipedia.org/wiki/ISO_3166">http://en.wikipedia.org/wiki/ISO_3166</a>).
<li>A charset encoding, which determines both how a byte stream should be
divided into characters, and which characters the subsequences of bytes
represent. Sometimes the combination of language and territory is used
to specify the encoding, for example to distinguish between traditional
and simplified Chinese.
<li>Optionally, a modifier, for example to indicate that Austria is to be
considered pre- or post-Euro. The modifier is also used to indicate the
script (<code>@latin</code>, <code>@cyrillic</code> for Serbian, <code>@iqtelif</code>)
or language dialect (e.g. <code>@saaho</code>, a dialect of Afar, and
<code>@bokmal</code> and <code>@nynorsk</code>, dialects of Norwegian regarded by
some OSes as separate languages, <code>no</code> and <code>nn</code>).
</ul>
<p>R is principally concerned with the first (for translations) and
third. Note that the charset may be deducible from the language, as
some OSes offer only one charset per language, and most OSes have only
one charset each for most languages.
<ul class="menu">
<li><a accesskey="1" href="#Locales-under-Unix_002dalikes">Locales under Unix-alikes</a>
<li><a accesskey="2" href="#Locales-under-Windows">Locales under Windows</a>
<li><a accesskey="3" href="#Locales-under-OS-X">Locales under OS X</a>
</ul>
<div class="node">
<a name="Locales-under-Unix-alikes"></a>
<a name="Locales-under-Unix_002dalikes"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Locales-under-Windows">Locales under Windows</a>,
Previous: <a rel="previous" accesskey="p" href="#Locales">Locales</a>,
Up: <a rel="up" accesskey="u" href="#Locales">Locales</a>
</div>
<h4 class="subsection">7.1.1 Locales under Unix-alikes</h4>
<p>Modern Linux uses the XPG<a rel="footnote" href="#fn-14" name="fnd-14"><sup>14</sup></a> locale specifications which have the form
‘<samp><span class="samp">en_GB</span></samp>’, ‘<samp><span class="samp">en_GB.UTF-8</span></samp>’, ‘<samp><span class="samp">aa_ER.UTF-8@saaho</span></samp>’,
‘<samp><span class="samp">de_AT.iso885915@euro</span></samp>’, the components being in the order listed
above. (See <samp><span class="command">man locale</span></samp> and <samp><span class="command">locale -a</span></samp> for more
details.) Similar schemes are used by most Unix-alikes: some (including
some distributions of Linux) use ‘<samp><span class="samp">.utf8</span></samp>’ rather than ‘<samp><span class="samp">.UTF-8</span></samp>’.
<p>Note that whereas UTF-8 locales are nowadays almost universally used,
locales such as ‘<samp><span class="samp">en_GB</span></samp>’ use 8-bit encodings for backwards
compatibility.
<div class="node">
<a name="Locales-under-Windows"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Locales-under-OS-X">Locales under OS X</a>,
Previous: <a rel="previous" accesskey="p" href="#Locales-under-Unix_002dalikes">Locales under Unix-alikes</a>,
Up: <a rel="up" accesskey="u" href="#Locales">Locales</a>
</div>
<h4 class="subsection">7.1.2 Locales under Windows</h4>
<p>Windows also uses locales, but specified in a rather less concise way.
Most users will encounter locales only via drop-down menus, but more
information and lists can be found at
<a href="http://msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80)">http://msdn.microsoft.com/en-us/library/hzz3tw78(v=vs.80)</a>
(or if Microsoft moves it yet again, search for ‘<samp><span class="samp">Windows language
country strings</span></samp>’).
<p>It offers only one encoding per language.
<p>Some care is needed with Windows' locale names. For example,
<code>chinese</code> is Traditional Chinese and not Simplified Chinese as used
in most of the Chinese-speaking world.
<div class="node">
<a name="Locales-under-OS-X"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Locales-under-Windows">Locales under Windows</a>,
Up: <a rel="up" accesskey="u" href="#Locales">Locales</a>
</div>
<h4 class="subsection">7.1.3 Locales under OS X</h4>
<p>OS X supports locales in its own particular way, but the R GUI tries to
make this easier for users. See
<a href="http://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/">http://developer.apple.com/documentation/MacOSX/Conceptual/BPInternational/</a>
for how users can set their locales. As with Windows, end users will
generally only see lists of languages/territories. Users of R in a
terminal may need to set the locale to something like ‘<samp><span class="samp">en_GB.UTF-8</span></samp>’
if it defaults to ‘<samp><span class="samp">C</span></samp>’ (as it sometimes does when logging it
remotely and in batch jobs: note whether <samp><span class="command">Terminal</span></samp> sets the
<samp><span class="env">LANG</span></samp> environment variable is an (advanced) option, but the
default).
<p>Internally OS X uses a form similar to Linux: the main difference from
other Unix-alikes is that where a character set is not specified it is
assumed to be <code>UTF-8</code>.
<div class="node">
<a name="Localization-of-messages"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Locales">Locales</a>,
Up: <a rel="up" accesskey="u" href="#Internationalization">Internationalization</a>
</div>
<h3 class="section">7.2 Localization of messages</h3>
<p>The preferred language for messages is by default taken from the locale.
This can be overridden first by the setting of the environment variable
<a name="index-LANGUAGE-62"></a><a name="index-LC_005fALL-63"></a><a name="index-LC_005fMESSAGES-64"></a><a name="index-LANG-65"></a><samp><span class="env">LANGUAGE</span></samp> and then<a rel="footnote" href="#fn-15" name="fnd-15"><sup>15</sup></a>
by the environment variables <samp><span class="env">LC_ALL</span></samp>, <samp><span class="env">LC_MESSAGES</span></samp> and
<samp><span class="env">LANG</span></samp>. (The last three are normally used to set the locale and so
should not be needed, but the first is only used to select the language
for messages.) The code tries hard to map locales to languages, but on
some systems (notably Windows) the locale names needed for the
environment variable <samp><span class="env">LC_ALL</span></samp> do not all correspond to XPG language
names and so <samp><span class="env">LANGUAGE</span></samp> may need to be set. (One example is
‘<samp><span class="samp">LC_ALL=es</span></samp>’ on Windows which sets the locale to Estonian and the
language to Spanish.)
<p>It is usually possible to change the language once R is running
<em>via</em> (not Windows) <code>Sys.setlocale("LC_MESSAGES",
"new_locale")</code>, or by setting an environment variable such as
<samp><span class="env">LANGUAGE</span></samp>, <em>provided</em><a rel="footnote" href="#fn-16" name="fnd-16"><sup>16</sup></a> the language you are changing to can be output in
the current character set. But this is OS-specific, and has been known
to stop working on an OS upgrade.
<p>Messages are divided into <em>domains</em>, and translations may be
available for some or all messages in a domain. R makes use of the
following domains.
<ul>
<li>Domain <code>R</code> for the C-level error and warning messages from the R
interpreter.
<li>Domain <code>R-</code><var>pkg</var> for the R <code>stop</code>, <code>warning</code> and
<code>message</code> messages in each package, including <code>R-base</code> for the
<strong>base</strong> package.
<li>Domain <var>pkg</var> for the C-level messages in each package.
<li>Domain <code>RGui</code> for the menus etc of the R for Windows GUI front-end.
</ul>
<p>Dividing up the messages in this way allows R to be extensible: as
packages are loaded, their message translation catalogues can be loaded
too.
<p>R can be built without support for translations, but it is enabled by
default.
<p>R-level and C-level domains are subtly different, for example in the way
strings are canonicalized before being passed for translation.
<p>Translations are looked for by domain according to the currently
specified language, as specifically as possible, so for example an
Austrian (‘<samp><span class="samp">de_AT</span></samp>’) translation catalogue will be used in preference
to a generic German one (‘<samp><span class="samp">de</span></samp>’) for an Austrian user. However, if a
specific translation catalogue exists but does not contain a
translation, the less specific catalogues are consulted. For example,
R has catalogues for ‘<samp><span class="samp">en_GB</span></samp>’ that translate the Americanisms
(e.g., ‘<samp><span class="samp">gray</span></samp>’) in the standard messages into English.<a rel="footnote" href="#fn-17" name="fnd-17"><sup>17</sup></a> Two other examples: there are catalogues
for ‘<samp><span class="samp">es</span></samp>’, which is Spanish as written in Spain and these will by
default also be used in Spanish-speaking Latin American countries, and
also for ‘<samp><span class="samp">pt_BR</span></samp>’, which are used for Brazilian locales but not for
locales specifying Portugal.
<p>Translations in the right language but the wrong charset are made use of
<a name="index-LANGUAGE-66"></a>by on-the-fly re-encoding. The <samp><span class="env">LANGUAGE</span></samp> variable (only) can be a
colon-separated list, for example ‘<samp><span class="samp">se:de</span></samp>’, giving a set of
languages in decreasing order of preference. One special value is
‘<samp><span class="samp">en@quot</span></samp>’, which can be used in a UTF-8 locale to have American
error messages with pairs of single quotes translated to Unicode directional
quotes.
<p>If no suitable translation catalogue is found or a particular message is
not translated in any suitable catalogue, ‘English’<a rel="footnote" href="#fn-18" name="fnd-18"><sup>18</sup></a> is used.
<p>See <a href="http://developer.r-project.org/Translations.html">http://developer.r-project.org/Translations.html</a> for how to
prepare and install translation catalogues.
<div class="node">
<a name="Choosing-between-32--and-64-bit-builds"></a>
<a name="Choosing-between-32_002d-and-64_002dbit-builds"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#The-standalone-Rmath-library">The standalone Rmath library</a>,
Previous: <a rel="previous" accesskey="p" href="#Internationalization">Internationalization</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">8 Choosing between 32- and 64-bit builds</h2>
<p>Almost all current <acronym>CPU</acronym>s have both 32- and 64-bit sets of
instructions. Most OSes running on such <acronym>CPU</acronym>s offer the choice
of building a 32-bit or a 64-bit version of R (and details are given
below under specific OSes). For most a 32-bit version is the default,
but for some (e.g., ‘<samp><span class="samp">x86_64</span></samp>’ Linux and OS X >= 10.6)
64-bit is.
<p>All current versions of R use 32-bit integers and
<acronym>ISO</acronym>/<acronym>IEC</acronym> 60559<a rel="footnote" href="#fn-19" name="fnd-19"><sup>19</sup></a> double-precision reals, and so compute to
the same precision<a rel="footnote" href="#fn-20" name="fnd-20"><sup>20</sup></a> and with the same limits on the sizes of
numerical quantities. The principal difference is in the size of the
pointers.
<p>64-bit builds have both advantages and disadvantages:
<ul>
<li>The total virtual memory space made available to a 32-bit process is
limited by the pointer size to 4GB, and on most OSes to 3GB (or even
2GB). The limits for 64-bit processes are much larger (e.g.
8–128TB).
<p>R allocates memory for large objects as needed, and removes any
unused ones at garbage collection. When the sizes of objects become an
appreciable fraction of the address limit, fragmentation of the address
space becomes an issue and there may be no hole available that is the
size requested. This can cause more frequent garbage collection or the
inability to allocate large objects. As a guide, this will become an
issue with objects more than 10% of the size of the address space
(around 300Mb) or when the total size of objects in use is around one
third (around 1Gb).
<li>Only 64-bit builds support ‘long vectors’, those with 2^31 or
more elements (each of which needs at least 8GB of storage, 16GB for a
numeric vector).
<li>Most 32-bit OSes by default limit file sizes to 2GB (and this may also
apply to 32-bit builds on 64-bit OSes). This can often be worked
around: and <samp><span class="command">configure</span></samp> selects suitable defines if this is
possible. (We have also largely worked around that limit on 32-bit
Windows.) 64-bit builds have much larger limits.
<li>Because the pointers are larger, R's basic structures are larger.
This means that R objects take more space and (usually) more time to
manipulate. So 64-bit builds of R will, all other things being
equal, run slower than 32-bit builds. (On Sparc Solaris the difference
was 15-20%.)
<li>However, ‘other things’ may not be equal. In the specific case of
‘<samp><span class="samp">x86_64</span></samp>’ <em>vs</em> ‘<samp><span class="samp">ix86</span></samp>’, the 64-bit CPU has features
(such as SSE2 instructions) which are guaranteed to be present but are
optional on the 32-bit CPU, and also has more general-purpose registers.
This means that on chips like a desktop Intel Core 2 Duo the vanilla
64-bit version of R has been around 10% faster on both Linux and OS
X. (Laptop CPUs are usually relatively slower in 64-bit mode.)
</ul>
<p>So, for speed you may want to use a 32-bit build (especially on a
laptop), but to handle large datasets (and perhaps large files) a 64-bit
build. You can often build both and install them in the same place:
See <a href="#Sub_002darchitectures">Sub-architectures</a>. (This is done for the Windows binary
distributions.)
<p>Even on 64-bit builds of R there are limits on the size of R
objects (see <code>help("Memory-limits")</code>, some of which stem from the
use of 32-bit integers (especially in FORTRAN code). For example, the
dimensions of an array are limited to 2^31 - 1.
<div class="node">
<a name="The-standalone-Rmath-library"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>,
Previous: <a rel="previous" accesskey="p" href="#Choosing-between-32_002d-and-64_002dbit-builds">Choosing between 32- and 64-bit builds</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="chapter">9 The standalone Rmath library</h2>
<p>The routines supporting the distribution and
special<a rel="footnote" href="#fn-21" name="fnd-21"><sup>21</sup></a> functions in R
and a few others are declared in C header file <samp><span class="file">Rmath.h</span></samp>. These
can be compiled into a standalone library for linking to other
applications. (Note that they are not a separate library when R is
built, and the standalone version differs in several ways.)
<p>The makefiles and other sources needed are in directory
<samp><span class="file">src/nmath/standalone</span></samp>, so the following instructions assume that
is the current working directory (in the build directory tree on a
Unix-alike if that is separate from the sources).
<p><samp><span class="file">Rmath.h</span></samp> contains ‘<samp><span class="samp">R_VERSION_STRING</span></samp>’, which is a character
string containing the current R version, for example <code>"3.0.0"</code>.
<p>There is full access to R's handling of <code>NaN</code>, <code>Inf</code> and
<code>-Inf</code> via special versions of the macros and functions
<pre class="example"> ISNAN, R_FINITE, R_log, R_pow and R_pow_di
</pre>
<p class="noindent">and (extern) constants <code>R_PosInf</code>, <code>R_NegInf</code> and <code>NA_REAL</code>.
<p>There is no support for R's notion of missing values, in particular
not for <code>NA_INTEGER</code> nor the distinction between <code>NA</code> and
<code>NaN</code> for doubles.
<p>A little care is needed to use the random-number routines. You will
need to supply the uniform random number generator
<pre class="example"> double unif_rand(void)
</pre>
<p class="noindent">or use the one supplied (and with a shared library or DLL you will
have to use the one supplied, which is the Marsaglia-multicarry with
an entry point
<pre class="example"> set_seed(unsigned int, unsigned int)
</pre>
<p class="noindent">to set its seeds).
<p>The facilities to change the normal random number generator are
available through the constant N01_kind. This takes values
from the enumeration type
<pre class="example"> typedef enum {
BUGGY_KINDERMAN_RAMAGE,
AHRENS_DIETER,
BOX_MULLER,
USER_NORM,
INVERSION,
KINDERMAN_RAMAGE
} N01type;
</pre>
<p class="noindent">(and ‘<samp><span class="samp">USER_NORM</span></samp>’ is not available).
<ul class="menu">
<li><a accesskey="1" href="#Unix_002dalike-standalone">Unix-alike standalone</a>
<li><a accesskey="2" href="#Windows-standalone">Windows standalone</a>
</ul>
<div class="node">
<a name="Unix-alike-standalone"></a>
<a name="Unix_002dalike-standalone"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Windows-standalone">Windows standalone</a>,
Previous: <a rel="previous" accesskey="p" href="#The-standalone-Rmath-library">The standalone Rmath library</a>,
Up: <a rel="up" accesskey="u" href="#The-standalone-Rmath-library">The standalone Rmath library</a>
</div>
<h3 class="section">9.1 Unix-alikes</h3>
<p>If R has not already be made in the directory tree,
<samp><span class="command">configure</span></samp> must be run as described in the main build
instructions.
<p>Then (in <samp><span class="file">src/nmath/standalone</span></samp>)
<pre class="example"> make
</pre>
<p class="noindent">will make standalone libraries <samp><span class="file">libRmath.a</span></samp> and <samp><span class="file">libRmath.so</span></samp>
(<samp><span class="file">libRmath.dylib</span></samp> on OS X): ‘<samp><span class="samp">make static</span></samp>’ and ‘<samp><span class="samp">make
shared</span></samp>’ will create just one of them.
<p>To use the routines in your own C or C++ programs, include
<pre class="example"> #define MATHLIB_STANDALONE
#include <Rmath.h>
</pre>
<p class="noindent">and link against ‘<samp><span class="samp">-lRmath</span></samp>’ (and ‘<samp><span class="samp">-lm</span></samp>’ if needed on your OS).
The example file <samp><span class="file">test.c</span></samp> does nothing useful, but is provided to
test the process (via <samp><span class="command">make test</span></samp>). Note that you will probably
not be able to run it unless you add the directory containing
<a name="index-LD_005fLIBRARY_005fPATH-67"></a><samp><span class="file">libRmath.so</span></samp> to the <samp><span class="env">LD_LIBRARY_PATH</span></samp> environment variable
(<samp><span class="file">libRmath.dylib</span></samp>, <samp><span class="env">DYLD_LIBRARY_PATH</span></samp> on OS X).
<p>The targets
<pre class="example"> make install
make uninstall
</pre>
<p class="noindent">will (un)install the header <samp><span class="file">Rmath.h</span></samp> and shared and static
<a name="index-DESTDIR-68"></a>libraries (if built). Both <code>prefix=</code> and <samp><span class="env">DESTDIR</span></samp> are
supported, together with more precise control as described for the main
build.
<p>‘<samp><span class="samp">make install</span></samp>’ installs a file for <samp><span class="command">pkg-config</span></samp> to use by
e.g.
<pre class="example"> $(CC) `pkg-config --cflags libRmath` -c test.c
$(CC) `pkg-config --libs libRmath` test.o -o test
</pre>
<p>On some systems ‘<samp><span class="samp">make install-strip</span></samp>’ will install a stripped shared
library.
<div class="node">
<a name="Windows-standalone"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Unix_002dalike-standalone">Unix-alike standalone</a>,
Up: <a rel="up" accesskey="u" href="#The-standalone-Rmath-library">The standalone Rmath library</a>
</div>
<h3 class="section">9.2 Windows</h3>
<p>You need to set up<a rel="footnote" href="#fn-22" name="fnd-22"><sup>22</sup></a> almost all the
tools to make R and then run (in a Unix-like shell)
<pre class="example"> (cd ../../gnuwin32; make MkRules)
(cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h)
make -f Makefile.win
</pre>
<p class="noindent">Alternatively, in a <samp><span class="file">cmd.exe</span></samp> shell use
<pre class="example"> cd ../../include
make -f Makefile.win config.h Rconfig.h Rmath.h
cd ../nmath/standalone
make -f Makefile.win
</pre>
<p>This creates a static library <samp><span class="file">libRmath.a</span></samp> and a DLL
<samp><span class="file">Rmath.dll</span></samp>. If you want an import library <samp><span class="file">libRmath.dll.a</span></samp>
(you don't need one), use
<pre class="example"> make -f Makefile.win shared implib
</pre>
<p>To use the routines in your own C or C++ programs using MinGW, include
<pre class="example"> #define MATHLIB_STANDALONE
#include <Rmath.h>
</pre>
<p class="noindent">and link against ‘<samp><span class="samp">-lRmath</span></samp>’. This will use the first found of
<samp><span class="file">libRmath.dll.a</span></samp>, <samp><span class="file">libRmath.a</span></samp> and <samp><span class="file">Rmath.dll</span></samp> in that
order, so the result depends on which files are present. You should be
able to force static or dynamic linking <em>via</em>
<pre class="example"> -Wl,-Bstatic -lRmath -Wl,dynamic
-Wl,-Bdynamic -lRmath
</pre>
<p class="noindent">or by linking to explicit files (as in the ‘<samp><span class="samp">test</span></samp>’ target in
<samp><span class="file">Makefile.win</span></samp>: this makes two executables, <samp><span class="file">test.exe</span></samp> which
is dynamically linked, and <samp><span class="file">test-static.exe</span></samp>, which is statically
linked).
<p>It is possible to link to <samp><span class="file">Rmath.dll</span></samp> using other compilers, either
directly or via an import library: if you make a MinGW import library as
above, you will create a file <samp><span class="file">Rmath.def</span></samp> which can be used
(possibly after editing) to create an import library for other systems
such as Visual C++.
<p>If you make use of dynamic linking you should use
<pre class="example"> #define MATHLIB_STANDALONE
#define RMATH_DLL
#include <Rmath.h>
</pre>
<p class="noindent">to ensure that the constants like <code>NA_REAL</code> are linked correctly.
(Auto-import will probably work with MinGW, but it is better to be
sure. This is likely to also work with VC++, Borland and similar
compilers.)
<div class="node">
<a name="Essential-and-useful-other-programs-under-a-Unix-alike"></a>
<a name="Essential-and-useful-other-programs-under-a-Unix_002dalike"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>,
Previous: <a rel="previous" accesskey="p" href="#The-standalone-Rmath-library">The standalone Rmath library</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="appendix">Appendix A Essential and useful other programs under a Unix-alike</h2>
<p>This appendix gives details of programs you will need to build R on
Unix-like platforms, or which will be used by R if found by
<samp><span class="command">configure</span></samp>.
<p>Remember that some package management systems (such as <acronym>RPM</acronym> and
deb) make a distinction between the user version of a package and the
development version. The latter usually has the same name but with the
extension ‘<samp><span class="samp">-devel</span></samp>’ or ‘<samp><span class="samp">-dev</span></samp>’: you need both versions
installed.
<ul class="menu">
<li><a accesskey="1" href="#Essential-programs-and-libraries">Essential programs and libraries</a>
<li><a accesskey="2" href="#Useful-libraries-and-programs">Useful libraries and programs</a>
<li><a accesskey="3" href="#Linear-algebra">Linear algebra</a>
</ul>
<div class="node">
<a name="Essential-programs-and-libraries"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Useful-libraries-and-programs">Useful libraries and programs</a>,
Previous: <a rel="previous" accesskey="p" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>,
Up: <a rel="up" accesskey="u" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>
</div>
<h3 class="section">A.1 Essential programs and libraries</h3>
<p>You need a means of compiling C and FORTRAN 90 (see <a href="#Using-FORTRAN">Using FORTRAN</a>). Some add-on packages also need a C++ compiler. Your C
compiler should be <acronym>ISO</acronym>/<acronym>IEC</acronym> 60059<a rel="footnote" href="#fn-23" name="fnd-23"><sup>23</sup></a>, POSIX 1003.1 and
C99-compliant.<a rel="footnote" href="#fn-24" name="fnd-24"><sup>24</sup></a> R tries to choose
suitable flags for the C compilers it knows about, but you may have to
set <code>CC</code> or <code>CFLAGS</code> suitably. For recent versions of
<samp><span class="command">gcc</span></samp> with <code>glibc</code> this means including
<samp><span class="option">-std=gnu99</span></samp><a rel="footnote" href="#fn-25" name="fnd-25"><sup>25</sup></a>. If the compiler is
detected as <samp><span class="command">gcc</span></samp>, <samp><span class="option">-std=gnu99</span></samp> will be appended to
<code>CC</code> unless it conflicts with a setting of <code>CFLAGS</code>. (Note
that options essential to run the compiler even for linking, such as
those to set the architecture, should be specified as part of <code>CC</code>
rather than in <code>CFLAGS</code>.)
<p>Unless you do not want to view graphs on-screen (or use a Mac) you need
‘<samp><span class="samp">X11</span></samp>’ installed, including its headers and client libraries. For
recent Fedora distributions it means (at least) RPMs ‘<samp><span class="samp">libX11</span></samp>’,
‘<samp><span class="samp">libX11-devel</span></samp>’, ‘<samp><span class="samp">libXt</span></samp>’ and ‘<samp><span class="samp">libXt-devel</span></samp>’. On Debian we
recommend the meta-package ‘<samp><span class="samp">xorg-dev</span></samp>’. If you really do not want
these you will need to explicitly configure R without X11, using
<samp><span class="option">--with-x=no</span></samp>.
<p>The command-line editing (and command completion) depends on the
<acronym>GNU</acronym> <code>readline</code> library: version 4.2 or later is needed
for all the features to be enabled. Otherwise you will need to
configure with <samp><span class="option">--with-readline=no</span></samp> (or equivalent).
<p>A suitably comprehensive <code>iconv</code> function is essential. The R
usage requires <code>iconv</code> to be able to translate between
<code>"latin1"</code> and <code>"UTF-8"</code>, to recognize <code>""</code> (as the
current encoding) and <code>"ASCII"</code>, and to translate to and from the
Unicode wide-character formats <code>"UCS-[24][BL]E"</code> — this is true
for <code>glibc</code> but not of most commercial Unixes. However, you can
make use of <acronym>GNU</acronym> <code>libiconv</code> (possibly as a plug-in
replacement: see <a href="http://www.gnu.org/software/libiconv/">http://www.gnu.org/software/libiconv/</a>).
<p>An implementation of <acronym>XDR</acronym> is required. This is part of
<acronym>RPC</acronym> and historically has been part of <samp><span class="file">libc</span></samp> on a
Unix-alike: however some builds<a rel="footnote" href="#fn-26" name="fnd-26"><sup>26</sup></a> of <code>glibc
2.14</code> hide it. The intention seems to be that the <acronym>TI-RPC</acronym>
library be used instead, in which case <code>libtirpc</code> (and its
development version) needs to be installed, and its headers need to be
on the C include path (and <samp><span class="command">configure</span></samp> tries
<samp><span class="file">/usr/include/tirpc</span></samp> if the headers are not found on the standard
include path). The R sources contain a fall-back implementation of
<acronym>XDR</acronym> which is likely to suffice on both 32- and 64-bit
platforms.
<p>The OS needs to have enough support<a rel="footnote" href="#fn-27" name="fnd-27"><sup>27</sup></a> for wide-character
types: this is checked at configuration.
<p>A <samp><span class="command">tar</span></samp> program is needed to unpack the sources and packages
(including the recommended packages). A version<a rel="footnote" href="#fn-28" name="fnd-28"><sup>28</sup></a> that can
automagically detect compressed archives is preferred for use with
<code>untar()</code>: the configure script looks for <samp><span class="command">gtar</span></samp> and
<samp><span class="command">gnutar</span></samp> before
<a name="index-TAR-69"></a><samp><span class="command">tar</span></samp>: use environment variable <samp><span class="env">TAR</span></samp> to override this.
<p>There need to be suitable versions of the tools <samp><span class="command">grep</span></samp> and
<samp><span class="command">sed</span></samp>: the problems are usually with old AT&T and BSD variants.
<samp><span class="command">configure</span></samp> will try to find suitable versions (including
looking in <samp><span class="file">/usr/xpg4/bin</span></samp> which is used on some commercial
Unixes).
<p>You will not be able to build most of the manuals unless you have
<samp><span class="command">makeinfo</span></samp> version 4.7 or later installed, and if not some of
the <acronym>HTML</acronym> manuals will be linked to <acronym>CRAN</acronym>. To make PDF
versions of the manuals you will also need file <samp><span class="file">texinfo.tex</span></samp>
installed (which is part of the <acronym>GNU</acronym> <strong>texinfo</strong> distribution
but is often made part of the TeX package in re-distributions) as
well as <samp><span class="command">texi2dvi</span></samp>.<a rel="footnote" href="#fn-29" name="fnd-29"><sup>29</sup></a> Further, the versions of <samp><span class="command">texi2dvi</span></samp> and
<samp><span class="file">texinfo.tex</span></samp> need to be compatible: we have seen problems with
older TeX distributions (TeXLive 2007 and MiKTeX 2.8) used with
<strong>texinfo</strong> 4.13. It should be possible to use <samp><span class="command">makeinfo</span></samp>
version 5.x.
<p><a name="index-Vignettes-70"></a>The PDF documentation (including <samp><span class="file">doc/NEWS.pdf</span></samp>) and building
vignettes needs <samp><span class="command">pdftex</span></samp> and <samp><span class="command">pdflatex</span></samp>. We require
LaTeX version <code>2005/12/01</code> or later (for UTF-8 support).
Building PDF package manuals (including the R reference manual) and
vignettes is sensitive to the version of the LaTeX package
<strong>hyperref</strong> and we recommend that the TeX distribution used is
kept up-to-date. A number of LaTeX packages are required (including
<strong>url.sty</strong>, and <strong>listings.sty</strong>) and others such as <strong>hyperref</strong>
and <strong>inconsolata</strong> are desirable (and without them you may need to change
R's defaults: see <a href="#Making-the-manuals">Making the manuals</a>).
<p>If you want to build from the R Subversion repository you need both
<samp><span class="command">makeinfo</span></samp> and <samp><span class="command">pdflatex</span></samp>.
<a name="index-Subversion-71"></a>
<a name="index-PATH-72"></a>The essential programs should be in your <samp><span class="env">PATH</span></samp> at the time
<samp><span class="command">configure</span></samp> is run: this will capture the full paths.
<div class="node">
<a name="Useful-libraries-and-programs"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Linear-algebra">Linear algebra</a>,
Previous: <a rel="previous" accesskey="p" href="#Essential-programs-and-libraries">Essential programs and libraries</a>,
Up: <a rel="up" accesskey="u" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>
</div>
<h3 class="section">A.2 Useful libraries and programs</h3>
<p>The ability to use translated messages makes use of <code>gettext</code> and
most likely needs <acronym>GNU</acronym> <code>gettext</code>: you do need this to work
with new translations, but otherwise the version contained in the R
sources will be used if no suitable external <code>gettext</code> is found.
<p>The ‘modern’ version of the <code>X11()</code>, <code>jpeg()</code>, <code>png()</code>
and <code>tiff()</code> graphics devices uses the <code>cairo</code> and
(optionally) <code>Pango</code> libraries. Cairo version 1.2.0 or later is
required. Pango needs to be at least version 1.10, and 1.12 is the
earliest version we have tested. (For Fedora users we believe the
<code>pango-devel</code> RPM and its dependencies suffice.) R checks for
<samp><span class="command">pkg-config</span></samp>, and uses that to check first that the
‘<samp><span class="samp">pangocairo</span></samp>’ package is installed (and if not, ‘<samp><span class="samp">cairo</span></samp>’) and if
additional flags are needed for the ‘<samp><span class="samp">cairo-xlib</span></samp>’ package, then if
suitable code can be compiled. These tests will fail if
<samp><span class="command">pkg-config</span></samp> is not installed, and are likely to fail if
<code>cairo</code> was built statically (unusual). Most systems with
<code>Gtk+</code> 2.8 or later installed will have suitable libraries. OS X
comes with none of these libraries (but XQuartz, as used for 10.8 and
later, ships <code>cairo</code>), but <code>cairo</code> support (without
<code>Pango</code>) has been added to the binary distribution (see
<a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a> you need <code>fontconfig</code>,
<code>freetype</code> and <code>pixman</code> too): <code>pkg-config</code> is still
needed when building R from source and can be installed from its
sources.
<p>For the best font experience with these devices you need suitable fonts
installed: Linux users will want the <code>urw-fonts</code> package. On
platforms which have it available, the <code>msttcorefonts</code>
package<a rel="footnote" href="#fn-30" name="fnd-30"><sup>30</sup></a> provides
TrueType versions of Monotype fonts such as Arial and Times New Roman.
Another useful set of fonts is the ‘liberation’ TrueType fonts available
at
<a href="https://fedorahosted.org/liberation-fonts/">https://fedorahosted.org/liberation-fonts/</a>,<a rel="footnote" href="#fn-31" name="fnd-31"><sup>31</sup></a> which cover the Latin, Greek and Cyrillic alphabets
plus a fair range of signs. These share metrics with Arial, Times New
Roman and Courier New, and contain fonts rather similar to the first two
(<a href="http://en.wikipedia.org/wiki/Liberation_fonts">http://en.wikipedia.org/wiki/Liberation_fonts</a>). Then there
is the ‘Free UCS Outline Fonts’ project
(<a href="http://www.gnu.org/software/freefont/">http://www.gnu.org/software/freefont/</a>) which are
OpenType/TrueType fonts based on the URW fonts but with extended Unicode
coverage. See the R help on <code>X11</code> on selecting such fonts.
<p>The bitmapped graphics devices <code>jpeg()</code>, <code>png()</code> and
<code>tiff()</code> need the appropriate headers and libraries installed:
<code>jpeg</code> (version 6b or later, or <code>libjpeg-turbo</code>) or
<code>libpng</code> (version 1.2.7 or later) and <code>zlib</code> or <code>libtiff</code>
(any recent version – 3.9.[4567] and 4.0.[23] have been tested)
respectively. They also need support for either <code>X11</code> or
<code>cairo</code> (see above). Should support for these devices <strong>not</strong>
be required or broken system libraries need to be avoided there are
<samp><span class="command">configure</span></samp> options <samp><span class="option">--without-libpng</span></samp>,
<samp><span class="option">--without-jpeglib</span></samp> and <samp><span class="option">--without-libtiff</span></samp>. For most
system installations the TIFF libraries will require JPEG libraries to
be present and perhaps linked explicitly, so <samp><span class="option">--without-jpeglib</span></samp>
may also disable the <code>tiff()</code> device. The <code>tiff()</code> devices
only require a basic build of <code>libtiff</code> (not even JPEG support is
needed). Recent versions allow several other libraries to be linked
into <code>libtiff</code> such as <code>lzma</code>, <code>jbig</code> and <code>jpeg12</code>,
and these may need also to be present.
<p>If you have them installed (including the appropriate headers and of
suitable versions), system versions of <code>zlib</code>, <code>libbz2</code> and
PCRE will be used if specified by <samp><span class="option">--with-system-zlib</span></samp> (version
1.2.5 or later), <samp><span class="option">--with-system-bzlib</span></samp> or
<samp><span class="option">--with-system-pcre</span></samp> (version 8.10 or later, preferably 8.33
which is what is supplied with R): otherwise versions in the R
sources will be compiled in. As the latter suffice and are tested with
R you should not need to change this.
<p><code>liblzma</code> from <code>xz-utils</code> version 5.0.3 or later will be used
if installed: the version in the R sources can be selected instead by
configuring with <samp><span class="option">--with-system-xz=no</span></samp>. Systems differ in what
they call the package including this: e.g. on Fedora the library is in
‘<samp><span class="samp">xz-libs</span></samp>’ and the headers in ‘<samp><span class="samp">xz-devel</span></samp>’.
<p>Use of the X11 clipboard selection requires the <code>Xmu</code> headers and
libraries. These are normally part of an X11 installation (e.g. the
Debian meta-package ‘<samp><span class="samp">xorg-dev</span></samp>’), but some distributions have split
this into smaller parts, so for example recent versions of Fedora
require the ‘<samp><span class="samp">libXmu</span></samp>’ and ‘<samp><span class="samp">libXmu-devel</span></samp>’ RPMs.
<p>Some systems (notably OS X and at least some FreeBSD systems) have
inadequate support for collation in multibyte locales. It is possible
to replace the OS's collation support by that from ICU (International
Components for Unicode, <a href="http://site.icu-project.org/">http://site.icu-project.org/</a>), and this
provides much more precise control over collation on all systems. ICU
is available as sources and as binary distributions for (at least) most
Linux distributions, Solaris, FreeBSD and AIX, usually as <code>libicu</code>
or <code>icu4c</code>. It will be used by default where available (including
on OS X >= 10.4): should a very old or broken version of ICU be found
this can be suppressed by <samp><span class="option">--without-ICU</span></samp>.
<p>The <code>bitmap</code> and <code>dev2bitmap</code> devices and also
<code>embedFonts()</code> use ghostscript
(<a href="http://www.ghostscript.com/">http://www.ghostscript.com/</a>). This should either be in your
path when the command is run, or its full path specified by the
environment variable <samp><span class="env">R_GSCMD</span></samp> at that time.
<a name="index-R_005fGSCMD-73"></a>
<ul class="menu">
<li><a accesskey="1" href="#Tcl_002fTk">Tcl/Tk</a>
<li><a accesskey="2" href="#Java-support">Java support</a>
</ul>
<div class="node">
<a name="Tcl%2fTk"></a>
<a name="Tcl_002fTk"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Java-support">Java support</a>,
Previous: <a rel="previous" accesskey="p" href="#Useful-libraries-and-programs">Useful libraries and programs</a>,
Up: <a rel="up" accesskey="u" href="#Useful-libraries-and-programs">Useful libraries and programs</a>
</div>
<h4 class="subsection">A.2.1 Tcl/Tk</h4>
<p>The <strong>tcltk</strong> package needs Tcl/Tk >= 8.4 installed: the sources are
available at <a href="http://www.tcl.tk/">http://www.tcl.tk/</a>. To specify the locations of the
Tcl/Tk files you may need the configuration options
<dl>
<dt><samp><span class="option">--with-tcltk</span></samp><dd>use Tcl/Tk, or specify its library directory
<br><dt><samp><span class="option">--with-tcl-config=</span><var>TCL_CONFIG</var></samp><dd>specify location of <samp><span class="file">tclConfig.sh</span></samp>
<br><dt><samp><span class="option">--with-tk-config=</span><var>TK_CONFIG</var></samp><dd>specify location of <samp><span class="file">tkConfig.sh</span></samp>
</dl>
<p class="noindent">or use the configure variables <code>TCLTK_LIBS</code> and
<code>TCLTK_CPPFLAGS</code> to specify the flags needed for linking against
the Tcl and Tk libraries and for finding the <samp><span class="file">tcl.h</span></samp> and
<samp><span class="file">tk.h</span></samp> headers, respectively. If you have both 32- and 64-bit
versions of Tcl/Tk installed, specifying the paths to the correct config
files may be necessary to avoid confusion between them.
<p>Versions of Tcl/Tk up to 8.5.12 and 8.6.0 have been tested (including
most versions of 8.4.x, but not recently).
<div class="node">
<a name="Java-support"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Tcl_002fTk">Tcl/Tk</a>,
Up: <a rel="up" accesskey="u" href="#Useful-libraries-and-programs">Useful libraries and programs</a>
</div>
<h4 class="subsection">A.2.2 Java support</h4>
<p>The build process looks for Java support on the host system, and if it
finds it sets some settings which are useful for Java-using packages.
<a name="index-JAVA_005fHOME-74"></a><samp><span class="env">JAVA_HOME</span></samp> can be set to point to a specific JRE/JDK.
<p>Principal amongst these are setting some library paths to the Java
libraries and JVM, which are stored in environment variable
<a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-75"></a><samp><span class="env">R_JAVA_LD_LIBRARY_PATH</span></samp> in file <samp><var>R_HOME</var><span class="file">/etc/ldpaths</span></samp> (or
a sub-architecture-specific version). A typical setting for
‘<samp><span class="samp">x86_64</span></samp>’ Linux is
<pre class="example"> JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.25.x86_64/jre
R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
</pre>
<p>Note that this unfortunately depends on the exact version of the JRE/JDK
installed, and so may need updating if the Java installation is updated.
This can be done by running <code>R CMD javareconf</code> which updates
settings in both <samp><span class="file">etc/Makeconf</span></samp> and
<samp><var>R_HOME</var><span class="file">/etc/ldpaths</span></samp>. See <code>R CMD javareconf --help</code> for
details.
<p>Another way of overriding those settings is to set the environment variable
<a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-76"></a><samp><span class="env">R_JAVA_LD_LIBRARY_PATH</span></samp> (before R is started, hence not in
<samp><span class="file">~/.Renviron</span></samp>), which suffices to run already-installed
Java-using packages. For example
<pre class="example"> R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.7.0/jre/lib/amd64/server
</pre>
<p>It may be possible to avoid this by specifying an invariant link as the
path. For example, on that system either of
<pre class="example"> JAVA_HOME=/usr/lib/jvm/java-1.7.0
JAVA_HOME=/usr/lib/jvm/java-1.7.0/jre
</pre>
<p class="noindent">worked.
<div class="node">
<a name="Linear-algebra"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Useful-libraries-and-programs">Useful libraries and programs</a>,
Up: <a rel="up" accesskey="u" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>
</div>
<h3 class="section">A.3 Linear algebra</h3>
<p><a name="index-BLAS-library-77"></a>
<ul class="menu">
<li><a accesskey="1" href="#BLAS">BLAS</a>
<li><a accesskey="2" href="#LAPACK">LAPACK</a>
<li><a accesskey="3" href="#Caveats">Caveats</a>
</ul>
<div class="node">
<a name="BLAS"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#LAPACK">LAPACK</a>,
Previous: <a rel="previous" accesskey="p" href="#Linear-algebra">Linear algebra</a>,
Up: <a rel="up" accesskey="u" href="#Linear-algebra">Linear algebra</a>
</div>
<h4 class="subsection">A.3.1 BLAS</h4>
<p>The linear algebra routines in R can make use of enhanced
<acronym>BLAS</acronym> (Basic Linear Algebra Subprograms,
<a href="http://www.netlib.org/blas/faq.html">http://www.netlib.org/blas/faq.html</a>) routines. However,
these have to be explicitly requested at configure time: R provides
an internal <acronym>BLAS</acronym> which is well-tested and will be adequate for
most uses of R.
<p>You can specify a particular <acronym>BLAS</acronym> library <em>via</em> a value
for the configuration option <samp><span class="option">--with-blas</span></samp> and not to use an
external <acronym>BLAS</acronym> library by <samp><span class="option">--without-blas</span></samp> (the
default). If <samp><span class="option">--with-blas</span></samp> is given with no <code>=</code>, its value
is taken from the
<a name="index-BLAS_005fLIBS-78"></a>environment variable <samp><span class="env">BLAS_LIBS</span></samp>, set for example in
<samp><span class="file">config.site</span></samp>. If neither the option nor the environment variable
supply a value, a search is made for a suitable <acronym>BLAS</acronym>. If the
value is not obviously a linker command (starting with a dash or giving
the path to a library), it is prefixed by ‘<samp><span class="samp">-l</span></samp>’, so
<pre class="example"> --with-blas="foo"
</pre>
<p class="noindent">is an instruction to link against ‘<samp><span class="samp">-lfoo</span></samp>’ to find an external
<acronym>BLAS</acronym> (which needs to be found both at link time and run time).
<p>The configure code checks that the external <acronym>BLAS</acronym> is complete
(it must include all double precision and double complex routines, as
well as <code>LSAME</code>), and appears to be usable. However, an external
<acronym>BLAS</acronym> has to be usable from a shared object (so must contain
position-independent code), and that is not checked.
<p>Some enhanced <acronym>BLAS</acronym>es are compiler-system-specific
(<code>sunperf</code> on Solaris<a rel="footnote" href="#fn-32" name="fnd-32"><sup>32</sup></a>, <code>libessl</code> on IBM,
<code>Accelerate</code> on OS X). The correct incantation for
these is usually found <em>via</em> <samp><span class="option">--with-blas</span></samp> with no value on
the appropriate platforms.
<p>Some of the external <acronym>BLAS</acronym>es are multi-threaded. One issue is
that R profiling (which uses the <code>SIGPROF</code> signal) may cause
problems, and you may want to disable profiling if you use a
multi-threaded <acronym>BLAS</acronym>. Note that using a multi-threaded
<acronym>BLAS</acronym> can result in taking more <acronym>CPU</acronym> time and even
more elapsed time (occasionally dramatically so) than using a similar
single-threaded <acronym>BLAS</acronym>.
<p>Note that under Unix (but not under Windows) if R is compiled against
a non-default <acronym>BLAS</acronym> and <samp><span class="option">--enable-BLAS-shlib</span></samp> is
<strong>not</strong> used, then all <acronym>BLAS</acronym>-using packages must also be.
So if R is re-built to use an enhanced <acronym>BLAS</acronym> then packages
such as <a href="http://CRAN.R-project.org/package=quantreg"><strong>quantreg</strong></a> will need to be re-installed.
<p>R relies on <acronym>ISO</acronym>/<acronym>IEC</acronym> 60559 compliance of an
external <acronym>BLAS</acronym>. This can be broken if for example the code
assumes that terms with a zero factor are always zero and do not need to
be computed—whereas <code>x*0</code> can be <code>NaN</code>. This is checked in
the test suite.
<ul class="menu">
<li><a accesskey="1" href="#ATLAS">ATLAS</a>
<li><a accesskey="2" href="#ACML">ACML</a>
<li><a accesskey="3" href="#Goto-and-OpenBLAS">Goto and OpenBLAS</a>
<li><a accesskey="4" href="#MKL">MKL</a>
<li><a accesskey="5" href="#Shared-BLAS">Shared BLAS</a>
</ul>
<div class="node">
<a name="ATLAS"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#ACML">ACML</a>,
Previous: <a rel="previous" accesskey="p" href="#BLAS">BLAS</a>,
Up: <a rel="up" accesskey="u" href="#BLAS">BLAS</a>
</div>
<h5 class="subsubsection">A.3.1.1 ATLAS</h5>
<p>ATLAS (<a href="http://math-atlas.sourceforge.net/">http://math-atlas.sourceforge.net/</a>) is a “tuned”
<acronym>BLAS</acronym> that runs on a wide range of Unix-alike platforms.
Unfortunately it is usually built as a static library that on some
platforms cannot be used with shared objects such as are used in R
packages. Be careful when using pre-built versions of ATLAS (they seem
to work on ‘<samp><span class="samp">ix86</span></samp>’ platforms, but not always on ‘<samp><span class="samp">x86_64</span></samp>’
ones).
<p>The usual way to specify ATLAS will be via
<pre class="example"> --with-blas="-lf77blas -latlas"
</pre>
<p class="noindent">if the libraries are in the library path, otherwise by
<pre class="example"> --with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas"
</pre>
<p class="noindent">For example, ‘<samp><span class="samp">x86_64</span></samp>’ Fedora needs
<pre class="example"> --with-blas="-L/usr/lib64/atlas -lf77blas -latlas"
</pre>
<p>For systems with multiple CPU cores it is possible to use a
multi-threaded version of ATLAS, by specifying
<pre class="example"> --with-blas="-lptf77blas -lpthread -latlas"
</pre>
<p>Consult its file <samp><span class="file">INSTALL.txt</span></samp> for how to build ATLAS with
position-independent code: that file also describes how to build ATLAS
as a shared library.
<div class="node">
<a name="ACML"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Goto-and-OpenBLAS">Goto and OpenBLAS</a>,
Previous: <a rel="previous" accesskey="p" href="#ATLAS">ATLAS</a>,
Up: <a rel="up" accesskey="u" href="#BLAS">BLAS</a>
</div>
<h5 class="subsubsection">A.3.1.2 ACML</h5>
<!-- : there used to be Solaris 10, but it seems no more. -->
<p>For ‘<samp><span class="samp">x86_64</span></samp>’ and ‘<samp><span class="samp">i686</span></samp>’ processors under Linux there is
the AMD Core Math Library (ACML) <a href="http://www.amd.com/acml">http://www.amd.com/acml</a>. For
the <samp><span class="command">gcc</span></samp> version we could use
<pre class="example"> --with-blas="-lacml"
</pre>
<p class="noindent">if the appropriate library directory (such as
<a name="index-LD_005fLIBRARY_005fPATH-79"></a><samp><span class="file">/opt/acml5.1.0/gfortran64/lib</span></samp>) is in the <samp><span class="env">LD_LIBRARY_PATH</span></samp>.
For other compilers, see the ACML documentation. There is a
multithreaded Linux version of ACML available for recent versions of
<samp><span class="command">gfortran</span></samp>. To make use of this you will need something like
<pre class="example"> --with-blas="-L/opt/acml5.1.0/gfortran64_mp/lib -lacml_mp"
</pre>
<p class="noindent">(and you may need to arrange for the directory to be in <samp><span class="command">ld.so</span></samp>
cache).
<p>See see <a href="#Shared-BLAS">Shared BLAS</a> for an alternative (and in many ways preferable)
way to use ACML.
<p>The version last tested (5.1.0) failed the <samp><span class="file">reg-BLAS.R</span></samp> test in its
handling of <code>NA</code>s.
<div class="node">
<a name="Goto-and-OpenBLAS"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#MKL">MKL</a>,
Previous: <a rel="previous" accesskey="p" href="#ACML">ACML</a>,
Up: <a rel="up" accesskey="u" href="#BLAS">BLAS</a>
</div>
<h5 class="subsubsection">A.3.1.3 Goto and OpenBLAS</h5>
<p>Dr Kazushige Goto wrote another tuned <acronym>BLAS</acronym> which is available
for several processors and OSes. The final version is known as
GotoBLAS2, and was re-released under a much less restrictive licence.
Source code can be obtained from
<a href="http://www.tacc.utexas.edu/tacc-projects/gotoblas2/">http://www.tacc.utexas.edu/tacc-projects/gotoblas2/</a>
<p>Once it is built and installed, it can be used by configuring R with
<pre class="example"> --with-blas="-lgoto2"
</pre>
<p>See see <a href="#Shared-BLAS">Shared BLAS</a> for an alternative (and in many ways preferable)
way to use it.
<p>Our understanding is that this project is now frozen and so will not be
updated for CPUs released since mid-2010. However, OpenBLAS
(<a href="http://xianyi.github.com/OpenBLAS/">http://xianyi.github.com/OpenBLAS/</a>) is a descendant project with
support for some current CPUs (e.g. Intel Sandy Bridge and AMD Bulldozer).
<div class="node">
<a name="MKL"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Shared-BLAS">Shared BLAS</a>,
Previous: <a rel="previous" accesskey="p" href="#Goto-and-OpenBLAS">Goto and OpenBLAS</a>,
Up: <a rel="up" accesskey="u" href="#BLAS">BLAS</a>
</div>
<h5 class="subsubsection">A.3.1.4 Intel MKL</h5>
<p>For Intel processors<a rel="footnote" href="#fn-33" name="fnd-33"><sup>33</sup></a> under Linux, there is
Intel's Math Kernel Library
(<a href="http://www.intel.com/software/products/mkl/">http://www.intel.com/software/products/mkl/</a>). You are
strongly encouraged to read the MKL User's Guide, which is installed
with the library, before attempting to link to MKL. There are also
versions of MKL for OS X and Windows, but they did not work with the
standard compilers used for R on those platforms.
<p>The MKL interface has changed several times, and may change again: the
following notes apply exactly only to version 10.3.
<p>Version 10 of MKL supports two linking models: the default model, which
is backward compatible with version 9 (see below), and the pure layered
model. The layered model gives the user fine-grained control over four
different library layers: interface, threading, computation, and
run-time library support. Some examples of linking to MKL using this
layered model are given below. (These examples are for GCC compilers on
‘<samp><span class="samp">x86_64</span></samp>’.) The choice of interface layer is important on
‘<samp><span class="samp">x86_64</span></samp>’ since the Intel Fortran compiler returns complex values
in different registers from the <acronym>GNU</acronym> Fortran compiler. You must
therefore use the interface layer that matches your compiler
(<code>mkl_intel*</code> or <code>mkl_gf*</code>).
<p>R can be linked to a sequential version of MKL by something like
<pre class="example"> MKL_LIB_PATH=/opt/intel/mkl/10.311.339/lib/intel64/
export LD_LIBRARY_PATH=$MKL_LIB_PATH
MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_sequential -lmkl_core"
./configure --with-blas="$MKL" --with-lapack
</pre>
<p class="noindent">where some versions may need <code>-lmkl_lapack</code> before
<code>-lmkl_core</code>. The order of the libraries is important. The option
<samp><span class="option">--with-lapack</span></samp> is used since MKL contains a tuned copy of LAPACK
as well as <acronym>BLAS</acronym> (see <a href="#LAPACK">LAPACK</a>), although this can be
omitted.
<p>Threaded MKL may be used (according to Zhang Zhang of Intel) by
replacing the line defining the variable <code>MKL</code> with (Intel OMP)
<pre class="example"> MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_intel_thread \
-lmkl_core -liomp5 -lpthread"
</pre>
<p class="noindent">or (GNU OMP)
<pre class="example"> MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_gnu_thread \
-lmkl_core -fopenmp -lpthread"
</pre>
<p class="noindent">The default number of threads will be chosen by the OpenMP software,
but can be controlled by setting <code>OMP_NUM_THREADS</code> or
<code>MKL_NUM_THREADS</code>, and in recent versions seems to produce a
sensible value for sole use of the machine.
<p>Static threaded MKL may be used (GNU OpenMP) with something like
<pre class="example"> MKL=" -L${MKL_LIB_PATH} \
-Wl,--start-group \
${MKL_LIB_PATH}/libmkl_gf_lp64.a \
${MKL_LIB_PATH}/libmkl_gnu_thread.a \
${MKL_LIB_PATH}/libmkl_core.a \
-Wl,--end-group \
-lgomp -lpthread"
</pre>
<p class="noindent">(Thanks to Ei-ji Nakama).
<p>The MKL documentation includes a ‘link line advisor’ which will suggest
appropriate incantations: an on-line version was available at
<a href="http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/">http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/</a>
<p>The default linking model, which was also used by version 9 of MKL, can
be used by
<pre class="example"> --with-blas="-lmkl -lguide -lpthread"
</pre>
<p class="noindent">but this may not match your compiler on a 64-bit platform. This is
multi-threaded, but in version 9 the number of threads defaults to 1.
It can be increased by setting <code>OMP_NUM_THREADS</code>. (Thanks to Andy
Liaw for the information.)
<div class="node">
<a name="Shared-BLAS"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#MKL">MKL</a>,
Up: <a rel="up" accesskey="u" href="#BLAS">BLAS</a>
</div>
<h5 class="subsubsection">A.3.1.5 Shared BLAS</h5>
<p>The <acronym>BLAS</acronym> library will be used for many of the add-on packages
as well as for R itself. This means that it is better to use a
shared/dynamic <acronym>BLAS</acronym> library, as most of a static library will
be compiled into the R executable and each <acronym>BLAS</acronym>-using
package.
<p>R offers the option of compiling the <acronym>BLAS</acronym> into a dynamic
library <code>libRblas</code> stored in <samp><var>R_HOME</var><span class="file">/lib</span></samp> and linking
both R itself and all the add-on packages against that library.
<p>This is the default on all platforms except AIX unless an external
<acronym>BLAS</acronym> is specified and found: for the latter it can be used by
specifying the option <samp><span class="option">--enable-BLAS-shlib</span></samp>, and it can always be
disabled via <samp><span class="option">--disable-BLAS-shlib</span></samp>.
<p>This has both advantages and disadvantages.
<ul>
<li>It saves space by having only a single copy of the <acronym>BLAS</acronym>
routines, which is helpful if there is an external static <acronym>BLAS</acronym>
such as used to be standard for ATLAS.
<li>There may be performance disadvantages in using a shared <acronym>BLAS</acronym>.
Probably the most likely is when R's internal <acronym>BLAS</acronym> is used
and R is <em>not</em> built as a shared library, when it is possible to
build the <acronym>BLAS</acronym> into <samp><span class="file">R.bin</span></samp> (and <samp><span class="file">libR.a</span></samp>) without
using position-independent code. However, experiments showed that in
many cases using a shared <acronym>BLAS</acronym> was as fast, provided high
levels of compiler optimization are used.
<li>It is easy to change the <acronym>BLAS</acronym> without needing to re-install
R and all the add-on packages, since all references to the
<acronym>BLAS</acronym> go through <code>libRblas</code>, and that can be replaced.
Note though that any dynamic libraries the replacement links to will
need to be found by the linker: this may need the library path to be
changed in <samp><var>R_HOME</var><span class="file">/etc/ldpaths</span></samp>.
</ul>
<p>Another option to change the <acronym>BLAS</acronym> in use is to symlink a
dynamic <acronym>BLAS</acronym> library (such as ACML or Goto's) to
<samp><var>R_HOME</var><span class="file">/lib/libRblas.so</span></samp>. For example, just
<pre class="example"> mv <var>R_HOME</var>/lib/libRblas.so <var>R_HOME</var>/lib/libRblas.so.keep
ln -s /opt/acml5.1.0/gfortran64_mp/lib/libacml_mp.so <var>R_HOME</var>/lib/libRblas.so
</pre>
<p>will change the <acronym>BLAS</acronym> in use to multithreaded ACML. A similar
link works for some versions of the Goto <acronym>BLAS</acronym> and perhaps
for MKL (provided the appropriate <samp><span class="file">lib</span></samp> directory is in the
run-time library path or <samp><span class="command">ld.so</span></samp> cache).
<div class="node">
<a name="LAPACK"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Caveats">Caveats</a>,
Previous: <a rel="previous" accesskey="p" href="#BLAS">BLAS</a>,
Up: <a rel="up" accesskey="u" href="#Linear-algebra">Linear algebra</a>
</div>
<h4 class="subsection">A.3.2 LAPACK</h4>
<p><a name="index-LAPACK-library-80"></a>Provision is made for using an external LAPACK library, principally to
cope with <acronym>BLAS</acronym> libraries which contain a copy of LAPACK (such
as <code>sunperf</code> on Solaris, <code>Accelerate</code> on OS X and ACML and MKL
on ‘<samp><span class="samp">ix86</span></samp>’/‘<samp><span class="samp">x86_64</span></samp>’ Linux). At least LAPACK version 3.2
is required. This can only be done if <samp><span class="option">--with-blas</span></samp> has been used.
<p>However, the likely performance gains are thought to be small (and may
be negative), and the default is not to search for a suitable LAPACK
library, and this is definitely <strong>not</strong> recommended. You can
specify a specific LAPACK library or a search for a generic library by
the configuration option <samp><span class="option">--with-lapack</span></samp>. The default for
<samp><span class="option">--with-lapack</span></samp> is to check the <acronym>BLAS</acronym> library and then
look for an external library ‘<samp><span class="samp">-llapack</span></samp>’. Sites searching for the
fastest possible linear algebra may want to build a LAPACK library using
the ATLAS-optimized subset of LAPACK. To do so specify something like
<pre class="example"> --with-lapack="-L/path/to/ATLAS/libs -llapack -lcblas"
</pre>
<p class="noindent">since the ATLAS subset of LAPACK depends on <code>libcblas</code>. A value
for <samp><span class="option">--with-lapack</span></samp> can be set <em>via</em> the environment
variable
<a name="index-LAPACK_005fLIBS-81"></a><samp><span class="env">LAPACK_LIBS</span></samp>, but this will only be used if <samp><span class="option">--with-lapack</span></samp>
is specified (as the default value is <code>no</code>) and the <acronym>BLAS</acronym> library
does not contain LAPACK.
<p>Since ACML contains a full LAPACK, if selected as the <acronym>BLAS</acronym> it
can be used as the LAPACK <em>via</em> <samp><span class="option">--with-lapack</span></samp>.
<p>If you do use <samp><span class="option">--with-lapack</span></samp>, be aware of potential problems
with bugs in the LAPACK sources (or in the posted corrections to those
sources). In particular, bugs in <code>DGEEV</code> and <code>DGESDD</code> have
resulted in error messages such as
<pre class="example"> DGEBRD gave error code -10
</pre>
<p class="noindent">. Other potential problems are incomplete versions of the libraries,
seen several times in Linux distributions over the years.
<p>Please <strong>do</strong> bear in mind that using <samp><span class="option">--with-lapack</span></samp> is
‘definitely <strong>not</strong> recommended’: it is provided <strong>only</strong>
because it is necessary on some platforms and because some users want to
experiment with claimed performance improvements. Reporting problems
where it is used unnecessarily will simply irritate the R helpers.
<p>Note too the comments about <acronym>ISO</acronym>/<acronym>IEC</acronym> 60559
compliance in the section of external <acronym>BLAS</acronym>: these apply
equally to an external LAPACK, and for example the Intel MKL
documentation says
<blockquote>
LAPACK routines assume that input matrices do not contain IEEE 754
special values such as INF or NaN values. Using these special values may
cause LAPACK to return unexpected results or become unstable.
</blockquote>
<p>We rely on limited support in LAPACK for matrices with 2^31 or
more elements: it is quite possible that an external LAPACK will not
have that support.
<p>If you have a pure FORTRAN 77 compiler which cannot compile LAPACK it
may be possible to use CLAPACK from
<a href="http://www.netlib.org/clapack/">http://www.netlib.org/clapack/</a> by something like
<pre class="example"> -with-lapack="-lclapack -lf2c"
</pre>
<p class="noindent">provided these were built with position-independent code and the calling
conventions for double complex function return values match those in the
BLAS used, so it may be simpler to use CLAPACK built to use CBLAS and
<pre class="example"> -with-lapack="-lclapack -lcblas -lf2c"
</pre>
<div class="node">
<a name="Caveats"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#LAPACK">LAPACK</a>,
Up: <a rel="up" accesskey="u" href="#Linear-algebra">Linear algebra</a>
</div>
<h4 class="subsection">A.3.3 Caveats</h4>
<p>As with all libraries, you need to ensure that they and R were
compiled with compatible compilers and flags. For example, this has
meant that on Sun Sparc using the native compilers the flag
<samp><span class="option">-dalign</span></samp> is needed so <code>sunperf</code> can be used.
<p>On some systems it is necessary that an external <acronym>BLAS</acronym>/LAPACK
was built with the same FORTRAN compiler used to build R: known
problems are with R built with <samp><span class="command">gfortran</span></samp>, see <a href="#Using-gfortran">Using gfortran</a>.
<div class="node">
<a name="Configuration-on-a-Unix-alike"></a>
<a name="Configuration-on-a-Unix_002dalike"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Platform-notes">Platform notes</a>,
Previous: <a rel="previous" accesskey="p" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="appendix">Appendix B Configuration on a Unix-alike</h2>
<ul class="menu">
<li><a accesskey="1" href="#Configuration-options">Configuration options</a>
<li><a accesskey="2" href="#Internationalization-support">Internationalization support</a>
<li><a accesskey="3" href="#Configuration-variables">Configuration variables</a>
<li><a accesskey="4" href="#Setting-the-shell">Setting the shell</a>
<li><a accesskey="5" href="#Using-make">Using make</a>
<li><a accesskey="6" href="#Using-FORTRAN">Using FORTRAN</a>
<li><a accesskey="7" href="#Compile-and-load-flags">Compile and load flags</a>
</ul>
<div class="node">
<a name="Configuration-options"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Internationalization-support">Internationalization support</a>,
Previous: <a rel="previous" accesskey="p" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.1 Configuration options</h3>
<p><samp><span class="command">configure</span></samp> has many options: running
<pre class="example"> ./configure --help
</pre>
<p class="noindent">will give a list. Probably the most important ones not covered
elsewhere are (defaults in brackets)
<dl>
<dt><samp><span class="option">--with-x</span></samp><dd>use the X Window System [yes]
<br><dt><samp><span class="option">--x-includes=</span><var>DIR</var></samp><dd>X include files are in <var>DIR</var>
<br><dt><samp><span class="option">--x-libraries=</span><var>DIR</var></samp><dd>X library files are in <var>DIR</var>
<br><dt><samp><span class="option">--with-readline</span></samp><dd>use readline library (if available) [yes]
<br><dt><samp><span class="option">--enable-R-profiling</span></samp><dd>attempt to compile support for <code>Rprof()</code> [yes]
<br><dt><samp><span class="option">--enable-memory-profiling</span></samp><dd>attempt to compile support for <code>Rprofmem()</code> and <code>tracemem()</code> [no]
<br><dt><samp><span class="option">--enable-R-shlib</span></samp><dd>build R as a shared/dynamic library [no]
<br><dt><samp><span class="option">--enable-BLAS-shlib</span></samp><dd>build the <acronym>BLAS</acronym> as a shared/dynamic library [yes, except on AIX]
</dl>
<p class="noindent">You can use <samp><span class="option">--without-foo</span></samp> or <samp><span class="option">--disable-foo</span></samp> for the
negatives.
<p>You will want to use <samp><span class="option">--disable-R-profiling</span></samp> if you are building
a profiled executable of R (e.g. with ‘<samp><span class="samp">-pg)</span></samp>’.
<p>Flag <samp><span class="option">--enable-R-shlib</span></samp> causes the make process to build R as
a dynamic (shared) library, typically called <samp><span class="file">libR.so</span></samp>, and link
the main R executable <samp><span class="file">R.bin</span></samp> against that library. This can
only be done if all the code (including system libraries) can be
compiled into a dynamic library, and there may be a
performance<a rel="footnote" href="#fn-34" name="fnd-34"><sup>34</sup></a> penalty. So you probably
only want this if you will be using an application which embeds R.
Note that C code in packages installed on an R system linked with
<samp><span class="option">--enable-R-shlib</span></samp> is linked against the dynamic library and so
such packages cannot be used from an R system built in the default
way. Also, because packages are linked against R they are on some
OSes also linked against the dynamic libraries R itself is linked
against, and this can lead to symbol conflicts.
<p>If you need to re-configure R with different options you may need to run
<code>make clean</code> or even <code>make distclean</code> before doing so.
<div class="node">
<a name="Internationalization-support"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Configuration-variables">Configuration variables</a>,
Previous: <a rel="previous" accesskey="p" href="#Configuration-options">Configuration options</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.2 Internationalization support</h3>
<p>Translation of messages is supported via <acronym>GNU</acronym> <code>gettext</code>
unless disabled by the configure option <samp><span class="option">--disable-nls</span></samp>.
The <code>configure</code> report will show <code>NLS</code> as one of the
‘Additional capabilities’ if support has been compiled in, and running
in an English locale (but not the <code>C</code> locale) will include
<pre class="example"> Natural language support but running in an English locale
</pre>
<p class="noindent">in the greeting on starting R.
<div class="node">
<a name="Configuration-variables"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Setting-the-shell">Setting the shell</a>,
Previous: <a rel="previous" accesskey="p" href="#Internationalization-support">Internationalization support</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.3 Configuration variables</h3>
<p><a name="index-configure-82"></a>If you need or want to set certain configure variables to something
other than their default, you can do that by either editing the file
<samp><span class="file">config.site</span></samp> (which documents many of the variables you might want
to set: others can be seen in file <samp><span class="file">etc/Renviron.in</span></samp>) or on the
command line as
<pre class="example"> ./configure <var>VAR</var>=<var>value</var>
</pre>
<p class="noindent">If you are building in a directory different from the sources, there can
be copies of <samp><span class="file">config.site</span></samp> in the source and the build directories,
and both will be read (in that order). In addition, if there is a file
<samp><span class="file">~/.R/config</span></samp>, it is read between the <samp><span class="file">config.site</span></samp> files in
the source and the build directories.
<p>There is also a general <samp><span class="command">autoconf</span></samp> mechanism for
<samp><span class="file">config.site</span></samp> files, which are read before any of those mentioned
in the previous paragraph. This looks first at a file specified by the
<a name="index-CONFIG_005fSITE-83"></a>environment variable <samp><span class="env">CONFIG_SITE</span></samp>, and if not is set at files such
as <samp><span class="file">/usr/local/share/config.site</span></samp> and
<samp><span class="file">/usr/local/etc/config.site</span></samp> in the area (exemplified by
<samp><span class="file">/usr/local</span></samp>) where R would be installed.
<p>These variables are <em>precious</em>, implying that they do not have to
be exported to the environment, are kept in the cache even if not
specified on the command line, checked for consistency between two
configure runs (provided that caching is used), and are kept during
automatic reconfiguration as if having been passed as command line
arguments, even if no cache is used.
<p>See the variable output section of <code>configure --help</code> for a list of
all these variables.
<p>If you find you need to alter configure variables, it is worth noting
that some settings may be cached in the file <samp><span class="file">config.cache</span></samp>, and it
is a good idea to remove that file (if it exists) before re-configuring.
Note that caching is turned <em>off</em> by default: use the command line
option <samp><span class="option">--config-cache</span></samp> (or <samp><span class="option">-C</span></samp>) to enable caching.
<ul class="menu">
<li><a accesskey="1" href="#Setting-paper-size">Setting paper size</a>
<li><a accesskey="2" href="#Setting-the-browsers">Setting the browsers</a>
<li><a accesskey="3" href="#Compilation-flags">Compilation flags</a>
<li><a accesskey="4" href="#Making-manuals">Making manuals</a>
</ul>
<div class="node">
<a name="Setting-paper-size"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Setting-the-browsers">Setting the browsers</a>,
Previous: <a rel="previous" accesskey="p" href="#Configuration-variables">Configuration variables</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-variables">Configuration variables</a>
</div>
<h4 class="subsection">B.3.1 Setting paper size</h4>
<p><a name="index-R_005fPAPERSIZE-84"></a>One common variable to change is <samp><span class="env">R_PAPERSIZE</span></samp>, which defaults to
‘<samp><span class="samp">a4</span></samp>’, not ‘<samp><span class="samp">letter</span></samp>’. (Valid values are ‘<samp><span class="samp">a4</span></samp>’,
‘<samp><span class="samp">letter</span></samp>’, ‘<samp><span class="samp">legal</span></samp>’ and ‘<samp><span class="samp">executive</span></samp>’.)
<p>This is used both when configuring R to set the default, and when
running R to override the default. It is also used to set the
paper size when making PDF manuals.
<p>The configure default will most often be ‘<samp><span class="samp">a4</span></samp>’ if <samp><span class="env">R_PAPERSIZE</span></samp>
is unset. (If the (Debian Linux) program <samp><span class="command">paperconf</span></samp> is found
<a name="index-PAPERSIZE-85"></a>or the environment variable <samp><span class="env">PAPERSIZE</span></samp> is set, these are used to
produce the default.)
<div class="node">
<a name="Setting-the-browsers"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Compilation-flags">Compilation flags</a>,
Previous: <a rel="previous" accesskey="p" href="#Setting-paper-size">Setting paper size</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-variables">Configuration variables</a>
</div>
<h4 class="subsection">B.3.2 Setting the browsers</h4>
<p><a name="index-R_005fBROWSER-86"></a>Another precious variable is <samp><span class="env">R_BROWSER</span></samp>, the default <acronym>HTML</acronym>
browser, which should take a value of an executable in the user's path
or specify a full path.
<p><a name="index-R_005fPDFVIEWER-87"></a>Its counterpart for PDF files is <samp><span class="env">R_PDFVIEWER</span></samp>.
<div class="node">
<a name="Compilation-flags"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Making-manuals">Making manuals</a>,
Previous: <a rel="previous" accesskey="p" href="#Setting-the-browsers">Setting the browsers</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-variables">Configuration variables</a>
</div>
<h4 class="subsection">B.3.3 Compilation flags</h4>
<p>If you have libraries and header files, e.g., for <acronym>GNU</acronym>
readline, in non-system directories, use the variables <code>LDFLAGS</code>
(for libraries, using ‘<samp><span class="samp">-L</span></samp>’ flags to be passed to the linker) and
<code>CPPFLAGS</code> (for header files, using ‘<samp><span class="samp">-I</span></samp>’ flags to be passed to
the C/C++ preprocessors), respectively, to specify these locations.
These default to ‘<samp><span class="samp">-L/usr/local/lib</span></samp>’ (<code>LDFLAGS</code>,
‘<samp><span class="samp">-L/usr/local/lib64</span></samp>’ on most 64-bit Linux OSes) and
‘<samp><span class="samp">-I/usr/local/include</span></samp>’ (<code>CPPFLAGS</code>) to catch the most common
cases. If libraries are still not found, then maybe your
compiler/linker does not support re-ordering of <samp><span class="option">-L</span></samp> and
<samp><span class="option">-l</span></samp> flags (this has been reported to be a problem on HP-UX with
the native <samp><span class="command">cc</span></samp>). In this case, use a different compiler (or a
front end shell script which does the re-ordering).
<p>These flags can also be used to build a faster-running version of R.
On most platforms using <samp><span class="command">gcc</span></samp>, having ‘<samp><span class="samp">-O3</span></samp>’ in
<code>CFLAGS</code> and <code>FFLAGS</code> produces worthwhile performance gains
with <samp><span class="command">gcc</span></samp> and <samp><span class="command">gfortran</span></samp>, but may result in a less
reliable build (both segfaults and incorrect numeric computations have
been seen). On systems using the <acronym>GNU</acronym> linker (especially those
using R as a shared library), it is likely that including
‘<samp><span class="samp">-Wl,-O1</span></samp>’ in <code>LDFLAGS</code> is worthwhile, and
‘<samp><span class="samp">'-Bdirect,--hash-style=both,-Wl,-O1'</span></samp>’ is recommended at
<a href="http://lwn.net/Articles/192624/">http://lwn.net/Articles/192624/</a>. Tuning compilation to a
specific <acronym>CPU</acronym> family (e.g. ‘<samp><span class="samp">-mtune=native</span></samp>’ for
<samp><span class="command">gcc</span></samp>) can give worthwhile performance gains, especially on
older architectures such as ‘<samp><span class="samp">ix86</span></samp>’.
<div class="node">
<a name="Making-manuals"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Compilation-flags">Compilation flags</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-variables">Configuration variables</a>
</div>
<h4 class="subsection">B.3.4 Making manuals</h4>
<p><a name="index-R_005fRD4PDF-88"></a><a name="index-R_005fPAPERSIZE-89"></a>The default settings for making the manuals are controlled by
<samp><span class="env">R_RD4PDF</span></samp> and <samp><span class="env">R_PAPERSIZE</span></samp>.
<div class="node">
<a name="Setting-the-shell"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Using-make">Using make</a>,
Previous: <a rel="previous" accesskey="p" href="#Configuration-variables">Configuration variables</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.4 Setting the shell</h3>
<p>By default the shell scripts such as <samp><span class="file">R</span></samp> will be ‘<samp><span class="samp">#!/bin/sh</span></samp>’
scripts (or using the <samp><span class="env">SHELL</span></samp> chosen by <samp><span class="file">configure</span></samp>). This is
almost always satisfactory, but on a few systems <samp><span class="file">/bin/sh</span></samp> is not a
Bourne shell or clone, and the shell to be used can be changed by
setting the configure variable <samp><span class="env">R_SHELL</span></samp> to a suitable value (a full
path to a shell, e.g. <samp><span class="file">/usr/local/bin/bash</span></samp>).
<div class="node">
<a name="Using-make"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Using-FORTRAN">Using FORTRAN</a>,
Previous: <a rel="previous" accesskey="p" href="#Setting-the-shell">Setting the shell</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.5 Using make</h3>
<p><a name="index-make-90"></a>
To compile R, you will most likely find it easiest to use
<acronym>GNU</acronym> <samp><span class="command">make</span></samp>, although the Sun <samp><span class="command">make</span></samp> works on
Solaris, as does the native FreeBSD <samp><span class="command">make</span></samp>. The native
<samp><span class="command">make</span></samp> has been reported to fail on SGI Irix 6.5 and Alpha/OSF1
(aka Tru64).
<p>To build in a separate directory you need a <samp><span class="command">make</span></samp> that uses the
<code>VPATH</code> variable, for example <acronym>GNU</acronym> <samp><span class="command">make</span></samp>, or Sun
<samp><span class="command">make</span></samp> on Solaris 7 or later.
<p><samp><span class="command">dmake</span></samp> has also been used. e.g, on Solaris 10.
<p>If you want to use a <samp><span class="command">make</span></samp> by another name, for example if your
<acronym>GNU</acronym> <samp><span class="command">make</span></samp> is called ‘<samp><span class="samp">gmake</span></samp>’, you need to set the
variable <code>MAKE</code> at configure time, for example
<p><a name="index-configure-91"></a>
<pre class="example"> ./configure MAKE=gmake
</pre>
<div class="node">
<a name="Using-FORTRAN"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Compile-and-load-flags">Compile and load flags</a>,
Previous: <a rel="previous" accesskey="p" href="#Using-make">Using make</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.6 Using FORTRAN</h3>
<p><a name="index-FORTRAN-92"></a>
<ul class="menu">
<li><a accesskey="1" href="#Using-gfortran">Using gfortran</a>
</ul>
<p>To compile R, you need a FORTRAN compiler. The default
is to search for
<!-- F95_compilers in m4/R.m4: -->
<samp><span class="command">f95</span></samp>, <samp><span class="command">fort</span></samp>, <samp><span class="command">xlf95</span></samp>,
<samp><span class="command">ifort</span></samp>, <samp><span class="command">ifc</span></samp>, <samp><span class="command">efc</span></samp>, <samp><span class="command">pgf95</span></samp>
<samp><span class="command">lf95</span></samp>, <samp><span class="command">gfortran</span></samp>, <samp><span class="command">ftn</span></samp>, <samp><span class="command">g95</span></samp>,
<!-- F90 compilers in m4/R.m4: -->
<samp><span class="command">f90</span></samp>, <samp><span class="command">xlf90</span></samp>, <samp><span class="command">pghpf</span></samp>, <samp><span class="command">pgf90</span></samp>,
<samp><span class="command">epcf90</span></samp>,
<!-- F77 compilers in m4/R.m4: -->
<samp><span class="command">g77</span></samp>, <samp><span class="command">f77</span></samp>, <samp><span class="command">xlf</span></samp>, <samp><span class="command">frt</span></samp>,
<samp><span class="command">pgf77</span></samp>, <samp><span class="command">cf77</span></samp>, <samp><span class="command">fort77</span></samp>, <samp><span class="command">fl32</span></samp>,
<samp><span class="command">af77</span></samp> (in that order)<a rel="footnote" href="#fn-35" name="fnd-35"><sup>35</sup></a>, and use whichever is found first; if none is found,
R cannot be compiled.
<!-- GCC_Fortran_compiler in m4/R.m4: -->
However, if <samp><span class="command">CC</span></samp> is <samp><span class="command">gcc</span></samp>, the matching FORTRAN compiler
(<samp><span class="command">g77</span></samp> for <samp><span class="command">gcc</span></samp> 3 and <code>gfortran</code> for
<samp><span class="command">gcc</span></samp> 4) is used if available.
<p>The search mechanism can be changed using the configure variable
<code>F77</code> which specifies the command that runs the FORTRAN 77
compiler. If your FORTRAN compiler is in a non-standard location, you
<a name="index-PATH-93"></a>should set the environment variable <samp><span class="env">PATH</span></samp> accordingly before
running <samp><span class="command">configure</span></samp>, or use the configure variable <code>F77</code> to
specify its full path.
<p>If your FORTRAN libraries are in slightly peculiar places, you should
<a name="index-LD_005fLIBRARY_005fPATH-94"></a>also look at <samp><span class="env">LD_LIBRARY_PATH</span></samp> or your system's equivalent to make
sure that all libraries are on this path.
<p>Note that only FORTRAN compilers which convert identifiers to lower case
are supported.
<p>You must set whatever compilation flags (if any) are needed to ensure
that FORTRAN <code>integer</code> is equivalent to a C <code>int</code> pointer and
FORTRAN <code>double precision</code> is equivalent to a C <code>double</code>
pointer. This is checked during the configuration process.
<p>Some of the FORTRAN code makes use of <code>COMPLEX*16</code> variables, which
is a Fortran 90 extension. This is checked for at configure
time<a rel="footnote" href="#fn-36" name="fnd-36"><sup>36</sup></a>, but you may need to avoid
compiler flags asserting FORTRAN 77 compliance.
<p>Compiling the version of LAPACK in the R sources also requires some
Fortran 90 extensions, but these are not needed if an external LAPACK is
used.
<p>It might be possible to use <samp><span class="command">f2c</span></samp>, the FORTRAN-to-C converter
(<a href="http://www.netlib.org/f2c">http://www.netlib.org/f2c</a>), via a script. (An example script
is given in <samp><span class="file">scripts/f77_f2c</span></samp>: this can be customized by setting
<a name="index-F2C-95"></a><a name="index-F2CLIBS-96"></a><a name="index-CC-97"></a>the environment variables <samp><span class="env">F2C</span></samp>, <samp><span class="env">F2CLIBS</span></samp>, <samp><span class="env">CC</span></samp> and
<a name="index-CPP-98"></a><samp><span class="env">CPP</span></samp>.) You will need to ensure that the FORTRAN type
<code>integer</code> is translated to the C type <code>int</code>. Normally
<samp><span class="file">f2c.h</span></samp> contains ‘<samp><span class="samp">typedef long int integer;</span></samp>’, which will work
on a 32-bit platform but needs to be changed to ‘<samp><span class="samp">typedef int
integer;</span></samp>’ on a 64-bit platform. If your compiler is not <samp><span class="command">gcc</span></samp>
you will need to set
<a name="index-FPICFLAGS-99"></a><samp><span class="env">FPICFLAGS</span></samp> appropriately. Also, the included LAPACK sources
contain constructs that <samp><span class="command">f2c</span></samp> is unlikely to be able to process,
so you would need to use an external LAPACK library (such as CLAPACK
from <a href="http://www.netlib.org/clapack/">http://www.netlib.org/clapack/</a>).
<div class="node">
<a name="Using-gfortran"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Using-FORTRAN">Using FORTRAN</a>,
Up: <a rel="up" accesskey="u" href="#Using-FORTRAN">Using FORTRAN</a>
</div>
<h4 class="subsection">B.6.1 Using gfortran</h4>
<p><samp><span class="command">gfortran</span></samp> is the F95 compiler that is part of
<samp><span class="command">gcc</span></samp> 4.<var>x</var>.<var>y</var>.
<p>On Linux ‘<samp><span class="samp">x86_64</span></samp>’ systems there is an incompatibility in the
return conventions for double-complex functions between
<samp><span class="command">gfortran</span></samp> and <samp><span class="command">g77</span></samp> which results in the final example
in <code>example(eigen)</code> hanging or segfaulting under external
<acronym>BLAS</acronym>s built under <samp><span class="command">g77</span></samp> (and also some external
LAPACKs). The commonest cases will be detected by a <samp><span class="command">configure</span></samp>
test. Although <samp><span class="command">g77</span></samp> is long obsolete this is still sometimes
seen with C versions of external software using <samp><span class="command">g77</span></samp>
conventions.
<p>The default <code>FFLAGS</code> and <code>FCFLAGS</code> chosen (by
<samp><span class="command">autoconf</span></samp>) for a <acronym>GNU</acronym> FORTRAN compiler is ‘<samp><span class="samp">-g
-O2</span></samp>’. This has caused problems (segfaults and infinite loops) on
‘<samp><span class="samp">x86_64</span></samp>’ Linux in the past, but seems fine with
<samp><span class="command">gfortran 4.4.4</span></samp> and later: for <code>gfortran 4.3.x</code> set
<code>FFLAGS</code> and <code>FCFLAGS</code> to use at most ‘<samp><span class="samp">-O</span></samp>’.
<div class="node">
<a name="Compile-and-load-flags"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Using-FORTRAN">Using FORTRAN</a>,
Up: <a rel="up" accesskey="u" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>
</div>
<h3 class="section">B.7 Compile and load flags</h3>
<p>A wide range of flags can be set in the file <samp><span class="file">config.site</span></samp> or as
configure variables on the command line. We have already mentioned
<dl>
<dt><code>CPPFLAGS</code><dd>header file search directory (<samp><span class="option">-I</span></samp>) and any other miscellaneous
options for the C and C++ preprocessors and compilers
<br><dt><code>LDFLAGS</code><dd>path (<samp><span class="option">-L</span></samp>), stripping (<samp><span class="option">-s</span></samp>) and any other miscellaneous
options for the linker
</dl>
<p class="noindent">and others include
<dl>
<dt><code>CFLAGS</code><dd>debugging and optimization flags, C
<br><dt><code>MAIN_CFLAGS</code><dd>ditto, for compiling the main program
<br><dt><code>SHLIB_CFLAGS</code><dd>for shared objects
<br><dt><code>FFLAGS</code><dd>debugging and optimization flags, FORTRAN
<br><dt><code>SAFE_FFLAGS</code><dd>ditto for source files which need exact floating point behaviour
<br><dt><code>MAIN_FFLAGS</code><dd>ditto, for compiling the main program
<br><dt><code>SHLIB_FFLAGS</code><dd>for shared objects
<br><dt><code>MAIN_LDFLAGS</code><dd>additional flags for the main link
<br><dt><code>SHLIB_LDFLAGS</code><dd>additional flags for linking the shared objects
<br><dt><code>LIBnn</code><dd>the primary library directory, <samp><span class="file">lib</span></samp> or <samp><span class="file">lib64</span></samp>
<br><dt><code>CPICFLAGS</code><dd>special flags for compiling C code to be turned into a shared object
<br><dt><code>FPICFLAGS</code><dd>special flags for compiling Fortran code to be turned into a shared object
<br><dt><code>CXXPICFLAGS</code><dd>special flags for compiling C++ code to be turned into a shared object
<br><dt><code>FCPICFLAGS</code><dd>special flags for compiling Fortran 95 code to be turned into a shared object
<br><dt><code>DEFS</code><dd>defines to be used when compiling C code in R itself
</dl>
<p class="noindent">Library paths specified as <samp><span class="option">-L/lib/path</span></samp> in <code>LDFLAGS</code> are
<a name="index-LD_005fLIBRARY_005fPATH-100"></a>collected together and prepended to <samp><span class="env">LD_LIBRARY_PATH</span></samp> (or your
system's equivalent), so there should be no need for <samp><span class="option">-R</span></samp> or
<samp><span class="option">-rpath</span></samp> flags.
<p>Variables such as <samp><span class="env">CPICFLAGS</span></samp> are determined where possible by
<samp><span class="command">configure</span></samp>. Some systems allows two types of PIC flags, for
example ‘<samp><span class="samp">-fpic</span></samp>’ and ‘<samp><span class="samp">-fPIC</span></samp>’, and if they differ the first
allows only a limited number of symbols in a shared object. Since R
as a shared library has about 6200 symbols, if in doubt use the larger
version.
<p>To compile a profiling version of R, one might for example want to
use ‘<samp><span class="samp">MAIN_CFLAGS=-pg</span></samp>’, ‘<samp><span class="samp">MAIN_FFLAGS=-pg</span></samp>’,
‘<samp><span class="samp">MAIN_LDFLAGS=-pg</span></samp>’ on platforms where ‘<samp><span class="samp">-pg</span></samp>’ cannot be used
with position-independent code.
<p><strong>Beware</strong>: it may be necessary to set <code>CFLAGS</code> and
<code>FFLAGS</code> in ways compatible with the libraries to be used: one
possible issue is the alignment of doubles, another is the way
structures are passed.
<p>On some platforms <samp><span class="command">configure</span></samp> will select additional flags for
<code>CFLAGS</code>, <code>CPPFLAGS</code>, <code>FFLAGS</code>, <code>CXXFLAGS</code> and
<code>LIBS</code> in <code>R_XTRA_CFLAGS</code> (and so on). These are for options
which are always required, for example to force <acronym>IEC</acronym> 60559
compliance.
<div class="node">
<a name="Platform-notes"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#The-Windows-toolset">The Windows toolset</a>,
Previous: <a rel="previous" accesskey="p" href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="appendix">Appendix C Platform notes</h2>
<p>This section provides some notes on building R on different Unix-alike
platforms. These notes are based on tests run on one or two systems in
each case with particular sets of compilers and support libraries.
Success in building R depends on the proper installation and functioning
of support software; your results may differ if you have other versions
of compilers and support libraries.
<p>Older versions of this manual (for R < 2.10.0) contain notes on
platforms such as HP-UX, IRIX and Alpha/OSF1 for which we have had no
recent reports.
<p>C macros to select particular platforms can be tricky to track down
(there is a fair amount of misinformation on the Web). The Wiki
(currently) at <a href="http://sourceforge.net/p/predef/wiki/Home/">http://sourceforge.net/p/predef/wiki/Home/</a> can be
helpful. The R sources currently use
<pre class="example"> AIX: _AIX
Cygwin: __CYGWIN__
FreeBSD: __FreeBSD__
HP-UX: __hpux__, __hpux
IRIX: sgi, __sgi
Linux: __linux__
OS X: __APPLE__
NetBSD: __NetBSD__
OpenBSD: __OpenBSD__
Solaris: __sun, sun
Windows: _WIN32, _WIN64
</pre>
<ul class="menu">
<li><a accesskey="1" href="#X11-issues">X11 issues</a>
<li><a accesskey="2" href="#Linux">Linux</a>
<li><a accesskey="3" href="#OS-X">OS X</a>
<li><a accesskey="4" href="#Solaris">Solaris</a>
<li><a accesskey="5" href="#AIX">AIX</a>
<li><a accesskey="6" href="#FreeBSD">FreeBSD</a>
<li><a accesskey="7" href="#Cygwin">Cygwin</a>
<li><a accesskey="8" href="#New-platforms">New platforms</a>
</ul>
<div class="node">
<a name="X11-issues"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Linux">Linux</a>,
Previous: <a rel="previous" accesskey="p" href="#Platform-notes">Platform notes</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.1 X11 issues</h3>
<p>The ‘<samp><span class="samp">X11()</span></samp>’ graphics device is the one started automatically on
Unix-alikes when plotting. As its name implies, it displays on a (local
or remote) X server, and relies on the services provided by the X
server.
<p>The ‘modern’ version of the ‘<samp><span class="samp">X11()</span></samp>’ device is based on ‘<samp><span class="samp">cairo</span></samp>’
graphics and (in most implementations) uses ‘<samp><span class="samp">fontconfig</span></samp>’ to pick and
render fonts. This is done on the server, and although there can be
selection issues, they are more amenable than the issues with
‘<samp><span class="samp">X11()</span></samp>’ discussed in the rest of this section.
<p>When X11 was designed, most displays were around 75dpi, whereas today
they are of the order of 100dpi or more. If you find that X11()
is reporting<a rel="footnote" href="#fn-37" name="fnd-37"><sup>37</sup></a> missing font sizes, especially larger ones, it is likely
that you are not using scalable fonts and have not installed the 100dpi
versions of the X11 fonts. The names and details differ by system, but
will likely have something like Fedora's
<pre class="example"> xorg-x11-fonts-75dpi
xorg-x11-fonts-100dpi
xorg-x11-fonts-ISO8859-2-75dpi
xorg-x11-fonts-Type1
xorg-x11-fonts-cyrillic
</pre>
<p class="noindent">and you need to ensure that the ‘<samp><span class="samp">-100dpi</span></samp>’ versions are installed
and on the X11 font path (check via <samp><span class="command">xset -q</span></samp>). The
‘<samp><span class="samp">X11()</span></samp>’ device does try to set a pointsize and not a pixel size:
laptop users may find the default setting of 12 too large (although very
frequently laptop screens are set to a fictitious dpi to appear like a
scaled-down desktop screen).
<p>More complicated problems can occur in non-Western-European locales, so
if you are using one, the first thing to check is that things work in
the <code>C</code> locale. The likely issues are a failure to find any fonts
or glyphs being rendered incorrectly (often as a pair of <acronym>ASCII</acronym>
characters). X11 works by being asked for a font specification and
coming up with its idea of a close match. For text (as distinct from
the symbols used by plotmath), the specification is the first element of
the option <code>"X11fonts"</code> which defaults to
<pre class="example"> "-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*"
</pre>
<p>If you are using a single-byte encoding, for example ISO 8859-2 in
Eastern Europe or KOI8-R in Russian, use <samp><span class="command">xlsfonts</span></samp> to find an
appropriate family of fonts in your encoding (the last field in the
listing). If you find none, it is likely that you need to install
further font packages, such as ‘<samp><span class="samp">xorg-x11-fonts-ISO8859-2-75dpi</span></samp>’ and
‘<samp><span class="samp">xorg-x11-fonts-cyrillic</span></samp>’ shown in the listing above.
<p>Multi-byte encodings (most commonly UTF-8) are even more complicated.
There are few fonts in ‘<samp><span class="samp">iso10646-1</span></samp>’, the Unicode encoding, and they
only contain a subset of the available glyphs (and are often fixed-width
designed for use in terminals). In such locales <em>fontsets</em> are
used, made up of fonts encoded in other encodings. If the locale you
are using has an entry in the ‘<samp><span class="samp">XLC_LOCALE</span></samp>’ directory (typically
<samp><span class="file">/usr/share/X11/locale</span></samp>, it is likely that all you need to do is to
pick a suitable font specification that has fonts in the encodings
specified there. If not, you may have to get hold of a suitable locale
entry for X11. This may mean that, for example, Japanese text can be
displayed when running in ‘<samp><span class="samp">ja_JP.UTF-8</span></samp>’ but not when running in
‘<samp><span class="samp">en_GB.UTF-8</span></samp>’ on the same machine (although on some systems many
UTF-8 X11 locales are aliased to ‘<samp><span class="samp">en_US.UTF-8</span></samp>’ which covers several
character sets, e.g. ISO 8859-1 (Western European), JISX0208 (Kanji),
KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)).
<p>On some systems scalable fonts are available covering a wide range of
glyphs. One source is TrueType/OpenType fonts, and these can provide
high coverage. Another is Type 1 fonts: the URW set of Type 1 fonts
provides standard typefaces such as Helvetica with a larger coverage of
Unicode glyphs than the standard X11 bitmaps, including Cyrillic. These
are generally not part of the default install, and the X server may need
to be configured to use them. They might be under the X11 <samp><span class="file">fonts</span></samp>
directory or elsewhere, for example,
<pre class="example"> /usr/share/fonts/default/Type1
/usr/share/fonts/ja/TrueType
</pre>
<div class="node">
<a name="Linux"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#OS-X">OS X</a>,
Previous: <a rel="previous" accesskey="p" href="#X11-issues">X11 issues</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.2 Linux</h3>
<p><a name="index-Linux-101"></a>
Linux is the main development platform for R, so compilation from the
sources is normally straightforward with the standard compilers.
<p>Remember that some package management systems (such as <acronym>RPM</acronym> and
deb) make a distinction between the user version of a package and the
developer version. The latter usually has the same name but with the
extension ‘<samp><span class="samp">-devel</span></samp>’ or ‘<samp><span class="samp">-dev</span></samp>’: you need both versions
installed. So please check the <code>configure</code> output to see if the
expected features are detected: if for example ‘<samp><span class="samp">readline</span></samp>’ is
missing add the developer package. (On most systems you will also need
‘<samp><span class="samp">ncurses</span></samp>’ and its developer package, although these should be
dependencies of the ‘<samp><span class="samp">readline</span></samp>’ package(s).)
<p>When R has been installed from a binary distribution there are
sometimes problems with missing components such as the FORTRAN
compiler. Searching the ‘<samp><span class="samp">R-help</span></samp>’ archives will normally reveal
what is needed.
<p>It seems that ‘<samp><span class="samp">ix86</span></samp>’ Linux accepts non-PIC code in shared
libraries, but this is not necessarily so on other platforms, in
particular on 64-bit <acronym>CPU</acronym>s such as ‘<samp><span class="samp">x86_64</span></samp>’. So care
can be needed with <acronym>BLAS</acronym> libraries and when building R as a
shared library to ensure that position-independent code is used in any
static libraries (such as the Tcl/Tk libraries, <code>libpng</code>,
<code>libjpeg</code> and <code>zlib</code>) which might be linked against.
Fortunately these are normally built as shared libraries with the
exception of the ATLAS <acronym>BLAS</acronym> libraries.
<p>The default optimization settings chosen for <code>CFLAGS</code> etc are
conservative. It is likely that using <samp><span class="option">-mtune</span></samp> will result in
significant performance improvements on recent CPUs (especially for
‘<samp><span class="samp">ix86</span></samp>’): one possibility is to add <samp><span class="option">-mtune=native</span></samp> for
the best possible performance on the machine on which R is being
installed: if the compilation is for a site-wide installation, it may
still be desirable to use something like
<samp><span class="option">-mtume=core2</span></samp>.<a rel="footnote" href="#fn-38" name="fnd-38"><sup>38</sup></a> It is also possible to increase the
optimization levels to <samp><span class="option">-O3</span></samp>: however for many versions of the
compilers this has caused problems in at least one <acronym>CRAN</acronym>
package.
<p>For platforms with both 64- and 32-bit support, it is likely that
<pre class="example"> LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib"
</pre>
<p class="noindent">is appropriate since most (but not all) software installs its 64-bit
libraries in <samp><span class="file">/usr/local/lib64</span></samp>. To build a 32-bit version of R
on ‘<samp><span class="samp">x86_64</span></samp>’ with Fedora 18 we used
<pre class="example"> CC="gcc -m32"
CXX="g++ -m32"
F77="gfortran -m32"
FC=${F77}
OBJC=${CC}
LDFLAGS="-L/usr/local/lib"
LIBnn=lib
</pre>
<p class="noindent">Note the use of ‘<samp><span class="samp">LIBnn</span></samp>’: ‘<samp><span class="samp">x86_64</span></samp>’ Fedora installs its
64-bit software in <samp><span class="file">/usr/lib64</span></samp> and 32-bit software in
<samp><span class="file">/usr/lib</span></samp>. Linking will skip over inappropriate binaries, but for
example the 32-bit Tcl/Tk configure scripts are in <samp><span class="file">/usr/lib</span></samp>. It
may also be necessary to set the <samp><span class="command">pkg-config</span></samp> path, e.g. by
<pre class="example"> export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
</pre>
<p>64-bit versions of Linux are built with support for files > 2Gb, and
32-bit versions will be if possible unless <samp><span class="option">--disable-largefile</span></samp>
is specified.
<p>To build a 64-bit version of R on ‘<samp><span class="samp">ppc64</span></samp>’ (also known as
‘<samp><span class="samp">powerpc64</span></samp>’) with <samp><span class="command">gcc</span></samp> 4.1.1, Ei-ji Nakama used
<pre class="example"> CC="gcc -m64"
CXX="gxx -m64"
F77="gfortran -m64"
FC="gfortran -m64"
CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2"
</pre>
<p class="noindent">the additional flags being needed to resolve problems linking against
<samp><span class="file">libnmath.a</span></samp> and when linking R as a shared library.
<ul class="menu">
<li><a accesskey="1" href="#Clang">Clang</a>
<li><a accesskey="2" href="#Intel-compilers">Intel compilers</a>
<li><a accesskey="3" href="#Oracle-Solaris-Studio-compilers">Oracle Solaris Studio compilers</a>
</ul>
<div class="node">
<a name="Clang"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Intel-compilers">Intel compilers</a>,
Previous: <a rel="previous" accesskey="p" href="#Linux">Linux</a>,
Up: <a rel="up" accesskey="u" href="#Linux">Linux</a>
</div>
<h4 class="subsection">C.2.1 Clang</h4>
<p>R has been built with Linux ‘<samp><span class="samp">ix86</span></samp>’ and ‘<samp><span class="samp">x86_64</span></samp>’ C and
C++ compilers (<a href="http://clang.llvm.org">http://clang.llvm.org</a>, versions 3.0, 3.2 and 3.3)
based on the Clang front-ends, invoked by <code>CC=clang CXX=clang++</code>,
together with <samp><span class="command">gfortran</span></samp>. These take very similar options to
the corresponding GCC compilers.
<p>This has to be used in conjunction with a Fortran compiler: the
<samp><span class="command">configure</span></samp> code will remove <samp><span class="option">-lgcc</span></samp> from <samp><span class="env">FLIBS</span></samp>,
which is needed for some versions of <samp><span class="command">gfortran</span></samp>.
<div class="node">
<a name="Intel-compilers"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Oracle-Solaris-Studio-compilers">Oracle Solaris Studio compilers</a>,
Previous: <a rel="previous" accesskey="p" href="#Clang">Clang</a>,
Up: <a rel="up" accesskey="u" href="#Linux">Linux</a>
</div>
<h4 class="subsection">C.2.2 Intel compilers</h4>
<p>Intel compilers have been used under ‘<samp><span class="samp">ix86</span></samp>’ and ‘<samp><span class="samp">x86_64</span></samp>’
Linux. Brian Ripley used version 9.0 of the compilers for
‘<samp><span class="samp">x86_64</span></samp>’ on Fedora Core 5 with
<pre class="example"> CC=icc
CFLAGS="-g -O3 -wd188 -ip -mp"
F77=ifort
FLAGS="-g -O3 -mp"
CXX=icpc
CXXFLAGS="-g -O3 -mp"
FC=ifort
FCFLAGS="-g -O3 -mp"
ICC_LIBS=/opt/compilers/intel/cce/9.1.039/lib
IFC_LIBS=/opt/compilers/intel/fce/9.1.033/lib
LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64"
SHLIB_CXXLD=icpc
</pre>
<p class="noindent"><samp><span class="command">configure</span></samp> will add ‘<samp><span class="samp">-c99</span></samp>’ to <code>CC</code> for
C99-compliance. This causes warnings with <code>icc</code> 10 and later, so
use <code>CC="icc -std=c99"</code> there. The flag <samp><span class="option">-wd188</span></samp> suppresses
a large number of warnings about the enumeration type ‘<samp><span class="samp">Rboolean</span></samp>’.
Because the Intel C compiler sets ‘<samp><span class="samp">__GNUC__</span></samp>’ without complete
emulation of <samp><span class="command">gcc</span></samp>, we suggest adding <code>CPPFLAGS=-no-gcc</code>.
<p>To maintain correct <acronym>IEC</acronym> 60559 arithmetic you most likely
need add flags to <code>CFLAGS</code>, <code>FFLAGS</code> and <code>CXXFLAGS</code> such
as <samp><span class="option">-mp</span></samp> (shown above) or <samp><span class="option">-fp-model precise -fp-model
source</span></samp>, depending on the compiler version.
<p>Others have reported success with versions 10.x and 11.x.
<div class="node">
<a name="Oracle-Solaris-Studio-compilers"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Intel-compilers">Intel compilers</a>,
Up: <a rel="up" accesskey="u" href="#Linux">Linux</a>
</div>
<h4 class="subsection">C.2.3 Oracle Solaris Studio compilers</h4>
<p>Brian Ripley tested the Sun Studio 12 compilers, since renamed to Oracle
Solaris Studio,
(<a href="http://developers.sun.com/sunstudio/index.jsp">http://developers.sun.com/sunstudio/index.jsp</a>)
On
‘<samp><span class="samp">x86_64</span></samp>’ Linux with
<pre class="example"> CC=suncc
CFLAGS="-xO5 -xc99 -xlibmil -nofstore"
CPICFLAGS=-Kpic
F77=sunf95
FFLAGS="-O5 -libmil -nofstore"
FPICFLAGS=-Kpic
CXX="sunCC -library=stlport4"
CXXFLAGS="-xO5 -xlibmil -nofstore -features=tmplrefstatic"
CXXPICFLAGS=-Kpic
FC=sunf95
FCFLAGS=$FFLAGS
FCPICFLAGS=-Kpic
LDFLAGS=-L/opt/sunstudio12.1/rtlibs/amd64
SHLIB_LDFLAGS=-shared
SHLIB_CXXLDFLAGS=-G
SHLIB_FCLDFLAGS=-G
SAFE_FFLAGS="-O5 -libmil"
</pre>
<p class="noindent"><samp><span class="option">-m64</span></samp> could be added, but was the default. Do not use
<samp><span class="option">-fast</span></samp>: see the warnings under Solaris. (The C++ options are
also explained under Solaris.)
<p>Others have found on at least some versions of ‘<samp><span class="samp">ix86</span></samp>’ Linux that
the configure flag <samp><span class="option">--disable-largefile</span></samp> was needed (since
<samp><span class="file">glob.h</span></samp> on that platform presumed <samp><span class="command">gcc</span></samp> was being used).
<div class="node">
<a name="OS-X"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Solaris">Solaris</a>,
Previous: <a rel="previous" accesskey="p" href="#Linux">Linux</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.3 OS X</h3>
<p><a name="index-OS-X-102"></a>
You can build R using Apple's ‘Command Line Tools for Xcode’ and and
suitable compilers. You will also need <code>readline</code> (or to configure
with <samp><span class="option">--without-readline</span></samp>).
<p>You may also need to install an X sub-system (or you will need to
configure with <samp><span class="option">--without-x</span></samp>): X is part of the standard OS X
distribution in versions prior to Mountain Lion, but not always
installed. For Mountain Lion and later, see
<a href="http://xquartz.macosforge.org/">http://xquartz.macosforge.org/</a>: some people prefer to use XQuartz
on earlier versions of OS X instead of the Apple version.
<p>In principle R can be built for 10.4.x, 10.5.x and for PowerPC Macs
but this has not been tested recently: 10.6 (Snow Leopard) is the
earliest version currently tested. 32-bit Intel builds of R 3.0.0
were tested: they would be needed for Snow Leopard running on very old
machines with Core Solo or Core Duo CPUs. The instructions here
concentrate on ‘<samp><span class="samp">x86_64</span></samp>’ builds.
<p>To use the <code>quartz()</code> graphics device you need to configure with
<samp><span class="option">--with-aqua</span></samp> (which is the default): <code>quartz()</code> then
becomes the default device when running R at the console and X11
would only be used for the data editor/viewer. (This needs an
Objective-C compiler<a rel="footnote" href="#fn-39" name="fnd-39"><sup>39</sup></a> which can compile the code for <code>quartz()</code>.)
<p>Use <samp><span class="option">--without-aqua</span></samp> if you want a standard Unix-alike build:
apart from disabling <code>quartz()</code> and the ability to use the build
with <span class="sc">R.app</span>, it also changes the default location of the personal
library (see <code>?.libPaths()</code>). Also use
<samp><span class="option">--disable-R-framework</span></samp> to install in the standard layout.
<p>‘Command Line Tools for Xcode’ used to be part of the Apple
Developer Tools (‘Xcode’) but nowadays need to be installed
separately. They can be downloaded from
<a href="http://developer.apple.com/devcenter/mac/">http://developer.apple.com/devcenter/mac/</a> (you will need to register
there) or if you have a recent Xcode installed (from the App Store or
from <a href="https://developer.apple.com/devcenter/mac/">https://developer.apple.com/devcenter/mac/</a>) you can install
the command-line tools from within Xcode, from the ‘<samp><span class="samp">Downloads</span></samp>’ pane
in the ‘<samp><span class="samp">Preferences</span></samp>’.
<p>Various compilers can be used. The <acronym>CRAN</acronym> distribution of R
is built using
<ul>
<li><samp><span class="command">gcc</span></samp>
from the Xcode distribution. This is a version of gcc 4.2.1 with an
LLVM backend. Note that Apple have announced that Xcode 4.6 will be the
last ‘release’ with this compiler (4.6.2 does contain it but 5 is
expected not to), and it is likely that <samp><span class="command">clang</span></samp> will be used
before R 3.1.0 is released.
<li><samp><span class="command">gfortran</span></samp>
from
<a href="http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg">http://cran.r-project.org/bin/macosx/tools/gfortran-4.2.3.pkg</a>.
Note that this installs into <samp><span class="file">/usr/local/bin</span></samp>, so make sure that is
on your path. Other compilers from
<a href="http://r.research.att.com/tools/">http://r.research.att.com/tools/</a> can also be used.
<li><samp><span class="command">clang</span></samp>
from the Xcode distribution, to compile the Objective-C parts of the
<code>quartz()</code> device.
</ul>
<p>To use these, have in <samp><span class="file">config.site</span></samp> something like
<pre class="example"> CC="llvm-gcc-4.2"
CXX="llvm-g++-4.2"
F77="gfortran-4.2 -arch x86_64"
FC=$F77
OBJC="clang"
</pre>
<p class="noindent">Full names are not needed, but help to ensure that the intended
compilers are used. The recommended Fortran compiler defaults to
32-bit, so <code>-arch x86_64</code> is needed. (For a 32-bit build, use
<code>-arch i386</code> for all compiler commands.)
<p>The OpenMP support in this version of <samp><span class="command">gcc</span></samp> is problematic, so
the <acronym>CRAN</acronym> build is configured with <samp><span class="option">--disable-openmp</span></samp>.
The alternative, <samp><span class="command">clang</span></samp>, has no OpenMP support.
<p>Pre-compiled versions of many of the <a href="#Useful-libraries-and-programs">Useful libraries and programs</a>
are available from <a href="http://r.research.att.com/libs/">http://r.research.att.com/libs/</a>. You will
most likely want at least <code>jpeg</code>, <code>libpng</code> and <code>readline</code>
(and perhaps <code>tiff</code>). <code>pkg-config</code> is not provided by Apple
and useful for many packages.
<p><a name="index-BLAS-library-103"></a><a name="index-LAPACK-library-104"></a>The <code>Accelerate</code> library can be used <em>via</em> the configuration options
<pre class="example"> --with-blas="-framework Accelerate" --with-lapack
</pre>
<p class="noindent">to provide higher-performance versions of the <acronym>BLAS</acronym> and LAPACK
routines. (Use of <code>Accelerate</code> with <samp><span class="option">--with-lapack</span></samp> does
not work on Snow Leopard: it may work there without.)
<p>Looking at the top of
<samp><span class="file">/Library/Frameworks/R.framework/Resources/etc/Makeconf</span></samp>
will show the compilers and configuration options used for the
<acronym>CRAN</acronym> binary package for R: at the time of writing
<pre class="example"> --with-system-zlib --enable-memory-profiling --disable-openmp
</pre>
<p class="noindent">was used.
<p>The TeX implementation used by the developers is MacTeX
(<a href="http://www.tug.org/mactex/">http://www.tug.org/mactex/</a>): the full installation is several
gigabytes, but a smaller version (ca 300MB) is available at
<a href="http://www.tug.org/mactex/morepackages.html">http://www.tug.org/mactex/morepackages.html</a>: you will want to add
some packages, including <strong>inconsolata</strong>.
<ul class="menu">
<li><a accesskey="1" href="#Snow-Leopard">Snow Leopard</a>
<li><a accesskey="2" href="#Lion">Lion</a>
<li><a accesskey="3" href="#Mountain-Lion">Mountain Lion</a>
<li><a accesskey="4" href="#Mavericks">Mavericks</a>
<li><a accesskey="5" href="#Tcl_002fTk-headers-and-libraries">Tcl/Tk headers and libraries</a>
<li><a accesskey="6" href="#Java-_0028OS-X_0029">Java (OS X)</a>
<li><a accesskey="7" href="#Frameworks">Frameworks</a>
<li><a accesskey="8" href="#Building-R_002eapp">Building R.app</a>
</ul>
<div class="node">
<a name="Snow-Leopard"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Lion">Lion</a>,
Previous: <a rel="previous" accesskey="p" href="#OS-X">OS X</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.1 Snow Leopard</h4>
<p>A quirk on Snow Leopard is that the X11 libraries are not in the default
linking path, so something like ‘<samp><span class="samp">LIBS=-L/usr/X11/lib</span></samp>’ may be
required in <samp><span class="file">config.site</span></samp>, or you can use the <samp><span class="command">configure</span></samp>
options <samp><span class="option">--x-includes=/usr/X11/include
--x-libraries=/usr/X11/lib.</span></samp>.
<p>The <acronym>CRAN</acronym> binaries are built using Xcode 4.2, a version
available only to subscribing developers. It is expected that 3.2.6 (the
last public free version for Snow Leopard) will work.
<div class="node">
<a name="Lion"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Mountain-Lion">Mountain Lion</a>,
Previous: <a rel="previous" accesskey="p" href="#Snow-Leopard">Snow Leopard</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.2 Lion</h4>
<p>No tweaks are known to be needed on Lion. See the notes on Mountain
Lion if XQuartz is in use.
<div class="node">
<a name="Mountain-Lion"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Mavericks">Mavericks</a>,
Previous: <a rel="previous" accesskey="p" href="#Lion">Lion</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.3 Mountain Lion</h4>
<p>The X11 system used with Mountain Lion is XQuartz (see above).
<p>To build the graphics devices depending on cairographics the XQuartz
path for <samp><span class="command">pkg-config</span></samp> files needs to be known to
<samp><span class="command">pkg-config</span></samp> when <samp><span class="command">configure</span></samp> is run: this usually means
adding it to the <samp><span class="env">PKG_CONFIG_PATH</span></samp> environment variable, e.g.
<pre class="example"> export PKG_CONFIG_PATH= \
/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
</pre>
<p>For some pre-compiled software, for example the GTK framework,
<samp><span class="file">/opt/X11/include</span></samp> may need to be added to the include paths.
<div class="node">
<a name="Mavericks"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Tcl_002fTk-headers-and-libraries">Tcl/Tk headers and libraries</a>,
Previous: <a rel="previous" accesskey="p" href="#Mountain-Lion">Mountain Lion</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.4 Mavericks</h4>
<p>Mavericks is associated with Xcode 5, and is said to download software
components as needed without installing all of Xcode.
<p>It is likely that <samp><span class="command">clang</span></samp> will be the preferred C compiler,
using something like
<pre class="example"> CC="clang"
CXX="clang++"
F77="gfortran-4.2 -arch x86_64"
FC=$F77
OBJC="clang"
</pre>
<p>See the comments under Mountain Lion about X11 and GTK.
<div class="node">
<a name="Tcl%2fTk-headers-and-libraries"></a>
<a name="Tcl_002fTk-headers-and-libraries"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Java-_0028OS-X_0029">Java (OS X)</a>,
Previous: <a rel="previous" accesskey="p" href="#Mavericks">Mavericks</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.5 Tcl/Tk headers and libraries</h4>
<p>If you plan to use the <code>tcltk</code> package for R, you need to
install a distribution of Tcl/Tk. There are two alternatives. If you
use <span class="sc">R.app</span> you will want to use X11-based Tcl/Tk (as used on other
Unix-alikes), which is installed as part of the CRAN binary for R.
This may need
<pre class="example"> --with-tcl-config=/usr/local/lib/tclConfig.sh
--with-tk-config=/usr/local/lib/tkConfig.sh
</pre>
<p>Note that this expects a fully-updated X11 installation: it was built
against the Apple X11 from Snow Leopard, but XQuartz will work if recent
enough (e.g. version 2.7.4).
<p>There is also a native (‘Aqua’) version of Tcl/Tk which produces widgets
in the native OS X style: this will not work with <span class="sc">R.app</span> because of
conflicting event loops, but for those only using command-line R this
provides a much more intuitive interface to Tk for experienced Mac
users. Most versions of OS X come with Aqua Tcl/Tk libraries, but these
are not current versions of Tcl/Tk (8.5.9 in Mountain Lion). It is
better to install Tcl/Tk 8.6.x or 8.5.x from the sources or the binary
distribution at <a href="http://www.activestate.com/activetcl/downloads">http://www.activestate.com/activetcl/downloads</a>.
Configure R with
<pre class="example"> --with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh
--with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh
</pre>
<p class="noindent">(for the versions bundled with OS X, use paths starting with
<samp><span class="file">/System/Library</span></samp>).
<div class="node">
<a name="Java-(OS-X)"></a>
<a name="Java-_0028OS-X_0029"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Frameworks">Frameworks</a>,
Previous: <a rel="previous" accesskey="p" href="#Tcl_002fTk-headers-and-libraries">Tcl/Tk headers and libraries</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.6 Java</h4>
<p>The situation with Java support on OS X is messy, with Apple essentially
no longer supporting Java (and what it does support is Java 6, which has
reached end-of-life). Snow Leopard and Lion shipped with a Java 6
runtime (JRE).
<p>Mountain Lion did not come with an installed JRE, and an upgrade to
Mountain Lion removed one if already installed. It is intended to be
installed at first use. Check if a JRE is installed by running
<samp><span class="command">java -version</span></samp> in a <samp><span class="command">Terminal</span></samp> window: if Java is not
installed this should prompt you to install it.
<p>However, for security reasons you may want/need to install the latest
Java from Oracle (currently Java 7 from
<a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">http://www.oracle.com/technetwork/java/javase/downloads/index.html</a>);
this is for Lion and later.
<p>To see what compatible versions of Java are currently installed, run
<samp><span class="command">/usr/libexec/java_home -V -a x86_64</span></samp>. If needed, set the
environment variable <samp><span class="env">JAVA_HOME</span></samp> to choose between these, both when
R is built from the sources and when <samp><span class="command">R CMD javareconf</span></samp> is
run.
<p>Configuring and building R both looks for a JRE and for support for
compiling JNI programs (used by packages <a href="http://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and
<a href="http://CRAN.R-project.org/package=JavaGD"><strong>JavaGD</strong></a>); the latter requires a JDK (Java SDK) and not just a
JRE.
<p>The build process tries to fathom out what JRE/JDK to use, but it may
need some help, e.g. by setting <samp><span class="env">JAVA_HOME</span></samp>. The Apple JRE can be
specified explicitly by something like
<pre class="example"> JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Home
JAVA_CPPFLAGS="-I/System/Library/Frameworks/JavaVM.framework/Headers"
JAVA_LD_LIBRARY_PATH=
JAVA_LIBS="-framework JavaVM"
</pre>
<p class="noindent">The Apple developer versions of the JDK install somewhere like
<pre class="example"> JAVA_HOME=/Library/Java/JavaVirtualMachines/1.6.0_43-b01-447.jdk/Contents/Home
</pre>
<p class="noindent">The Oracle JDK can be specified explicitly by something like
<pre class="example"> JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.7.0_17.jdk/Contents/Home
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"
</pre>
<p>in <samp><span class="file">config.site</span></samp>. <samp><span class="env">JAVA_LD_LIBRARY_PATH</span></samp> is used as part of
<samp><span class="env">DYLD_FALLBACK_LIBRARY_PATH</span></samp> and so is less likely to cause
conflicts, but <samp><span class="file">${JAVA_HOME}/jre/lib</span></samp> is still best avoided as in
some JDKs it contains libraries which conflict with system libraries.
<p>Note that it is necessary to set the environment variable <samp><span class="env">NOAWT</span></samp>
to <code>1</code> to install many of the Java-using packages.
<div class="node">
<a name="Frameworks"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Building-R_002eapp">Building R.app</a>,
Previous: <a rel="previous" accesskey="p" href="#Java-_0028OS-X_0029">Java (OS X)</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.7 Frameworks</h4>
<p>The <acronym>CRAN</acronym> build of R is installed as a framework, which is
selected by the default option
<pre class="example"> ./configure --enable-R-framework
</pre>
<p>This is only needed if you want to build R for use with the
<span class="sc">R.app</span> console, and implies <samp><span class="option">--enable-R-shlib</span></samp> to build
R as a dynamic library. This option configures R to be built and
installed as a framework called <samp><span class="file">R.framework</span></samp>. The default
installation path for <samp><span class="file">R.framework</span></samp> is <samp><span class="file">/Library/Frameworks</span></samp>
but this can be changed at configure time by specifying the flag
<samp><span class="option">--enable-R-framework[=</span><var>DIR</var><span class="option">]</span></samp> or at install time as
<pre class="example"> make prefix=/where/you/want/R.framework/to/go install
</pre>
<div class="node">
<a name="Building-R.app"></a>
<a name="Building-R_002eapp"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Frameworks">Frameworks</a>,
Up: <a rel="up" accesskey="u" href="#OS-X">OS X</a>
</div>
<h4 class="subsection">C.3.8 Building R.app</h4>
<p>Note that building the <span class="sc">R.app</span> GUI console is a separate project, using
Xcode. Before compiling <span class="sc">R.app</span> make sure the current version of R
is installed in <samp><span class="file">/Library/Frameworks/R.framework</span></samp> and working at
the command-line (this can be a binary install).
<p>The current sources can be checked out by
<pre class="example"> svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI
</pre>
<p class="noindent">This can be built by loading the <code>R.xcodeproj</code> project (select the
<code>R</code> target and the <code>SnowLeopard64</code> or <code>Lion64</code>
configuration), or from the command-line by e.g.
<pre class="example"> xcodebuild -target R -configuration SnowLeopard64
</pre>
<p>See also the <samp><span class="file">INSTALL</span></samp> file in the checkout or directly at <a href="https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL">https://svn.r-project.org/R-packages/trunk/Mac-GUI/INSTALL</a>.
<p><span class="sc">R.app</span> does not need to be installed in any specific way. Building
<span class="sc">R.app</span> results in the <span class="sc">R.app</span> bundle which appears as one R icon. This
application bundle can be run anywhere and it is customary to place it
in the <em>Applications</em> folder.
<div class="node">
<a name="Solaris"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#AIX">AIX</a>,
Previous: <a rel="previous" accesskey="p" href="#OS-X">OS X</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.4 Solaris</h3>
<p><a name="index-Solaris-105"></a>
R has been built successfully on Solaris 10 (both Sparc and
‘<samp><span class="samp">x86</span></samp>’) using the (zero cost) Oracle Solaris Studio compilers:
there has been some success with
<samp><span class="command">gcc</span></samp> 4/<samp><span class="command">gfortran</span></samp>. (Recent Sun machines are AMD
Opterons or Intel Xeons (‘<samp><span class="samp">amd64</span></samp>’) rather than ‘<samp><span class="samp">x86</span></samp>’, but
32-bit ‘<samp><span class="samp">x86</span></samp>’ executables are the default.)
<p>There have been few reports on Solaris 11, with no known extra issues.
Solaris 9 and earlier are now so old that it is unlikely that R is
still used with them, and they will not be considered here.
<p>The Solaris versions of several of the tools needed to build R
(e.g. <samp><span class="command">make</span></samp>, <samp><span class="command">ar</span></samp> and <samp><span class="command">ld</span></samp>) are in
<samp><span class="file">/usr/ccs/bin</span></samp>, so if using those tools ensure this is in your
path. A version of the preferred <acronym>GNU</acronym> <samp><span class="command">tar</span></samp> is (if
installed) in <samp><span class="file">/usr/sfw/bin</span></samp>, as sometimes are tools like
<samp><span class="command">makeinfo</span></samp>. It may be necessary to avoid the tools in
<samp><span class="file">/usr/ucb</span></samp>: POSIX-compliant versions of some tools can be found in
<samp><span class="file">/usr/xpg4/bin</span></samp> and <samp><span class="file">/usr/xpg6/bin</span></samp>.
<p>A large selection of Open Source software can be installed from
<a href="http://www.opencsw.org">http://www.opencsw.org</a>, by default installed under
<samp><span class="file">/opt/csw</span></samp>.
<p>You will need <acronym>GNU</acronym> <code>libiconv</code> and <code>readline</code>: the
Solaris version of <code>iconv</code> is not sufficiently powerful.
<p>The native <samp><span class="command">make</span></samp> suffices to build R but a small number of
packages require <acronym>GNU</acronym> <samp><span class="command">make</span></samp> (some without good reason
and without declaring it as ‘<samp><span class="samp">SystemRequirements</span></samp>’ in the
<samp><span class="file">DESCRIPTION</span></samp> file).
<p>Some people have reported that the Solaris <code>libintl</code> needs to be
avoided, for example by using <samp><span class="option">--disable-nls</span></samp> or
<samp><span class="option">--with-included-gettext</span></samp> or using <code>libintl</code> from OpenCSW.
<p>The support for the C99 <code>long double</code> type on Sparc hardware uses
quad-precision arithmetic, and this is usually slow because it is done
by software emulation. On such systems <samp><span class="command">configure</span></samp> option
<samp><span class="option">--disable-long-double</span></samp> can be used for faster but less accurate
computations.
<p>When using the Oracle compilers<a rel="footnote" href="#fn-40" name="fnd-40"><sup>40</sup></a> do <em>not</em> specify <samp><span class="option">-fast</span></samp>, as this
disables <acronym>IEEE</acronym> arithmetic and <samp><span class="command">make check</span></samp> will fail.
<p>A little juggling of paths was needed to ensure <acronym>GNU</acronym>
<code>libiconv</code> (in <samp><span class="file">/usr/local</span></samp>) was used rather than the Solaris
<code>iconv</code>:
<pre class="example"> CC="cc -xc99"
CFLAGS="-O -xlibmieee"
F77=f95
FFLAGS=-O
CXX="CC -library=stlport4"
CXXFLAGS=-O
FC=f95
FCFLAGS=$FFLAGS
FCLIBS="-lfai -lfsu"
R_LD_LIBRARY_PATH="/usr/local/lib:/opt/csw/gcc4/lib:/opt/csw/lib"
</pre>
<p class="noindent">For a 64-bit target add <samp><span class="option">-m64</span></samp> to the compiler macros
and use something like <code>LDFLAGS=-L/usr/local/lib/sparcv9</code> or
<code>LDFLAGS=-L/usr/local/lib/amd64</code> as appropriate.
It will also be necessary to point <samp><span class="command">pkg-config</span></samp> at the 64-bit
directories, e.g. one of
<pre class="example"> PKG_CONFIG_PATH=/opt/csw/lib/amd64/pkgconfig:/usr/lib/amd64/pkgconfig
PKG_CONFIG_PATH=/opt/csw/lib/sparcv9/pkgconfig:/usr/lib/sparcv9/pkgconfig
</pre>
<p class="noindent">and to specify a 64-bit Java VM by e.g.
<pre class="example"> JAVA_CPPFLAGS="-I${JAVA_HOME}/../include -I${JAVA_HOME}/../include/solaris"
JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/amd64/server
JAVA_LIBS="-L${JAVA_HOME}/lib/amd64/server \
-R${JAVA_HOME}/lib/amd64/server -ljvm"
</pre>
<p class="noindent">With Solaris Studio 12.[23] on Sparc, <code>FCLIBS</code> needs to be
<pre class="example"> FCLIBS="-lfai -lfai2 -lfsu"
</pre>
<p class="noindent">(and possibly other Fortran libraries, but this suffices for the
packages currently on CRAN).
<p>Currently ‘<samp><span class="samp">amd64</span></samp>’ and ‘<samp><span class="samp">sparcv9</span></samp>’ builds work
out-of-the-box with Sun Studio 12u1 but not Solaris Studio 12.2 and
later: <samp><span class="file">libRblas.so</span></samp> and <samp><span class="file">lapack.so</span></samp> are generated with code
that causes relocation errors (which is being linked in from the Fortran
libraries). This means that building R as a shared library may be
impossible with Solaris Studio >= 12.2. For a standard build the trick
seems to be to manually set <code>FLIBS</code> to avoid the troublesome
libraries. For example, on ‘<samp><span class="samp">amd64</span></samp>’ set in <samp><span class="file">config.site</span></samp>
something like
<pre class="example"> FLIBS_IN_SO="-R/opt/solarisstudio12.3/lib/amd64
/opt/solarisstudio12.3/lib/amd64/libfui.so
/opt/solarisstudio12.3/lib/amd64/libfsu.so"
</pre>
<p class="noindent">For 64-bit Sparc, set in <samp><span class="file">config.site</span></samp> something like
<pre class="example"> FLIBS="-R/opt/solarisstudio12.3/prod/lib/sparc/64
-lifai -lsunimath -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai
-lfminvai -lfmaxvai -lfui -lsunmath -lmtsk
/opt/solarisstudio12.3/prod/lib/sparc/64/libfsu.so.1"
</pre>
<p>By default the Solaris Studio compilers do not by default conform to the C99
standard (appendix F 8.9) on the return values of functions such as
<code>log</code>: use <samp><span class="option">-xlibmieee</span></samp> to ensure this.
<p>You can target specific Sparc architectures for (slightly) higher
performance: <samp><span class="option">-xtarget=native</span></samp> (in <code>CFLAGS</code> etc) tunes the
compilation to the current machine.
<p>Using <code>-xlibmil</code> in <code>CFLAGS</code> and <code>-xlibmil</code> in
<code>FFLAGS</code> allows more system mathematical functions to be inlined.
<p>On ‘<samp><span class="samp">x86</span></samp>’ you will get marginally higher performance <em>via</em>
<pre class="example"> CFLAGS="-xO5 -xc99 -xlibmieee -xlibmil -nofstore -xtarget=native"
FFLAGS="-O5 -libmil -nofstore -xtarget=native"
CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native"
SAFE_FFLAGS="-libmil -fstore -xtarget=native"
</pre>
<p class="noindent">but the use of <code>-nofstore</code> can be less numerically stable, and some
packages (notably <a href="http://CRAN.R-project.org/package=mgcv"><strong>mgcv</strong></a> on ‘<samp><span class="samp">x86</span></samp>’) failed to compile at
higher optimization levels with version 12.3.
<p>The Solaris Studio compilers provide several implementations of the C++
standard which select both the set of headers and a C++ runtime library.
These are selected by the <samp><span class="option">-library</span></samp> flag, which as it is needed
for both compiling and linking is best specified as part of the
compiler. The examples above use ‘<samp><span class="samp">stlport4</span></samp>’, currently the most
modern of the options: the default (but still needed to be specified as
it is needed for linking) is ‘<samp><span class="samp">Cstd</span></samp>’: see
<a href="http://developers.sun.com/solaris/articles/cmp_stlport_libCstd.html">http://developers.sun.com/solaris/articles/cmp_stlport_libCstd.html</a>.
Note though that most external Solaris C++ libraries will have been
built with ‘<samp><span class="samp">Cstd</span></samp>’ and so an R package using such libraries also
needs to be. Occasionally the flag <samp><span class="option">-library=stlport4,Crun</span></samp> has
been needed.
<p>Several <acronym>CRAN</acronym> packages using C++ need the more liberal interpretation
given by adding
<pre class="example"> CXXFLAGS="-features=tmplrefstatic"
</pre>
<p><a name="index-BLAS-library-106"></a><a name="index-LAPACK-library-107"></a>
The performance library <code>sunperf</code> is available for use with the
Solaris Studio compilers. If selected as a <acronym>BLAS</acronym>, it must also
be selected as LAPACK <em>via</em> (for Solaris Studio 12.2)
<pre class="example"> ./configure --with-blas='-library=sunperf' --with-lapack
</pre>
<p class="noindent">This has often given test failures in the past, in several different
places. At the time of writing it fails in <samp><span class="file">tests/reg-BLAS.R</span></samp>, and on
some builds, including for ‘<samp><span class="samp">amd64</span></samp>’, it fails in
<code>example(eigen)</code>.
<p>Parsing very complex expressions needs a lot of stack space when the
Oracle compilers are used: several packages require the stack increased
to say 20MB.
<ul class="menu">
<li><a accesskey="1" href="#Using-gcc">Using gcc</a>
</ul>
<div class="node">
<a name="Using-gcc"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Solaris">Solaris</a>,
Up: <a rel="up" accesskey="u" href="#Solaris">Solaris</a>
</div>
<h4 class="subsection">C.4.1 Using gcc</h4>
<p>If using <samp><span class="command">gcc</span></samp>, ensure that the compiler was compiled for the
version of Solaris in use. (This can be ascertained from <samp><span class="command">gcc
-v</span></samp>.) <samp><span class="command">gcc</span></samp> makes modified versions of some header files, and
several reports of problems were due to using <samp><span class="command">gcc</span></samp> compiled on
one version of Solaris on a later version.
<p>The notes here are for <samp><span class="command">gcc</span></samp> set up to use the Solaris linker:
it can also be set up to use GNU <samp><span class="command">ld</span></samp>, but that has not been
tested.
<p>Compilation for a 32-bit Sparc target with <samp><span class="command">gcc</span></samp> 4.8.1
needed
<pre class="example"> CPPFLAGS=-I/opt/csw/include
LDFLAGS="-L/opt/csw/gcc4/lib -L/opt/csw/lib"
</pre>
<p class="noindent">and for a 64-bit Sparc target
<pre class="example"> CC="gcc -m64"
F77="gfortran -m64"
CXX="g++ -m64"
FC=$F77
CPPFLAGS=-I/opt/csw/include
LDFLAGS="-L/opt/csw/gcc4/lib/sparcv9 -L/opt/csw/lib/sparcv9"
</pre>
<p class="noindent">Note that paths such as <samp><span class="file">/opt/csw/gcc4/lib/sparcv9</span></samp> may need to
be in the
<a name="index-LD_005fLIBRARY_005fPATH-108"></a><samp><span class="env">LD_LIBRARY_PATH</span></samp> during configuration.
<p>The compilation can be tuned to a particular cpu: the <acronym>CRAN</acronym>
check system uses <code>-mtune=niagara2</code>.
<p>Compilation for an ‘<samp><span class="samp">x86</span></samp>’ target with <samp><span class="command">gcc</span></samp> 4.8.1
needed
<pre class="example"> CC="/opt/csw/gcc4/bin/gcc -m32"
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="/opt/csw/gcc4/bin/gfortran -m32"
CXX="/opt/csw/gcc4/bin/g++ -m32"
FC="/opt/csw/gcc4/bin/gfortran -m32"
LDFLAGS="-L/opt/csw/gcc4/lib -L/opt/csw/lib -L/usr/local/lib"
</pre>
<p class="noindent">(<code>-L/opt/csw/lib</code> is needed since TeXLive was built using
32-bit <code>gcc</code>, and we need <samp><span class="file">/opt/csw/lib</span></samp> in
<code>R_LD_LIBRARY_PATH</code>.)
<p>For an ‘<samp><span class="samp">amd64</span></samp>’ target with <samp><span class="command">gcc</span></samp> 4.8.1
we used
<pre class="example"> CC="/opt/csw/gcc4/bin/gcc -m64"
CPPFLAGS="-I/opt/csw/include -I/usr/local/include"
F77="/opt/csw/gcc4/bin/gfortran -m64"
FPICFLAGS=-fPIC
CXX="/opt/csw/gcc4/bin/g++ -m64"
FC=$F77
FCPICFLAGS=$FPICFLAGS
LDFLAGS="-L/opt/csw/gcc4/lib/amd64 -L/opt/csw/lib/amd64"
</pre>
<div class="node">
<a name="AIX"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#FreeBSD">FreeBSD</a>,
Previous: <a rel="previous" accesskey="p" href="#Solaris">Solaris</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.5 AIX</h3>
<p><a name="index-AIX-109"></a>
We no longer support AIX prior to 4.2, and <samp><span class="command">configure</span></samp> will
throw an error on such systems.
<p>Ei-ji Nakama was able to build under AIX 5.2 on ‘<samp><span class="samp">powerpc</span></samp>’ with
GCC 4.0.3 in several configurations. 32-bit versions could be
configured with <samp><span class="option">--without-iconv</span></samp> as well as
<samp><span class="option">--enable-R-shlib</span></samp>. For 64-bit versions he used
<pre class="example"> OBJECT_MODE=64
CC="gcc -maix64"
CXX="g++ -maix64"
F77="gfortran -maix64"
FC="gfortran -maix64"
</pre>
<p class="noindent">and was also able to build with the IBM <code>xlc</code> and Hitachi
<code>f90</code> compilers by
<pre class="example"> OBJECT_MODE=64
CC="xlc -q64"
CXX="g++ -maix64"
F77="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FC="f90 -cpu=pwr4 -hf77 -parallel=0 -i,L -O3 -64"
FLIBS="-L/opt/ofort90/lib -lhf90vecmath -lhf90math -lf90"
</pre>
<p>Some systems have <samp><span class="command">f95</span></samp> as an IBM compiler that does not by
default accept FORTRAN 77. It needs the flag <samp><span class="option">-qfixed=72</span></samp>, or to
be invoked as <samp><span class="command">xlf_r</span></samp>.
<!-- http://publib.boulder.ibm.com/infocenter/comphelp/v7v91/index.jsp?topic=/com.ibm.xlf91a.doc/xlfug/hu00465.htm -->
<p>The AIX native <code>iconv</code> does not support encodings ‘<samp><span class="samp">latin1</span></samp>’ nor
‘<samp><span class="samp">""</span></samp>’ and so cannot be used. (As far as we know <acronym>GNU</acronym>
<code>libiconv</code> could be installed.)
<p>Fan Long reports success on AIX 5.3 using
<!-- https://stat.ethz.ch/pipermail/r-devel/2008-August/050318.html -->
<pre class="example"> OBJECT_MODE=64
LIBICONV=<var>/where/libiconv/installed</var>
CC="xlc_r -q64"
CFLAGS="-O -qstrict"
CXX="xlC_r -q64"
CXXFLAGS="-O -qstrict"
F77="xlf_r -q64"
AR="ar -X64"
CPPFLAGS="-I$LIBICONV/include -I/usr/lpp/X11/include/X11"
LDFLAGS="-L$LIBICONV/lib -L/usr/lib -L/usr/X11R6/lib"
</pre>
<p><a name="index-R_005fSHELL-110"></a>On one AIX 6.x system it was necessary to use <samp><span class="env">R_SHELL</span></samp> to set the
default shell to be Bash rather than Zsh.
<p>Kurt Hornik and Stefan Theussl at WU (Wirtschaftsuniversität Wien)
successfully built R on a ‘<samp><span class="samp">powerpc</span></samp>’ (8-<acronym>CPU</acronym> Power6
system) running AIX 6.1, configuring with or without
<samp><span class="option">--enable-R-shlib</span></samp> (Ei-ji Nakama's support is gratefully
acknowledged).
<p>It helps to describe the WU build environment first. A small part of
the software needed to build R and/or install packages is available
directly from the AIX Installation DVDs, e.g., Java 6, X11, and Perl.
Additional open source software (OSS) is packaged for AIX in <samp><span class="file">.rpm</span></samp>
files and available from both IBM's “AIX Toolbox for Linux
Applications”
(<a href="http://www-03.ibm.com/systems/power/software/aix/linux/">http://www-03.ibm.com/systems/power/software/aix/linux/</a>) and
<a href="http://www.oss4aix.org/download/">http://www.oss4aix.org/download/</a>. The latter website typically
offers more recent versions of the available OSS. All tools needed and
libraries downloaded from these repositories (e.g., GCC, Make,
<code>libreadline</code>, etc.) are typically installed to
<samp><span class="file">/opt/freeware</span></samp>, hence corresponding executables are found in
<a name="index-PATH-111"></a><samp><span class="file">/opt/freeware/bin</span></samp> which thus needs to be in <samp><span class="env">PATH</span></samp> for using
these tools. As on other Unix systems one needs <acronym>GNU</acronym>
<code>libiconv</code> as the AIX version of iconv is not sufficiently
powerful. Additionally, for proper Unicode compatibility one should
install the corresponding package from the ICU project
(<a href="http://www.icu-project.org/download/">http://www.icu-project.org/download/</a>), which offers pre-compiled
binaries for various platforms which in case of AIX can be installed via
unpacking the tarball to the root file system. For full LaTeX
support one can install the TeX Live DVD distribution
(<a href="http://www.tug.org/texlive/">http://www.tug.org/texlive/</a>): it is recommended to update the
distribution using the <code>tlmgr</code> update manager. For 64-bit R builds
supporting Tcl/Tk this needs to installed from the sources as available
pre-compiled binaries supply only 32-bit shared objects.
<p>The recent WU testing was done using compilers from both the
<acronym>GNU</acronym> Compiler Collection (version 4.2.4) which is available
from one of the above OSS repositories, and the IBM C/C++ (XL C/C++
10.01) as well as FORTRAN (XL Fortran 12.01) compilers
(<a href="http://www14.software.ibm.com/webapp/download/byproduct.jsp#X">http://www14.software.ibm.com/webapp/download/byproduct.jsp#X</a>).
<p>To compile for a 64-bit ‘<samp><span class="samp">powerpc</span></samp>’ (Power6 <acronym>CPU</acronym>) target
one can use
<pre class="example"> CC ="gcc -maix64 -pthread"
CXX="g++ -maix64 -pthread"
FC="gfortran -maix64 -pthread"
F77="gfortran -maix64 -pthread"
CFLAGS="-O2 -g -mcpu=power6"
FFLAGS="-O2 -g -mcpu=power6"
FCFLAGS="-O2 -g -mcpu=power6"
</pre>
<p class="noindent">for the GCC and
<pre class="example"> CC=xlc
CXX=xlc++
FC=xlf
F77=xlf
CFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict -ma"
FFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
FCFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
CXXFLAGS="-qarch=auto -qcache=auto -qtune=auto -O3 -qstrict"
</pre>
<p class="noindent">for the IBM XL compilers. For the latter, it is important to note that
the decision for generating 32-bit or 64-bit code is done by setting the
<a name="index-OBJECT_005fMODE-112"></a><samp><span class="env">OBJECT_MODE</span></samp> environment variable appropriately (recommended) or
using an additional compiler flag (<samp><span class="option">-q32</span></samp> or <samp><span class="option">-q64</span></samp>). By
default the IBM XL compilers produce 32 bit code. Thus, to build R with
64-bit support one needs to either export <samp><span class="env">OBJECT_MODE=64</span></samp> in the
environment or, alternatively, use the <samp><span class="option">-q64</span></samp> compiler options.
<p>It is strongly recommended to install Bash and use it as the configure
shell, e.g., via setting <code>CONFIG_SHELL=/usr/bin/bash</code> in the
environment, and to use <acronym>GNU</acronym> Make (e.g., via
(<code>MAKE=/opt/freeware/bin/make</code>).
<p>Further installation instructions to set up a proper R development
environment can be found in the “R on AIX” project on R-Forge
(<a href="http://R-Forge.R-project.org/projects/aix/">http://R-Forge.R-project.org/projects/aix/</a>).
<div class="node">
<a name="FreeBSD"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Cygwin">Cygwin</a>,
Previous: <a rel="previous" accesskey="p" href="#AIX">AIX</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.6 FreeBSD</h3>
<p><a name="index-FreeBSD-113"></a>
The reports here were for R 2.15.x.
<p>Rainer Hurling has reported success on ‘<samp><span class="samp">amd64</span></samp>’ FreeBSD 9.0 (and
on earlier versions in the past), and Brian Ripley tested
‘<samp><span class="samp">amd64</span></samp>’ FreeBSD 8.2. Since Darwin (the base OS of OS X) is
based on FreeBSD we find testing on Darwin tends to pick up most
potential problems on FreeBSD. However, FreeBSD lacks adequate
character type (e.g. which are alphabetic) and collation support for
multi-byte locales (but a port of ICU is available), and does not yet
implement C99 complex math functions (for which R's substitutes are
used).
<p>The native BSD <samp><span class="command">make</span></samp> suffices to build R but a number of
packages require <acronym>GNU</acronym> <samp><span class="command">make</span></samp>, despite the
recommendations of the “Writing R Extensions” manual.
<p>The simplest way to get the additional software needed to build R is
to install a pre-compiled version first, e.g. by
<pre class="example"> pkg_add -r R
</pre>
<p class="noindent">(on the system this was tested on, this installed Tcl, Tk, blas, lapack
and <code>gcc-4.6.2</code> which includes <samp><span class="command">gfortran46</span></samp>). A listing of
dependencies (not necessarily for current R) can be found at
<a href="http://www.freebsd.org/ports/lang.html">http://www.freebsd.org/ports/lang.html</a>: you will however also
need a TeX system<a rel="footnote" href="#fn-41" name="fnd-41"><sup>41</sup></a> to build the
manuals.
<p>Then R itself can be built by something like
<pre class="example"> ./configure CC=gcc46 F77=gfortran46 CXX=g++46 FC=gfortran46
</pre>
<p>There are also FreeBSD packages for a small eclectic collection of
<acronym>CRAN</acronym> packages.
<p>Beware that the lack of adequate support for non-<acronym>ASCII</acronym>
characters in UTF-8 locales has many consequences in R: for example
names will not be recognized as alphabetic by <code>make.names</code>.
<div class="node">
<a name="Cygwin"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#New-platforms">New platforms</a>,
Previous: <a rel="previous" accesskey="p" href="#FreeBSD">FreeBSD</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.7 Cygwin</h3>
<p>The Cygwin emulation layer on Windows can be treated as a Unix-alike OS.
This is unsupported, but experiments have been conducted and a few
workarounds added. R requires C99 complex type support, which is
available as from Cygwin 1.7.8 (March 2011). However, the (new)
implementation of <code>cacos</code> gives incorrect results, so we undefine
<code>HAVE_CACOS</code> in <samp><span class="file">src/main/complex.c</span></samp> on that platform.
<p>Many versions of Cygwin during 2011 were unable to build R: 1.7.9-1
with <acronym>GCC</acronym> 4.5.3-3 in November 2011 was able to do so. Cygwin
has not been tested for R 3.0.0 or later.
<p>Only building as a shared library can possibly work,<a rel="footnote" href="#fn-42" name="fnd-42"><sup>42</sup></a> so use e.g
<pre class="example"> ./configure --disable-nls --enable-R-shlib FLIBS=-lgfortran
make
</pre>
<p class="noindent">Enabling NLS does work if required, although adding
<samp><span class="option">--with-included-gettext</span></samp> is preferable. You will see many
warnings about the use of auto-import. Setting ‘<samp><span class="samp">FLIBS</span></samp>’ explicitly
seems needed currently as the auto-detection gives an incorrect value.
<p>You will need the <strong>tetex-extra</strong> Cygwin package to build
<samp><span class="file">NEWS.pdf</span></samp> and the vignettes.
<p>Note that this gives you a command-line application using <code>readline</code>
for command editing. The ‘<samp><span class="samp">X11</span></samp>’ graphics device will work if a
suitable X server is running, and the standard Unix-alike ways of
installing source packages work. There was a bug in the
<samp><span class="file">/usr/lib/tkConfig.sh</span></samp> script in the version we looked at, which
needs to have
<pre class="example"> TK_LIB_SPEC='-ltk84'
</pre>
<p>The overhead of using shell scripts makes this noticeably slower than a
native build of R on Windows.
<p>Even when R can be built, not all the tests passed: there were
incorrect results from wide-character regular expressions code and from
sourcing CR-delimited files.
<p>Do not use Cygwin's BLAS library: it is known to give incorrect results.
<div class="node">
<a name="New-platforms"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Cygwin">Cygwin</a>,
Up: <a rel="up" accesskey="u" href="#Platform-notes">Platform notes</a>
</div>
<h3 class="section">C.8 New platforms</h3>
<p>There are a number of sources of problems when installing R on a new
hardware/OS platform. These include
<p><strong>Floating Point Arithmetic</strong>: R requires arithmetic compliant
with <acronym>IEC</acronym> 60559, also known as <acronym>IEEE</acronym> 754.
This mandates the use of plus and minus infinity and <code>NaN</code> (not a
number) as well as specific details of rounding. Although almost all
current FPUs can support this, selecting such support can be a pain.
The problem is that there is no agreement on how to set the signalling
behaviour; Sun/Sparc, SGI/IRIX and ‘<samp><span class="samp">ix86</span></samp>’ Linux require no
special action, FreeBSD requires a call to (the macro)
<code>fpsetmask(0)</code> and OSF1 required that computation be done with a
<samp><span class="option">-ieee_with_inexact</span></samp> flag etc. On a new platform you must find
out the magic recipe and add some code to make it work. This can often
be done via the file <samp><span class="file">config.site</span></samp> which resides in the top level
directory.
<p>Beware of using high levels of optimization, at least initially. On
many compilers these reduce the degree of compliance to the
<acronym>IEEE</acronym> model. For example, using <samp><span class="option">-fast</span></samp> on the Solaris
Studio compilers has caused R's <code>NaN</code> to be set incorrectly, and
<samp><span class="command">gcc</span></samp>'s <samp><span class="option">-ffast-math</span></samp> has given incorrect results.
<p><strong>Shared Objects</strong>: There seems to be very little agreement
across platforms on what needs to be done to build shared objects.
there are many different combinations of flags for the compilers and
loaders. <acronym>GNU</acronym> libtool cannot be used (yet), as it currently
does not fully support FORTRAN: one would need a shell wrapper for
this). The technique we use is to first interrogate the X window system
about what it does (using <samp><span class="command">xmkmf</span></samp>), and then override this in
situations where we know better (for tools from the <acronym>GNU</acronym>
Compiler Collection and/or platforms we know about). This typically
works, but you may have to manually override the results. Scanning the
manual entries for <samp><span class="command">cc</span></samp> and <samp><span class="command">ld</span></samp> usually reveals the
correct incantation. Once you know the recipe you can modify the file
<samp><span class="file">config.site</span></samp> (following the instructions therein) so that the
build will use these options.
<p>It seems that <samp><span class="command">gcc</span></samp> 3.4.x and later on ‘<samp><span class="samp">ix86</span></samp>’ Linux
defeat attempts by the LAPACK code to avoid computations entirely in
extended-precision registers, so file <samp><span class="file">src/modules/lapack/dlamc.f</span></samp>
may need to be compiled without optimization. Set the configure
variable <samp><span class="env">SAFE_FFLAGS</span></samp> to the flags to be used for this file. If
configure detects <acronym>GNU</acronym> FORTRAN it adds flag
<samp><span class="option">-ffloat-store</span></samp> to <samp><span class="env">FFLAGS</span></samp>. (Other settings are needed when
using <samp><span class="command">icc</span></samp> on ‘<samp><span class="samp">ix86</span></samp>’ Linux, for example. Using
<samp><span class="option">-mpc64</span></samp> is preferable on more recent GCC compilers.)
<p>If you do manage to get R running on a new platform please let us
know about it so we can modify the configuration procedures to include
that platform.
<p>If you are having trouble getting R to work on your platform please
feel free to use the ‘<samp><span class="samp">R-devel</span></samp>’ mailing list to ask questions. We
have had a fair amount of practice at porting R to new platforms
<small class="enddots">...</small>
<div class="node">
<a name="The-Windows-toolset"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Function-and-variable-index">Function and variable index</a>,
Previous: <a rel="previous" accesskey="p" href="#Platform-notes">Platform notes</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="appendix">Appendix D The Windows toolset</h2>
<p>If you want to build R or add-on packages from source in Windows, you
will need to collect, install and test an extensive set of tools. See
<a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a> for the current
locations and other updates to these instructions. (Most Windows users
will not need to build add-on packages from source; see <a href="#Add_002don-packages">Add-on packages</a> for details.)
<p>We have found that the build process for R is quite sensitive to
the choice of tools: please follow our instructions <strong>exactly</strong>,
even to the choice of particular versions of the tools.<a rel="footnote" href="#fn-43" name="fnd-43"><sup>43</sup></a> The build process for add-on packages is somewhat more
forgiving, but we recommend using the exact toolset at first, and only
substituting other tools once you are familiar with the process.
<p><em>This appendix contains a lot of prescriptive comments. They are
here as a result of bitter experience. Please do not report problems to
the R mailing lists unless you have followed all the prescriptions.</em>
<p>We have collected most of the necessary tools (unfortunately not all,
due to license or size limitations) into an executable installer
named<a rel="footnote" href="#fn-44" name="fnd-44"><sup>44</sup></a> <samp><span class="file">Rtools30.exe</span></samp>,
available from <a href="http://CRAN.R-project.org/bin/windows/Rtools/">http://CRAN.R-project.org/bin/windows/Rtools/</a>. You
should download and run it, choosing the default “Package authoring
installation” to build add-on packages, or the “full installation” if
you intend to build R.
<p>You will need the following items to build R and packages.
See the subsections below for detailed descriptions.
<ul>
<li>The command line tools (in <samp><span class="file">Rtools*.exe</span></samp>)
<li>The MinGW-w64 32/64-bit toolchain to compile C, Fortran and C++.
</ul>
For installing simple source packages containing data or R source but
no compiled code, none of these are needed. Perl is no longer needed to
build R nor to install nor develop source packages.
<p>A complete build of R including PDF manuals, and producing the
installer will also need the following:
<ul>
<li>LaTeX
<li>The Inno Setup installer
<li>(optional) <code>qpdf</code>
</ul>
<p><a name="index-PATH-114"></a>It is important to set your <samp><span class="env">PATH</span></samp> properly. The installer
<samp><span class="file">Rtools*.exe</span></samp> optionally sets the path to components that it
installs.
<p>Your <samp><span class="env">PATH</span></samp> may include <samp><span class="file">.</span></samp> first, then the <samp><span class="file">bin</span></samp>
directories of the tools, the compiler toolchain and LaTeX. Do not
use filepaths containing spaces: you can always use the short forms
(found by <code>dir /x</code> at the Windows command line). Network shares
(with paths starting <code>\\</code>) are not supported.
<p>For example for a 32-bit build, all on one line,
<pre class="example"> PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\MiKTeX\miktex\bin;
c:\R\R-3.0\bin\i386;c:\windows;c:\windows\system32
</pre>
<p class="noindent">It is essential that the directory containing the command line tools
comes first or second in the path: there are typically like-named
tools<a rel="footnote" href="#fn-45" name="fnd-45"><sup>45</sup></a> in other directories, and they will <strong>not</strong>
work. The ordering of the other directories is less important, but if in
doubt, use the order above.
<p>Our toolset contains copies of Cygwin DLLs that may conflict with other
ones on your system if both are in the path at once. The normal
recommendation is to delete the older ones; however, at one time we
found our tools did not work with a newer version of the Cygwin DLLs, so
it may be safest not to have any other version of the Cygwin DLLs in your
path.
<ul class="menu">
<li><a accesskey="1" href="#LaTeX">LaTeX</a>
<li><a accesskey="2" href="#The-Inno-Setup-installer">The Inno Setup installer</a>
<li><a accesskey="3" href="#The-command-line-tools">The command line tools</a>
<li><a accesskey="4" href="#The-MinGW_002dw64-toolchain">The MinGW-w64 toolchain</a>
<li><a accesskey="5" href="#Useful-additional-programs">Useful additional programs</a>
</ul>
<div class="node">
<a name="LaTeX"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#The-Inno-Setup-installer">The Inno Setup installer</a>,
Previous: <a rel="previous" accesskey="p" href="#The-Windows-toolset">The Windows toolset</a>,
Up: <a rel="up" accesskey="u" href="#The-Windows-toolset">The Windows toolset</a>
</div>
<h3 class="section">D.1 LaTeX</h3>
<p>The ‘<samp><span class="samp">MiKTeX</span></samp>’ (<a href="http://www.miktex.org/">http://www.miktex.org/</a>) distribution of
LaTeX includes a suitable port of <code>pdftex</code>. The ‘basic’ version
of ‘<samp><span class="samp">MiKTeX</span></samp>’ almost suffices (the <strong>grid</strong> vignettes need
<samp><span class="file">fancyvrb.sty</span></samp>), but it will install the 15Mb ‘<samp><span class="samp">lm</span></samp>’ package if
allowed to (although that is not actually used). The <samp><span class="file">Rtools*.exe</span></samp>
installer does <em>not</em> include any version of LaTeX.
<p>It is also possible to use the TeXLive distribution from
<a href="http://www.tug.org/texlive/">http://www.tug.org/texlive/</a>.
<p><a name="index-R_005fRD4PDF-115"></a>Please read <a href="#Making-the-manuals">Making the manuals</a> about how to make <samp><span class="file">fullrefman.pdf</span></samp>
and set the environment variable <samp><span class="env">R_RD4PDF</span></samp> suitably; ensure you
have the required fonts installed or that ‘<samp><span class="samp">MiKTeX</span></samp>’ is set up to
install LaTeX packages on first use. (In any case ensure that the
<strong>inconsolata</strong> package is installed—you can check with the MiKTeX
Package Manager.)
<div class="node">
<a name="The-Inno-Setup-installer"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#The-command-line-tools">The command line tools</a>,
Previous: <a rel="previous" accesskey="p" href="#LaTeX">LaTeX</a>,
Up: <a rel="up" accesskey="u" href="#The-Windows-toolset">The Windows toolset</a>
</div>
<h3 class="section">D.2 The Inno Setup installer</h3>
<p>To make the installer package (<samp><span class="file">R-3.0.2-win.exe</span></samp>) we
currently require the Unicode version of Inno Setup 5.3.7 or later from
<a href="http://jrsoftware.org/">http://jrsoftware.org/</a>. This is <em>not</em> included in
<samp><span class="file">Rtools*.exe</span></samp>.
<p>Copy file <samp><span class="file">src/gnuwin32/MkRules.dist</span></samp> to
<samp><span class="file">src/gnuwin32/MkRules.local</span></samp> and edit it to set <code>ISDIR</code> to the
location where Inno Setup was installed.
<div class="node">
<a name="The-command-line-tools"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#The-MinGW_002dw64-toolchain">The MinGW-w64 toolchain</a>,
Previous: <a rel="previous" accesskey="p" href="#The-Inno-Setup-installer">The Inno Setup installer</a>,
Up: <a rel="up" accesskey="u" href="#The-Windows-toolset">The Windows toolset</a>
</div>
<h3 class="section">D.3 The command line tools</h3>
<p>This item is installed by the <samp><span class="file">Rtools*.exe</span></samp> installer.
<!-- INSTALL may use sh make zip (and tar if R_INSTALL_TAR is used) -->
<!-- build may use make and sh. -->
<!-- Rdiff.sh USED to use diff echo grep sed tr: grep and tr are no longer used. -->
<!-- basename is used in src/library/Recommended/Makefile.win -->
<!-- comm, sort, uniq are used in producing .def files -->
<!-- cmp is used in src/include/Makefile.win, tools/{copy,move}-if-change -->
<!-- cp is used as $(CP) in numerous Makefiles -->
<!-- cut is used to make RVER -->
<!-- date is used when building base and tools -->
<!-- diff is used by tools::Rdiff and tests/Makefile.common -->
<!-- du is used by R CMD check -->
<!-- expr is used in tools/GETVERSION -->
<!-- find is used in installer/Makefile -->
<!-- expr is used in tools/GETCONFIG -->
<!-- gzip is used in src/library/Makefile.win, R CMD build -->
<!-- ls is used in src/library/*/Makefile.win -->
<!-- mkdir is used in numerous Makefiles -->
<!-- rsync is only needed if building from svn -->
<!-- sed is used in tools/GETVERSION, many Makefiles -->
<!-- touch is used in Makefiles -->
<!-- unzip is used in making R, e.g. for zoneinfo.zip -->
<!-- AFAICS [g]awk, egrep, grep, head, rmdir, tail, tr, wc are no longer used -->
<p>If you choose to install these yourself, you will need suitable versions
of at least <code>basename</code>, <code>cat</code>, <code>cmp</code>, <code>comm</code>,
<code>cp</code>, <code>cut</code>, <code>date</code>, <code>diff</code>, <code>du</code>, <code>echo</code>,
<code>expr</code>, <code>gzip</code>, <code>ls</code>, <code>make</code>, <code>makeinfo</code>,
<code>mkdir</code>, <code>mv</code>, <code>rm</code>, <code>rsync</code>, <code>sed</code>, <code>sh</code>,
<code>sort</code>, <code>tar</code>, <code>texindex</code>, <code>touch</code> and <code>uniq</code>;
we use those from the Cygwin distribution
(<a href="http://www.cygwin.com/">http://www.cygwin.com/</a>) or compiled from the sources. You will
also need <code>zip</code> and <code>unzip</code> from the Info-ZIP project
(<a href="http://www.info-zip.org/">http://www.info-zip.org/</a>). All of these tools are in
<samp><span class="file">Rtools*.exe</span></samp>.
<!-- So needed for end users: -->
<!-- comm cp diff echo gzip make mkdir rm sh sort tar uniq zip -->
<p><strong>Beware</strong>: ‘Native’ ports of make are <strong>not</strong> suitable
(including those called ‘MinGW make’ at the MinGW SourceForge site and
<samp><span class="command">mingw32-make</span></samp> in some MinGW-w64 distributions). There were
also problems with other versions of the Cygwin tools and DLLs. To
avoid frustration, please use our tool set, and make sure it is at the
front of your path (including before the Windows system directories).
If you are using a Windows shell, type <code>PATH</code> at the prompt to find
out.
<p><a name="index-CYGWIN-116"></a>You may need to set the environment variable <samp><span class="env">CYGWIN</span></samp> to a value
including ‘<samp><span class="samp">nodosfilewarning</span></samp>’ to suppress messages about
Windows-style paths.
<div class="node">
<a name="The-MinGW-w64-toolchain"></a>
<a name="The-MinGW_002dw64-toolchain"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Useful-additional-programs">Useful additional programs</a>,
Previous: <a rel="previous" accesskey="p" href="#The-command-line-tools">The command line tools</a>,
Up: <a rel="up" accesskey="u" href="#The-Windows-toolset">The Windows toolset</a>
</div>
<h3 class="section">D.4 The MinGW-w64 toolchain</h3>
<p>Technically you need more than just a compiler so the set of tools is
referred to as a ‘toolchain’.
<p>The preferred toolchain since R 2.14.2 is part of
<code>Rtools30.exe</code>: this uses a beta version of <samp><span class="command">gcc 4.6.3</span></samp>
and version 2.0.1 of the MinGW-w64 project's runtime.
<p>This toolchain uses <em>multilib</em>: that is there is a single front-end
such as <samp><span class="command">gcc.exe</span></samp> for each of the compilers and 32-bit (the
default) and 64-bit compilation are selected by the flags<a rel="footnote" href="#fn-46" name="fnd-46"><sup>46</sup></a> <samp><span class="option">-m32</span></samp> and <samp><span class="option">-m64</span></samp>
respectively. The tools are all 32-bit Windows executables and should
be able to run on any current version of Windows—however you do need a
64-bit version of Windows to build 64-bit R as the build process runs
R.
<p>To select a 32-bit or 64-bit build of R, set the options in
<samp><span class="file">MkRules.local</span></samp> appropriately (following the comments in the file).
<p>Some external software libraries will need to be re-compiled under the
new toolchain: especially those providing a C++ interface. Many of
those used by <acronym>CRAN</acronym> packages are available from
<a href="http://www.stats.ox.ac.uk/pub/Rtools/multilib/">http://www.stats.ox.ac.uk/pub/Rtools/multilib/</a>. Users
developing packages with <a href="http://CRAN.R-project.org/package=Rcpp"><strong>Rcpp</strong></a> need to ensure that they use a
version built with exactly the same toolchain as their package: the
recommendation is to build <a href="http://CRAN.R-project.org/package=Rcpp"><strong>Rcpp</strong></a> from its sources yourself.
<p>There is support for OpenMP and pthreads in this toolchain. As the
performance of OpenMP on Windows is poor for small tasks, it is not used
for R itself.
<div class="node">
<a name="Useful-additional-programs"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#The-MinGW_002dw64-toolchain">The MinGW-w64 toolchain</a>,
Up: <a rel="up" accesskey="u" href="#The-Windows-toolset">The Windows toolset</a>
</div>
<h3 class="section">D.5 Useful additional programs</h3>
<p>The process of making the installer will make use of <code>qpdf</code> to
compact some of the package vignettes, if it is available. Windows
binaries of <code>qpdf</code> are available from
<a href="http://sourceforge.net/projects/qpdf/files/">http://sourceforge.net/projects/qpdf/files/</a>. Set the path
to the <code>qpdf</code> installation in file <samp><span class="file">MkRules.local</span></samp>.
<p>Developers of packages will find some of the ‘goodies’ at
<a href="http://www.stats.ox.ac.uk/pub/Rtools/goodies">http://www.stats.ox.ac.uk/pub/Rtools/goodies</a> useful.
<p>There is a version of the <samp><span class="command">file</span></samp> command that identifies the
type of files, and is used by <samp><span class="command">Rcmd check</span></samp> if available. The
binary distribution is included in <samp><span class="file">Rtools30.exe</span></samp>.
<p>The file <samp><span class="file">xzutils.zip</span></samp> contains the program <samp><span class="command">xz</span></samp> which can
be used to (de)compress files with that form of compression.
<div class="node">
<a name="Function-and-variable-index"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Concept-index">Concept index</a>,
Previous: <a rel="previous" accesskey="p" href="#The-Windows-toolset">The Windows toolset</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="unnumbered">Function and variable index</h2>
<ul class="index-vr" compact>
<li><a href="#index-configure-91"><code>configure</code></a>: <a href="#Using-make">Using make</a></li>
<li><a href="#index-configure-82"><code>configure</code></a>: <a href="#Configuration-variables">Configuration variables</a></li>
<li><a href="#index-configure-17"><code>configure</code></a>: <a href="#Installation">Installation</a></li>
<li><a href="#index-configure-10"><code>configure</code></a>: <a href="#Simple-compilation">Simple compilation</a></li>
<li><a href="#index-install_002epackages-50"><code>install.packages</code></a>: <a href="#Installing-packages">Installing packages</a></li>
<li><a href="#index-make-90"><code>make</code></a>: <a href="#Using-make">Using make</a></li>
<li><a href="#index-R_005fHOME-9"><code>R_HOME</code></a>: <a href="#Simple-compilation">Simple compilation</a></li>
<li><a href="#index-remove_002epackages-55"><code>remove.packages</code></a>: <a href="#Removing-packages">Removing packages</a></li>
<li><a href="#index-update_002epackages-53"><code>update.packages</code></a>: <a href="#Updating-packages">Updating packages</a></li>
</ul><div class="node">
<a name="Concept-index"></a>
<p><hr>
Next: <a rel="next" accesskey="n" href="#Environment-variable-index">Environment variable index</a>,
Previous: <a rel="previous" accesskey="p" href="#Function-and-variable-index">Function and variable index</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="unnumbered">Concept index</h2>
<ul class="index-cp" compact>
<li><a href="#index-AIX-109">AIX</a>: <a href="#AIX">AIX</a></li>
<li><a href="#index-BLAS-library-106">BLAS library</a>: <a href="#Solaris">Solaris</a></li>
<li><a href="#index-BLAS-library-103">BLAS library</a>: <a href="#OS-X">OS X</a></li>
<li><a href="#index-BLAS-library-77">BLAS library</a>: <a href="#Linear-algebra">Linear algebra</a></li>
<li><a href="#index-FORTRAN-92">FORTRAN</a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-FreeBSD-113">FreeBSD</a>: <a href="#FreeBSD">FreeBSD</a></li>
<li><a href="#index-Installation-16">Installation</a>: <a href="#Installation">Installation</a></li>
<li><a href="#index-Installing-under-Unix_002dalikes-5">Installing under Unix-alikes</a>: <a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></li>
<li><a href="#index-Installing-under-Windows-24">Installing under Windows</a>: <a href="#Installing-R-under-Windows">Installing R under Windows</a></li>
<li><a href="#index-Internationalization-58">Internationalization</a>: <a href="#Internationalization">Internationalization</a></li>
<li><a href="#index-LAPACK-library-107">LAPACK library</a>: <a href="#Solaris">Solaris</a></li>
<li><a href="#index-LAPACK-library-104">LAPACK library</a>: <a href="#OS-X">OS X</a></li>
<li><a href="#index-LAPACK-library-80">LAPACK library</a>: <a href="#LAPACK">LAPACK</a></li>
<li><a href="#index-Libraries-37">Libraries</a>: <a href="#Add_002don-packages">Add-on packages</a></li>
<li><a href="#index-Libraries_002c-managing-41">Libraries, managing</a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-Libraries_002c-site-42">Libraries, site</a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-Libraries_002c-user-45">Libraries, user</a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-Linux-101">Linux</a>: <a href="#Linux">Linux</a></li>
<li><a href="#index-Linux-6">Linux</a>: <a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></li>
<li><a href="#index-Locale-61">Locale</a>: <a href="#Locales">Locales</a></li>
<li><a href="#index-Locale-60">Locale</a>: <a href="#Internationalization">Internationalization</a></li>
<li><a href="#index-Localization-59">Localization</a>: <a href="#Internationalization">Internationalization</a></li>
<li><a href="#index-Manuals-13">Manuals</a>: <a href="#Making-the-manuals">Making the manuals</a></li>
<li><a href="#index-Manuals_002c-installing-19">Manuals, installing</a>: <a href="#Installation">Installation</a></li>
<li><a href="#index-Obtaining-R-1">Obtaining R</a>: <a href="#Obtaining-R">Obtaining R</a></li>
<li><a href="#index-OS-X-102">OS X</a>: <a href="#OS-X">OS X</a></li>
<li><a href="#index-OS-X-29">OS X</a>: <a href="#Installing-R-under-OS-X">Installing R under OS X</a></li>
<li><a href="#index-OS-X-7">OS X</a>: <a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></li>
<li><a href="#index-Packages-36">Packages</a>: <a href="#Add_002don-packages">Add-on packages</a></li>
<li><a href="#index-Packages_002c-default-39">Packages, default</a>: <a href="#Default-packages">Default packages</a></li>
<li><a href="#index-Packages_002c-installing-48">Packages, installing</a>: <a href="#Installing-packages">Installing packages</a></li>
<li><a href="#index-Packages_002c-removing-56">Packages, removing</a>: <a href="#Removing-packages">Removing packages</a></li>
<li><a href="#index-Packages_002c-updating-54">Packages, updating</a>: <a href="#Updating-packages">Updating packages</a></li>
<li><a href="#index-Rbitmap_002edll-27">Rbitmap.dll</a>: <a href="#Building-the-bitmap-files">Building the bitmap files</a></li>
<li><a href="#index-Repositories-57">Repositories</a>: <a href="#Setting-up-a-package-repository">Setting up a package repository</a></li>
<li><a href="#index-Site-libraries-43">Site libraries</a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-Solaris-105">Solaris</a>: <a href="#Solaris">Solaris</a></li>
<li><a href="#index-Sources-for-R-2">Sources for R</a>: <a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></li>
<li><a href="#index-Subversion-71">Subversion</a>: <a href="#Essential-programs-and-libraries">Essential programs and libraries</a></li>
<li><a href="#index-Subversion-4">Subversion</a>: <a href="#Using-Subversion-and-rsync">Using Subversion and rsync</a></li>
<li><a href="#index-User-libraries-46">User libraries</a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-Vignettes-70">Vignettes</a>: <a href="#Essential-programs-and-libraries">Essential programs and libraries</a></li>
<li><a href="#index-winCairo_002edll-28">winCairo.dll</a>: <a href="#Building-the-cairo-devices-files">Building the cairo devices files</a></li>
</ul><div class="node">
<a name="Environment-variable-index"></a>
<p><hr>
Previous: <a rel="previous" accesskey="p" href="#Concept-index">Concept index</a>,
Up: <a rel="up" accesskey="u" href="#Top">Top</a>
</div>
<h2 class="unnumbered">Environment variable index</h2>
<ul class="index-en" compact>
<li><a href="#index-BLAS_005fLIBS-78"><code>BLAS_LIBS</code></a>: <a href="#BLAS">BLAS</a></li>
<li><a href="#index-CC-97"><code>CC</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-CONFIG_005fSITE-83"><code>CONFIG_SITE</code></a>: <a href="#Configuration-variables">Configuration variables</a></li>
<li><a href="#index-CPP-98"><code>CPP</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-CYGWIN-116"><code>CYGWIN</code></a>: <a href="#The-command-line-tools">The command line tools</a></li>
<li><a href="#index-DESTDIR-68"><code>DESTDIR</code></a>: <a href="#Unix_002dalike-standalone">Unix-alike standalone</a></li>
<li><a href="#index-DESTDIR-20"><code>DESTDIR</code></a>: <a href="#Installation">Installation</a></li>
<li><a href="#index-F2C-95"><code>F2C</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-F2CLIBS-96"><code>F2CLIBS</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-FPICFLAGS-99"><code>FPICFLAGS</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-JAVA_005fHOME-74"><code>JAVA_HOME</code></a>: <a href="#Java-support">Java support</a></li>
<li><a href="#index-LANG-65"><code>LANG</code></a>: <a href="#Localization-of-messages">Localization of messages</a></li>
<li><a href="#index-LANGUAGE-62"><code>LANGUAGE</code></a>: <a href="#Localization-of-messages">Localization of messages</a></li>
<li><a href="#index-LAPACK_005fLIBS-81"><code>LAPACK_LIBS</code></a>: <a href="#LAPACK">LAPACK</a></li>
<li><a href="#index-LC_005fALL-63"><code>LC_ALL</code></a>: <a href="#Localization-of-messages">Localization of messages</a></li>
<li><a href="#index-LC_005fCOLLATE-23"><code>LC_COLLATE</code></a>: <a href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a></li>
<li><a href="#index-LC_005fMESSAGES-64"><code>LC_MESSAGES</code></a>: <a href="#Localization-of-messages">Localization of messages</a></li>
<li><a href="#index-LD_005fLIBRARY_005fPATH-108"><code>LD_LIBRARY_PATH</code></a>: <a href="#Using-gcc">Using gcc</a></li>
<li><a href="#index-LD_005fLIBRARY_005fPATH-100"><code>LD_LIBRARY_PATH</code></a>: <a href="#Compile-and-load-flags">Compile and load flags</a></li>
<li><a href="#index-LD_005fLIBRARY_005fPATH-94"><code>LD_LIBRARY_PATH</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-LD_005fLIBRARY_005fPATH-79"><code>LD_LIBRARY_PATH</code></a>: <a href="#ACML">ACML</a></li>
<li><a href="#index-LD_005fLIBRARY_005fPATH-67"><code>LD_LIBRARY_PATH</code></a>: <a href="#Unix_002dalike-standalone">Unix-alike standalone</a></li>
<li><a href="#index-LOCAL_005fSOFT-52"><code>LOCAL_SOFT</code></a>: <a href="#Windows-packages">Windows packages</a></li>
<li><a href="#index-OBJECT_005fMODE-112"><code>OBJECT_MODE</code></a>: <a href="#AIX">AIX</a></li>
<li><a href="#index-PAPERSIZE-85"><code>PAPERSIZE</code></a>: <a href="#Setting-paper-size">Setting paper size</a></li>
<li><a href="#index-PATH-114"><code>PATH</code></a>: <a href="#The-Windows-toolset">The Windows toolset</a></li>
<li><a href="#index-PATH-111"><code>PATH</code></a>: <a href="#AIX">AIX</a></li>
<li><a href="#index-PATH-93"><code>PATH</code></a>: <a href="#Using-FORTRAN">Using FORTRAN</a></li>
<li><a href="#index-PATH-72"><code>PATH</code></a>: <a href="#Essential-programs-and-libraries">Essential programs and libraries</a></li>
<li><a href="#index-R_005fARCH-21"><code>R_ARCH</code></a>: <a href="#Sub_002darchitectures">Sub-architectures</a></li>
<li><a href="#index-R_005fBROWSER-86"><code>R_BROWSER</code></a>: <a href="#Setting-the-browsers">Setting the browsers</a></li>
<li><a href="#index-R_005fDEFAULT_005fPACKAGES-40"><code>R_DEFAULT_PACKAGES</code></a>: <a href="#Default-packages">Default packages</a></li>
<li><a href="#index-R_005fDISABLE_005fHTTPD-12"><code>R_DISABLE_HTTPD</code></a>: <a href="#Help-options">Help options</a></li>
<li><a href="#index-R_005fGSCMD-73"><code>R_GSCMD</code></a>: <a href="#Useful-libraries-and-programs">Useful libraries and programs</a></li>
<li><a href="#index-R_005fINSTALL_005fTAR-51"><code>R_INSTALL_TAR</code></a>: <a href="#Windows-packages">Windows packages</a></li>
<li><a href="#index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-75"><code>R_JAVA_LD_LIBRARY_PATH</code></a>: <a href="#Java-support">Java support</a></li>
<li><a href="#index-R_005fLIBS-38"><code>R_LIBS</code></a>: <a href="#Add_002don-packages">Add-on packages</a></li>
<li><a href="#index-R_005fLIBS_005fSITE-44"><code>R_LIBS_SITE</code></a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-R_005fLIBS_005fUSER-47"><code>R_LIBS_USER</code></a>: <a href="#Managing-libraries">Managing libraries</a></li>
<li><a href="#index-R_005fPAPERSIZE-89"><code>R_PAPERSIZE</code></a>: <a href="#Making-manuals">Making manuals</a></li>
<li><a href="#index-R_005fPAPERSIZE-84"><code>R_PAPERSIZE</code></a>: <a href="#Setting-paper-size">Setting paper size</a></li>
<li><a href="#index-R_005fPAPERSIZE-30"><code>R_PAPERSIZE</code></a>: <a href="#Running-R">Running R</a></li>
<li><a href="#index-R_005fPAPERSIZE-14"><code>R_PAPERSIZE</code></a>: <a href="#Making-the-manuals">Making the manuals</a></li>
<li><a href="#index-R_005fPDFVIEWER-87"><code>R_PDFVIEWER</code></a>: <a href="#Setting-the-browsers">Setting the browsers</a></li>
<li><a href="#index-R_005fRD4PDF-115"><code>R_RD4PDF</code></a>: <a href="#LaTeX">LaTeX</a></li>
<li><a href="#index-R_005fRD4PDF-88"><code>R_RD4PDF</code></a>: <a href="#Making-manuals">Making manuals</a></li>
<li><a href="#index-R_005fRD4PDF-15"><code>R_RD4PDF</code></a>: <a href="#Making-the-manuals">Making the manuals</a></li>
<li><a href="#index-R_005fSHELL-110"><code>R_SHELL</code></a>: <a href="#AIX">AIX</a></li>
<li><a href="#index-R_005fUSER-34"><code>R_USER</code></a>: <a href="#Running-R">Running R</a></li>
<li><a href="#index-TAR-69"><code>TAR</code></a>: <a href="#Essential-programs-and-libraries">Essential programs and libraries</a></li>
<li><a href="#index-TAR_005fOPTIONS-25"><code>TAR_OPTIONS</code></a>: <a href="#Getting-the-source-files">Getting the source files</a></li>
<li><a href="#index-TAR_005fOPTIONS-3"><code>TAR_OPTIONS</code></a>: <a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></li>
<li><a href="#index-TEMP-33"><code>TEMP</code></a>: <a href="#Running-R">Running R</a></li>
<li><a href="#index-TMP-32"><code>TMP</code></a>: <a href="#Running-R">Running R</a></li>
<li><a href="#index-TMPDIR-49"><code>TMPDIR</code></a>: <a href="#Installing-packages">Installing packages</a></li>
<li><a href="#index-TMPDIR-31"><code>TMPDIR</code></a>: <a href="#Running-R">Running R</a></li>
<li><a href="#index-TMPDIR-26"><code>TMPDIR</code></a>: <a href="#Building-the-core-files">Building the core files</a></li>
<li><a href="#index-TMPDIR-8"><code>TMPDIR</code></a>: <a href="#Simple-compilation">Simple compilation</a></li>
</ul><div class="footnote">
<hr>
<a name="texinfo-footnotes-in-document"></a><h4>Footnotes</h4><p class="footnote"><small>[<a name="fn-1" href="#fnd-1">1</a>]</small> e.g. <acronym>GNU</acronym>
<samp><span class="command">tar</span></samp> version 1.15 or later, or that from the ‘<samp><span class="samp">libarchive</span></samp>’
(as used on OS 10.6 and later) or ‘Heirloom Toolchest’ distributions.</p>
<p class="footnote"><small>[<a name="fn-2" href="#fnd-2">2</a>]</small> for some Subversion clients
‘<samp><span class="samp">http:</span></samp>’ may appear to work, but requires continual redirection.</p>
<p class="footnote"><small>[<a name="fn-3" href="#fnd-3">3</a>]</small> Most aspects will work with paths containing spaces,
but external software used by R, e.g. <samp><span class="command">texi2dvi</span></samp> version
<code>4.8</code>, may not.</p>
<p class="footnote"><small>[<a name="fn-4" href="#fnd-4">4</a>]</small> which use <samp><span class="file">lib</span></samp> rather than
<samp><span class="file">lib64</span></samp> for their primary 64-bit library directories.</p>
<p class="footnote"><small>[<a name="fn-5" href="#fnd-5">5</a>]</small> for example, if you configured R with
<samp><span class="option">--without-recommended</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-6" href="#fnd-6">6</a>]</small> on a
Unix-alike, ‘<samp><span class="samp">incosolata</span></samp>’ is omitted if not found by
<samp><span class="command">configure</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-7" href="#fnd-7">7</a>]</small> with possible values
‘<samp><span class="samp">i386</span></samp>’, ‘<samp><span class="samp">x64</span></samp>’, ‘<samp><span class="samp">32</span></samp>’ and ‘<samp><span class="samp">64</span></samp>’.</p>
<p class="footnote"><small>[<a name="fn-8" href="#fnd-8">8</a>]</small> mainly on RedHat and Fedora, whose layout is described
here.</p>
<p class="footnote"><small>[<a name="fn-9" href="#fnd-9">9</a>]</small> unless they were excluded in the build.</p>
<p class="footnote"><small>[<a name="fn-10" href="#fnd-10">10</a>]</small> its binding is locked once the startup files have been
read, so users cannot easily change it.</p>
<p class="footnote"><small>[<a name="fn-11" href="#fnd-11">11</a>]</small> If a proxy needs to be set, see
<samp><span class="command">?download.file</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-12" href="#fnd-12">12</a>]</small> for a small number of
<acronym>CRAN</acronym> packages where this is known to be safe and is needed by
the autobuilder this is the default. Look at the source of
<samp><span class="file">tools:::.install_packages</span></samp> for the list. It can also be specified
in the package's <samp><span class="file">DESCRIPTION</span></samp> file.</p>
<p class="footnote"><small>[<a name="fn-13" href="#fnd-13">13</a>]</small> or by adding it in
a file such as <samp><span class="file">etc/i386/Makevars.site</span></samp>, which does not exist by
default.</p>
<p class="footnote"><small>[<a name="fn-14" href="#fnd-14">14</a>]</small> ‘X/Open Portability Guide’, which has
had several versions.</p>
<p class="footnote"><small>[<a name="fn-15" href="#fnd-15">15</a>]</small> On some systems setting
<samp><span class="env">LC_ALL</span></samp> or <samp><span class="env">LC_MESSAGES</span></samp> to ‘<samp><span class="samp">C</span></samp>’ disables <samp><span class="env">LANGUAGE</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-16" href="#fnd-16">16</a>]</small> If you try changing from French
to Russian except in a UTF-8 locale, you will most likely find messages
change to English.</p>
<p class="footnote"><small>[<a name="fn-17" href="#fnd-17">17</a>]</small> the
language written in England: some people living in the USA appropriate
this name for their language.</p>
<p class="footnote"><small>[<a name="fn-18" href="#fnd-18">18</a>]</small> with
Americanisms.</p>
<p class="footnote"><small>[<a name="fn-19" href="#fnd-19">19</a>]</small> also known as
<acronym>IEEE</acronym> 754</p>
<p class="footnote"><small>[<a name="fn-20" href="#fnd-20">20</a>]</small> at least when storing quantities: the on-FPU
precision is allowed to vary</p>
<p class="footnote"><small>[<a name="fn-21" href="#fnd-21">21</a>]</small> e.g. Bessel, beta and gamma functions</p>
<p class="footnote"><small>[<a name="fn-22" href="#fnd-22">22</a>]</small> including copying <samp><span class="file">MkRules.dist</span></samp> to
<samp><span class="file">MkRule.local</span></samp> and selecting the architecture.</p>
<p class="footnote"><small>[<a name="fn-23" href="#fnd-23">23</a>]</small> also
known as <acronym>IEEE</acronym> 754</p>
<p class="footnote"><small>[<a name="fn-24" href="#fnd-24">24</a>]</small> Note that C11 compilers (when they appear) need
not be C99-compliant: R requires support for <code>double complex</code>
which is optional in C11 but is mandatory in C99.</p>
<p class="footnote"><small>[<a name="fn-25" href="#fnd-25">25</a>]</small> <samp><span class="option">-std=c99</span></samp> excludes POSIX
functionality, but <samp><span class="file">config.h</span></samp> will turn on all <acronym>GNU</acronym>
extensions to include the POSIX functionality.</p>
<p class="footnote"><small>[<a name="fn-26" href="#fnd-26">26</a>]</small> apparently when built by
default, but not for example as built for Fedora 15.</p>
<p class="footnote"><small>[<a name="fn-27" href="#fnd-27">27</a>]</small> specifically, the C99
functionality of headers <samp><span class="file">wchar.h</span></samp> and <samp><span class="file">wctype.h</span></samp>, types
<code>wctans_t</code> and <code>mbstate_t</code> and functions <code>mbrtowc</code>,
<code>mbstowcs</code>, <code>wcrtomb</code>, <code>wcscoll</code>, <code>wcstombs</code>,
<code>wctrans</code>, <code>wctype</code>, and <code>iswctype</code>.</p>
<p class="footnote"><small>[<a name="fn-28" href="#fnd-28">28</a>]</small> Such as
<acronym>GNU</acronym> <samp><span class="command">tar</span></samp> 1.15 or later, <samp><span class="command">bsdtar</span></samp> (from
<a href="http://code.google.com/p/libarchive/">http://code.google.com/p/libarchive/</a>, as used by FreeBSD and OS
10.6 and later) or <samp><span class="command">tar</span></samp> from the Heirloom Toolchest
(<a href="http://heirloom.sourceforge.net/tools.html">http://heirloom.sourceforge.net/tools.html</a>).</p>
<p class="footnote"><small>[<a name="fn-29" href="#fnd-29">29</a>]</small> <samp><span class="command">texi2dvi</span></samp> is normally a
shell script. Some versions, e.g. that from <strong>texinfo</strong> 4.13a, need
to be run under <samp><span class="command">bash</span></samp> rather than a Bourne shell as on, say,
Solaris.</p>
<p class="footnote"><small>[<a name="fn-30" href="#fnd-30">30</a>]</small> also known as <code>ttf-mscorefonts-installer</code> in the
Debian/Ubuntu world: see also
<a href="http://en.wikipedia.org/wiki/Core_fonts_for_the_Web">http://en.wikipedia.org/wiki/Core_fonts_for_the_Web</a>.</p>
<p class="footnote"><small>[<a name="fn-31" href="#fnd-31">31</a>]</small> <code>ttf-liberation</code>
in Debian/Ubuntu.</p>
<p class="footnote"><small>[<a name="fn-32" href="#fnd-32">32</a>]</small> Using the Oracle Solaris Studio
<samp><span class="command">cc</span></samp> and <samp><span class="command">f95</span></samp> compilers</p>
<p class="footnote"><small>[<a name="fn-33" href="#fnd-33">33</a>]</small> and perhaps others</p>
<p class="footnote"><small>[<a name="fn-34" href="#fnd-34">34</a>]</small> We have measured 15–20% on ‘<samp><span class="samp">i686</span></samp>’ Linux
and around 10% on ‘<samp><span class="samp">x86_64</span></samp>’ Linux.</p>
<p class="footnote"><small>[<a name="fn-35" href="#fnd-35">35</a>]</small> On HP-UX <samp><span class="command">fort77</span></samp> is the
<acronym>POSIX</acronym> compliant FORTRAN compiler, and comes after
<samp><span class="command">g77</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-36" href="#fnd-36">36</a>]</small> as well as its equivalence to the <code>Rcomplex</code>
structure defined in <samp><span class="file">R_ext/Complex.h</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-37" href="#fnd-37">37</a>]</small> for example, <code>X11 font at size 14 could not
be loaded</code>.</p>
<p class="footnote"><small>[<a name="fn-38" href="#fnd-38">38</a>]</small> or <code>-mtune=corei7</code> for Intel Core
i3/15/17 with <samp><span class="command">gcc >= 4.6.0</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-39" href="#fnd-39">39</a>]</small> Apple's <code>clang</code> should be able to:
some builds of <code>gcc</code> can, but not all built with Objective C
support work.</p>
<p class="footnote"><small>[<a name="fn-40" href="#fnd-40">40</a>]</small> including <samp><span class="command">gcc</span></samp> for
Sparc from Oracle.</p>
<p class="footnote"><small>[<a name="fn-41" href="#fnd-41">41</a>]</small> TeXLive is recommended.</p>
<p class="footnote"><small>[<a name="fn-42" href="#fnd-42">42</a>]</small> Windows
DLLs need to have all links resolved at build time and so cannot resolve
against <samp><span class="file">R.bin</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-43" href="#fnd-43">43</a>]</small> For
example, the Cygwin version of <code>make 3.81</code> fails to work
correctly.</p>
<p class="footnote"><small>[<a name="fn-44" href="#fnd-44">44</a>]</small> for R 2.15.3 and later.</p>
<p class="footnote"><small>[<a name="fn-45" href="#fnd-45">45</a>]</small> such as <samp><span class="command">sort</span></samp>, <samp><span class="command">find</span></samp> and perhaps
<samp><span class="command">make</span></samp>.</p>
<p class="footnote"><small>[<a name="fn-46" href="#fnd-46">46</a>]</small> these
flags apply to the compilers: some of the tools use different flags.
32-bit builds are the default.</p>
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