EVOLUTION-MANAGER
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> <html> <!-- This manual is for R, version 3.6.0 (2019-04-26). Copyright (C) 2001-2018 R Core Team 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. 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. 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background: white; color: rgb(25%, 25%, 25%); font-family: monospace; font-size: xx-large; text-align: center; } h2 { background: white; color: rgb(40%, 40%, 40%); font-family: monospace; font-size: x-large; text-align: center; } h3 { background: white; color: rgb(40%, 40%, 40%); font-family: monospace; font-size: large; } h4 { background: white; color: rgb(40%, 40%, 40%); font-family: monospace; } span.samp { font-family: monospace; } span.command { font-family: monospace; } span.option { font-family: monospace; } span.file { font-family: monospace; } span.env { font-family: monospace; } ul { margin-top: 0.25ex; margin-bottom: 0.25ex; } li { margin-top: 0.25ex; margin-bottom: 0.25ex; } p { margin-top: 0.6ex; margin-bottom: 1.2ex; } --> </style> </head> <body lang="en" bgcolor="#FFFFFF" text="#000000" link="#0000FF" vlink="#800080" alink="#FF0000"> <h1 class="settitle" align="center">R Installation and Administration</h1> <a name="SEC_Contents"></a> <h2 class="contents-heading">Table of Contents</h2> <div class="contents"> <ul class="no-bullet"> <li><a name="toc-Obtaining-R-1" href="#Obtaining-R">1 Obtaining R</a> <ul class="no-bullet"> <li><a name="toc-Getting-and-unpacking-the-sources-1" href="#Getting-and-unpacking-the-sources">1.1 Getting and unpacking the sources</a></li> <li><a name="toc-Getting-patched-and-development-versions-1" href="#Getting-patched-and-development-versions">1.2 Getting patched and development versions</a> <ul class="no-bullet"> <li><a name="toc-Using-Subversion-and-rsync-1" href="#Using-Subversion-and-rsync">1.2.1 Using Subversion and rsync</a></li> </ul></li> </ul></li> <li><a name="toc-Installing-R-under-Unix_002dalikes-1" href="#Installing-R-under-Unix_002dalikes">2 Installing R under Unix-alikes</a> <ul class="no-bullet"> <li><a name="toc-Simple-compilation-1" href="#Simple-compilation">2.1 Simple compilation</a></li> <li><a name="toc-Help-options-1" href="#Help-options">2.2 Help options</a></li> <li><a name="toc-Making-the-manuals-1" href="#Making-the-manuals">2.3 Making the manuals</a></li> <li><a name="toc-Installation-1" href="#Installation">2.4 Installation</a></li> <li><a name="toc-Uninstallation-1" href="#Uninstallation">2.5 Uninstallation</a></li> <li><a name="toc-Sub_002darchitectures-1" href="#Sub_002darchitectures">2.6 Sub-architectures</a> <ul class="no-bullet"> <li><a name="toc-Multilib-1" href="#Multilib">2.6.1 Multilib</a></li> </ul></li> <li><a name="toc-Other-Options-1" href="#Other-Options">2.7 Other Options</a> <ul class="no-bullet"> <li><a name="toc-Debugging-Symbols-1" href="#Debugging-Symbols">2.7.1 Debugging Symbols</a></li> <li><a name="toc-OpenMP-Support-1" href="#OpenMP-Support">2.7.2 OpenMP Support</a></li> <li><a name="toc-C_002b_002b-Support-1" href="#C_002b_002b-Support">2.7.3 C++ Support</a></li> </ul></li> <li><a name="toc-Testing-an-Installation" href="#Testing-a-Unix_002dalike-Installation">2.8 Testing an Installation</a></li> </ul></li> <li><a name="toc-Installing-R-under-Windows-1" href="#Installing-R-under-Windows">3 Installing R under Windows</a> <ul class="no-bullet"> <li><a name="toc-Building-from-source-1" href="#Building-from-source">3.1 Building from source</a> <ul class="no-bullet"> <li><a name="toc-Getting-the-tools-1" href="#Getting-the-tools">3.1.1 Getting the tools</a></li> <li><a name="toc-Getting-the-source-files-1" href="#Getting-the-source-files">3.1.2 Getting the source files</a></li> <li><a name="toc-Building-the-core-files-1" href="#Building-the-core-files">3.1.3 Building the core files</a></li> <li><a name="toc-Building-the-cairo-devices" href="#Building-the-cairo-devices-files">3.1.4 Building the cairo devices</a></li> <li><a name="toc-Using-ICU-for-collation-1" href="#Using-ICU-for-collation">3.1.5 Using ICU for collation</a></li> <li><a name="toc-Support-for-libcurl-1" href="#Support-for-libcurl">3.1.6 Support for libcurl</a></li> <li><a name="toc-Checking-the-build-1" href="#Checking-the-build">3.1.7 Checking the build</a></li> <li><a name="toc-Building-the-manuals-1" href="#Building-the-manuals">3.1.8 Building the manuals</a></li> <li><a name="toc-Building-the-Inno-Setup-installer-1" href="#Building-the-Inno-Setup-installer">3.1.9 Building the Inno Setup installer</a></li> <li><a name="toc-Building-the-MSI-installer-1" href="#Building-the-MSI-installer">3.1.10 Building the MSI installer</a></li> <li><a name="toc-64_002dbit-Windows-builds-1" href="#g_t64_002dbit-Windows-builds">3.1.11 64-bit Windows builds</a></li> </ul></li> <li><a name="toc-Testing-an-Installation-1" href="#Testing-a-Windows-Installation">3.2 Testing an Installation</a></li> </ul></li> <li><a name="toc-Installing-R-under-macOS-1" href="#Installing-R-under-macOS">4 Installing R under macOS</a> <ul class="no-bullet"> <li><a name="toc-Running-R-under-macOS-1" href="#Running-R-under-macOS">4.1 Running R under macOS</a></li> <li><a name="toc-Uninstalling-under-macOS-1" href="#Uninstalling-under-macOS">4.2 Uninstalling under macOS</a></li> <li><a name="toc-Multiple-versions-1" href="#Multiple-versions">4.3 Multiple versions</a></li> </ul></li> <li><a name="toc-Running-R-1" href="#Running-R">5 Running R</a></li> <li><a name="toc-Add_002don-packages-1" href="#Add_002don-packages">6 Add-on packages</a> <ul class="no-bullet"> <li><a name="toc-Default-packages-1" href="#Default-packages">6.1 Default packages</a></li> <li><a name="toc-Managing-libraries-1" href="#Managing-libraries">6.2 Managing libraries</a></li> <li><a name="toc-Installing-packages-1" href="#Installing-packages">6.3 Installing packages</a> <ul class="no-bullet"> <li><a name="toc-Windows" href="#Windows-packages">6.3.1 Windows</a></li> <li><a name="toc-macOS-1" href="#macOS-packages">6.3.2 macOS</a></li> <li><a name="toc-Customizing-package-compilation-1" href="#Customizing-package-compilation">6.3.3 Customizing package compilation</a></li> <li><a name="toc-Multiple-sub_002darchitectures-1" href="#Multiple-sub_002darchitectures">6.3.4 Multiple sub-architectures</a></li> <li><a name="toc-Byte_002dcompilation-1" href="#Byte_002dcompilation">6.3.5 Byte-compilation</a></li> <li><a name="toc-External-software-1" href="#External-software">6.3.6 External software</a></li> </ul></li> <li><a name="toc-Updating-packages-1" href="#Updating-packages">6.4 Updating packages</a></li> <li><a name="toc-Removing-packages-1" href="#Removing-packages">6.5 Removing packages</a></li> <li><a name="toc-Setting-up-a-package-repository-1" href="#Setting-up-a-package-repository">6.6 Setting up a package repository</a></li> <li><a name="toc-Checking-installed-source-packages-1" href="#Checking-installed-source-packages">6.7 Checking installed source packages</a></li> </ul></li> <li><a name="toc-Internationalization-and-Localization" href="#Internationalization">7 Internationalization and Localization</a> <ul class="no-bullet"> <li><a name="toc-Locales-1" href="#Locales">7.1 Locales</a> <ul class="no-bullet"> <li><a name="toc-Locales-under-Unix_002dalikes-1" href="#Locales-under-Unix_002dalikes">7.1.1 Locales under Unix-alikes</a></li> <li><a name="toc-Locales-under-Windows-1" href="#Locales-under-Windows">7.1.2 Locales under Windows</a></li> <li><a name="toc-Locales-under-macOS-1" href="#Locales-under-macOS">7.1.3 Locales under macOS</a></li> </ul></li> <li><a name="toc-Localization-of-messages-1" href="#Localization-of-messages">7.2 Localization of messages</a></li> </ul></li> <li><a name="toc-Choosing-between-32_002d-and-64_002dbit-builds-1" href="#Choosing-between-32_002d-and-64_002dbit-builds">8 Choosing between 32- and 64-bit builds</a></li> <li><a name="toc-The-standalone-Rmath-library-1" href="#The-standalone-Rmath-library">9 The standalone Rmath library</a> <ul class="no-bullet"> <li><a name="toc-Unix_002dalikes" href="#Unix_002dalike-standalone">9.1 Unix-alikes</a></li> <li><a name="toc-Windows-1" href="#Windows-standalone">9.2 Windows</a></li> </ul></li> <li><a name="toc-Essential-and-useful-other-programs-under-a-Unix_002dalike-1" href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Appendix A Essential and useful other programs under a Unix-alike</a> <ul class="no-bullet"> <li><a name="toc-Essential-programs-and-libraries-1" href="#Essential-programs-and-libraries">A.1 Essential programs and libraries</a></li> <li><a name="toc-Useful-libraries-and-programs-1" href="#Useful-libraries-and-programs">A.2 Useful libraries and programs</a> <ul class="no-bullet"> <li><a name="toc-Tcl_002fTk-1" href="#Tcl_002fTk">A.2.1 Tcl/Tk</a></li> <li><a name="toc-Java-support-1" href="#Java-support">A.2.2 Java support</a></li> <li><a name="toc-Other-compiled-languages-1" href="#Other-compiled-languages">A.2.3 Other compiled languages</a></li> </ul></li> <li><a name="toc-Linear-algebra-1" href="#Linear-algebra">A.3 Linear algebra</a> <ul class="no-bullet"> <li><a name="toc-BLAS-1" href="#BLAS">A.3.1 BLAS</a> <ul class="no-bullet"> <li><a name="toc-ATLAS-1" href="#ATLAS">A.3.1.1 ATLAS</a></li> <li><a name="toc-OpenBLAS-1" href="#OpenBLAS">A.3.1.2 OpenBLAS</a></li> <li><a name="toc-Intel-MKL" href="#MKL">A.3.1.3 Intel MKL</a></li> <li><a name="toc-Shared-BLAS-1" href="#Shared-BLAS">A.3.1.4 Shared BLAS</a></li> </ul></li> <li><a name="toc-LAPACK-1" href="#LAPACK">A.3.2 LAPACK</a></li> <li><a name="toc-Caveats-1" href="#Caveats">A.3.3 Caveats</a></li> </ul></li> </ul></li> <li><a name="toc-Configuration-on-a-Unix_002dalike-1" href="#Configuration-on-a-Unix_002dalike">Appendix B Configuration on a Unix-alike</a> <ul class="no-bullet"> <li><a name="toc-Configuration-options-1" href="#Configuration-options">B.1 Configuration options</a></li> <li><a name="toc-Internationalization-support-1" href="#Internationalization-support">B.2 Internationalization support</a></li> <li><a name="toc-Configuration-variables-1" href="#Configuration-variables">B.3 Configuration variables</a> <ul class="no-bullet"> <li><a name="toc-Setting-paper-size-1" href="#Setting-paper-size">B.3.1 Setting paper size</a></li> <li><a name="toc-Setting-the-browsers-1" href="#Setting-the-browsers">B.3.2 Setting the browsers</a></li> <li><a name="toc-Compilation-flags-1" href="#Compilation-flags">B.3.3 Compilation flags</a></li> <li><a name="toc-Making-manuals-1" href="#Making-manuals">B.3.4 Making manuals</a></li> </ul></li> <li><a name="toc-Setting-the-shell-1" href="#Setting-the-shell">B.4 Setting the shell</a></li> <li><a name="toc-Using-make-1" href="#Using-make">B.5 Using make</a></li> <li><a name="toc-Using-Fortran-1" href="#Using-Fortran">B.6 Using Fortran</a></li> <li><a name="toc-Compile-and-load-flags-1" href="#Compile-and-load-flags">B.7 Compile and load flags</a></li> <li><a name="toc-Maintainer-mode-1" href="#Maintainer-mode">B.8 Maintainer mode</a></li> </ul></li> <li><a name="toc-Platform-notes-1" href="#Platform-notes">Appendix C Platform notes</a> <ul class="no-bullet"> <li><a name="toc-X11-issues-1" href="#X11-issues">C.1 X11 issues</a></li> <li><a name="toc-Linux-1" href="#Linux">C.2 Linux</a> <ul class="no-bullet"> <li><a name="toc-Clang-1" href="#Clang">C.2.1 Clang</a></li> <li><a name="toc-Intel-compilers-1" href="#Intel-compilers">C.2.2 Intel compilers</a></li> </ul></li> <li><a name="toc-macOS-2" href="#macOS">C.3 macOS</a> <ul class="no-bullet"> <li><a name="toc-Tcl_002fTk-headers-and-libraries-1" href="#Tcl_002fTk-headers-and-libraries">C.3.1 Tcl/Tk headers and libraries</a></li> <li><a name="toc-Java" href="#Java-_0028macOS_0029">C.3.2 Java</a></li> <li><a name="toc-Frameworks-1" href="#Frameworks">C.3.3 Frameworks</a></li> <li><a name="toc-Building-R_002eapp-1" href="#Building-R_002eapp">C.3.4 Building R.app</a></li> </ul></li> <li><a name="toc-Solaris-1" href="#Solaris">C.4 Solaris</a> <ul class="no-bullet"> <li><a name="toc-64_002dbit-builds-1" href="#g_t64_002dbit-builds">C.4.1 64-bit builds</a></li> <li><a name="toc-Using-gcc-1" href="#Using-gcc">C.4.2 Using gcc</a></li> </ul></li> <li><a name="toc-FreeBSD-1" href="#FreeBSD">C.5 FreeBSD</a></li> <li><a name="toc-OpenBSD-1" href="#OpenBSD">C.6 OpenBSD</a></li> <li><a name="toc-Cygwin-1" href="#Cygwin">C.7 Cygwin</a></li> <li><a name="toc-New-platforms-1" href="#New-platforms">C.8 New platforms</a></li> </ul></li> <li><a name="toc-The-Windows-toolset-1" href="#The-Windows-toolset">Appendix D The Windows toolset</a> <ul class="no-bullet"> <li><a name="toc-LaTeX-1" href="#LaTeX">D.1 LaTeX</a></li> <li><a name="toc-The-Inno-Setup-installer-1" href="#The-Inno-Setup-installer">D.2 The Inno Setup installer</a></li> <li><a name="toc-The-command-line-tools-1" href="#The-command-line-tools">D.3 The command line tools</a></li> <li><a name="toc-The-MinGW_002dw64-toolchain-1" href="#The-MinGW_002dw64-toolchain">D.4 The MinGW-w64 toolchain</a></li> <li><a name="toc-Useful-additional-programs-1" href="#Useful-additional-programs">D.5 Useful additional programs</a></li> </ul></li> <li><a name="toc-Function-and-variable-index-1" href="#Function-and-variable-index">Function and variable index</a></li> <li><a name="toc-Concept-index-1" href="#Concept-index">Concept index</a></li> <li><a name="toc-Environment-variable-index-1" href="#Environment-variable-index">Environment variable index</a></li> </ul> </div> <a name="Top"></a> <div class="header"> <p> Next: <a href="#Obtaining-R" accesskey="n" rel="next">Obtaining R</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="R-Installation-and-Administration"></a> <h1 class="top">R Installation and Administration</h1> <p>This is a guide to installation and administration for R. </p> <p>This manual is for R, version 3.6.0 (2019-04-26). </p> <p>Copyright © 2001–2018 R Core Team </p> <blockquote> <p>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> <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> <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. </p></blockquote> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Obtaining-R" accesskey="1">Obtaining R</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Installing-R-under-Unix_002dalikes" accesskey="2">Installing R under Unix-alikes</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Installing-R-under-Windows" accesskey="3">Installing R under Windows</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Installing-R-under-macOS" accesskey="4">Installing R under macOS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Running-R" accesskey="5">Running R</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Add_002don-packages" accesskey="6">Add-on packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Internationalization" accesskey="7">Internationalization</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="8">Choosing between 32- and 64-bit builds</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#The-standalone-Rmath-library" accesskey="9">The standalone Rmath library</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike">Essential and useful other programs under a Unix-alike</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Configuration-on-a-Unix_002dalike">Configuration on a Unix-alike</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Platform-notes">Platform notes</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#The-Windows-toolset">The Windows toolset</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Function-and-variable-index">Function and variable index</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Concept-index">Concept index</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Environment-variable-index">Environment variable index</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Obtaining-R"></a> <div class="header"> <p> Next: <a href="#Installing-R-under-Unix_002dalikes" accesskey="n" rel="next">Installing R under Unix-alikes</a>, Previous: <a href="#Top" accesskey="p" rel="previous">Top</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Obtaining-R-1"></a> <h2 class="chapter">1 Obtaining R</h2> <a name="index-Obtaining-R"></a> <p>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="https://CRAN.R-project.org/mirrors.html">https://CRAN.R-project.org/mirrors.html</a>. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Getting-and-unpacking-the-sources" accesskey="1">Getting and unpacking the sources</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Getting-patched-and-development-versions" accesskey="2">Getting patched and development versions</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Getting-and-unpacking-the-sources"></a> <div class="header"> <p> Next: <a href="#Getting-patched-and-development-versions" accesskey="n" rel="next">Getting patched and development versions</a>, Previous: <a href="#Obtaining-R" accesskey="p" rel="previous">Obtaining R</a>, Up: <a href="#Obtaining-R" accesskey="u" rel="up">Obtaining R</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Getting-and-unpacking-the-sources-1"></a> <h3 class="section">1.1 Getting and unpacking the sources</h3> <a name="index-Sources-for-R"></a> <p>The simplest way is to download the most recent <samp>R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz</samp> file, and unpack it with </p> <div class="example"> <pre class="example">tar -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz </pre></div> <p>on systems that have a suitable<a name="DOCF1" href="#FOOT1"><sup>1</sup></a> <code>tar</code> installed. On other systems you need to have the <code>gzip</code> program installed, when you can use </p> <div class="example"> <pre class="example">gzip -dc R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz | tar -xf - </pre></div> <p>The pathname of the directory into which the sources are unpacked should not contain spaces, as most <code>make</code> programs (and specifically <acronym>GNU</acronym> <code>make</code>) do not expect spaces. </p> <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> <p>If you use a fairly recent <acronym>GNU</acronym> version of <code>tar</code> 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 </p> <div class="example"> <pre class="example">tar --no-same-owner -xf R-<var>x</var>.<var>y</var>.<var>z</var>.tar.gz </pre></div> <p>and perhaps also include the option <samp>--no-same-permissions</samp>. <a name="index-TAR_005fOPTIONS"></a> (These options can also be set in the <code>TAR_OPTIONS</code> environment variable: if more than one option is included they should be separated by spaces.) </p> <hr> <a name="Getting-patched-and-development-versions"></a> <div class="header"> <p> Previous: <a href="#Getting-and-unpacking-the-sources" accesskey="p" rel="previous">Getting and unpacking the sources</a>, Up: <a href="#Obtaining-R" accesskey="u" rel="up">Obtaining R</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Getting-patched-and-development-versions-1"></a> <h3 class="section">1.2 Getting patched and development versions</h3> <p>A patched version of the current release, ‘<samp>r-patched</samp>’, and the current development version, ‘<samp>r-devel</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>r-patched</samp>’ tarballs may refer to beta/release candidates of the upcoming release, the patched version of the current release being available via Subversion.) </p> <p>The tarballs are available from <a href="https://stat.ethz.ch/R/daily">https://stat.ethz.ch/R/daily</a>. Download <samp>R-patched.tar.gz</samp> or <samp>R-devel.tar.gz</samp> (or the <samp>.tar.bz2</samp> versions) and unpack as described in the previous section. They are built in exactly the same way as distributions of R releases. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Using-Subversion-and-rsync" accesskey="1">Using Subversion and rsync</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Using-Subversion-and-rsync"></a> <div class="header"> <p> Previous: <a href="#Getting-patched-and-development-versions" accesskey="p" rel="previous">Getting patched and development versions</a>, Up: <a href="#Getting-patched-and-development-versions" accesskey="u" rel="up">Getting patched and development versions</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Using-Subversion-and-rsync-1"></a> <h4 class="subsection">1.2.1 Using Subversion and rsync</h4> <a name="index-Subversion"></a> <p>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="https://subversion.apache.org/">https://subversion.apache.org/</a>), you can check out and update the current ‘<samp>r-devel</samp>’ from <a href="https://svn.r-project.org/R/trunk/">https://svn.r-project.org/R/trunk/</a> and the current ‘<samp>r-patched</samp>’ from ‘<samp>https://svn.r-project.org/R/branches/R-<var>x</var>-<var>y</var>-branch/</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 </p> <div class="example"> <pre class="example">svn checkout https://svn.r-project.org/R/trunk/ <var>path</var> </pre></div> <p>to check out ‘<samp>r-devel</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>https://svn.r-project.org/R/branches/R-<var>x</var>-<var>y</var>-branch/</samp>’ in the four-week period prior to the release. </p> <p>Note that ‘<samp>https:</samp>’ is required<a name="DOCF2" href="#FOOT2"><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> <p>Note that retrieving the sources by e.g. <code>wget -r</code> or <code>svn export</code> from that URL will not work (and will give a error early in the <code>make</code> process): the Subversion information is needed to build R. </p> <p>The Subversion repository does not contain the current sources for the recommended packages, which can be obtained by <code>rsync</code> 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> <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>VERSION</samp> is ‘<samp><var>x</var>.<var>y</var>.<var>z</var></samp>’ you need to download the contents of ‘<samp>https://CRAN.R-project.org/src/contrib/<var>dir</var></samp>’, where <var>dir</var> is ‘<samp><var>x</var>.<var>y</var>.<var>z</var>/Recommended</samp>’ for r-devel or <samp><var>x</var>.<var>y</var>-patched/Recommended</samp> for r-patched, respectively, to directory <samp>src/library/Recommended</samp> in the sources you have unpacked. After downloading manually you need to execute <code>tools/link-recommended</code> from the top level of the sources to make the requisite links in <samp>src/library/Recommended</samp>. A suitable incantation from the top level of the R sources using <code>wget</code> might be (for the correct value of <samp><var>dir</var></samp>) </p> <div class="example"> <pre class="example">wget -r -l1 --no-parent -A\*.gz -nd -P src/library/Recommended \ https://CRAN.R-project.org/src/contrib/<var>dir</var> ./tools/link-recommended </pre></div> <hr> <a name="Installing-R-under-Unix_002dalikes"></a> <div class="header"> <p> Next: <a href="#Installing-R-under-Windows" accesskey="n" rel="next">Installing R under Windows</a>, Previous: <a href="#Obtaining-R" accesskey="p" rel="previous">Obtaining R</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Installing-R-under-Unix_002dalikes-1"></a> <h2 class="chapter">2 Installing R under Unix-alikes</h2> <a name="index-Installing-under-Unix_002dalikes"></a> <p>R will configure and build under most common Unix and Unix-alike platforms including ‘<samp><var>cpu</var>-*-linux-gnu</samp>’ for the ‘<samp>alpha</samp>’, ‘<samp>arm64</samp>’, ‘<samp>hppa</samp>’, ‘<samp>ix86</samp>’, ‘<samp>m68k</samp>’, ‘<samp>mips</samp>’, ‘<samp>mipsel</samp>’, ‘<samp>ppc64</samp>’, ‘<samp>s390</samp>’, ‘<samp>sparc64</samp>’, and ‘<samp>x86_64</samp>’ <acronym>CPU</acronym>s, ‘<samp>x86_64-apple-darwin</samp>’, ‘<samp>i386-sun-solaris</samp>’ and ‘<samp>sparc-sun-solaris</samp>’ as well as perhaps (it is tested less frequently on these platforms) ‘<samp>i386-*-freebsd</samp>’, ‘<samp>x86_64-*-freebsd</samp>’, ‘<samp>i386-*-netbsd</samp>’, ‘<samp>x86_64/*-openbsd</samp>’ and ‘<samp>powerpc-ibm-aix6*</samp>’ </p> <a name="index-Linux"></a> <a name="index-macOS"></a> <p>In addition, binary distributions are available for some common Linux distributions and for macOS (formerly OS X and 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. </p> <p>Cross-building is not possible: installing R builds a minimal version of R and then runs many R scripts to complete the build. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Simple-compilation" accesskey="1">Simple compilation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Help-options" accesskey="2">Help options</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Making-the-manuals" accesskey="3">Making the manuals</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Installation" accesskey="4">Installation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Uninstallation" accesskey="5">Uninstallation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Sub_002darchitectures" accesskey="6">Sub-architectures</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Other-Options" accesskey="7">Other Options</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Testing-a-Unix_002dalike-Installation" accesskey="8">Testing a Unix-alike Installation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Simple-compilation"></a> <div class="header"> <p> Next: <a href="#Help-options" accesskey="n" rel="next">Help options</a>, Previous: <a href="#Installing-R-under-Unix_002dalikes" accesskey="p" rel="previous">Installing R under Unix-alikes</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Simple-compilation-1"></a> <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"></a> want or need. Ensure that either the environment variable <code>TMPDIR</code> is either unset (and <samp>/tmp</samp> exists and can be written in and scripts can be executed from) or points to the absolute path to a valid temporary directory (one from which execution of scripts is allowed) which does not contain spaces.<a name="DOCF3" href="#FOOT3"><sup>3</sup></a> </p> <a name="index-R_005fHOME"></a> <p>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>src</samp>, <samp>doc</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"></a> <div class="example"> <pre class="example">./configure make </pre></div> <p>(See <a href="#Using-make">Using make</a> if your make is not called ‘<samp>make</samp>’.) Users of Debian-based 64-bit systems<a name="DOCF4" href="#FOOT4"><sup>4</sup></a> may need </p> <div class="example"> <pre class="example">./configure LIBnn=lib make </pre></div> <p>Then check the built system works correctly by </p> <div class="example"> <pre class="example">make check </pre></div> <p>Failures are not necessarily problems as they might be caused by missing functionality, 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>tests/ok-errors.R</samp> may indicate inadequate resource limits (see <a href="#Running-R">Running R</a>). </p> <p>More comprehensive testing can be done by </p> <div class="example"> <pre class="example">make check-devel </pre></div> <p>or </p> <div class="example"> <pre class="example">make check-all </pre></div> <p>see file <samp>tests/README</samp> and <a href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a> for the possibilities of doing this in parallel. Note that these checks are only run completely if the recommended packages are installed. </p> <p>If the <code>configure</code> and <code>make</code> commands execute successfully, a shell-script front-end called <samp>R</samp> will be created and copied to <samp><var>R_HOME</var>/bin</samp>. You can link or copy this script to a place where users can invoke it, for example to <samp>/usr/local/bin/R</samp>. You could also copy the man page <samp>R.1</samp> to a place where your <code>man</code> reader finds it, such as <samp>/usr/local/man/man1</samp>. If you want to install the complete R tree to, e.g., <samp>/usr/local/lib/R</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> <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-1"></a> <div class="example"> <pre class="example">cd <var>BUILDDIR</var> <var>TOP_SRCDIR</var>/configure make </pre></div> <p>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> <code>make</code> to allow this, and you will need no spaces in the path to the build directory. It is unlikely to work if the source directory has previously been used for a build.) </p> <p>Now <code>rehash</code> if necessary, type <kbd>R</kbd>, and read the R manuals and the R <acronym>FAQ</acronym> (files <samp>FAQ</samp> or <samp>doc/manual/R-FAQ.html</samp>, or <a href="https://CRAN.R-project.org/doc/FAQ/R-FAQ.html">https://CRAN.R-project.org/doc/FAQ/R-FAQ.html</a> which always has the version for the latest release of R). </p> <p>Note: if you already have R installed, check that where you installed R replaces or comes earlier in your path than the previous installation. Some systems are set up to have <samp>/usr/bin</samp> (the standard place for a system installation) ahead of <samp>/usr/local/bin</samp> (the default place for installation of R) in their default path, and some do not have <samp>/usr/local/bin</samp> on the default path. </p> <hr> <a name="Help-options"></a> <div class="header"> <p> Next: <a href="#Making-the-manuals" accesskey="n" rel="next">Making the manuals</a>, Previous: <a href="#Simple-compilation" accesskey="p" rel="previous">Simple compilation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Help-options-1"></a> <h3 class="section">2.2 Help options</h3> <p>R by default provides help pages a plain text displayed in a pager, with the options (see the help for <code>help</code> of displaying help as HTML or PDF. </p> <p>By default <acronym>HTML</acronym> help pages are created when needed rather than being built at install time. </p> <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 <code>configure</code> option <samp>--enable-prebuilt-html</samp>. Whether <code>R CMD INSTALL</code> (and hence <code>install.packages</code>) pre-builds <acronym>HTML</acronym> pages is determined by looking at the R installation and is reported by <code>R CMD INSTALL --help</code>: it can be overridden by specifying one of the <code>INSTALL</code> options <samp>--html</samp> or <samp>--no-html</samp>. </p> <p>The server is disabled by setting the environment variable <a name="index-R_005fDISABLE_005fHTTPD"></a> <code>R_DISABLE_HTTPD</code> 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. </p> <hr> <a name="Making-the-manuals"></a> <div class="header"> <p> Next: <a href="#Installation" accesskey="n" rel="next">Installation</a>, Previous: <a href="#Help-options" accesskey="p" rel="previous">Help options</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Making-the-manuals-1"></a> <h3 class="section">2.3 Making the manuals</h3> <a name="index-Manuals"></a> <p>There is a set of manuals that can be built from the sources, </p> <dl compact="compact"> <dt>‘<samp>fullrefman</samp>’</dt> <dd><p>Printed versions of all the help pages for base and recommended packages (around 3600 pages). </p></dd> <dt>‘<samp>refman</samp>’</dt> <dd><p>Printed versions of the help pages for selected base packages (around 2200 pages) </p></dd> <dt>‘<samp>R-FAQ</samp>’</dt> <dd><p>R <acronym>FAQ</acronym> </p></dd> <dt>‘<samp>R-intro</samp>’</dt> <dd><p>“An Introduction to R”. </p></dd> <dt>‘<samp>R-data</samp>’</dt> <dd><p>“R Data Import/Export”. </p></dd> <dt>‘<samp>R-admin</samp>’</dt> <dd><p>“R Installation and Administration”, this manual. </p></dd> <dt>‘<samp>R-exts</samp>’</dt> <dd><p>“Writing R Extensions”. </p></dd> <dt>‘<samp>R-lang</samp>’</dt> <dd><p>“The R Language Definition”. </p></dd> </dl> <p>To make these (with ‘<samp>fullrefman</samp>’ rather than ‘<samp>refman</samp>’), use </p> <div class="example"> <pre class="example">make pdf <span class="roman">to create PDF versions</span> make info <span class="roman">to create info files (not ‘<samp>refman</samp>’ nor ‘<samp>fullrefman</samp>’).</span> </pre></div> <p>You will not be able to build any of these unless you have <code>texi2any</code> version 5.1 or later installed, and for PDF you must have <code>texi2dvi</code> and <samp>texinfo.tex</samp> installed (which are part of the <acronym>GNU</acronym> <strong>texinfo</strong> distribution but are, especially <samp>texinfo.tex</samp>, often made part of the TeX package in re-distributions). The path to <code>texi2any</code> can be set by macro ‘<samp>TEXI2ANY</samp>’ in <samp>config.site</samp>. </p> <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> <code>info</code> program. The PDF versions will be created using the paper size selected at configuration (default ISO a4): this can be overridden by setting <code>R_PAPERSIZE</code> <a name="index-R_005fPAPERSIZE"></a> on the <code>make</code> command line, or setting <code>R_PAPERSIZE</code> in the environment and using <code>make -e</code>. (If re-making the manuals for a different paper size, you should first delete the file <samp>doc/manual/version.texi</samp>. The usual value for North America would be ‘<samp>letter</samp>’.) </p> <p>There are some issues with making the PDF reference manual, <samp>fullrefman.pdf</samp> or <samp>refman.pdf</samp>. The help files contain both ISO Latin1 characters (e.g. in <samp>text.Rd</samp>) and upright quotes, neither of which are contained in the standard LaTeX Computer Modern fonts. We have provided four alternatives: </p> <dl compact="compact"> <dt><code>times</code></dt> <dd><p>(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 <code>configure</code>) 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><a name="DOCF5" href="#FOOT5"><sup>5</sup></a> or <strong>bera</strong> installed.) </p> <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. </p> <p>This needs LaTeX packages <strong>times</strong>, <strong>helvetic</strong> and (if used) <strong>courier</strong> installed. </p> </dd> <dt><code>lm</code></dt> <dd><p>Using the <em>Latin Modern</em> fonts. These are not often installed as part of a TeX distribution, but can obtained from <a href="https://www.ctan.org/tex-archive/fonts/ps-type1/lm/">https://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>. </p> </dd> <dt><code>cm-super</code></dt> <dd><p>Using type-1 versions of the Computer Modern fonts by Vladimir Volovich. This is a large installation, obtainable from <a href="https://www.ctan.org/tex-archive/fonts/ps-type1/cm-super/">https://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. </p> </dd> <dt><code>ae</code></dt> <dd><p>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>tctt0900.600pk</samp>, <samp>tctt1000.600pk</samp> and <samp>tcrm1000.600pk</samp>. Unfortunately, if those files are not available, Acrobat Reader will substitute completely incorrect glyphs so you need to examine the logs carefully. </p></dd> </dl> <p>The default can be overridden by setting the environment variable <a name="index-R_005fRD4PDF"></a> <code>R_RD4PDF</code>. (On Unix-alikes, this will be picked up at install time and stored in <samp>etc/Renviron</samp>, but can still be overridden when the manuals are built, using <code>make -e</code>.) The usual<a name="DOCF6" href="#FOOT6"><sup>6</sup></a> default value for <code>R_RD4PDF</code> is ‘<samp>times,inconsolata,hyper</samp>’: omit ‘<samp>hyper</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>inconsolata</samp>’ if you do not have LaTeX package <strong>inconsolata</strong> installed. </p> <p>Further options, e.g for <strong>hyperref</strong>, can be included in a file <samp>Rd.cfg</samp> somewhere on your LaTeX search path. For example, if you prefer to hyperlink the text and not the page number in the table of contents use </p><div class="example"> <pre class="example">\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=section}}{} </pre></div> <p>or </p><div class="example"> <pre class="example">\ifthenelse{\boolean{Rd@use@hyper}}{\hypersetup{linktoc=all}}{} </pre></div> <p>to hyperlink both text and page number. </p> <p>Ebook versions of most of the manuals in one or both of <samp>.epub</samp> and <samp>.mobi</samp> formats can be made by running in <samp>doc/manual</samp> one of </p><div class="example"> <pre class="example">make ebooks make epub make mobi </pre></div> <p>This requires <code>ebook-convert</code> from <code>Calibre</code> (<a href="http://calibre-ebook.com/download">http://calibre-ebook.com/download</a>), or from most Linux distributions. If necessary the path to <code>ebook-convert</code> can be set as make macro <code>EBOOK</code> to by editing <samp>doc/manual/Makefile</samp> (which contains a commented value suitable for macOS) or using <code>make -e</code>. </p> <hr> <a name="Installation"></a> <div class="header"> <p> Next: <a href="#Uninstallation" accesskey="n" rel="next">Uninstallation</a>, Previous: <a href="#Making-the-manuals" accesskey="p" rel="previous">Making the manuals</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Installation-1"></a> <h3 class="section">2.4 Installation</h3> <a name="index-Installation"></a> <p>To ensure that the installed tree is usable by the right group of users, set <code>umask</code> appropriately (perhaps to ‘<samp>022</samp>’) before unpacking the sources and throughout the build process. </p> <p>After </p> <a name="index-configure-2"></a> <div class="example"> <pre class="example">./configure make make check </pre></div> <p>(or, when building outside the source, <code><var>TOP_SRCDIR</var>/configure</code>, etc) have been completed successfully, you can install the complete R tree to your system by typing </p> <div class="example"> <pre class="example">make install </pre></div> <p>A parallel make can be used (but run <code>make</code> before <code>make install</code>). Those using GNU <code>make</code> 4.0 or later may want to use <code>make -j <var>n</var> -O</code> to avoid interleaving of output. </p> <p>This will install to the following directories: </p> <dl compact="compact"> <dt><samp><var>prefix</var>/bin</samp> or <samp><var>bindir</var></samp></dt> <dd><p>the front-end shell script and other scripts and executables </p></dd> <dt><samp><var>prefix</var>/man/man1</samp> or <samp><var>mandir</var>/man1</samp></dt> <dd><p>the man page </p></dd> <dt><samp><var>prefix</var>/<var>LIBnn</var>/R</samp> or <samp><var>libdir</var>/R</samp></dt> <dd><p>all the rest (libraries, on-line help system, …). Here <var>LIBnn</var> is usually ‘<samp>lib</samp>’, but may be ‘<samp>lib64</samp>’ on some 64-bit Linux systems. This is known as the R home directory. </p></dd> </dl> <p>where <var>prefix</var> is determined during configuration (typically <samp>/usr/local</samp>) and can be set by running <code>configure</code> with the option <samp>--prefix</samp>, as in </p> <a name="index-configure-3"></a> <div class="example"> <pre class="example">./configure --prefix=/where/you/want/R/to/go </pre></div> <p>where the value should be an absolute path. This causes <code>make install</code> to install the R script to <samp>/where/you/want/R/to/go/bin</samp>, and so on. The prefix of the installation directories can be seen in the status message that is displayed at the end of <code>configure</code>. The installation may need to be done by the owner of <samp><var>prefix</var></samp>, often a root account. </p> <p>There is the option of using <code>make install-strip</code> (see <a href="#Debugging-Symbols">Debugging Symbols</a>). </p> <p>You can install into another directory tree by using </p> <div class="example"> <pre class="example">make prefix=/path/to/here install </pre></div> <p>at least with <acronym>GNU</acronym> <code>make</code> (but not some other Unix makes). </p> <p>More precise control is available at configure time via options: see <code>configure --help</code> for details. (However, most of the ‘Fine tuning of the installation directories’ options are not used by R.) </p> <p>Configure options <samp>--bindir</samp> and <samp>--mandir</samp> are supported and govern where a copy of the <code>R</code> script and the <code>man</code> page are installed. </p> <p>The configure option <samp>--libdir</samp> controls where the main R files are installed: the default is ‘<samp><var>eprefix</var>/<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>--exec-prefix</samp>. </p> <p>Each of <code>bindir</code>, <code>mandir</code> and <code>libdir</code> can also be specified on the <code>make install</code> command line (at least for <acronym>GNU</acronym> <code>make</code>). </p> <p>The <code>configure</code> or <code>make</code> variables <code>rdocdir</code> and <code>rsharedir</code> can be used to install the system-independent <samp>doc</samp> and <samp>share</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-3.6.0</code>. </p> <p>If you want the R home to be something other than <samp><var>libdir</var>/R</samp>, use <samp>rhome</samp>: for example </p> <div class="example"> <pre class="example">make install rhome=/usr/local/lib64/R-3.6.0 </pre></div> <p>will use a version-specific R home on a non-Debian Linux 64-bit system. </p> <p>If you have made R as a shared/static library you can install it in your system’s library directory by </p> <div class="example"> <pre class="example">make prefix=/path/to/here install-libR </pre></div> <p>where <code>prefix</code> is optional, and <code>libdir</code> will give more precise control.<a name="DOCF7" href="#FOOT7"><sup>7</sup></a> However, you should not install to a directory mentioned in <code>LDPATHS</code> (e.g. <samp>/usr/local/lib64</samp>) if you intend to work with multiple versions of R, since that directory may be given precedence over the <samp>lib</samp> directory of other R installations. </p> <div class="example"> <pre class="example">make install-strip </pre></div> <p>will install stripped executables, and on platforms where this is supported, stripped libraries in directories <samp>lib</samp> and <samp>modules</samp> and in the standard packages. </p> <p>Note that installing R into a directory whose path contains spaces is not supported, and some aspects (such as installing source packages) will not work. </p> <a name="index-Manuals_002c-installing"></a> <p>To install info and PDF versions of the manuals, use one or both of </p> <div class="example"> <pre class="example">make install-info make install-pdf </pre></div> <p>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). (<code>make install-info</code> needs <code>Perl</code> installed if there is no command <code>install-info</code> on the system.) </p> <p>More precise control is possible. For info, the setting used is that of <code>infodir</code> (default <samp><var>prefix</var>/info</samp>, set by configure option <samp>--infodir</samp>). The PDF files are installed into the R <samp>doc</samp> tree, set by the <code>make</code> variable <code>rdocdir</code>. </p> <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"></a> final destination, and <code>DESTDIR</code> should be used: see <a href="https://www.gnu.org/prep/standards/html_node/DESTDIR.html">https://www.gnu.org/prep/standards/html_node/DESTDIR.html</a>. </p> <p>You can optionally install the run-time tests that are part of <code>make check-all</code> by </p> <div class="example"> <pre class="example">make install-tests </pre></div> <p>which populates a <samp>tests</samp> directory in the installation. </p> <hr> <a name="Uninstallation"></a> <div class="header"> <p> Next: <a href="#Sub_002darchitectures" accesskey="n" rel="next">Sub-architectures</a>, Previous: <a href="#Installation" accesskey="p" rel="previous">Installation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Uninstallation-1"></a> <h3 class="section">2.5 Uninstallation</h3> <p>You can uninstall R by </p> <div class="example"> <pre class="example">make uninstall </pre></div> <p>optionally specifying <code>prefix</code> etc in the same way as specified for installation. </p> <p>This will also uninstall any installed manuals. There are specific targets to uninstall info and PDF manuals in file <samp>doc/manual/Makefile</samp>. </p> <p>Target <code>uninstall-tests</code> will uninstall any installed tests, as well as removing the directory <samp>tests</samp> containing the test results. </p> <p>An installed shared/static <code>libR</code> can be uninstalled by </p> <div class="example"> <pre class="example">make prefix=/path/to/here uninstall-libR </pre></div> <hr> <a name="Sub_002darchitectures"></a> <div class="header"> <p> Next: <a href="#Other-Options" accesskey="n" rel="next">Other Options</a>, Previous: <a href="#Uninstallation" accesskey="p" rel="previous">Uninstallation</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Sub_002darchitectures-1"></a> <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> <p>R supports the idea of architecture-specific builds, specified by adding ‘<samp>r_arch=<var>name</var></samp>’ to the <code>configure</code> line. Here <var>name</var> can be anything non-empty, and is used to name subdirectories of <samp>lib</samp>, <samp>etc</samp>, <samp>include</samp> and the package <samp>libs</samp> subdirectories. Example names from other software are the use of <samp>sparcv9</samp> on Sparc Solaris and <samp>32</samp> by <code>gcc</code> on ‘<samp>x86_64</samp>’ Linux. </p> <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>r_arch</samp>’). The space savings can be considerable: on ‘<samp>x86_64</samp>’ Linux a basic install (without debugging symbols) took 74Mb, and adding a 32-bit build added 6Mb. If you have installed multiple builds you can select which build to run by </p> <div class="example"> <pre class="example">R --arch=<var>name</var> </pre></div> <p>and just running ‘<samp>R</samp>’ will run the last build that was installed. </p> <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>src/Makefile</samp> file. In such cases you can install for extra builds by </p> <div class="example"> <pre class="example">R --arch=<var>name</var> CMD INSTALL --libs-only <var>pkg1</var> <var>pkg2</var> … </pre></div> <p>If you want to mix sub-architectures compiled on different platforms (for example ‘<samp>x86_64</samp>’ Linux and ‘<samp>i686</samp>’ Linux), it is wise to use explicit names for each, and you may also need to set <samp>libdir</samp> to ensure that they install into the same place. </p> <p>When sub-architectures are used the version of <code>Rscript</code> in e.g. <samp>/usr/bin</samp> will be the last installed, but architecture-specific versions will be available in e.g. <samp>/usr/lib64/R/bin/exec${<var>R_ARCH</var>}</samp>. Normally all installed architectures will run on the platform so the architecture of <code>Rscript</code> itself does not matter. The executable <code>Rscript</code> will run the <code>R</code> script, and at that time the <a name="index-R_005fARCH"></a> setting of the <code>R_ARCH</code> environment variable determines the architecture which is run. </p> <p>When running post-install tests with sub-architectures, use </p> <div class="example"> <pre class="example">R --arch=<var>name</var> CMD make check[-devel|all] </pre></div> <p>to select a sub-architecture to check. </p> <p>Sub-architectures are also used on Windows, but by selecting executables within the appropriate <samp>bin</samp> directory, <samp><var>R_HOME</var>/bin/i386</samp> or <samp><var>R_HOME</var>/bin/x64</samp>. For backwards compatibility there are executables <samp><var>R_HOME</var>/bin/R.exe</samp> and <samp><var>R_HOME</var>/bin/Rscript.exe</samp>: these will run an executable from one of the subdirectories, which one being taken first from the <a name="index-R_005fARCH-1"></a> <code>R_ARCH</code> environment variable, then from the <samp>--arch</samp> command-line option<a name="DOCF8" href="#FOOT8"><sup>8</sup></a> and finally from the installation default (which is 32-bit for a combined 32/64 bit R installation). </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Multilib" accesskey="1">Multilib</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Multilib"></a> <div class="header"> <p> Previous: <a href="#Sub_002darchitectures" accesskey="p" rel="previous">Sub-architectures</a>, Up: <a href="#Sub_002darchitectures" accesskey="u" rel="up">Sub-architectures</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Multilib-1"></a> <h4 class="subsection">2.6.1 Multilib</h4> <p>For some Linux distributions<a name="DOCF9" href="#FOOT9"><sup>9</sup></a>, there is an alternative mechanism for mixing 32-bit and 64-bit libraries known as <em>multilib</em>. If the Linux distribution supports multilib, then parallel builds of R may be installed in the sub-directories <samp>lib</samp> (32-bit) and <samp>lib64</samp> (64-bit). The build to be run may then be selected using the <code>setarch</code> command. For example, a 32-bit build may be run by </p> <div class="example"> <pre class="example">setarch i686 R </pre></div> <p>The <code>setarch</code> 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 <code>setarch</code> command. </p> <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> <p>There is a potential problem with packages using Java, as the post-install for a ‘<samp>i686</samp>’ RPM on ‘<samp>x86_64</samp>’ Linux reconfigures Java and will find the ‘<samp>x86_64</samp>’ Java. If you know where a 32-bit Java is installed you may be able to run (as root) </p> <div class="example"> <pre class="example">export JAVA_HOME=<path to jre directory of 32-bit Java> setarch i686 R CMD javareconf </pre></div> <p>to get a suitable setting. </p> <p>When this mechanism is used, the version of <code>Rscript</code> in e.g. <samp>/usr/bin</samp> will be the last installed, but an architecture-specific version will be available in e.g. <samp>/usr/lib64/R/bin</samp>. Normally all installed architectures will run on the platform so the architecture of <code>Rscript</code> does not matter. </p> <hr> <a name="Other-Options"></a> <div class="header"> <p> Next: <a href="#Testing-a-Unix_002dalike-Installation" accesskey="n" rel="next">Testing a Unix-alike Installation</a>, Previous: <a href="#Sub_002darchitectures" accesskey="p" rel="previous">Sub-architectures</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Other-Options-1"></a> <h3 class="section">2.7 Other Options</h3> <p>There are many other installation options, most of which are listed by <code>configure --help</code>. Almost all of those not listed elsewhere in this manual are either standard <code>autoconf</code> options not relevant to R or intended for specialist uses by the R developers. </p> <p>One that may be useful when working on R itself is the option <samp>--disable-byte-compiled-packages</samp>, which ensures that the base and recommended packages are not byte-compiled. (Alternatively the (make or environment) variable <code>R_NO_BASE_COMPILE</code> can be set to a non-empty value for the duration of the build.) </p> <p>Option <samp>--with-internal-tzcode</samp> makes use of R’s own code and copy of the Olson database for managing timezones. This will be preferred where there are issues with the system implementation, usually involving times after 2037 or before 1916. An alternative time-zone directory<a name="DOCF10" href="#FOOT10"><sup>10</sup></a> can be used, pointed to by environment variable <code>TZDIR</code>: this should contain files such as <samp>Europe/London</samp>. On all tested OSes the system timezone was deduced correctly, but if necessary it can be set as the value of environment variable <code>TZ</code>. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Debugging-Symbols" accesskey="1">Debugging Symbols</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#OpenMP-Support" accesskey="2">OpenMP Support</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#C_002b_002b-Support" accesskey="3">C++ Support</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Debugging-Symbols"></a> <div class="header"> <p> Next: <a href="#OpenMP-Support" accesskey="n" rel="next">OpenMP Support</a>, Previous: <a href="#Other-Options" accesskey="p" rel="previous">Other Options</a>, Up: <a href="#Other-Options" accesskey="u" rel="up">Other Options</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Debugging-Symbols-1"></a> <h4 class="subsection">2.7.1 Debugging Symbols</h4> <p>By default, <code>configure</code> adds a flag (usually <samp>-g</samp>) to the compilation flags for C, Fortran and CXX sources. This will slow down compilation and increase object sizes of both R and packages, so it may be a good idea to change those flags (set ‘<samp>CFLAGS</samp>’ etc in <samp>config.site</samp> before configuring, or edit files <samp>Makeconf</samp> and <samp>etc/Makeconf</samp> between running <code>configure</code> and <code>make</code>). </p> <p>Having debugging symbols available is useful both when running R under a debugger (e.g., <code>R -d gdb</code>) and when using sanitizers and <code>valgrind</code>, all things intended for experts. </p> <p>Debugging symbols (and some others) can be ‘stripped’ on installation by using </p><div class="example"> <pre class="example">make install-strip </pre></div> <p>How well this is supported depends on the platform: it works best on those using GNU <code>binutils</code>. On ‘<samp>x86_64</samp>’ Linux a typical reduction in overall size was from 92MB to 66MB. On macOS debugging symbols are not by default included in <samp>.dylib</samp> and <samp>.so</samp> files, so there is negligible difference. </p> <hr> <a name="OpenMP-Support"></a> <div class="header"> <p> Next: <a href="#C_002b_002b-Support" accesskey="n" rel="next">C++ Support</a>, Previous: <a href="#Debugging-Symbols" accesskey="p" rel="previous">Debugging Symbols</a>, Up: <a href="#Other-Options" accesskey="u" rel="up">Other Options</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="OpenMP-Support-1"></a> <h4 class="subsection">2.7.2 OpenMP Support</h4> <p>By default <code>configure</code> searches for suitable flags<a name="DOCF11" href="#FOOT11"><sup>11</sup></a> for OpenMP support for the C, C++ (default standard) and Fortran compilers. </p> <p>Only the C result is currently used for R itself, and only if <code>MAIN_LD</code>/<code>DYLIB_LD</code> were not specified. This can be overridden by specifying </p><div class="example"> <pre class="example">R_OPENMP_CFLAGS </pre></div> <p>Use for packages has similar restrictions (involving <code>SHLIB_LD</code> and similar: note that as Fortran code is linked by the C (or C++) compiler, both need to support OpenMP) and can be overridden by specifying some of </p><div class="example"> <pre class="example">SHLIB_OPENMP_CFLAGS SHLIB_OPENMP_CXXFLAGS SHLIB_OPENMP_FFLAGS </pre></div> <p>Setting these to an empty value will disable OpenMP for that compiler (and configuring with <samp>--disable-openmp</samp> will disable all detection<a name="DOCF12" href="#FOOT12"><sup>12</sup></a> of OpenMP). The <code>configure</code> detection test is to compile and link a standalone OpenMP program, which is not the same as compiling a shared object and loading it into the C program of R’s executable. Note that overridden values are not tested. </p> <hr> <a name="C_002b_002b-Support"></a> <div class="header"> <p> Previous: <a href="#OpenMP-Support" accesskey="p" rel="previous">OpenMP Support</a>, Up: <a href="#Other-Options" accesskey="u" rel="up">Other Options</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="C_002b_002b-Support-1"></a> <h4 class="subsection">2.7.3 C++ Support</h4> <p>C++ is not used by R itself, but support is provided for installing packages with C++ code via <code>make</code> macros defined in file <samp>etc/Makeconf</samp> (and with explanations in file <samp>config.site</samp>): </p><div class="example"> <pre class="example">CXX CXXFLAGS CXXPICFLAGS CXXSTD CXX98 CXX98STD CXX98FLAGS CXX98PICFLAGS CXX11 CXX11STD CXX11FLAGS CXX11PICFLAGS CXX14 CXX14STD CXX14FLAGS CXX14PICFLAGS CXX17 CXX17STD CXX17FLAGS CXX17PICFLAGS </pre></div> <p>The macros <code>CXX</code> etc are those used by default for C++ code. <code>configure</code> will attempt to set the rest suitably, choosing for <code>CXX11STD</code> a suitable flag such as <samp>-std=c++11</samp> for C++11 support. Similarly, configure will if possible choose for <code>CXX14STD</code> a flag<a name="DOCF13" href="#FOOT13"><sup>13</sup></a> such as <samp>-std=c++14</samp> for C++14 support and <samp>-std=c++17</samp> or <samp>-std=c++1z</samp> for support for the C++17 standard. The inferred values can be overridden in file <samp>config.site</samp> or on the <code>configure</code> command line: user-supplied values will be tested by compiling some C++11/14/17 code. </p> <p>R versions 3.1.0 to 3.3.3 used <code>CXX1X</code> rather than <code>CXX11</code>: these forms were deprecated in 3.4.4 and removed in 3.6.0. </p> <p>It may be<a name="DOCF14" href="#FOOT14"><sup>14</sup></a> that there is no suitable flag for C++11 support, in which case a different compiler could be selected for <code>CXX11</code> and its corresponding flags. Likewise, a different compiler can be specified for C++14 support with <code>CXX14</code> and for C++17 support with <code>CXX17</code>. Some compilers<a name="DOCF15" href="#FOOT15"><sup>15</sup></a> by default assume a later standard than C++98 whereas the latter has been assumed by some packages. So users of GCC 6 might like to specify </p><div class="example"> <pre class="example">CXX='g++ -std=gnu++98' CXX11=g++ CXX11STD='-std=c++11' CXX14=g++ CXX14STD='-std=c++14' </pre></div> <p>The <samp>-std</samp> flag is supported by the GCC, <code>clang++</code>, Intel and Solaris compilers (the latter from version 12.4). Currently accepted values are (plus some synonyms) </p><div class="example"> <pre class="example">g++: c++98 gnu++98 c++11 gnu+11 c++14 gnu++14 c++17 gnu++17 Intel: gnu+98 c++11 c++14 (from 16.0) c++17 (from 17.0) Solaris: c++03 c++11 c++14 (from 12.5) </pre></div> <p>(Those for <code>clang++</code> are not documented, but seem to be based on <code>g++</code>.) Versions 4.3.x to 4.8.x of <code>g++</code> accepted flag <samp>-std=c++0x</samp> with partial support<a name="DOCF16" href="#FOOT16"><sup>16</sup></a> for C++11: this is currently still accepted as a deprecated synonym for <samp>-std=c++11</samp>. (At least for versions 4.8.x it has sufficient support to be picked by <code>configure</code>.) Option <samp>-std=c++14</samp> was introduced in version 5.x. </p> <p>‘Standards’ for <code>g++</code> starting with ‘<samp>gnu</samp>’ enable ‘GNU extensions’: what those are is hard to track down. </p> <p>For the use of C++11 and later in R packages see the ‘Writing R Extensions’ manual. Prior to R 3.6.0 the default C++ standard was that of the compiler used: currently it is C++11 if supported by the compiler: this can be overridden by setting ‘<samp>CXXSTD</samp>’ when R is configured, for example to ‘<samp>-std=gnu++14</samp>’. </p> <hr> <a name="Testing-a-Unix_002dalike-Installation"></a> <div class="header"> <p> Previous: <a href="#Other-Options" accesskey="p" rel="previous">Other Options</a>, Up: <a href="#Installing-R-under-Unix_002dalikes" accesskey="u" rel="up">Installing R under Unix-alikes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Testing-an-Installation"></a> <h3 class="section">2.8 Testing an Installation</h3> <p>Full post-installation testing is possible only if the test files have been installed with </p> <div class="example"> <pre class="example">make install-tests </pre></div> <p>which populates a <samp>tests</samp> directory in the installation. </p> <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 RHOME</code> or from R as <code>R.home()</code>) and run </p> <div class="example"> <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></div> <p>and other useful targets are <code>test-BasePackages</code> and <code>test-Recommended</code> to run tests of the standard and recommended packages (if installed) respectively. </p> <p>This re-runs all the tests relevant to the installed R (including for example the 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> <p>Parallel checking of packages may be possible: set the environment variable <code>TEST_MC_CORES</code> to the maximum number of processes to be run in parallel. This affects both checking the package examples (part of <code>make check</code>) and package sources (part of <code>make check-devel</code> and <code>make check-recommended</code>). It does require a <code>make</code> command which supports the <code>make -j <var>n</var></code> option: most do but on Solaris you need to select GNU <code>make</code> or <code>dmake</code>. </p> <p>Alternatively, the installed R can be run, preferably with <samp>--vanilla</samp>. Then <a name="index-LC_005fCOLLATE"></a> </p> <div class="example"> <pre class="example">Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en") tools::testInstalledBasic("both") tools::testInstalledPackages(scope = "base") tools::testInstalledPackages(scope = "recommended") </pre></div> <p>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>tests</samp> folder of the R home directory and run fewer tests than the first approach: in particular they do not test things which need Internet access—that can be tested by </p><div class="example"> <pre class="example">tools::testInstalledBasic("internet") </pre></div> <p>These tests work best if <code>diff</code> (in <samp>Rtools*.exe</samp> for Windows users) is in the path. </p> <p>It is possible to test the installed packages (but not their package-specific tests) by <code>testInstalledPackages</code> even if <code>make install-tests</code> was not run. </p> <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 (before starting the R session) </p> <div class="example"> <pre class="example">LANGUAGE=en </pre></div> <p>and use a UTF-8 or Latin-1 locale. </p> <hr> <a name="Installing-R-under-Windows"></a> <div class="header"> <p> Next: <a href="#Installing-R-under-macOS" accesskey="n" rel="next">Installing R under macOS</a>, Previous: <a href="#Installing-R-under-Unix_002dalikes" accesskey="p" rel="previous">Installing R under Unix-alikes</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Installing-R-under-Windows-1"></a> <h2 class="chapter">3 Installing R under Windows</h2> <a name="index-Installing-under-Windows"></a> <p>The <samp>bin/windows</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 32- or 64-bit Windows (Windows 7 and later are tested; XP is known to fail some tests) on ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’ <acronym>CPU</acronym>s. </p> <p>Your file system must allow long file names (as is likely except perhaps for some network-mounted systems). If it doesn’t also support conversion to short name equivalents (a.k.a. DOS 8.3 names), then R <em>must</em> be installed in a path that does not contain spaces. </p> <p>Installation is <em>via</em> the installer <samp>R-3.6.0-win.exe</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> <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> <p>See the <a href="https://CRAN.R-project.org/bin/windows/base/rw-FAQ.html">R Windows <acronym>FAQ</acronym></a> for more details on the binary installer. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Building-from-source" accesskey="1">Building from source</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Testing-a-Windows-Installation" accesskey="2">Testing a Windows Installation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Building-from-source"></a> <div class="header"> <p> Next: <a href="#Testing-a-Windows-Installation" accesskey="n" rel="next">Testing a Windows Installation</a>, Previous: <a href="#Installing-R-under-Windows" accesskey="p" rel="previous">Installing R under Windows</a>, Up: <a href="#Installing-R-under-Windows" accesskey="u" rel="up">Installing R under Windows</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-from-source-1"></a> <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> <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>.exe</samp> and <samp>.dll</samp> files and some configuration files in the <samp>etc</samp> directory. </p> <p>Building is only tested in a 8-bit locale: using a multi-byte locale (as used for CJK languages) is unsupported and may not work (the scripts do try to select a ‘<samp>C</samp>’ locale; Windows may not honour this). </p> <p><strong>NB:</strong> The build process is currently being changed to require external binary distributions of third-party software. Their location is set using macro <code>EXT_LIBS</code> with default setting <samp>$(LOCAL_SOFT)</samp>; the $(LOCAL_SOFT) macro defaults to <samp>$(R_HOME)/extsoft</samp>. This directory can be populated using <code>make rsync-extsoft</code>. The location can be overridden by setting <code>EXT_LIBS</code> to a different path in <samp>src/gnuwin32/MkRules.local</samp>. A suitable collection of files can also be obtained from <a href="https://CRAN.R-project.org/bin/windows/extsoft">https://CRAN.R-project.org/bin/windows/extsoft</a> or <a href="https://www.stats.ox.ac.uk/pub/Rtools/libs.html">https://www.stats.ox.ac.uk/pub/Rtools/libs.html</a>. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Getting-the-tools" accesskey="1">Getting the tools</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Getting-the-source-files" accesskey="2">Getting the source files</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-the-core-files" accesskey="3">Building the core files</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-the-cairo-devices-files" accesskey="4">Building the cairo devices files</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Using-ICU-for-collation" accesskey="5">Using ICU for collation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Support-for-libcurl" accesskey="6">Support for libcurl</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Checking-the-build" accesskey="7">Checking the build</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-the-manuals" accesskey="8">Building the manuals</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-the-Inno-Setup-installer" accesskey="9">Building the Inno Setup installer</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-the-MSI-installer">Building the MSI installer</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#g_t64_002dbit-Windows-builds">64-bit Windows builds</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Getting-the-tools"></a> <div class="header"> <p> Next: <a href="#Getting-the-source-files" accesskey="n" rel="next">Getting the source files</a>, Previous: <a href="#Building-from-source" accesskey="p" rel="previous">Building from source</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Getting-the-tools-1"></a> <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="https://CRAN.R-project.org/bin/windows/Rtools/">https://CRAN.R-project.org/bin/windows/Rtools/</a>) for details. </p> <p>The <samp>Rtools*.exe</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>C:/R</samp>. The directory name <em>should not contain spaces</em>. We will call this directory <samp><var>R_HOME</var></samp> below. </p> <hr> <a name="Getting-the-source-files"></a> <div class="header"> <p> Next: <a href="#Building-the-core-files" accesskey="n" rel="next">Building the core files</a>, Previous: <a href="#Getting-the-tools" accesskey="p" rel="previous">Getting the tools</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Getting-the-source-files-1"></a> <h4 class="subsection">3.1.2 Getting the source files</h4> <p>You need to collect the following sets of files: </p><ul> <li> Get the R source code tarball <samp>R-3.6.0.tar.gz</samp> from <acronym>CRAN</acronym>. Open a command window (or another shell) at directory <var>R_HOME</var>, and run <div class="example"> <pre class="example">tar -xf R-3.6.0.tar.gz </pre></div> <p>to create the source tree in <var>R_HOME</var>. <strong>Beware</strong>: do use <code>tar</code> 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 </p> <div class="example"> <pre class="example">tar --no-same-owner -xf R-3.6.0.tar.gz </pre></div> <a name="index-TAR_005fOPTIONS-1"></a> <p>or perhaps better, set the environment variable <code>TAR_OPTIONS</code> to the value ‘<samp>--no-same-owner --no-same-permissions</samp>’. </p> <p>It is also possible to obtain the source code using Subversion; see <a href="#Obtaining-R">Obtaining R</a> for details. </p> </li><li> If you are not using a tarball you need to obtain copies of the recommended packages from <acronym>CRAN</acronym>. Put the <samp>.tar.gz</samp> files in <samp><var>R_HOME</var>/src/library/Recommended</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>/src/gnuwin32</samp> <div class="example"> <pre class="example">make rsync-recommended </pre></div> </li><li> The binary distributions of external software. Download <div class="example"> <pre class="example">https://www.stats.ox.ac.uk/pub/Rtools/goodies/multilib/local323.zip </pre></div> <p>(or a more recent version if appropriate), create an empty directory, say <samp>c:/R/extsoft</samp>, and unpack it in that directory by e.g. </p> <div class="example"> <pre class="example">unzip local323.zip -d c:/R/extsoft </pre></div> </li><li> Make a local copy of the configuration rules by <div class="example"> <pre class="example">cd <var>R_HOME</var>/src/gnuwin32 cp MkRules.dist MkRules.local </pre></div> <p>and edit <samp>MkRules.local</samp>, uncommenting <code>EXT_LIBS</code> and setting it to the appropriate path (in our example <samp>c:/R/extsoft</samp>). </p> <p>Look through the file <samp>MkRules.local</samp> and make any other changes needed: in particular, this is where a 64-bit build is selected and the locations are set of external software for ICU collation and the cairo-based devices. </p> </li></ul> <p>The following additional item is normally installed by <samp>Rtools*.exe</samp>. If instead you choose to do a completely manual build you will also need </p> <ul> <li> The Tcl/Tk support files are contained in <samp>Rtools*.exe</samp>. 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>Tcl</samp> there. </li></ul> <hr> <a name="Building-the-core-files"></a> <div class="header"> <p> Next: <a href="#Building-the-cairo-devices-files" accesskey="n" rel="next">Building the cairo devices files</a>, Previous: <a href="#Getting-the-source-files" accesskey="p" rel="previous">Getting the source files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-the-core-files-1"></a> <h4 class="subsection">3.1.3 Building the core files</h4> <a name="index-TMPDIR-1"></a> <p>Set the environment variable <code>TMPDIR</code> to the absolute path to a writable directory, with a path specified with forward slashes and no spaces. (The default is <samp>/tmp</samp>, which may not be useful on Windows.) </p> <p>You may need to compile under a case-honouring file system: we found that a <code>samba</code>-mounted file system (which maps all file names to lower case) did not work. </p> <p>Open a command window at <samp><var>R_HOME</var>/src/gnuwin32</samp>, then run </p> <div class="example"> <pre class="example">make all recommended vignettes </pre></div> <p>and sit back and wait while the basic compile takes place. </p> <p>Notes: </p><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><li> You can run a parallel make by e.g. <div class="example"> <pre class="example">make -j4 all make -j4 recommended make vignettes </pre></div> <p>but this is only likely to be worthwhile on a multi-core machine with ample memory, and is not 100% reliable. </p> </li><li> It is possible (mainly for those working on R itself) to set the (make or environment) variable <code>R_NO_BASE_COMPILE</code> to a non-empty value, which inhibits the byte-compilation of the base and recommended packages. </li></ul> <hr> <a name="Building-the-cairo-devices-files"></a> <div class="header"> <p> Next: <a href="#Using-ICU-for-collation" accesskey="n" rel="next">Using ICU for collation</a>, Previous: <a href="#Building-the-core-files" accesskey="p" rel="previous">Building the core files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-the-cairo-devices"></a> <h4 class="subsection">3.1.4 Building the cairo devices</h4> <a name="index-winCairo_002edll"></a> <p>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>winCairo.dll</samp> which is loaded when one of these devices is first used. It is not built by default, and needs to be built (after <code>make all</code>) by <code>make cairodevices</code>. </p> <p>To enable the building of these devices you need to install the static cairographics libraries built by Simon Urbanek at <a href="https://www.rforge.net/Cairo/files/cairo-current-win.tar.gz">https://www.rforge.net/Cairo/files/cairo-current-win.tar.gz</a>. Set the macro ‘<samp>CAIRO_HOME</samp>’ in <samp>MkRules.local</samp>. (Note that this tarball unpacks with a top-level directory <samp>src/</samp>: ‘<samp>CAIRO_HOME</samp>’ needs to include that directory in its path.) </p> <hr> <a name="Using-ICU-for-collation"></a> <div class="header"> <p> Next: <a href="#Support-for-libcurl" accesskey="n" rel="next">Support for libcurl</a>, Previous: <a href="#Building-the-cairo-devices-files" accesskey="p" rel="previous">Building the cairo devices files</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Using-ICU-for-collation-1"></a> <h4 class="subsection">3.1.5 Using ICU for collation</h4> <p>It is recommended to build R to support ICU (International Components for Unicode, <a href="http://site.icu-project.org/">http://site.icu-project.org/</a>) for collation, as is commonly done on Unix-alikes. </p> <p>Two settings are needed in <samp>MkRules.local</samp>, </p><div class="example"> <pre class="example"># set to use ICU # USE_ICU = YES # path to parent of ICU headers ICU_PATH = /path/to/ICU </pre></div> <p>The first should be uncommented and the second set to the top-level directory of a suitably packaged binary build of ICU, for example that at <a href="https://www.stats.ox.ac.uk/pub/Rtools/goodies/ICU_531.zip">https://www.stats.ox.ac.uk/pub/Rtools/goodies/ICU_531.zip</a>. Depending on the build, it may be necessary to edit the macro <code>ICU_LIBS</code>. </p> <p>Unlike on a Unix-alike, it is normally necessary to call <code>icuSetCollate</code> to set a locale before ICU is actually used for collation, or set the environment variable <code>R_ICU_LOCALE</code>. </p> <hr> <a name="Support-for-libcurl"></a> <div class="header"> <p> Next: <a href="#Checking-the-build" accesskey="n" rel="next">Checking the build</a>, Previous: <a href="#Using-ICU-for-collation" accesskey="p" rel="previous">Using ICU for collation</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Support-for-libcurl-1"></a> <h4 class="subsection">3.1.6 Support for libcurl</h4> <p><code>libcurl</code> version 7.28.0 or later is used to support <code>curlGetHeaders</code> and the <code>"libcurl"</code> methods of <code>download.file</code> and <code>url</code>. </p> <p>A suitable distribution can be found <em>via</em> <a href="https://www.stats.ox.ac.uk/pub/Rtools/libs.html">https://www.stats.ox.ac.uk/pub/Rtools/libs.html</a> and its unpacked location should be specified in file <samp>MkRules.local</samp>. </p> <p>For secure use of e.g. ‘<samp>https://</samp>’ URLs Windows users may need to specify the path to up-to-date <em>CA root certificates</em>: see <code>?download.file</code>. </p> <hr> <a name="Checking-the-build"></a> <div class="header"> <p> Next: <a href="#Building-the-manuals" accesskey="n" rel="next">Building the manuals</a>, Previous: <a href="#Support-for-libcurl" accesskey="p" rel="previous">Support for libcurl</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Checking-the-build-1"></a> <h4 class="subsection">3.1.7 Checking the build</h4> <p>You can test a build by running </p> <div class="example"> <pre class="example">make check </pre></div> <p>The recommended packages can be checked by </p> <div class="example"> <pre class="example">make check-recommended </pre></div> <p>Other levels of checking are </p> <div class="example"> <pre class="example">make check-devel </pre></div> <p>for a more thorough check of the R functionality, and </p> <div class="example"> <pre class="example">make check-all </pre></div> <p>for both <code>check-devel</code> and <code>check-recommended</code>. </p> <p>If a test fails, there will almost always be a <samp>.Rout.fail</samp> file in the directory being checked (often <samp>tests/Examples</samp> or <samp>tests</samp>): examine the file to help pinpoint the problem. </p> <p>Parallel checking of package sources (part of <code>make check-devel</code> and <code>make check-recommended</code>) is possible: see the environment variable <code>TEST_MC_CORES</code> to the maximum number of processes to be run in parallel. </p> <hr> <a name="Building-the-manuals"></a> <div class="header"> <p> Next: <a href="#Building-the-Inno-Setup-installer" accesskey="n" rel="next">Building the Inno Setup installer</a>, Previous: <a href="#Checking-the-build" accesskey="p" rel="previous">Checking the build</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-the-manuals-1"></a> <h4 class="subsection">3.1.8 Building the manuals</h4> <p>The PDF manuals require <strong>texinfo</strong> 5.1 or later, and can be made by </p> <div class="example"> <pre class="example">make manuals </pre></div> <p>If you want to make the info versions (not including the Reference Manual), use </p> <div class="example"> <pre class="example">cd ../../doc/manual make -f Makefile.win info </pre></div> <p>(all assuming you have <code>pdftex</code>/<code>pdflatex</code> installed and in your path). </p> <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. </p> <p>By default it is assumed that <strong>texinfo</strong> is not installed, and the manuals will not be built. The comments in file <samp>MkRules.dist</samp> describe settings to build them. (Copy that file to <samp>MkRules.local</samp> and edit it.) The <strong>texinfo</strong> 5.x package for use on Windows is available at <a href="https://www.stats.ox.ac.uk/pub/Rtools/">https://www.stats.ox.ac.uk/pub/Rtools/</a>: you will also need to install <code>Perl</code><a name="DOCF17" href="#FOOT17"><sup>17</sup></a> </p> <hr> <a name="Building-the-Inno-Setup-installer"></a> <div class="header"> <p> Next: <a href="#Building-the-MSI-installer" accesskey="n" rel="next">Building the MSI installer</a>, Previous: <a href="#Building-the-manuals" accesskey="p" rel="previous">Building the manuals</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-the-Inno-Setup-installer-1"></a> <h4 class="subsection">3.1.9 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 (which requires <strong>texinfo</strong> installed), as well as the recommended packages and Inno Setup (see <a href="#The-Inno-Setup-installer">The Inno Setup installer</a>). </p> <p>Once everything is set up </p> <div class="example"> <pre class="example">make distribution make check-all </pre></div> <p>will make all the pieces and the installer and put them in the <samp>gnuwin32/cran</samp> subdirectory, then check the build. This works by building all the parts in the sequence: </p> <div class="example"> <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> 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 <code>svn</code> 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></div> <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>Makefile</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 <code>make</code> (or <code>make all</code>) is run. </p> <p>Parallel make is not supported and likely to fail. </p> <p>If you want to customize the installation by adding extra packages, replace <code>make rinstaller</code> by something like </p> <div class="example"> <pre class="example">make rinstaller EXTRA_PKGS='pkg1 pkg2 pkg3' </pre></div> <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>MkRules</samp>, possibly <em>via</em> <samp>MkRules.local</samp>, and having made R in the source tree) in <samp>src/gnuwin32/installer</samp> run </p> <div class="example"> <pre class="example">make myR IMAGEDIR=rootdir </pre></div> <p>where <samp>rootdir</samp> is the path to the root of the customized installation (in double quotes if it contains spaces or backslashes). </p> <p>Both methods create an executable with a standard name such as <samp>R-3.6.0-win.exe</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 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> <p>The defaults for the startup parameters may also be customized. For example </p> <div class="example"> <pre class="example">make myR IMAGEDIR=rootdir MDISDI=1 </pre></div> <p>will create an installer that defaults to installing R to run in SDI mode. See <samp>src/gnuwin32/installer/Makefile</samp> for the names and values that can be set. </p> <p>The standard <acronym>CRAN</acronym> distribution of a 32/64-bit installer is made by first building 32-bit R (just </p> <div class="example"> <pre class="example">make 32-bit </pre></div> <p>is needed), and then (in a separate directory) building 64-bit R with the macro <code>HOME32</code> set in file <samp>MkRules.local</samp> to the top-level directory of the 32-bit build. Then the <code>make rinstaller</code> step copies the files that differ between architectures from the 32-bit build as it builds the installer image. </p> <hr> <a name="Building-the-MSI-installer"></a> <div class="header"> <p> Next: <a href="#g_t64_002dbit-Windows-builds" accesskey="n" rel="next">64-bit Windows builds</a>, Previous: <a href="#Building-the-Inno-Setup-installer" accesskey="p" rel="previous">Building the Inno Setup installer</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-the-MSI-installer-1"></a> <h4 class="subsection">3.1.10 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> <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://wixtoolset.org/">http://wixtoolset.org/</a>. Once WiX is installed, set the path to its home directory in <samp>MkRules.local</samp>. </p> <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>etc/Rconsole</samp> and <samp>etc/Rprofile.site</samp> to set these as required. Then </p> <div class="example"> <pre class="example">cd installer make msi </pre></div> <p>which will result in a file with a name like <samp>R-3.6.0-win32.msi</samp>. This can be double-clicked to be installed, but those who need it will know what to do with it (usually by running <code>msiexec /i</code> with additional options). Properties that users might want to set from the <code>msiexec</code> command line include ‘<samp>ALLUSERS</samp>’, ‘<samp>INSTALLDIR</samp>’ (something like <samp>c:\Program Files\R\R-3.6.0</samp>) and ‘<samp>RMENU</samp>’ (the path to the ‘<samp>R</samp>’ folder on the start menu) and ‘<samp>STARTDIR</samp>’ (the starting directory for R shortcuts, defaulting to something like <samp>c:\Users\name\Documents\R</samp>). </p> <p>The MSI installer can be built both from a 32-bit build of R (<samp>R-3.6.0-win32.msi</samp>) and from a 64-bit build of R (<samp>R-3.6.0-win64.msi</samp>, optionally including 32-bit files by setting the macro <code>HOME32</code>, when the name is <samp>R-3.6.0-win.msi</samp>). Unlike the main installer, a 64-bit MSI installer can only be run on 64-bit Windows. </p> <p>Thanks to David del Campo (Dept of Statistics, University of Oxford) for suggesting WiX and building a prototype installer. </p> <hr> <a name="g_t64_002dbit-Windows-builds"></a> <div class="header"> <p> Previous: <a href="#Building-the-MSI-installer" accesskey="p" rel="previous">Building the MSI installer</a>, Up: <a href="#Building-from-source" accesskey="u" rel="up">Building from source</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="g_t64_002dbit-Windows-builds-1"></a> <h4 class="subsection">3.1.11 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> <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> <p>Windows 64-bit is now completely integrated into the R and package build systems: a 64-bit build is selected in file <samp>MkRules.local</samp>. </p> <hr> <a name="Testing-a-Windows-Installation"></a> <div class="header"> <p> Previous: <a href="#Building-from-source" accesskey="p" rel="previous">Building from source</a>, Up: <a href="#Installing-R-under-Windows" accesskey="u" rel="up">Installing R under Windows</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Testing-an-Installation-1"></a> <h3 class="section">3.2 Testing an Installation</h3> <p>The Windows installer contains a set of test files used when building R. </p> <p>The <code>Rtools</code> are not needed to run these tests, but more comprehensive analysis of errors will be given if <code>diff</code> is in the path (and <code>errorsAreFatal = FALSE</code> is then not needed below). </p> <p>Launch either <code>Rgui</code> or <code>Rterm</code>, preferably with <samp>--vanilla</samp>. Then run </p> <div class="example"> <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></div> <p>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>tests</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> <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. </p> <hr> <a name="Installing-R-under-macOS"></a> <div class="header"> <p> Next: <a href="#Running-R" accesskey="n" rel="next">Running R</a>, Previous: <a href="#Installing-R-under-Windows" accesskey="p" rel="previous">Installing R under Windows</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Installing-R-under-macOS-1"></a> <h2 class="chapter">4 Installing R under macOS</h2> <a name="index-macOS-1"></a> <p>(‘macOS’ was known as ‘OS X’ from 2012–2016 and as ‘Mac OS X’ before that.) </p> <p>The front page of a <acronym>CRAN</acronym> site has a link ‘Download R for (Mac) OS X’. Click on that, then download the file <samp>R-3.6.0.pkg</samp> and install it. This runs on macOS 10.11 and later (El Capitan, Sierra, High Sierra, Mojave, …). </p> <p>Installers for R-patched and R-devel are usually available from <a href="https://mac.R-project.org">https://mac.R-project.org</a>. (Some of these packages are unsigned: to install those Control/right/two-finger click, select ‘<samp>Open with</samp>’ and ‘<samp>Installer</samp>’.) </p> <p>For some older versions of the OS you can in principle (it is little tested) install R from the sources (see <a href="#macOS">macOS</a>). </p> <p>It is important that if you use a binary installer package that your OS is fully updated: look at ‘Updates’ from the ‘App Store’ to be sure. (If using XQuartz, check that is current.) </p> <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 four components: everyone will need the ‘R Framework’ component: the remaining components are optional. (The ‘Tcl/Tk’ component is needed to use package <strong>tcltk</strong>. The ‘Texinfo’ component is only needed by those installing source packages or R from its sources.) </p> <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. Note the the installer is clever enough to try to upgrade the last-installed version of the application where you installed it (which may not be where you want this time …). </p> <p>Various parts of the build require XQuartz to be installed: see <a href="https://xquartz.macosforge.org/">https://xquartz.macosforge.org/</a>. These include the <strong>tcltk</strong> package and the <code>X11</code> device: attempting to use these without XQuartz will remind you. Also for the cairographics-based devices (which are not often used on macOS) such as <code>png(type = "cairo")</code>. </p> <p>If you update your macOS version, you should re-install R (and perhaps XQuartz): the installer may tailor the installation to the current version of the OS. </p> <p>For building R from source, see <a href="#macOS">macOS</a>. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Running-R-under-macOS" accesskey="1">Running R under macOS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Uninstalling-under-macOS" accesskey="2">Uninstalling under macOS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Multiple-versions" accesskey="3">Multiple versions</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Running-R-under-macOS"></a> <div class="header"> <p> Next: <a href="#Uninstalling-under-macOS" accesskey="n" rel="next">Uninstalling under macOS</a>, Previous: <a href="#Installing-R-under-macOS" accesskey="p" rel="previous">Installing R under macOS</a>, Up: <a href="#Installing-R-under-macOS" accesskey="u" rel="up">Installing R under macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Running-R-under-macOS-1"></a> <h3 class="section">4.1 Running R under macOS</h3> <p>There are two ways to run R on macOS from a <acronym>CRAN</acronym> binary distribution. </p> <p>There is a GUI console normally installed with the R icon in <samp>/Applications</samp> which you can run by double-clicking (e.g. from Launchpad or Finder). (If you cannot find it there it was possibly installed elsewhere so try searching for it in Spotlight.) This is usually referred to as <small>R.APP</small> to distinguish it from command-line R: its user manual is currently part of the macOS FAQ at <a href="https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html">https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html</a> and can be viewed from <small>R.APP</small>’s ‘Help’ menu. </p> <p>You can run command-line R and <code>Rscript</code> from a Terminal<a name="DOCF18" href="#FOOT18"><sup>18</sup></a> so these can be typed as commands 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 location of the personal library directory (under <samp>~/Library/R</samp>, e.g. <samp>~/Library/R/3.6/library</samp>), and that warnings, messages and other output to <samp>stderr</samp> are highlighted in bold. </p> <p>It has been reported that running <small>R.APP</small> may fail if no preferences are stored, so if it fails when launched for the very first time, try it again (the first attempt will store some preferences). </p> <p>Users of <small>R.APP</small> need to be aware of the ‘App Nap’ feature (<a href="https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html">https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html</a>) which can cause R tasks to appear to run very slowly when not producing output in the console. Here are ways to avoid it: </p> <ul> <li> Ensure that the console is completely visible (or at least the activity indicator at the top right corner is visible). </li><li> In a Terminal, run <div class="example"> <pre class="example">defaults write org.R-project.R NSAppSleepDisabled -bool YES </pre></div> <p>(see <a href="https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html">https://developer.apple.com/library/mac/releasenotes/MacOSX/WhatsNewInOSX/Articles/MacOSX10_9.html</a>). </p></li></ul> <p>Using the <code>X11</code> device or the X11-based versions of <code>View()</code> and <code>edit()</code> for data frames and matrices (the latter are the default for command-line R but not <small>R.APP</small>) requires an X sub-system to be installed: see <a href="#macOS">macOS</a>. So do the <strong>tcltk</strong> package and some third-party packages. </p> <hr> <a name="Uninstalling-under-macOS"></a> <div class="header"> <p> Next: <a href="#Multiple-versions" accesskey="n" rel="next">Multiple versions</a>, Previous: <a href="#Running-R-under-macOS" accesskey="p" rel="previous">Running R under macOS</a>, Up: <a href="#Installing-R-under-macOS" accesskey="u" rel="up">Installing R under macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Uninstalling-under-macOS-1"></a> <h3 class="section">4.2 Uninstalling under macOS</h3> <p>R for macOS consists of two parts: the GUI (<small>R.APP</small>) and the R framework. The un-installation is as simple as removing those folders (e.g. by dragging them onto the Trash). The typical installation will install the GUI into the <samp>/Applications/R.app</samp> folder and the R framework into the <samp>/Library/Frameworks/R.framework</samp> folder. The links to <samp>R</samp> and <samp>Rscript</samp> in <samp>/usr/local/bin</samp> should also be removed. </p> <p>If you want to get rid of R more completely using a Terminal, simply run: </p> <div class="example"> <pre class="example">sudo rm -Rf /Library/Frameworks/R.framework /Applications/R.app \ /usr/local/bin/R /usr/local/bin/Rscript </pre></div> <p>The installation consists of up to four Apple packages:<a name="DOCF19" href="#FOOT19"><sup>19</sup></a> <code>org.r-project.R.el-capitan.fw.pkg</code>, <code>org.r-project.R.el-capitan.GUI.pkg</code>, <code>org.r-project.x86_64.tcltk.x11</code> and <code>org.r-project.x86_64.texinfo</code>. You can use <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> <p>Uninstalling the Tcl/Tk or Texinfo components (which are installed under <samp>/usr/local</samp>) is not as simple. You can list the files they installed in a Terminal by </p> <div class="example"> <pre class="example">pkgutil --files org.r-project.x86_64.tcltk.x11 pkgutil --files org.r-project.x86_64.texinfo </pre></div> <p>These are paths relative to <samp>/</samp>, the root of the file system. </p> <hr> <a name="Multiple-versions"></a> <div class="header"> <p> Previous: <a href="#Uninstalling-under-macOS" accesskey="p" rel="previous">Uninstalling under macOS</a>, Up: <a href="#Installing-R-under-macOS" accesskey="u" rel="up">Installing R under macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Multiple-versions-1"></a> <h3 class="section">4.3 Multiple versions</h3> <p>The installer will remove any previous version<a name="DOCF20" href="#FOOT20"><sup>20</sup></a> of the R framework which it finds installed. This can be avoided by using <code>pkgutil --forget</code> (see the previous section). However, note that different versions are installed under <samp>/Library/Frameworks/R.framework/Versions</samp> as <samp>3.5</samp>, <samp>3.6</samp> and so on, so it is not possible to have different ‘<samp>3.x.y</samp>’ versions installed for the same ‘<samp>x</samp>’. </p> <p>A version of R can be run directly from the command-line as e.g. </p><div class="example"> <pre class="example">/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R </pre></div> <p>However, <small>R.APP</small> will always run the ‘current’ version, that is the last installed version. A small utility, <code>Rswitch.app</code> (available at <a href="https://mac.R-project.org/#other">https://mac.R-project.org/#other</a>), can be used to change the ‘current’ version. This is of limited use as <small>R.APP</small> 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 <small>R.APP</small>) and then switch back to the release version. </p> <hr> <a name="Running-R"></a> <div class="header"> <p> Next: <a href="#Add_002don-packages" accesskey="n" rel="next">Add-on packages</a>, Previous: <a href="#Installing-R-under-macOS" accesskey="p" rel="previous">Installing R under macOS</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Running-R-1"></a> <h2 class="chapter">5 Running R</h2> <p>How to start R and what command-line options are available is discussed in <a href="http://cran.r-project.org/doc/manuals//R-intro.html#Invoking-R">Invoking R</a> in <cite>An Introduction to R</cite>. </p> <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 should have default limits at least as large as these, but apparently NetBSD may not. Use the shell command <code>ulimit</code> (<code>sh</code>/<code>bash</code>) or <code>limit</code> (<code>csh</code>/<code>tcsh</code>) to check.) </p> <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>/etc/Renviron</samp> (there are none set by default on Windows and hence no such file). These are set at <code>configure</code> time, and you would not normally want to <a name="index-R_005fPAPERSIZE-1"></a> change them – a possible exception is <code>R_PAPERSIZE</code> (see <a href="#Setting-paper-size">Setting paper size</a>). The paper size will be deduced from the ‘<samp>LC_PAPER</samp>’ locale category if it exists and <code>R_PAPERSIZE</code> is unset, and this will normally produce the right choice from ‘<samp>a4</samp>’ and ‘<samp>letter</samp>’ on modern Unix-alikes (but can always be overridden by setting <code>R_PAPERSIZE</code>). </p> <p>Various environment variables can be set to determine where R creates its per-session temporary directory. The environment variables <a name="index-TMPDIR-2"></a> <a name="index-TMP"></a> <a name="index-TEMP"></a> <code>TMPDIR</code>, <code>TMP</code> and <code>TEMP</code> 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>/tmp</samp> on Unix-alikes and the value of <a name="index-R_005fUSER"></a> <code>R_USER</code> on Windows. The path should be an absolute path not containing spaces (and it is best to avoid non-alphanumeric characters such as <code>+</code>). </p> <p>Some Unix-alike systems are set up to remove files and directories periodically from <samp>/tmp</samp>, for example by a <code>cron</code> job <a name="index-TMPDIR-3"></a> running <code>tmpwatch</code>. Set <code>TMPDIR</code> to another directory before starting long-running jobs on such a system. </p> <p>Note that <code>TMPDIR</code> will be used to execute <code>configure</code> scripts when installing packages, so if <samp>/tmp</samp> has been mounted as ‘<samp>noexec</samp>’, <code>TMPDIR</code> needs to be set to a directory from which execution is allowed. </p> <hr> <a name="Add_002don-packages"></a> <div class="header"> <p> Next: <a href="#Internationalization" accesskey="n" rel="next">Internationalization</a>, Previous: <a href="#Running-R" accesskey="p" rel="previous">Running R</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Add_002don-packages-1"></a> <h2 class="chapter">6 Add-on packages</h2> <a name="index-Packages"></a> <a name="index-Libraries"></a> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Default-packages" accesskey="1">Default packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Managing-libraries" accesskey="2">Managing libraries</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Installing-packages" accesskey="3">Installing packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Updating-packages" accesskey="4">Updating packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Removing-packages" accesskey="5">Removing packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Setting-up-a-package-repository" accesskey="6">Setting up a package repository</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Checking-installed-source-packages" accesskey="7">Checking installed source packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <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>/library</samp>, but others can be used, for example by <a name="index-R_005fLIBS"></a> setting the environment variable <code>R_LIBS</code> or using the R function <code>.libPaths()</code>. To avoid any confusion you will often see a library directory referred to as a ‘library tree’. </p> <hr> <a name="Default-packages"></a> <div class="header"> <p> Next: <a href="#Managing-libraries" accesskey="n" rel="next">Managing libraries</a>, Previous: <a href="#Add_002don-packages" accesskey="p" rel="previous">Add-on packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Default-packages-1"></a> <h3 class="section">6.1 Default packages</h3> <a name="index-Packages_002c-default"></a> <p>The set of packages loaded on startup is by default </p> <div class="example"> <pre class="example">> getOption("defaultPackages") [1] "datasets" "utils" "grDevices" "graphics" "stats" "methods" </pre></div> <p>(plus, of course, <strong>base</strong>) and this can be changed by setting the option in startup code (e.g. in <samp>~/.Rprofile</samp>). It is initially <a name="index-R_005fDEFAULT_005fPACKAGES"></a> set to the value of the environment variable <code>R_DEFAULT_PACKAGES</code> if set (as a comma-separated list). Setting <code>R_DEFAULT_PACKAGES=NULL</code> ensures that only package <strong>base</strong> is loaded. </p> <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. But it can also be used to customize R, e.g. for class use. <code>Rscript</code> also checks the environment variable <code>R_SCRIPT_DEFAULT_PACKAGES</code>; <a name="index-R_005fSCRIPT_005fDEFAULT_005fPACKAGES"></a> if set, this takes precedence over <code>R_DEFAULT_PACKAGES</code>. </p> <hr> <a name="Managing-libraries"></a> <div class="header"> <p> Next: <a href="#Installing-packages" accesskey="n" rel="next">Installing packages</a>, Previous: <a href="#Default-packages" accesskey="p" rel="previous">Default packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Managing-libraries-1"></a> <h3 class="section">6.2 Managing libraries</h3> <a name="index-Libraries_002c-managing"></a> <p>R packages are installed into <em>libraries</em>, which are directories in the file system containing a subdirectory for each package installed there. </p> <p>R comes with a single library, <samp><var>R_HOME</var>/library</samp> which is the value of the R object ‘<samp>.Library</samp>’ containing the standard and recommended<a name="DOCF21" href="#FOOT21"><sup>21</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>.libPaths()</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"></a> <a name="index-Site-libraries"></a> <p>R will automatically make use of a site-specific library <samp><var>R_HOME</var>/site-library</samp> if this exists (it does not in a vanilla R installation). This location can be overridden by setting<a name="DOCF22" href="#FOOT22"><sup>22</sup></a> ‘<samp>.Library.site</samp>’ in <samp><var>R_HOME</var>/etc/Rprofile.site</samp>, or (not recommended) by setting the <a name="index-R_005fLIBS_005fSITE"></a> environment variable <code>R_LIBS_SITE</code>. Like ‘<samp>.Library</samp>’, the site libraries are always included by ‘<samp>.libPaths()</samp>’. </p> <a name="index-Libraries_002c-user"></a> <a name="index-User-libraries"></a> <a name="index-R_005fLIBS_005fUSER"></a> <p>Users can have one or more libraries, normally specified by the environment variable <code>R_LIBS_USER</code>. This has a default value (to see it, use ‘<samp>Sys.getenv("R_LIBS_USER")</samp>’ within an R session), but that is only used if the corresponding directory actually exists (which by default it will not). </p> <p>Both <code>R_LIBS_USER</code> and <code>R_LIBS_SITE</code> can specify multiple library paths, separated by colons (semicolons on Windows). </p> <hr> <a name="Installing-packages"></a> <div class="header"> <p> Next: <a href="#Updating-packages" accesskey="n" rel="next">Updating packages</a>, Previous: <a href="#Managing-libraries" accesskey="p" rel="previous">Managing libraries</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Installing-packages-1"></a> <h3 class="section">6.3 Installing packages</h3> <a name="index-Packages_002c-installing"></a> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Windows-packages" accesskey="1">Windows packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#macOS-packages" accesskey="2">macOS packages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Customizing-package-compilation" accesskey="3">Customizing package compilation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Multiple-sub_002darchitectures" accesskey="4">Multiple sub-architectures</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Byte_002dcompilation" accesskey="5">Byte-compilation</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#External-software" accesskey="6">External software</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <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> <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. </p> <a name="index-TMPDIR-4"></a> <p>Ensure that the environment variable <code>TMPDIR</code> is either unset (and <samp>/tmp</samp> exists and can be written in and executed from) or is the absolute path to a valid temporary directory, not containing spaces. </p> <p>For most users it suffices to call ‘<samp>install.packages(<var>pkgname</var>)</samp>’ or its GUI equivalent if the intention is to install a <acronym>CRAN</acronym> package and internet access is available.<a name="DOCF23" href="#FOOT23"><sup>23</sup></a> On most systems ‘<samp>install.packages()</samp>’ will allow packages to be selected from a list box (typically with thousands of items). </p> <p>To install packages from source on a Unix-alike use in a terminal </p> <div class="example"> <pre class="example">R CMD INSTALL -l /path/to/library <var>pkg1</var> <var>pkg2</var> … </pre></div> <p>The part ‘<samp>-l /path/to/library</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> <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"></a> <p>Alternatively, packages can be downloaded and installed from within R. First choose your nearest <acronym>CRAN</acronym> mirror using <code>chooseCRANmirror()</code>. Then download and install packages <strong>pkg1</strong> and <strong>pkg2</strong> by </p> <div class="example"> <pre class="example">> install.packages(c("pkg1", "pkg2")) </pre></div> <p>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> <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. </p> <div class="example"> <pre class="example">> install.packages("Rcmdr", dependencies = TRUE) </pre></div> <p><code>install.packages</code> can install a source package from a local <samp>.tar.gz</samp> file (or a URL to such a file) by setting argument <code>repos</code> to <code>NULL</code>: this will be selected automatically if the name given is a single <samp>.tar.gz</samp> file. </p> <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, R-forge, rforge.net, local archives, local files, …). Function <code>setRepositories()</code> can select amongst those repositories that the R installation is aware of. </p> <p>Naive users sometimes forget that as well as installing a package, they have to use <code>library</code> to make its functionality available. </p> <hr> <a name="Windows-packages"></a> <div class="header"> <p> Next: <a href="#macOS-packages" accesskey="n" rel="next">macOS packages</a>, Previous: <a href="#Installing-packages" accesskey="p" rel="previous">Installing packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Windows"></a> <h4 class="subsection">6.3.1 Windows</h4> <p>What <code>install.packages</code> does by default is different on Unix-alikes (except macOS) 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) first at the list of <em>binary</em> versions of packages available for your version of R and downloads the latest versions (if any). If no binary version is available or the source version is newer, it will install the source versions of packages without compiled C/C++/Fortran code, and offer to do so for those with, if <code>make</code> is available (and this can be tuned by option <code>"install.packages.compile.from.source"</code>). </p> <p>On Windows <code>install.packages</code> can also install a binary package from a local <samp>zip</samp> file (or the URL of such a 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> <p>Windows binary packages for R are distributed as a single binary containing either or both architectures (32- and 64-bit). </p> <p>A few of the binary packages need other software to be installed on your system: see for example <a href="https://CRAN.R-project.org/bin/windows/contrib/3.2/@ReadMe">https://CRAN.R-project.org/bin/windows/contrib/3.2/@ReadMe</a>. Packages using Gtk+ (<a href="https://CRAN.R-project.org/package=Cairo"><strong>Cairo</strong></a>, <a href="https://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>, <a href="https://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them) need the <samp>bin</samp> directory of a bundled distribution of Gtk2 from <a href="http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+">http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+</a> or <a href="http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+">http://ftp.gnome.org/pub/gnome/binaries/win64/gtk+</a> in the path: it should work to have both 32- and 64-bit Gtk+ <samp>bin</samp> directories in the path on a 64-bit version of R. </p> <p><code>R CMD INSTALL</code> 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 on the path, and the variables <code>BINPREF</code> and <code>BINPREF64</code> are set properly; see the discussion below). We have seen occasional permission problems after unpacking source packages on some systems: these have been circumvented by setting the environment variable <code>R_INSTALL_TAR</code> to ‘<samp>tar.exe</samp>’. <a name="index-R_005fINSTALL_005fTAR"></a> </p> <p>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="https://win-builder.r-project.org/">https://win-builder.r-project.org/</a>. </p> <p>For almost all packages <code>R CMD INSTALL</code> 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 <code>R</code> succeeded, whether or not the other architecture was successfully installed. The exceptions are packages with a non-empty <samp>configure.win</samp> script or which make use of <samp>src/Makefile.win</samp>. If <samp>configure.win</samp> does something appropriate to both architectures use<a name="DOCF24" href="#FOOT24"><sup>24</sup></a> option <samp>--force-biarch</samp>: otherwise <code>R CMD INSTALL --merge-multiarch</code> 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> <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 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"></a> <a name="index-BINPREF"></a> <a name="index-BINPREF64"></a> <p>Packages with compiled code may need to have paths to the compilers set explicitly, and there is provision to make use of a system-wide library of installed external software. The compiler paths are set using the <code>make</code> variables <code>BINPREF</code> and (usually) <code>BINPREF64</code>. The library location is set using <code>make</code> variable <code>LOCAL_SOFT</code>, to give an equivalent of <samp>/usr/local</samp> on a Unix-alike. All of these can be set in <samp>src/gnuwin32/MkRules.local</samp> when R is built from sources (see the comments in <samp>src/gnuwin32/MkRules.dist</samp>), or in file<a name="DOCF25" href="#FOOT25"><sup>25</sup></a> <samp>etc/i386/Makeconf</samp> or <samp>etc/x64/Makeconf</samp> for an installed version of R. In the latter case only <code>BINPREF</code> is used, with the 64 bit path used in <samp>etc/x64/Makeconf</samp>. The version used by <acronym>CRAN</acronym> can be installed as described in <a href="#Building-from-source">Building from source</a>. </p> <hr> <a name="macOS-packages"></a> <div class="header"> <p> Next: <a href="#Customizing-package-compilation" accesskey="n" rel="next">Customizing package compilation</a>, Previous: <a href="#Windows-packages" accesskey="p" rel="previous">Windows packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="macOS-1"></a> <h4 class="subsection">6.3.2 macOS</h4> <p>On macOS (formerly OS X) <code>install.packages</code> works as it does on other Unix-alike systems, but there are additional types starting with <code>mac.binary</code> (available for the <acronym>CRAN</acronym> distribution but not when compiling R from source: <code>mac.binary.el-capitan</code> for an ‘El Capitan and later’ build with <code>"default"</code> a synonym for the appropriate variant) which can be passed to <code>install.packages</code> in order to download and install binary packages from a suitable repository. These binary package files for macOS have the extension ‘<samp>.tgz</samp>’. The <small>R.APP</small> GUI provides menus for installation of either binary or source packages, from <acronym>CRAN</acronym> or local files. </p> <p>On R builds using binary packages, the default is type <code>both</code>: this looks first at the list of binary packages available for your version of R and installs the latest versions (if any). If no binary version is available or the source version is newer, it will install the source versions of packages without compiled C/C++/Fortran code and offer to do so for those with, if <code>make</code> is available. </p> <p>Note that most binary packages which include compiled code are tied to a particular series (e.g. R 3.6.x or 3.5.x) of R. </p> <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 <code>Xcode</code> and compilers which match those used to build R: see <a href="#macOS">macOS</a>. </p> <p>Package <a href="https://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. See <a href="#macOS">macOS</a> and <a href="#Java-_0028macOS_0029">Java (macOS)</a>. </p> <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> <p>A few of the binary packages need other software to be installed on your system. In particular packages using Gtk+ (<a href="https://CRAN.R-project.org/package=RGtk2"><strong>RGtk2</strong></a>, <a href="https://CRAN.R-project.org/package=cairoDevice"><strong>cairoDevice</strong></a> and those that depend on them) need the GTK framework installed from <a href="https://mac.R-project.org/libs/">https://mac.R-project.org/libs/</a>: the appropriate version at the time of writing was <a href="https://mac.R-project.org/libs/GTK_2.24.17-X11.pkg">https://mac.R-project.org/libs/GTK_2.24.17-X11.pkg</a> </p> <p>The default compilers specified are shown in file <samp>/Library/Frameworks/R.framework/Resources/etc/Makeconf</samp>. At the time of writing these setting assumed that the C, Fortran and C++ compilers were on the path, using <code>gfortran</code> 6.1.0 (see <a href="#macOS">macOS</a>). The settings can be changed, either by editing that file or in a file such as <samp>~/.R/Makevars</samp> (see the next section). Entries which may need to be changed include ‘<samp>CC</samp>’, ‘<samp>CXX</samp>’, ‘<samp>FC</samp>’, ‘<samp>FLIBS</samp>’ and the corresponding flags, and perhaps ‘<samp>CXXCPP</samp>’, ‘<samp>DYLIB_LD</samp>’, ‘<samp>MAIN_LD</samp>’, ‘<samp>SHLIB_CXXLD</samp>’ and ‘<samp>SHLIB_LD</samp>’, as well as the ‘<samp>CXX11</samp>’, ‘<samp>CXX14</samp>’ and ‘<samp>CXX17</samp>’ variants </p> <p>So for example you could select a specific build of <code>clang</code> for both C and C++ with extensive checking by having in <samp>~/.R/Makevars</samp> </p><div class="example"> <pre class="example">CC = /usr/local/clang7/bin/clang CXX = /usr/local/clang7/bin/clang++ CFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXXFLAGS = -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion CXX11 = $CXX CXX14 = $CXX CXX17 = $CXX </pre></div> <p>and the Sierra build of <code>gfortran</code> by </p><div class="example"> <pre class="example">FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm </pre></div> <p>(line split for legibility here). </p> <p>If using the C/C++ compilers from the Command Line Tools (which do not have OpenMP support) one will need to include </p><div class="example"> <pre class="example">SHLIB_OPENMP_CFLAGS = SHLIB_OPENMP_CXXFLAGS = </pre></div> <p>to compile OpenMP-using packages. </p> <p>Apple includes many Open Source libraries in macOS but increasingly without the corresponding headers (not even in Xcode nor the Command Line Tools): they are often rather old versions. If installing packages from source using them it is usually easiest to install a statically-linked up-to-date copy of the Open Source package from its sources or from <a href="https://mac.R-project.org/libs">https://mac.R-project.org/libs</a>. But sometimes it is desirable/necessary to use Apple’s dynamically linked library, in which case appropriate headers could be extracted from the sources<a name="DOCF26" href="#FOOT26"><sup>26</sup></a> available <em>via</em> <a href="https://opensource.apple.com">https://opensource.apple.com</a>. </p> <hr> <a name="Customizing-package-compilation"></a> <div class="header"> <p> Next: <a href="#Multiple-sub_002darchitectures" accesskey="n" rel="next">Multiple sub-architectures</a>, Previous: <a href="#macOS-packages" accesskey="p" rel="previous">macOS packages</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Customizing-package-compilation-1"></a> <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>/.R/Makevars-<var>R_PLATFORM</var></samp> (but <samp><var>HOME</var>/.R/Makevars.win</samp> or <samp><var>HOME</var>/.R/Makevars.win64</samp> on Windows), or if that does not exist, <samp><var>HOME</var>/.R/Makevars</samp>, where ‘<samp>R_PLATFORM</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>. The path to an alternative personal file<a name="DOCF27" href="#FOOT27"><sup>27</sup></a> can be specified <em>via</em> the environment variable <code>R_MAKEVARS_USER</code>. </p> <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>-Wall -pedantic</samp> for tools from GCC, the GNU Compiler Collection. </p> <p>Note that this mechanism can also be used when it necessary to change the optimization level for a particular package. For example </p> <div class="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 fixed-form Fortran code</span> FFLAGS = -g -O -mtune=native ## <span class="roman">for free-form Fortran code</span> FCFLAGS = -g -O -mtune=native </pre></div> <p>Another use is to override the settings in a binary installation of R. For example, to use a different Fortran compiler on macOS </p> <div class="example"> <pre class="example">FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm </pre></div> <p>(line split for legibility here). </p> <p>There is also provision for a site-wide <samp>Makevars.site</samp> file under <samp><var>R_HOME</var>/etc</samp> (in a sub-architecture-specific directory if appropriate). This is read immediately after <samp>Makeconf</samp>, and the path to an alternative file can be specified by environment variable <code>R_MAKEVARS_SITE</code>. </p> <p>Note that these mechanisms do not work with packages which fail to pass settings down to sub-makes, perhaps reading <samp>etc/Makeconf</samp> in makefiles in subdirectories. Fortunately such packages are unusual. </p> <hr> <a name="Multiple-sub_002darchitectures"></a> <div class="header"> <p> Next: <a href="#Byte_002dcompilation" accesskey="n" rel="next">Byte-compilation</a>, Previous: <a href="#Customizing-package-compilation" accesskey="p" rel="previous">Customizing package compilation</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Multiple-sub_002darchitectures-1"></a> <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> <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 </p> <dl compact="compact"> <dt><em>Unix-alikes</em></dt> <dd> <p>where there is an <samp>configure</samp> script, or a file <samp>src/Makefile</samp>. </p> </dd> <dt><em>Windows</em></dt> <dd> <p>where there is a non-empty <samp>configure.win</samp> script, or a file <samp>src/Makefile.win</samp> (with some exceptions where the package is known to have an architecture-independent <samp>configure.win</samp>, or if <samp>--force-biarch</samp> or field ‘<samp>Biarch</samp>’ in the <samp>DESCRIPTION</samp> file is used to assert so). </p> </dd> </dl> <p>In those cases only the current architecture is installed. Further sub-architectures can be installed by </p> <div class="example"> <pre class="example">R CMD INSTALL --libs-only <var>pkg</var> </pre></div> <p>using the path to <code>R</code> or <code>R --arch</code> to select the additional sub-architecture. There is also <code>R CMD INSTALL --merge-multiarch</code> to build and merge the two architectures, starting with a source tarball. </p> <hr> <a name="Byte_002dcompilation"></a> <div class="header"> <p> Next: <a href="#External-software" accesskey="n" rel="next">External software</a>, Previous: <a href="#Multiple-sub_002darchitectures" accesskey="p" rel="previous">Multiple sub-architectures</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Byte_002dcompilation-1"></a> <h4 class="subsection">6.3.5 Byte-compilation</h4> <p>As from R 3.6.0, all packages are by default byte-compiled. </p> <p>Byte-compilation can be controlled on a per-package basis by the ‘<samp>ByteCompile</samp>’ field in the <samp>DESCRIPTION</samp> file. </p> <hr> <a name="External-software"></a> <div class="header"> <p> Previous: <a href="#Byte_002dcompilation" accesskey="p" rel="previous">Byte-compilation</a>, Up: <a href="#Installing-packages" accesskey="u" rel="up">Installing packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="External-software-1"></a> <h4 class="subsection">6.3.6 External software</h4> <p>Some R packages contain compiled code which links to external software libraries. Unless the external library is statically linked (which is done as much as possible for binary packages on Windows and macOS), the libraries have to be found when the package is loaded and not just when it is installed. How this should be done depends on the OS (and in some cases the version). </p> <p>For Unix-alikes except macOS the primary mechanism is the <code>ld.so</code> cache controlled by <code>ldconfig</code>: external dynamic libraries recorded in that cache will be found. Standard library locations will be covered by the cache, and well-designed software will add its locations (as for example <strong>openmpi</strong> does on Fedora). The secondary mechanism is to consult the environment variable <code>LD_LIBRARY_PATH</code>. The R script controls that variable, and sets it to the concatenation of <code>R_LD_LIBRARY_PATH</code>, <code>R_JAVA_LD_LIBRARY_PATH</code> and the environment value of <code>LD_LIBRARY_PATH</code>. The first two have defaults which are normally set when R is installed (but can be overridden in the environment) so <code>LD_LIBRARY_PATH</code> is the best choice for a user to set. </p> <p>On macOS the primary mechanism is to embed the absolute path to dependent dynamic libraries into an object when it is compiled. Few R packages arrange to do so, but it can be edited<a name="DOCF28" href="#FOOT28"><sup>28</sup></a> <em>via</em> <code>install_name_tool</code> — that only deals with direct dependencies and those would also need to be compiled to include the absolute paths of their dependencies. If the choice of absolute path is to be deferred to load time, how they are resolved is described in <code>man dyld</code>: the role of <code>LD_LIBRARY_PATH</code> is replaced on macOS by <code>DYLD_LIBRARY_PATH</code> and <code>DYLD_FALLBACK_LIBRARY_PATH</code>. Running <code>R CMD otool -L</code> on the package shared object will show where (if anywhere) its dependencies are resolved. <code>DYLD_FALLBACK_LIBRARY_PATH</code> is preferred (and it is that which is manipulated by the R script), but as from 10.11 (‘El Capitan’) the default behaviour had been changed for security reasons to discard these environment variables when invoking a shell script (and <samp>R</samp> is a shell script). That makes the only portable option to set <code>R_LD_LIBRARY_PATH</code> in the environment, something like </p> <div class="example"> <pre class="example">export R_LD_LIBRARY_PATH="`R RHOME`/lib:/opt/local/lib" </pre></div> <p>The precise rules for where Windows looks for DLLs are complex and depend on the version of Windows. But for present purposes the main solution is to put the directories containing the DLLs the package links to (and any those DLLs link to) on the <code>PATH</code>. 64-bit versions of Windows will ignore 32-bit DLLs from 64-bit R and <em>vice versa</em>. </p> <p>The danger with any of the methods which involve setting environment variables is of inadvertently masking a system library. This is less for <code>DYLD_FALLBACK_LIBRARY_PATH</code> and for <em>appending</em> to <code>PATH</code> on Windows (as it should already contain the system library paths). </p> <hr> <a name="Updating-packages"></a> <div class="header"> <p> Next: <a href="#Removing-packages" accesskey="n" rel="next">Removing packages</a>, Previous: <a href="#Installing-packages" accesskey="p" rel="previous">Installing packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Updating-packages-1"></a> <h3 class="section">6.4 Updating packages</h3> <a name="index-update_002epackages"></a> <a name="index-Packages_002c-updating"></a> <p>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> <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> <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 </p> <div class="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> <hr> <a name="Removing-packages"></a> <div class="header"> <p> Next: <a href="#Setting-up-a-package-repository" accesskey="n" rel="next">Setting up a package repository</a>, Previous: <a href="#Updating-packages" accesskey="p" rel="previous">Updating packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Removing-packages-1"></a> <h3 class="section">6.5 Removing packages</h3> <a name="index-remove_002epackages"></a> <a name="index-Packages_002c-removing"></a> <p>Packages can be removed in a number of ways. From a command prompt they can be removed by </p> <div class="example"> <pre class="example">R CMD REMOVE -l /path/to/library <var>pkg1</var> <var>pkg2</var> … </pre></div> <p>From a running R process they can be removed by </p> <div class="example"> <pre class="example">> remove.packages(c("pkg1", "pkg2"), lib = file.path("path", "to", "library")) </pre></div> <p>Finally, one can just remove the package directory from the library. </p> <hr> <a name="Setting-up-a-package-repository"></a> <div class="header"> <p> Next: <a href="#Checking-installed-source-packages" accesskey="n" rel="next">Checking installed source packages</a>, Previous: <a href="#Removing-packages" accesskey="p" rel="previous">Removing packages</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Setting-up-a-package-repository-1"></a> <h3 class="section">6.6 Setting up a package repository</h3> <a name="index-Repositories"></a> <p>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.stats.ox.ac.uk/pub/RWin">http://www.stats.ox.ac.uk/pub/RWin</a>: this must be an URL scheme that <code>download.packages</code> supports (which also includes ‘<samp>https://</samp>’, ‘<samp>ftp://</samp>’ and ‘<samp>file://</samp>’). Under that base URL there should be directory trees for one or more of the following types of package distributions: </p> <ul> <li> <code>"source"</code>: located at <samp>src/contrib</samp> and containing <samp>.tar.gz</samp> files. Other forms of compression can be used, e.g. <samp>.tar.bz2</samp> or <samp>.tar.xz</samp> files. Complete repositories contain the sources corresponding to any binary packages, and in any case it is wise to have a <samp>src/contrib</samp> area with a possibly empty <samp>PACKAGES</samp> file. </li><li> <code>"win.binary"</code>: located at <samp>bin/windows/contrib/<var>x.y</var></samp> for R versions <var>x.y.z</var> and containing <samp>.zip</samp> files for Windows. </li><li> <code>"mac.binary.el-capitan"</code>: located at <samp>bin/macosx/el-capitan/contrib/<var>3.y</var></samp> for the CRAN builds for ‘El Capitan (and later) for R versions <var>3.y.z</var>, containing <samp>.tgz</samp> files. </li></ul> <p>Each terminal directory must also contain a <samp>PACKAGES</samp> file. This can be a concatenation of the <samp>DESCRIPTION</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 <samp>PACKAGES.rds</samp> and <samp>PACKAGES.gz</samp> files, downloaded in preference to <samp>PACKAGES</samp>. (These files will be smaller: <samp>PACKAGES.rds</samp> is used only from R 3.4.0. If you have a mis-configured server that does not report correctly non-existent files you may need these files.) </p> <p>To add your repository to the list offered by <code>setRepositories()</code>, see the help file for that function. </p> <p>Incomplete repositories are better specified <em>via</em> a <code>contriburl</code> argument than <em>via</em> being set as a repository. </p> <p>A repository can contain subdirectories, when the descriptions in the <samp>PACKAGES</samp> file of packages in subdirectories must include a line of the form </p> <div class="example"> <pre class="example">Path: <var>path/to/subdirectory</var> </pre></div> <p>—once again <code>write_PACKAGES</code> is the simplest way to set this up. </p> <hr> <a name="Checking-installed-source-packages"></a> <div class="header"> <p> Previous: <a href="#Setting-up-a-package-repository" accesskey="p" rel="previous">Setting up a package repository</a>, Up: <a href="#Add_002don-packages" accesskey="u" rel="up">Add-on packages</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Checking-installed-source-packages-1"></a> <h3 class="section">6.7 Checking installed source packages</h3> <p>It can be convenient to run <code>R CMD check</code> 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): </p> <div class="example"> <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></div> <p>Where sub-architectures are in use the <code>R CMD check</code> line can be repeated with additional architectures by </p> <div class="example"> <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></div> <p>where <samp>--extra-arch</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>--no-multiarch</samp> may need to be added to the <code>INSTALL</code> lines.) On Unix-alikes the architecture to run is selected by <samp>--arch</samp>: this can also be used on Windows with <samp><var>R_HOME</var>/bin/R.exe</samp>, but it is more usual to select the path to the <code>Rcmd.exe</code> of the desired architecture. </p> <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 </p> <div class="example"> <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></div> <p>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> <p><code>R CMD INSTALL</code> can do a <code>i386</code> install and then add the <code>x64</code> DLL from a single command by </p> <div class="example"> <pre class="example">R CMD INSTALL --merge-multiarch -l <var>libdir</var> <var>tarball</var> </pre></div> <p>and <samp>--build</samp> can be added to zip up the installation. </p> <hr> <a name="Internationalization"></a> <div class="header"> <p> Next: <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="n" rel="next">Choosing between 32- and 64-bit builds</a>, Previous: <a href="#Add_002don-packages" accesskey="p" rel="previous">Add-on packages</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Internationalization-and-Localization"></a> <h2 class="chapter">7 Internationalization and Localization</h2> <a name="index-Internationalization"></a> <a name="index-Localization"></a> <p><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. </p> <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"></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> <p>The other aspect of the internationalization is support for the translation of messages. This is enabled in almost all builds of R. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Locales" accesskey="1">Locales</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Localization-of-messages" accesskey="2">Localization of messages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Locales"></a> <div class="header"> <p> Next: <a href="#Localization-of-messages" accesskey="n" rel="next">Localization of messages</a>, Previous: <a href="#Internationalization" accesskey="p" rel="previous">Internationalization</a>, Up: <a href="#Internationalization" accesskey="u" rel="up">Internationalization</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Locales-1"></a> <h3 class="section">7.1 Locales</h3> <a name="index-Locale-1"></a> <p>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> <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 </p><ul> <li> A human language. These are generally specified by a lower-case two-character abbreviation following ISO 639 (see e.g. <a href="https://en.wikipedia.org/wiki/ISO_639-1">https://en.wikipedia.org/wiki/ISO_639-1</a>). </li><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="https://en.wikipedia.org/wiki/ISO_3166">https://en.wikipedia.org/wiki/ISO_3166</a>). </li><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><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>). </li></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. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Locales-under-Unix_002dalikes" accesskey="1">Locales under Unix-alikes</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Locales-under-Windows" accesskey="2">Locales under Windows</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Locales-under-macOS" accesskey="3">Locales under macOS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Locales-under-Unix_002dalikes"></a> <div class="header"> <p> Next: <a href="#Locales-under-Windows" accesskey="n" rel="next">Locales under Windows</a>, Previous: <a href="#Locales" accesskey="p" rel="previous">Locales</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Locales-under-Unix_002dalikes-1"></a> <h4 class="subsection">7.1.1 Locales under Unix-alikes</h4> <p>Modern Linux uses the XPG<a name="DOCF29" href="#FOOT29"><sup>29</sup></a> locale specifications which have the form ‘<samp>en_GB</samp>’, ‘<samp>en_GB.UTF-8</samp>’, ‘<samp>aa_ER.UTF-8@saaho</samp>’, ‘<samp>de_AT.iso885915@euro</samp>’, the components being in the order listed above. (See <code>man locale</code> and <code>locale -a</code> for more details.) Similar schemes are used by most Unix-alikes: some (including some distributions of Linux) use ‘<samp>.utf8</samp>’ rather than ‘<samp>.UTF-8</samp>’. </p> <p>Note that whereas UTF-8 locales are nowadays almost universally used, locales such as ‘<samp>en_GB</samp>’ use 8-bit encodings for backwards compatibility. </p> <hr> <a name="Locales-under-Windows"></a> <div class="header"> <p> Next: <a href="#Locales-under-macOS" accesskey="n" rel="next">Locales under macOS</a>, Previous: <a href="#Locales-under-Unix_002dalikes" accesskey="p" rel="previous">Locales under Unix-alikes</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Locales-under-Windows-1"></a> <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 by searching for ‘<samp>Windows language country strings</samp>’). </p> <p>It offers only one encoding per language. </p> <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. </p> <hr> <a name="Locales-under-macOS"></a> <div class="header"> <p> Previous: <a href="#Locales-under-Windows" accesskey="p" rel="previous">Locales under Windows</a>, Up: <a href="#Locales" accesskey="u" rel="up">Locales</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Locales-under-macOS-1"></a> <h4 class="subsection">7.1.3 Locales under macOS</h4> <p>macOS supports locales in its own particular way, but the R GUI tries to make this easier for users. See <a href="https://developer.apple.com/library/content/documentation/MacOSX/Conceptual/BPInternational/">https://developer.apple.com/library/content/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>en_GB.UTF-8</samp>’ if it defaults to ‘<samp>C</samp>’ (as it sometimes does when logging in remotely and for batch jobs: note whether <code>Terminal</code> sets the <code>LANG</code> environment variable is an (advanced) preference, but does so by default). </p> <p>Internally macOS 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>. </p> <hr> <a name="Localization-of-messages"></a> <div class="header"> <p> Previous: <a href="#Locales" accesskey="p" rel="previous">Locales</a>, Up: <a href="#Internationalization" accesskey="u" rel="up">Internationalization</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Localization-of-messages-1"></a> <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"></a> <a name="index-LC_005fALL"></a> <a name="index-LC_005fMESSAGES"></a> <a name="index-LANG"></a> <code>LANGUAGE</code> and then<a name="DOCF30" href="#FOOT30"><sup>30</sup></a> by the environment variables <code>LC_ALL</code>, <code>LC_MESSAGES</code> and <code>LANG</code>. (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 <code>LC_ALL</code> do not all correspond to XPG language names and so <code>LANGUAGE</code> may need to be set. (One example is ‘<samp>LC_ALL=es</samp>’ on Windows which sets the locale to Estonian and the language to Spanish.) </p> <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 <code>LANGUAGE</code>, <em>provided</em><a name="DOCF31" href="#FOOT31"><sup>31</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> <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. </p> <ul> <li> Domain <code>R</code> for the C-level error and warning messages from the R interpreter. </li><li> Domain <code>R-<var>pkg</var></code> 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><li> Domain <code><var>pkg</var></code> for the C-level messages in each package. </li><li> Domain <code>RGui</code> for the menus etc of the R for Windows GUI front-end. </li></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> <p>R can be built without support for translations, but it is enabled by default. </p> <p>R-level and C-level domains are subtly different, for example in the way strings are canonicalized before being passed for translation. </p> <p>Translations are looked for by domain according to the currently specified language, as specifically as possible, so for example an Austrian (‘<samp>de_AT</samp>’) translation catalogue will be used in preference to a generic German one (‘<samp>de</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>en_GB</samp>’ that translate the Americanisms (e.g., ‘<samp>gray</samp>’) in the standard messages into English.<a name="DOCF32" href="#FOOT32"><sup>32</sup></a> Two other examples: there are catalogues for ‘<samp>es</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>pt_BR</samp>’, which are used for Brazilian locales but not for locales specifying Portugal. </p> <p>Translations in the right language but the wrong charset are made use of <a name="index-LANGUAGE-1"></a> by on-the-fly re-encoding. The <code>LANGUAGE</code> variable (only) can be a colon-separated list, for example ‘<samp>se:de</samp>’, giving a set of languages in decreasing order of preference. One special value is ‘<samp>en@quot</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> <p>If no suitable translation catalogue is found or a particular message is not translated in any suitable catalogue, ‘English’<a name="DOCF33" href="#FOOT33"><sup>33</sup></a> is used. </p> <p>See <a href="https://developer.r-project.org/Translations30.html">https://developer.r-project.org/Translations30.html</a> for how to prepare and install translation catalogues. </p> <hr> <a name="Choosing-between-32_002d-and-64_002dbit-builds"></a> <div class="header"> <p> Next: <a href="#The-standalone-Rmath-library" accesskey="n" rel="next">The standalone Rmath library</a>, Previous: <a href="#Internationalization" accesskey="p" rel="previous">Internationalization</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Choosing-between-32_002d-and-64_002dbit-builds-1"></a> <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>x86_64</samp>’ Linux and macOS ≥ 10.6) 64-bit is. </p> <p>All current versions of R use 32-bit integers (this is enforced in the build) and <acronym>ISO</acronym>/<acronym>IEC</acronym> 60559<a name="DOCF34" href="#FOOT34"><sup>34</sup></a> double-precision reals, and so compute to the same precision<a name="DOCF35" href="#FOOT35"><sup>35</sup></a> and with the same limits on the sizes of numerical quantities. The principal difference is in the size of the pointers. </p> <p>64-bit builds have both advantages and disadvantages: </p><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 for 32-bit builds 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). </p> </li><li> Only 64-bit builds support ‘long vectors’, those with <em>2^{31}</em> or more elements (which needs at least 16GB of storage for each numeric vector). </li><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: <code>configure</code> 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><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><li> However, ‘other things’ may not be equal. In the specific case of ‘<samp>x86_64</samp>’ <em>vs</em> ‘<samp>ix86</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 i7 the vanilla 64-bit version of R has been around 10% faster on both Linux and macOS. (Laptop CPUs are usually relatively slower in 64-bit mode.) </li></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> <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, each dimension of an array is limited to <em>2^{31} - 1</em>. </p> <hr> <a name="The-standalone-Rmath-library"></a> <div class="header"> <p> Next: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="n" rel="next">Essential and useful other programs under a Unix-alike</a>, Previous: <a href="#Choosing-between-32_002d-and-64_002dbit-builds" accesskey="p" rel="previous">Choosing between 32- and 64-bit builds</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="The-standalone-Rmath-library-1"></a> <h2 class="chapter">9 The standalone Rmath library</h2> <p>The routines supporting the distribution and special<a name="DOCF36" href="#FOOT36"><sup>36</sup></a> functions in R and a few others are declared in C header file <samp>Rmath.h</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> <p>The makefiles and other sources needed are in directory <samp>src/nmath/standalone</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> <p><samp>Rmath.h</samp> contains ‘<samp>R_VERSION_STRING</samp>’, which is a character string containing the current R version, for example <code>"3.6.0"</code>. </p> <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 </p> <div class="example"> <pre class="example"> ISNAN, R_FINITE, R_log, R_pow and R_pow_di </pre></div> <p>and (extern) constants <code>R_PosInf</code>, <code>R_NegInf</code> and <code>NA_REAL</code>. </p> <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> <p>A little care is needed to use the random-number routines. You will need to supply the uniform random number generator </p> <div class="example"> <pre class="example"> double unif_rand(void) </pre></div> <p>or use the one supplied (and with a shared library or DLL you may have to use the one supplied, which is the Marsaglia-multicarry with an entry point </p> <div class="example"> <pre class="example"> set_seed(unsigned int, unsigned int) </pre></div> <p>to set its seeds). </p> <p>The facilities to change the normal random number generator are available through the constant <code>N01_kind</code>. This takes values from the enumeration type </p> <div class="example"> <pre class="example">typedef enum { BUGGY_KINDERMAN_RAMAGE, AHRENS_DIETER, BOX_MULLER, USER_NORM, INVERSION, KINDERMAN_RAMAGE } N01type; </pre></div> <p>(and ‘<samp>USER_NORM</samp>’ is not available). </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Unix_002dalike-standalone" accesskey="1">Unix-alike standalone</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Windows-standalone" accesskey="2">Windows standalone</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Unix_002dalike-standalone"></a> <div class="header"> <p> Next: <a href="#Windows-standalone" accesskey="n" rel="next">Windows standalone</a>, Previous: <a href="#The-standalone-Rmath-library" accesskey="p" rel="previous">The standalone Rmath library</a>, Up: <a href="#The-standalone-Rmath-library" accesskey="u" rel="up">The standalone Rmath library</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Unix_002dalikes"></a> <h3 class="section">9.1 Unix-alikes</h3> <p>If R has not already been made in the directory tree, <code>configure</code> must be run as described in the main build instructions. </p> <p>Then (in <samp>src/nmath/standalone</samp>) </p> <div class="example"> <pre class="example">make </pre></div> <p>will make standalone libraries <samp>libRmath.a</samp> and <samp>libRmath.so</samp> (<samp>libRmath.dylib</samp> on macOS): ‘<samp>make static</samp>’ and ‘<samp>make shared</samp>’ will create just one of them. </p> <p>To use the routines in your own C or C++ programs, include </p> <div class="example"> <pre class="example">#define MATHLIB_STANDALONE #include <Rmath.h> </pre></div> <p>and link against ‘<samp>-lRmath</samp>’ (and ‘<samp>-lm</samp>’ if needed on your OS). The example file <samp>test.c</samp> does nothing useful, but is provided to test the process (via <code>make test</code>). Note that you will probably not be able to run it unless you add the directory containing <a name="index-LD_005fLIBRARY_005fPATH"></a> <samp>libRmath.so</samp> to the <code>LD_LIBRARY_PATH</code> environment variable (<samp>libRmath.dylib</samp>, <code>DYLD_FALLBACK_LIBRARY_PATH</code> on macOS). </p> <p>The targets </p> <div class="example"> <pre class="example">make install make uninstall </pre></div> <p>will (un)install the header <samp>Rmath.h</samp> and shared and static <a name="index-DESTDIR-1"></a> libraries (if built). Both <code>prefix=</code> and <code>DESTDIR</code> are supported, together with more precise control as described for the main build. </p> <p>‘<samp>make install</samp>’ installs a file for <code>pkg-config</code> to use by e.g. </p> <div class="example"> <pre class="example">$(CC) `pkg-config --cflags libRmath` -c test.c $(CC) `pkg-config --libs libRmath` test.o -o test </pre></div> <p>On some systems ‘<samp>make install-strip</samp>’ will install a stripped shared library. </p> <hr> <a name="Windows-standalone"></a> <div class="header"> <p> Previous: <a href="#Unix_002dalike-standalone" accesskey="p" rel="previous">Unix-alike standalone</a>, Up: <a href="#The-standalone-Rmath-library" accesskey="u" rel="up">The standalone Rmath library</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Windows-1"></a> <h3 class="section">9.2 Windows</h3> <p>You need to set up<a name="DOCF37" href="#FOOT37"><sup>37</sup></a> almost all the tools to make R and then run (in a Unix-like shell) </p> <div class="example"> <pre class="example">(cd ../../gnuwin32; make MkRules) (cd ../../include; make -f Makefile.win config.h Rconfig.h Rmath.h) make -f Makefile.win </pre></div> <p>Alternatively, in a <samp>cmd.exe</samp> shell use </p> <div class="example"> <pre class="example">cd ../../include make -f Makefile.win config.h Rconfig.h Rmath.h cd ../nmath/standalone make -f Makefile.win </pre></div> <p>This creates a static library <samp>libRmath.a</samp> and a DLL <samp>Rmath.dll</samp>. If you want an import library <samp>libRmath.dll.a</samp> (you don’t need one), use </p> <div class="example"> <pre class="example">make -f Makefile.win shared implib </pre></div> <p>To use the routines in your own C or C++ programs using MinGW-w64, include </p> <div class="example"> <pre class="example">#define MATHLIB_STANDALONE #include <Rmath.h> </pre></div> <p>and link against ‘<samp>-lRmath</samp>’. This will use the first found of <samp>libRmath.dll.a</samp>, <samp>libRmath.a</samp> and <samp>Rmath.dll</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> </p> <div class="example"> <pre class="example">-Wl,-Bstatic -lRmath -Wl,Bdynamic -Wl,-Bdynamic -lRmath </pre></div> <p>or by linking to explicit files (as in the ‘<samp>test</samp>’ target in <samp>Makefile.win</samp>: this makes two executables, <samp>test.exe</samp> which is dynamically linked, and <samp>test-static.exe</samp>, which is statically linked). </p> <p>It is possible to link to <samp>Rmath.dll</samp> using other compilers, either directly or via an import library: if you make a MinGW-w64 import library as above, you will create a file <samp>Rmath.def</samp> which can be used (possibly after editing) to create an import library for other systems such as Visual C++. </p> <p>If you make use of dynamic linking you should use </p> <div class="example"> <pre class="example">#define MATHLIB_STANDALONE #define RMATH_DLL #include <Rmath.h> </pre></div> <p>to ensure that the constants like <code>NA_REAL</code> are linked correctly. (Auto-import will probably work with MinGW-w64, but it is better to be sure. This is likely to also work with VC++, Borland and similar compilers.) </p> <hr> <a name="Essential-and-useful-other-programs-under-a-Unix_002dalike"></a> <div class="header"> <p> Next: <a href="#Configuration-on-a-Unix_002dalike" accesskey="n" rel="next">Configuration on a Unix-alike</a>, Previous: <a href="#The-standalone-Rmath-library" accesskey="p" rel="previous">The standalone Rmath library</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Essential-and-useful-other-programs-under-a-Unix_002dalike-1"></a> <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 <code>configure</code>. </p> <p>Remember that some package management systems (such as <acronym>RPM</acronym> and Debian/Ubuntu’s) 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>-devel</samp>’ or ‘<samp>-dev</samp>’: you need both versions installed. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Essential-programs-and-libraries" accesskey="1">Essential programs and libraries</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Useful-libraries-and-programs" accesskey="2">Useful libraries and programs</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Linear-algebra" accesskey="3">Linear algebra</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Essential-programs-and-libraries"></a> <div class="header"> <p> Next: <a href="#Useful-libraries-and-programs" accesskey="n" rel="next">Useful libraries and programs</a>, Previous: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="p" rel="previous">Essential and useful other programs under a Unix-alike</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Essential-programs-and-libraries-1"></a> <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>). Your C compiler should be <acronym>ISO</acronym>/<acronym>IEC</acronym> 60059<a name="DOCF38" href="#FOOT38"><sup>38</sup></a>, POSIX 1003.1 and C99-compliant.<a name="DOCF39" href="#FOOT39"><sup>39</sup></a> R tries to choose suitable flags<a name="DOCF40" href="#FOOT40"><sup>40</sup></a> for the C compilers it knows about, but you may have to set <code>CC</code> or <code>CFLAGS</code> suitably. For versions of <code>gcc</code> prior to 5.1 with <code>glibc</code>-based Linux this means including <samp>-std=gnu99</samp><a name="DOCF41" href="#FOOT41"><sup>41</sup></a>. (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> <p>Unless you do not want to view graphs on-screen (or use macOS) you need ‘<samp>X11</samp>’ installed, including its headers and client libraries. For recent Fedora/RedHat distributions it means (at least) RPMs ‘<samp>libX11</samp>’, ‘<samp>libX11-devel</samp>’, ‘<samp>libXt</samp>’ and ‘<samp>libXt-devel</samp>’. On Debian/Ubuntu we recommend the meta-package ‘<samp>xorg-dev</samp>’. If you really do not want these you will need to explicitly configure R without X11, using <samp>--with-x=no</samp>. </p> <p>The command-line editing (and command completion) depends on the <acronym>GNU</acronym> <code>readline</code> library (including its headers): version 4.2 or later is needed for all the features to be enabled. Otherwise you will need to configure with <samp>--with-readline=no</samp> (or equivalent). </p> <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 by default for <code>glibc</code><a name="DOCF42" href="#FOOT42"><sup>42</sup></a> but not of most commercial Unixes. However, you can make use of <acronym>GNU</acronym> <code>libiconv</code> (as used on macOS: see <a href="https://www.gnu.org/software/libiconv/">https://www.gnu.org/software/libiconv/</a>). </p> <p>The OS needs to have enough support<a name="DOCF43" href="#FOOT43"><sup>43</sup></a> for wide-character types: this is checked at configuration. Some C99 functions<a name="DOCF44" href="#FOOT44"><sup>44</sup></a> are required and checked for at configuration. A small number of POSIX functions<a name="DOCF45" href="#FOOT45"><sup>45</sup></a> are essential, and others<a name="DOCF46" href="#FOOT46"><sup>46</sup></a> will be used if available. </p> <p>Installations of <code>zlib</code> (version 1.2.5 or later), <code>libbz2</code> (version 1.0.6 or later: called <strong>bzip2-libs</strong>/<strong>bzip2-devel</strong> or <strong>libbz2-1.0</strong>/<strong>libbz2-dev</strong> by some Linux distributions) and <code>liblzma</code><a name="DOCF47" href="#FOOT47"><sup>47</sup></a> version 5.0.3 or later are required. </p> <p>PCRE<a name="DOCF48" href="#FOOT48"><sup>48</sup></a> (version 8.32 or later, although versions 8.20–8.31 will be accepted with a deprecation warning) is required (or just its library and headers if packaged separately). Only the ‘8-bit’ interface is used (and only that is built by default when installing from sources). PCRE must be built with UTF-8 support (not the default, and checked by <code>configure</code>) and support for Unicode properties is assumed by some R packages. JIT support (optionally available) is desirable for the best performance: support for this and Unicode properties can be checked at run-time by calling <code>pcre_config()</code>. If building PCRE for use with R a suitable <code>configure</code> command might be </p><div class="example"> <pre class="example">./configure --enable-utf --enable-unicode-properties --enable-jit --disable-cpp </pre></div> <p>The <samp>--enable-jit</samp> flag is supported for most common CPUs. (See also the comments for Solaris.) </p> <p>Library <code>libcurl</code> (version 7.22.0 or later<a name="DOCF49" href="#FOOT49"><sup>49</sup></a>) is required, with at least 7.28.0 being desirable. Information on <code>libcurl</code> is found from the <code>curl-config</code> script: if that is missing or needs to be overridden<a name="DOCF50" href="#FOOT50"><sup>50</sup></a> there are macros to do so described in file <samp>config.site</samp>. </p> <p>A <code>tar</code> program is needed to unpack the sources and packages (including the recommended packages). A version<a name="DOCF51" href="#FOOT51"><sup>51</sup></a> that can automagically detect compressed archives is preferred for use with <code>untar()</code>: the configure script looks for <code>gtar</code> and <code>gnutar</code> before <a name="index-TAR"></a> <code>tar</code> – use environment variable <code>TAR</code> to override this. (On NetBSD/OpenBSD systems set this to <code>bsdtar</code> if that is installed.) </p> <p>There need to be suitable versions of the tools <code>grep</code> and <code>sed</code>: the problems are usually with old AT&T and BSD variants. <code>configure</code> will try to find suitable versions (including looking in <samp>/usr/xpg4/bin</samp> which is used on some commercial Unixes). </p> <p>You will not be able to build most of the manuals unless you have <code>texi2any</code> version 5.1 or later installed, and if not most of the <acronym>HTML</acronym> manuals will be linked to a version on <acronym>CRAN</acronym>. To make PDF versions of the manuals you will also need file <samp>texinfo.tex</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 <code>texi2dvi</code>.<a name="DOCF52" href="#FOOT52"><sup>52</sup></a> Further, the versions of <code>texi2dvi</code> and <samp>texinfo.tex</samp> need to be compatible: we have seen problems with older TeX distributions. </p> <a name="index-Subversion-1"></a> <p>If you want to build from the R Subversion repository then <code>texi2any</code> is highly recommended as it is used to create files which are in the tarball but not stored in the Subversion repository. </p> <a name="index-Vignettes"></a> <p>The PDF documentation (including <samp>doc/NEWS.pdf</samp>) and building vignettes needs <code>pdftex</code> and <code>pdflatex</code>. 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 standard LaTeX packages are required (including <strong>url</strong> and some of the font packages such as <strong>times</strong>, <strong>helvetic</strong>, <strong>ec</strong> and <strong>cm-super</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>). Note that package <strong>hyperref</strong> (currently) requires packages <strong>kvoptions</strong>, <strong>ltxcmds</strong> and <strong>refcount</strong>. For distributions based on TeX Live the simplest approach may be to install collections <strong>collection-latex</strong>, <strong>collection-fontsrecommended</strong>, <strong>collection-latexrecommended</strong>, <strong>collection-fontsextra</strong> and <strong>collection-latexextra</strong> (assuming they are not installed by default): Fedora uses names like <strong>texlive-collection-fontsextra</strong> and Debian/Ubuntu like <strong>texlive-fonts-extra</strong>. </p> <a name="index-PATH"></a> <p>The essential programs should be in your <code>PATH</code> at the time <code>configure</code> is run: this will capture the full paths. </p> <p>Those distributing binary versions of R may need to be aware of the licences of the external libraries it is linked to (including ‘useful’ libraries from the next section). The <code>liblzma</code> library is in the public domain and X11, <code>libbzip2</code>, <code>libcurl</code> and <code>zlib</code> have MIT-style licences. PCRE has a BSD-style licence which requires distribution of the licence (included in R’s <samp>COPYRIGHTS</samp> file) in binary distributions. GNU <code>readline</code> is licensed under GPL (which version(s) depending on the <code>readline</code> version). </p> <hr> <a name="Useful-libraries-and-programs"></a> <div class="header"> <p> Next: <a href="#Linear-algebra" accesskey="n" rel="next">Linear algebra</a>, Previous: <a href="#Essential-programs-and-libraries" accesskey="p" rel="previous">Essential programs and libraries</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Useful-libraries-and-programs-1"></a> <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> <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 <code>pkg-config</code>, and uses that to check first that the ‘<samp>pangocairo</samp>’ package is installed (and if not, ‘<samp>cairo</samp>’) and if additional flags are needed for the ‘<samp>cairo-xlib</samp>’ package, then if suitable code can be compiled. These tests will fail if <code>pkg-config</code> is not installed<a name="DOCF53" href="#FOOT53"><sup>53</sup></a>, 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 </p> <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 name="DOCF54" href="#FOOT54"><sup>54</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 name="DOCF55" href="#FOOT55"><sup>55</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="https://en.wikipedia.org/wiki/Liberation_fonts">https://en.wikipedia.org/wiki/Liberation_fonts</a>). Then there is the ‘Free UCS Outline Fonts’ project (<a href="https://www.gnu.org/software/freefont/">https://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> <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> (versions 4.0.[5-10] have been tested) respectively. <code>pkg-config</code> is used if available and so needs the appropriate <samp>.pc</samp> file (which requires <code>libtiff</code> version 4.0.x and is not available on all platforms for <code>jpeg</code> before version 9c). 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 <code>configure</code> options <samp>--without-libpng</samp>, <samp>--without-jpeglib</samp> and <samp>--without-libtiff</samp>. The TIFF library has many optional features such as <code>jpeg</code>, <code>libz</code>, <code>lzma</code>, <code>jbig</code> and <code>jpeg12</code>, none of which is required for the <code>tiff()</code> devices but may need to be present to link the library (usually only an issue for static linking). </p> <p>Option <samp>--with-system-tre</samp> is also available: it needs a recent version of TRE. (The latest (2016) sources are in the <code>git</code> repository at <a href="https://github.com/laurikari/tre/">https://github.com/laurikari/tre/</a>, but at the time of writing the resulting build will not pass its checks.). </p> <p>An implementation of <acronym>XDR</acronym> is required, and the R sources contain one which is likely to suffice (although a system version may have higher performance). <acronym>XDR</acronym> is part of <acronym>RPC</acronym> and historically has been part of <samp>libc</samp> on a Unix-alike. (In principle <code>man xdr_string</code> should tell you which library is needed, but it often does not: on Solaris and others it is provided by <code>libnsl</code>.) However some builds<a name="DOCF56" href="#FOOT56"><sup>56</sup></a> of <code>glibc</code> omit or hide it with the intention that the <acronym>TI-RPC</acronym> library be used, in which case <code>libtirpc</code> (and its development version) should be installed, and its headers<a name="DOCF57" href="#FOOT57"><sup>57</sup></a> need to be on the C include path or under <samp>/usr/include/tirpc</samp>. </p> <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>xorg-dev</samp>’), but some distributions have split this into smaller parts, so for example recent versions of Fedora require the ‘<samp>libXmu</samp>’ and ‘<samp>libXmu-devel</samp>’ RPMs. </p> <p>Some systems (notably macOS 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: should a very old or broken version of ICU be found this can be suppressed by <samp>--without-ICU</samp>. </p> <p>The <code>bitmap</code> and <code>dev2bitmap</code> devices and function <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 <code>R_GSCMD</code> at that time. <a name="index-R_005fGSCMD"></a> </p> <p>At the time of writing a full installation on Fedora Linux used the following packages and their development versions, and this may provide a useful checklist for other systems: </p><div class="example"> <pre class="example">bzip2 cairo fontconfig freetype fribidi glib2 libX11 libXext libXt libcurl libicu libjpeg libpng libtiff libtirpc libxcrypt ncurses pango pcre readline tcl tk xz zlib </pre></div> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Tcl_002fTk" accesskey="1">Tcl/Tk</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Java-support" accesskey="2">Java support</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Other-compiled-languages" accesskey="3">Other compiled languages</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Tcl_002fTk"></a> <div class="header"> <p> Next: <a href="#Java-support" accesskey="n" rel="next">Java support</a>, Previous: <a href="#Useful-libraries-and-programs" accesskey="p" rel="previous">Useful libraries and programs</a>, Up: <a href="#Useful-libraries-and-programs" accesskey="u" rel="up">Useful libraries and programs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Tcl_002fTk-1"></a> <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="https://www.tcl.tk/">https://www.tcl.tk/</a>. To specify the locations of the Tcl/Tk files you may need the configuration options </p> <dl compact="compact"> <dt><samp>--with-tcltk</samp></dt> <dd><p>use Tcl/Tk, or specify its library directory </p></dd> <dt><samp>--with-tcl-config=<var>TCL_CONFIG</var></samp></dt> <dd><p>specify location of <samp>tclConfig.sh</samp> </p></dd> <dt><samp>--with-tk-config=<var>TK_CONFIG</var></samp></dt> <dd><p>specify location of <samp>tkConfig.sh</samp> </p></dd> </dl> <p>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>tcl.h</samp> and <samp>tk.h</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> <p>Versions of Tcl/Tk up to 8.5.19 and 8.6.9 have been tested (including most versions of 8.4.x, but not recently). </p> <p>Note that the <samp>tk.h</samp> header includes<a name="DOCF58" href="#FOOT58"><sup>58</sup></a> X11 headers, so you will need X11 and its development files installed. </p> <hr> <a name="Java-support"></a> <div class="header"> <p> Next: <a href="#Other-compiled-languages" accesskey="n" rel="next">Other compiled languages</a>, Previous: <a href="#Tcl_002fTk" accesskey="p" rel="previous">Tcl/Tk</a>, Up: <a href="#Useful-libraries-and-programs" accesskey="u" rel="up">Useful libraries and programs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Java-support-1"></a> <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 (such as <a href="https://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and <a href="https://CRAN.R-project.org/package=JavaGD"><strong>JavaGD</strong></a>: these require a full JDK). This check can be suppressed by configure option <samp>--disable-java</samp>. <a name="index-JAVA_005fHOME"></a> Configure variable <code>JAVA_HOME</code> can be set to point to a specific JRE/JDK, on the <code>configure</code> command line or in the environment. </p> <p>Principal amongst these settings are some paths to the Java libraries and JVM, which are stored in environment variable <a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH"></a> <code>R_JAVA_LD_LIBRARY_PATH</code> in file <samp><var>R_HOME</var>/etc/ldpaths</samp> (or a sub-architecture-specific version). A typical setting for ‘<samp>x86_64</samp>’ Linux is </p> <div class="example"> <pre class="example">JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.191-1.b12.fc28.x86_64/jre R_JAVA_LD_LIBRARY_PATH=${JAVA_HOME}/lib/that/server </pre></div> <p>Unfortunately this 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><var>R_HOME</var>/etc/Makeconf</samp> and <samp><var>R_HOME</var>/etc/ldpaths</samp>. See <code>R CMD javareconf --help</code> for details: note that this needs to be done by the account owning the R installation. </p> <p>Another way of overriding those settings is to set the environment variable <a name="index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-1"></a> <code>R_JAVA_LD_LIBRARY_PATH</code> (before R is started, hence not in <samp>~/.Renviron</samp>), which suffices to run already-installed Java-using packages. For example </p> <div class="example"> <pre class="example">R_JAVA_LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server </pre></div> <p>It may be possible to avoid this by specifying an invariant link as the path when configuring. For example, on that system any of </p> <div class="example"> <pre class="example">JAVA_HOME=/usr/lib/jvm/java JAVA_HOME=/usr/lib/jvm/java-1.8.0 JAVA_HOME=/usr/lib/jvm/java-1.8.0/jre </pre></div> <p>worked. </p> <p>‘Non-server’ distributions of Java as from version 11 are of a full JDK. However, Linux distributions can be confusing: for example Fedora 28 had </p><div class="example"> <pre class="example">java-1.8.0-openjdk java-1.8.0-openjdk-devel java-9-openjdk java-9-openjdk-devel java-openjdk java-openjdk-devel java-11-openjdk java-11-openjdk-devel </pre></div> <p>where the <code>-devel</code> RPMs are needed to complete the JDK. (At the time of writing <code>java-openjdk</code> was Java 10.) Debian/Ubuntu use ‘<samp>-jre</samp>’ and ‘<samp>-jdk</samp>’, e.g. </p><div class="example"> <pre class="example">sudo apt install default-jdk </pre></div> <hr> <a name="Other-compiled-languages"></a> <div class="header"> <p> Previous: <a href="#Java-support" accesskey="p" rel="previous">Java support</a>, Up: <a href="#Useful-libraries-and-programs" accesskey="u" rel="up">Useful libraries and programs</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Other-compiled-languages-1"></a> <h4 class="subsection">A.2.3 Other compiled languages</h4> <p>Some add-on packages need a C++ compiler. This is specified by the configure variables <code>CXX</code>, <code>CXXFLAGS</code> and similar. <code>configure</code> will normally find a suitable compiler. However, in many cases this will be a C++98 compiler, and it is possible to specify an alternative compiler for use with C++11 by the configure variables <code>CXX11</code>, <code>CXX11STD</code>, <code>CXX11FLAGS</code> and similar (see <a href="#C_002b_002b-Support">C++ Support</a>). Again, <code>configure</code> will normally find a suitable value for <code>CXX11STD</code> if the compiler given by <code>CXX</code> is capable of compiling C++11 code, but it is possible that a completely different compiler will be needed. </p> <p>For source files with extension <samp>.f90</samp> or <samp>.f95</samp> containing free-form Fortran, the compiler defined by the macro <code>FC</code> is used by <code>R CMD INSTALL</code>. Note that it is detected by the name of the command without a test that it can actually compile Fortran 90 code. Set the configure variable <code>FC</code> to override this if necessary: variables <code>FCFLAGS</code> and <code>FCLIBS_XTRA</code> might also need to be set. </p> <p>See file <samp>config.site</samp> in the R source for more details about these variables. </p> <hr> <a name="Linear-algebra"></a> <div class="header"> <p> Previous: <a href="#Useful-libraries-and-programs" accesskey="p" rel="previous">Useful libraries and programs</a>, Up: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="u" rel="up">Essential and useful other programs under a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Linear-algebra-1"></a> <h3 class="section">A.3 Linear algebra</h3> <a name="index-BLAS-library"></a> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#BLAS" accesskey="1">BLAS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#LAPACK" accesskey="2">LAPACK</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Caveats" accesskey="3">Caveats</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="BLAS"></a> <div class="header"> <p> Next: <a href="#LAPACK" accesskey="n" rel="next">LAPACK</a>, Previous: <a href="#Linear-algebra" accesskey="p" rel="previous">Linear algebra</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="BLAS-1"></a> <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> <p>You can specify a particular <acronym>BLAS</acronym> library <em>via</em> a value for the configuration option <samp>--with-blas</samp> and not to use an external <acronym>BLAS</acronym> library by <samp>--without-blas</samp> (the default). If <samp>--with-blas</samp> is given with no <code>=</code>, its value is taken from the <a name="index-BLAS_005fLIBS"></a> environment variable <code>BLAS_LIBS</code>, set for example in <samp>config.site</samp>. If neither the option nor the environment variable supply a value, a search is made for a suitable<a name="DOCF59" href="#FOOT59"><sup>59</sup></a> <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>-l</samp>’, so </p> <div class="example"> <pre class="example">--with-blas="foo" </pre></div> <p>is an instruction to link against ‘<samp>-lfoo</samp>’ to find an external <acronym>BLAS</acronym> (which needs to be found both at link time and run time). </p> <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> <p>Some enhanced <acronym>BLAS</acronym>es are compiler-system-specific (<code>sunperf</code> on Solaris<a name="DOCF60" href="#FOOT60"><sup>60</sup></a>, <code>libessl</code> on IBM, <code>Accelerate</code> on macOS). The correct incantation for these is often found <em>via</em> <samp>--with-blas</samp> with no value on the appropriate platforms. </p> <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>. On a machine running other tasks, there can be contention for CPU caches that reduces the effectiveness of the optimization of cache use by a <acronym>BLAS</acronym> implementation: some people warn that this is especially problematic for hyperthreaded CPUs. </p> <p>Note that under Unix (but not under Windows) if R is compiled against a non-default <acronym>BLAS</acronym> and <samp>--enable-BLAS-shlib</samp> is <strong>not</strong> used (it is the default on all platforms except AIX), 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="https://CRAN.R-project.org/package=quantreg"><strong>quantreg</strong></a> will need to be re-installed; they may be under other circumstances. </p> <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. </p> <p>External <acronym>BLAS</acronym> implementations often make less use of extended-precision floating-point registers (where available) and will almost certainly re-order computations. This can result in less accuracy than using a reference <acronym>BLAS</acronym>, and may result in different solutions, e.g. different signs in SVD and eigendecompositions. </p> <p>Debian/Ubuntu systems provide a system-specific way to switch the BLAS in use. Build R with <samp>-with-blas</samp> to select the OS version of the reference BLAS, and then use <code>update-alternatives</code> to switch between the available BLAS libraries. See <a href="https://wiki.debian.org/DebianScience/LinearAlgebraLibraries">https://wiki.debian.org/DebianScience/LinearAlgebraLibraries</a>. </p> <p>The URIs for several of these BLAS have been subject to frequent gratuitous changes, so you will need to search for their current locations. </p> <p>BLAS (and LAPACK) routines may be used inside threaded code, for example in OpenMP sections in packages such as <strong>mgcv</strong>. The reference implementations are thread-safe but external ones may not be (even single-threaded ones): this can lead to hard-to-track-down incorrect results or segfaults. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#ATLAS" accesskey="1">ATLAS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#OpenBLAS" accesskey="2">OpenBLAS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#MKL" accesskey="3">MKL</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Shared-BLAS" accesskey="4">Shared BLAS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="ATLAS"></a> <div class="header"> <p> Next: <a href="#OpenBLAS" accesskey="n" rel="next">OpenBLAS</a>, Previous: <a href="#BLAS" accesskey="p" rel="previous">BLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="ATLAS-1"></a> <h4 class="subsubsection">A.3.1.1 ATLAS</h4> <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 built by default as a static library that on some platforms may not be able to be used with shared objects such as are used in R packages. Be careful when using pre-built versions of ATLAS static libraries (they seem to work on ‘<samp>ix86</samp>’ platforms, but not always on ‘<samp>x86_64</samp>’ ones). </p> <p>ATLAS contains replacements for a small number of LAPACK routines, but can be built to merge these with LAPACK sources to include a full LAPACK library. </p> <p>Recent versions of ATLAS can be built as a single shared library, either <code>libsatlas</code> or <code>libtatlas</code> (serial or threaded respectively): these may even contain a full LAPACK. Such builds can be used by one of </p><div class="example"> <pre class="example">--with-blas=satlas --with-blas=tatlas </pre></div> <p>or, as on ‘<samp>x86_64</samp>’ Fedora where a path needs to be specified, </p><div class="example"> <pre class="example">--with-blas="-L/usr/lib64/atlas -lsatlas" --with-blas="-L/usr/lib64/atlas -ltatlas" </pre></div> <p>Distributed ATLAS libraries cannot be tuned to your machine and so are a compromise: for example Fedora tunes ‘<samp>x86_64</samp>’ for CPUs with SSE3 extensions, and separate ‘<samp>atlas-sse2</samp>’ and ‘<samp>atlas-sse3</samp>’ ‘<samp>i686</samp>’ RPMs are available.<a name="DOCF61" href="#FOOT61"><sup>61</sup></a> </p> <p>Note that building R on Linux against distributed shared libraries may need ‘<samp>-devel</samp>’ or ‘<samp>-dev</samp>’ packages installed. </p> <p>Linking against multiple static libraries requires one of </p><div class="example"> <pre class="example">--with-blas="-lf77blas -latlas" --with-blas="-lptf77blas -lpthread -latlas" --with-blas="-L/path/to/ATLAS/libs -lf77blas -latlas" --with-blas="-L/path/to/ATLAS/libs -lptf77blas -lpthread -latlas" </pre></div> <p>Consult its installation guide<a name="DOCF62" href="#FOOT62"><sup>62</sup></a> for how to build ATLAS as a shared library or as a static library with position-independent code (on platforms where that matters). </p> <p>According to the ATLAS FAQ<a name="DOCF63" href="#FOOT63"><sup>63</sup></a> the maximum number of threads used by multi-threaded ATLAS is set at compile time. Also, the author advises against using multi-threaded ATLAS on hyperthreaded CPUs without restricting affinities at compile-time to one virtual core per physical CPU. (For the Fedora libraries the compile-time flag specifies 4 threads.) </p> <hr> <a name="OpenBLAS"></a> <div class="header"> <p> Next: <a href="#MKL" accesskey="n" rel="next">MKL</a>, Previous: <a href="#ATLAS" accesskey="p" rel="previous">ATLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="OpenBLAS-1"></a> <h4 class="subsubsection">A.3.1.2 OpenBLAS</h4> <p>Dr Kazushige Goto wrote a tuned <acronym>BLAS</acronym> for several processors and OSes, which was frozen in mid-2010. OpenBLAS (<a href="http://www.openblas.net/">http://www.openblas.net/</a>) is a descendant project with support for some later CPUs. </p> <p>This can be used by configuring R with something like </p> <div class="example"> <pre class="example">--with-blas="-lopenblas" </pre></div> <p>See see <a href="#Shared-BLAS">Shared BLAS</a> for an alternative (and in many ways preferable) way to use them. </p> <p>Some platforms provide multiple builds of OpenBLAS: for example Fedora 28 has RPMs<a name="DOCF64" href="#FOOT64"><sup>64</sup></a> </p><div class="example"> <pre class="example">openblas openblas-threads openblas-openmp </pre></div> <p>providing shared libraries </p><div class="example"> <pre class="example">libopenblas.so libopenblasp.so libopenblaso.so </pre></div> <p>respectively, each of which can be used as a shared BLAS. For the second and third the number of threads is controlled by <code>OPENBLAS_NUM_THREADS</code> and <code>OMP_NUM_THREADS</code> (as usual for OpenMP) respectively. There is also a Fedora RPM ‘<samp>openblas-Rblas</samp>’ to replace <samp>libRblas.so</samp> in their distribution of R. </p> <p>Note that building R on Linux against distributed libraries may need ‘<samp>-devel</samp>’ or ‘<samp>-dev</samp>’ packages installed. </p> <p>For ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’ most distributed libraries contain several alternatives for different CPU microarchitectures with the choice being made at run time. </p> <hr> <a name="MKL"></a> <div class="header"> <p> Next: <a href="#Shared-BLAS" accesskey="n" rel="next">Shared BLAS</a>, Previous: <a href="#OpenBLAS" accesskey="p" rel="previous">OpenBLAS</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Intel-MKL"></a> <h4 class="subsubsection">A.3.1.3 Intel MKL</h4> <p>For Intel processors (and perhaps others) and some distributions of Linux, there is Intel’s Math Kernel Library. You are strongly encouraged to read the MKL User’s Guide, which is installed with the library, before attempting to link to MKL. This includes a ‘link line advisor’ which will suggest appropriate incantations: its use is recommended. Or see <a href="https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor">https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor</a>. </p> <p>There are also versions of MKL for macOS<a name="DOCF65" href="#FOOT65"><sup>65</sup></a> and Windows, but when these have been tried they did not work with the default compilers used for R on those platforms. </p> <p>The MKL interface has changed several times and may change again: the following examples have been used with versions 10.3 to 2019.1, for GCC compilers on ‘<samp>x86_64</samp>’. </p> <p>To use a sequential version of MKL we used </p> <div class="example"> <pre class="example">MKL_LIB_PATH=/path/to/intel_mkl/mkl/lib/intel64 export LD_LIBRARY_PATH=$MKL_LIB_PATH MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core -lmkl_sequential" ./configure --with-blas="$MKL" --with-lapack </pre></div> <p>The option <samp>--with-lapack</samp> is used since MKL contains a tuned copy of LAPACK (often older than the current version) as well as <acronym>BLAS</acronym> (see <a href="#LAPACK">LAPACK</a>), although this can be omitted. </p> <p>Threaded MKL may be used by replacing the line defining the variable <code>MKL</code> by (for version 2019.1) </p> <div class="example"> <pre class="example">MKL="-L${MKL_LIB_PATH} -lmkl_gf_lp64 -lmkl_core \ -lmkl_gnu_thread -dl -fopenmp" </pre></div> <p>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 default to a sensible value for sole use of the machine. (Parallel MKL has not always passed <code>make check-all</code>, but did with MKL 2019.1.) </p> <p>It was reported in 2015 that </p> <div class="example"> <pre class="example">--with-blas='-mkl=parallel' --with-lapack </pre></div> <p>worked with the Intel 2015.3 compilers on Centos 6. </p> <hr> <a name="Shared-BLAS"></a> <div class="header"> <p> Previous: <a href="#MKL" accesskey="p" rel="previous">MKL</a>, Up: <a href="#BLAS" accesskey="u" rel="up">BLAS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Shared-BLAS-1"></a> <h4 class="subsubsection">A.3.1.4 Shared BLAS</h4> <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> <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>/lib</samp> and linking both R itself and all the add-on packages against that library. </p> <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>--enable-BLAS-shlib</samp>, and it can always be disabled via <samp>--disable-BLAS-shlib</samp>. </p> <p>This has both advantages and disadvantages. </p> <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> (as used to be standard for ATLAS). </li><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>R.bin</samp> (and <samp>libR.a</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><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>/etc/ldpaths</samp>. </li></ul> <p>Another option to change the <acronym>BLAS</acronym> in use is to symlink a single dynamic <acronym>BLAS</acronym> library to <samp><var>R_HOME</var>/lib/libRblas.so</samp>. For example, just </p> <div class="example"> <pre class="example">mv <var>R_HOME</var>/lib/libRblas.so <var>R_HOME</var>/lib/libRblas.so.keep ln -s /usr/lib64/libopenblasp.so.0 <var>R_HOME</var>/lib/libRblas.so </pre></div> <p>on ‘<samp>x86_64</samp>’ Fedora will change the <acronym>BLAS</acronym> used to multithreaded OpenBLAS. A similar link works for most versions of the OpenBLAS (provided the appropriate <samp>lib</samp> directory is in the run-time library path or <code>ld.so</code> cache). It can also be used for a single-library ATLAS, so on ‘<samp>x86_64</samp>’ Fedora </p> <div class="example"> <pre class="example">ln -s /usr/lib64/atlas/libsatlas.so.3 <var>R_HOME</var>/lib/libRblas.so ln -s /usr/lib64/atlas/libtatlas.so.3 <var>R_HOME</var>/lib/libRblas.so </pre></div> <p>can be used with its distributed ATLAS libraries. (If you have the ‘<samp>-devel</samp>’ RPMS installed you can omit the <code>.0</code>/<code>.3</code>.) </p> <p>Note that rebuilding or symlinking <samp>libRblas.so</samp> may not suffice if the intention is to use a modified LAPACK contained in an external BLAS: the latter could even cause conflicts. However, on Fedora where the OpenBLAS distribution contains a copy of LAPACK, it is the latter which is used. </p> <hr> <a name="LAPACK"></a> <div class="header"> <p> Next: <a href="#Caveats" accesskey="n" rel="next">Caveats</a>, Previous: <a href="#BLAS" accesskey="p" rel="previous">BLAS</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="LAPACK-1"></a> <h4 class="subsection">A.3.2 LAPACK</h4> <a name="index-LAPACK-library"></a> <p>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 macOS and ATLAS and MKL on ‘<samp>ix86</samp>’/‘<samp>x86_64</samp>’ Linux). At least LAPACK version 3.2 is required. This can only be done if <samp>--with-blas</samp> has been used. </p> <p>However, the likely performance gains are thought to be small (and may be negative). 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>--with-lapack</samp>. The default for <samp>--with-lapack</samp> is to check the <acronym>BLAS</acronym> library and then look for an external library ‘<samp>-llapack</samp>’. Sites searching for the fastest possible linear algebra may want to build a LAPACK library using the ATLAS-optimized subset of LAPACK: this is simplest with a dynamic ATLAS library which contains a full LAPACK, when <samp>--with-lapack</samp> suffices. </p> <p>A value for <samp>--with-lapack</samp> can be set <em>via</em> the environment variable <a name="index-LAPACK_005fLIBS"></a> <code>LAPACK_LIBS</code>, but this will only be used if <samp>--with-lapack</samp> is specified (as the default value is <code>no</code>) and the <acronym>BLAS</acronym> library does not contain LAPACK. </p> <p>If you do use <samp>--with-lapack</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 </p> <div class="example"> <pre class="example">DGEBRD gave error code -10 </pre></div> <p>. Other potential problems are incomplete versions of the libraries, seen several times in Linux distributions over the years. </p> <p>Please <strong>do</strong> bear in mind that using <samp>--with-lapack</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> <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 has said </p><blockquote> <p>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. </p></blockquote> <p>We rely on limited support in LAPACK for matrices with <em>2^{31}</em> or more elements: it is possible that an external LAPACK will not have that support. </p> <hr> <a name="Caveats"></a> <div class="header"> <p> Previous: <a href="#LAPACK" accesskey="p" rel="previous">LAPACK</a>, Up: <a href="#Linear-algebra" accesskey="u" rel="up">Linear algebra</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Caveats-1"></a> <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 Oracle compilers the flag <samp>-dalign</samp> is needed if <code>sunperf</code> is to be used. </p> <p>On some systems it has been necessary that an external <acronym>BLAS</acronym>/LAPACK was built with the same Fortran compiler used to build R. </p> <hr> <a name="Configuration-on-a-Unix_002dalike"></a> <div class="header"> <p> Next: <a href="#Platform-notes" accesskey="n" rel="next">Platform notes</a>, Previous: <a href="#Essential-and-useful-other-programs-under-a-Unix_002dalike" accesskey="p" rel="previous">Essential and useful other programs under a Unix-alike</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Configuration-on-a-Unix_002dalike-1"></a> <h2 class="appendix">Appendix B Configuration on a Unix-alike</h2> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Configuration-options" accesskey="1">Configuration options</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Internationalization-support" accesskey="2">Internationalization support</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Configuration-variables" accesskey="3">Configuration variables</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Setting-the-shell" accesskey="4">Setting the shell</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Using-make" accesskey="5">Using make</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Using-Fortran" accesskey="6">Using Fortran</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Compile-and-load-flags" accesskey="7">Compile and load flags</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Maintainer-mode" accesskey="8">Maintainer mode</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Configuration-options"></a> <div class="header"> <p> Next: <a href="#Internationalization-support" accesskey="n" rel="next">Internationalization support</a>, Previous: <a href="#Configuration-on-a-Unix_002dalike" accesskey="p" rel="previous">Configuration on a Unix-alike</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Configuration-options-1"></a> <h3 class="section">B.1 Configuration options</h3> <p><code>configure</code> has many options: running </p> <div class="example"> <pre class="example">./configure --help </pre></div> <p>will give a list. Probably the most important ones not covered elsewhere are (defaults in brackets) </p> <dl compact="compact"> <dt><samp>--with-x</samp></dt> <dd><p>use the X Window System [yes] </p></dd> <dt><samp>--x-includes=<var>DIR</var></samp></dt> <dd><p>X include files are in <var>DIR</var> </p></dd> <dt><samp>--x-libraries=<var>DIR</var></samp></dt> <dd><p>X library files are in <var>DIR</var> </p></dd> <dt><samp>--with-readline</samp></dt> <dd><p>use readline library (if available) [yes] </p></dd> <dt><samp>--enable-R-profiling</samp></dt> <dd><p>attempt to compile support for <code>Rprof()</code> [yes] </p></dd> <dt><samp>--enable-memory-profiling</samp></dt> <dd><p>attempt to compile support for <code>Rprofmem()</code> and <code>tracemem()</code> [no] </p></dd> <dt><samp>--enable-R-shlib</samp></dt> <dd><p>build R as a shared/dynamic library [no] </p></dd> <dt><samp>--enable-BLAS-shlib</samp></dt> <dd><p>build the <acronym>BLAS</acronym> as a shared/dynamic library [yes, except on AIX] </p></dd> </dl> <p>You can use <samp>--without-foo</samp> or <samp>--disable-foo</samp> for the negatives. </p> <p>You will want to use <samp>--disable-R-profiling</samp> if you are building a profiled executable of R (e.g. with ‘<samp>-pg)</samp>’. Support for R profiling requires OS support for POSIX threads (<em>aka</em> ‘<samp>pthreads</samp>’), which are available on all mainstream Unix-alike platforms. </p> <p>Flag <samp>--enable-R-shlib</samp> causes the make process to build R as a dynamic (shared) library, typically called <samp>libR.so</samp>, and link the main R executable <samp>R.bin</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 name="DOCF66" href="#FOOT66"><sup>66</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>--enable-R-shlib</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> <p>For maximally effective use of <code>valgrind</code>, R should be compiled with valgrind instrumentation. The <code>configure</code> option is <samp>--with-valgrind-instrumentation=<var>level</var></samp>, where <var>level</var> is 0, 1 or 2. (Level 0 is the default and does not add anything.) The system headers for <code>valgrind</code> can be requested by option <samp>--with-system-valgrind-headers</samp>: they will be used if present (on Linux they may be in a separate package such as <strong>valgrind-devel</strong>). Note though that there is no guarantee that the code in R will be compatible with very old<a name="DOCF67" href="#FOOT67"><sup>67</sup></a> or future <code>valgrind</code> headers. </p> <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. </p> <p>The <samp>configure</samp> script has other generic options added by <code>autoconf</code> and which are not supported for R: in particular building for one architecture on a different host is not possible. </p> <hr> <a name="Internationalization-support"></a> <div class="header"> <p> Next: <a href="#Configuration-variables" accesskey="n" rel="next">Configuration variables</a>, Previous: <a href="#Configuration-options" accesskey="p" rel="previous">Configuration options</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Internationalization-support-1"></a> <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>--disable-nls</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 </p> <div class="example"> <pre class="example"> Natural language support but running in an English locale </pre></div> <p>in the greeting on starting R. </p> <hr> <a name="Configuration-variables"></a> <div class="header"> <p> Next: <a href="#Setting-the-shell" accesskey="n" rel="next">Setting the shell</a>, Previous: <a href="#Internationalization-support" accesskey="p" rel="previous">Internationalization support</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Configuration-variables-1"></a> <h3 class="section">B.3 Configuration variables</h3> <a name="index-configure-4"></a> <p>If you need or want to set certain configure variables to something other than their default, you can do that by either editing the file <samp>config.site</samp> (which documents many of the variables you might want to set: others can be seen in file <samp>etc/Renviron.in</samp>) or on the command line as </p> <div class="example"> <pre class="example">./configure <var>VAR</var>=<var>value</var> </pre></div> <p>If you are building in a directory different from the sources, there can be copies of <samp>config.site</samp> in the source and the build directories, and both will be read (in that order). In addition, if there is a file <samp>~/.R/config</samp>, it is read between the <samp>config.site</samp> files in the source and the build directories. </p> <p>There is also a general <code>autoconf</code> mechanism for <samp>config.site</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"></a> environment variable <code>CONFIG_SITE</code>, and if not is set at files such as <samp>/usr/local/share/config.site</samp> and <samp>/usr/local/etc/config.site</samp> in the area (exemplified by <samp>/usr/local</samp>) where R would be installed. </p> <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> <p>See the variable output section of <code>configure --help</code> for a list of all these variables. </p> <p>If you find you need to alter configure variables, it is worth noting that some settings may be cached in the file <samp>config.cache</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>--config-cache</samp> (or <samp>-C</samp>) to enable caching. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Setting-paper-size" accesskey="1">Setting paper size</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Setting-the-browsers" accesskey="2">Setting the browsers</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Compilation-flags" accesskey="3">Compilation flags</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Making-manuals" accesskey="4">Making manuals</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Setting-paper-size"></a> <div class="header"> <p> Next: <a href="#Setting-the-browsers" accesskey="n" rel="next">Setting the browsers</a>, Previous: <a href="#Configuration-variables" accesskey="p" rel="previous">Configuration variables</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Setting-paper-size-1"></a> <h4 class="subsection">B.3.1 Setting paper size</h4> <a name="index-R_005fPAPERSIZE-2"></a> <p>One common variable to change is <code>R_PAPERSIZE</code>, which defaults to ‘<samp>a4</samp>’, not ‘<samp>letter</samp>’. (Valid values are ‘<samp>a4</samp>’, ‘<samp>letter</samp>’, ‘<samp>legal</samp>’ and ‘<samp>executive</samp>’.) </p> <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> <p>The configure default will most often be ‘<samp>a4</samp>’ if <code>R_PAPERSIZE</code> is unset. (If the (Debian Linux) program <code>paperconf</code> is found <a name="index-PAPERSIZE"></a> or the environment variable <code>PAPERSIZE</code> is set, these are used to produce the default.) </p> <hr> <a name="Setting-the-browsers"></a> <div class="header"> <p> Next: <a href="#Compilation-flags" accesskey="n" rel="next">Compilation flags</a>, Previous: <a href="#Setting-paper-size" accesskey="p" rel="previous">Setting paper size</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Setting-the-browsers-1"></a> <h4 class="subsection">B.3.2 Setting the browsers</h4> <a name="index-R_005fBROWSER"></a> <p>Another precious variable is <code>R_BROWSER</code>, 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"></a> <p>Its counterpart for PDF files is <code>R_PDFVIEWER</code>. </p> <hr> <a name="Compilation-flags"></a> <div class="header"> <p> Next: <a href="#Making-manuals" accesskey="n" rel="next">Making manuals</a>, Previous: <a href="#Setting-the-browsers" accesskey="p" rel="previous">Setting the browsers</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Compilation-flags-1"></a> <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>-L</samp>’ flags to be passed to the linker) and <code>CPPFLAGS</code> (for header files, using ‘<samp>-I</samp>’ flags to be passed to the C/C++ preprocessors), respectively, to specify these locations. These default to ‘<samp>-L/usr/local/lib</samp>’ (<code>LDFLAGS</code>, ‘<samp>-L/usr/local/lib64</samp>’ on most 64-bit Linux OSes) and ‘<samp>-I/usr/local/include</samp>’ (<code>CPPFLAGS</code>, but note that on most systems <samp>/usr/local/include</samp> is regarded as a system include directory and so instances in that macro will be skipped) to catch the most common cases. If libraries are still not found, then maybe your compiler/linker does not support re-ordering of <samp>-L</samp> and <samp>-l</samp> flags. In this case, use a different compiler (or a front-end shell script which does the re-ordering). </p> <p>These flags can also be used to build a faster-running version of R. On most platforms using <code>gcc</code>, having ‘<samp>-O3</samp>’ in <code>CFLAGS</code> and <code>FFLAGS</code>/<code>FCFLAGS</code> produces worthwhile performance gains with <code>gcc</code> and <code>gfortran</code>, 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>-Wl,-O1</samp>’ in <code>LDFLAGS</code> is worthwhile, and ‘<samp>'-Bdirect,--hash-style=both,-Wl,-O1'</samp>’ is recommended at <a href="https://lwn.net/Articles/192624/">https://lwn.net/Articles/192624/</a>. Tuning compilation to a specific <acronym>CPU</acronym> family (e.g. ‘<samp>-mtune=native</samp>’ for <code>gcc</code>) can give worthwhile performance gains, especially on older architectures such as ‘<samp>ix86</samp>’. </p> <hr> <a name="Making-manuals"></a> <div class="header"> <p> Previous: <a href="#Compilation-flags" accesskey="p" rel="previous">Compilation flags</a>, Up: <a href="#Configuration-variables" accesskey="u" rel="up">Configuration variables</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Making-manuals-1"></a> <h4 class="subsection">B.3.4 Making manuals</h4> <a name="index-R_005fRD4PDF-1"></a> <a name="index-R_005fPAPERSIZE-3"></a> <p>The default settings for making the manuals are controlled by <code>R_RD4PDF</code> and <code>R_PAPERSIZE</code>. </p> <hr> <a name="Setting-the-shell"></a> <div class="header"> <p> Next: <a href="#Using-make" accesskey="n" rel="next">Using make</a>, Previous: <a href="#Configuration-variables" accesskey="p" rel="previous">Configuration variables</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Setting-the-shell-1"></a> <h3 class="section">B.4 Setting the shell</h3> <p>By default the shell scripts such as <samp>R</samp> will be ‘<samp>#!/bin/sh</samp>’ scripts (or using the <code>SHELL</code> chosen by <samp>configure</samp>). This is almost always satisfactory, but on a few systems <samp>/bin/sh</samp> is not a Bourne shell or clone, and the shell to be used can be changed by setting the configure variable <code>R_SHELL</code> to a suitable value (a full path to a shell, e.g. <samp>/usr/local/bin/bash</samp>). </p> <hr> <a name="Using-make"></a> <div class="header"> <p> Next: <a href="#Using-Fortran" accesskey="n" rel="next">Using Fortran</a>, Previous: <a href="#Setting-the-shell" accesskey="p" rel="previous">Setting the shell</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Using-make-1"></a> <h3 class="section">B.5 Using make</h3> <a name="index-make"></a> <p>To compile R, you will most likely find it easiest to use <acronym>GNU</acronym> <code>make</code>, although the Sun <code>make</code> works on Solaris. </p> <p>To build in a separate directory you need a <code>make</code> that supports the <code>VPATH</code> variable, for example <acronym>GNU</acronym> <code>make</code> and Sun <code>make</code>. </p> <p><code>dmake</code> has also been used. e.g, on Solaris 10. </p> <p>If you want to use a <code>make</code> by another name, for example if your <acronym>GNU</acronym> <code>make</code> is called ‘<samp>gmake</samp>’, you need to set the variable <code>MAKE</code> at configure time, for example </p> <a name="index-configure-5"></a> <div class="example"> <pre class="example">./configure MAKE=gmake </pre></div> <hr> <a name="Using-Fortran"></a> <div class="header"> <p> Next: <a href="#Compile-and-load-flags" accesskey="n" rel="next">Compile and load flags</a>, Previous: <a href="#Using-make" accesskey="p" rel="previous">Using make</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Using-Fortran-1"></a> <h3 class="section">B.6 Using Fortran</h3> <a name="index-Fortran"></a> <p>To compile R, you need a Fortran 90 compiler. The current default is to search for <code>gfortran</code>, <code>g95</code>, <code>xlf95</code> <code>f95</code>, <code>fort</code>, <code>ifort</code>, <code>ifc</code>, <code>efc</code>, <code>pgfortran</code>, <code>pgf95</code> <code>lf95</code>, <code>ftn</code>, <code>nagfor</code>, <code>xlf90</code>, <code>f90</code>, <code>pgf90</code>, <code>pghpf</code>, <code>epcf90</code>. (Note that these are searched for by name, without checking the standard of Fortran they support.) </p> <p>The search mechanism can be changed using the configure variable <code>FC</code> which specifies the command that runs the Fortran compiler. If your Fortran compiler is in a non-standard location, you <a name="index-PATH-1"></a> should set the environment variable <code>PATH</code> accordingly before running <code>configure</code>, or use the configure variable <code>FC</code> to specify its full path. </p> <p>If your Fortran libraries are in slightly peculiar places, you should <a name="index-LD_005fLIBRARY_005fPATH-1"></a> also look at <code>LD_LIBRARY_PATH</code> or your system’s equivalent to make sure that all libraries are on this path. </p> <p>Note that only Fortran compilers which convert identifiers to lower case are supported. </p> <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> <p>Some of the Fortran code makes use of <code>DOUBLE COMPLEX</code> and <code>COMPLEX*16</code> variables. This is checked for at configure time, as well as its equivalence to the <code>Rcomplex</code> C structure defined in <samp>R_ext/Complex.h</samp>. </p> <hr> <a name="Compile-and-load-flags"></a> <div class="header"> <p> Next: <a href="#Maintainer-mode" accesskey="n" rel="next">Maintainer mode</a>, Previous: <a href="#Using-Fortran" accesskey="p" rel="previous">Using Fortran</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Compile-and-load-flags-1"></a> <h3 class="section">B.7 Compile and load flags</h3> <p>A wide range of flags can be set in the file <samp>config.site</samp> or as configure variables on the command line. We have already mentioned </p> <dl compact="compact"> <dt><code>CPPFLAGS</code></dt> <dd><p>header file search directory (<samp>-I</samp>) and any other miscellaneous options for the C and C++ preprocessors and compilers </p></dd> <dt><code>LDFLAGS</code></dt> <dd><p>path (<samp>-L</samp>), stripping (<samp>-s</samp>) and any other miscellaneous options for the linker </p></dd> </dl> <p>and others include </p> <dl compact="compact"> <dt><code>CFLAGS</code></dt> <dd><p>debugging and optimization flags, C </p></dd> <dt><code>MAIN_CFLAGS</code></dt> <dd><p>ditto, for compiling the main program (e.g. when profiling) </p></dd> <dt><code>SHLIB_CFLAGS</code></dt> <dd><p>for shared objects (no known examples) </p></dd> <dt><code>FFLAGS</code></dt> <dd><p>debugging and optimization flags, fixed-form Fortran </p></dd> <dt><code>FCFLAGS</code></dt> <dd><p>debugging and optimization flags, free-form Fortran </p></dd> <dt><code>SAFE_FFLAGS</code></dt> <dd><p>ditto for source files which need exact floating point behaviour </p></dd> <dt><code>MAIN_FFLAGS</code></dt> <dd><p>ditto, for compiling the main program (e.g. when profiling) </p></dd> <dt><code>SHLIB_FFLAGS</code></dt> <dd><p>for shared objects (no known examples) </p></dd> <dt><code>MAIN_LDFLAGS</code></dt> <dd><p>additional flags for the main link </p></dd> <dt><code>SHLIB_LDFLAGS</code></dt> <dd><p>additional flags for linking the shared objects </p></dd> <dt><code>LIBnn</code></dt> <dd><p>the primary library directory, <samp>lib</samp> or <samp>lib64</samp> </p></dd> <dt><code>CPICFLAGS</code></dt> <dd><p>special flags for compiling C code to be turned into a shared object </p></dd> <dt><code>FPICFLAGS</code></dt> <dd><p>special flags for compiling Fortran code to be turned into a shared object </p></dd> <dt><code>CXXPICFLAGS</code></dt> <dd><p>special flags for compiling C++ code to be turned into a shared object </p></dd> <dt><code>DEFS</code></dt> <dd><p>defines to be used when compiling C code in R itself </p></dd> </dl> <p>Library paths specified as <samp>-L/lib/path</samp> in <code>LDFLAGS</code> are <a name="index-LD_005fLIBRARY_005fPATH-2"></a> collected together and prepended to <code>LD_LIBRARY_PATH</code> (or your system’s equivalent), so there should be no need for <samp>-R</samp> or <samp>-rpath</samp> flags. </p> <p>Variables such as <code>CPICFLAGS</code> are determined where possible by <code>configure</code>. Some systems allows two types of PIC flags, for example ‘<samp>-fpic</samp>’ and ‘<samp>-fPIC</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> <p>Other variables often set by <code>configure</code> include ‘<samp>MAIN_LDFLAGS</samp>’, ‘<samp>SAFE_FFLAGS</samp>’, ‘<samp>SHLIB_LDFLAGS</samp>’ and ‘<samp>SHLIB_CXXLDFLAGS</samp>’: see file <samp>config.site</samp> in the sources for more documentation on these and others. </p> <p>To compile a profiling version of R, one might for example want to use ‘<samp>MAIN_CFLAGS=-pg</samp>’, ‘<samp>MAIN_FFLAGS=-pg</samp>’, ‘<samp>MAIN_LDFLAGS=-pg</samp>’ on platforms where ‘<samp>-pg</samp>’ cannot be used with position-independent code. </p> <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> <p>On some platforms <code>configure</code> will select additional flags for <code>CFLAGS</code>, <code>CPPFLAGS</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. </p> <hr> <a name="Maintainer-mode"></a> <div class="header"> <p> Previous: <a href="#Compile-and-load-flags" accesskey="p" rel="previous">Compile and load flags</a>, Up: <a href="#Configuration-on-a-Unix_002dalike" accesskey="u" rel="up">Configuration on a Unix-alike</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Maintainer-mode-1"></a> <h3 class="section">B.8 Maintainer mode</h3> <p>There are several files that are part of the R sources but can be re-generated from their own sources by configuring with option <samp>--enable-maintainer-mode</samp> and then running <code>make</code> in the build directory. This requires other tools to be installed, discussed in the rest of this section. </p> <p>File <samp>configure</samp> is created from <samp>configure.ac</samp> and the files under <samp>m4</samp> by <code>autoconf</code> and <code>aclocal</code> (part of the <strong>automake</strong> package). There is a formal version requirement on <code>autoconf</code> of 2.69 or later, but it is unlikely that anything other than the most recent versions<a name="DOCF68" href="#FOOT68"><sup>68</sup></a> have been thoroughly tested. </p> <p>File <samp>src/include/config.h</samp> is created by <code>autoheader</code> (part of <strong>autoconf</strong>). </p> <p>Grammar files <samp>*.y</samp> are converted to C sources by an implementation of <code>yacc</code>, usually <code>bison -y</code>: these are found in <samp>src/main</samp> and <samp>src/library/tools/src</samp>. It is known that earlier versions of <code>bison</code> generate code which reads (and in some cases writes) outside array bounds: <code>bison</code> 2.6.1 was found to be satisfactory. </p> <p>The ultimate sources for package <strong>compiler</strong> are in its <samp>noweb</samp> directory. To re-create the sources from <samp>src/library/compiler/noweb/compiler.nw</samp>, the command <code>notangle</code> is required. Some Linux distributions include this command in package <strong>noweb</strong>. It can also be installed from the sources at <a href="https://www.cs.tufts.edu/~nr/noweb/">https://www.cs.tufts.edu/~nr/noweb/</a><a name="DOCF69" href="#FOOT69"><sup>69</sup></a>. The package sources are only re-created even in maintainer mode if <samp>src/library/compiler/noweb/compiler.nw</samp> has been updated. </p> <hr> <a name="Platform-notes"></a> <div class="header"> <p> Next: <a href="#The-Windows-toolset" accesskey="n" rel="next">The Windows toolset</a>, Previous: <a href="#Configuration-on-a-Unix_002dalike" accesskey="p" rel="previous">Configuration on a Unix-alike</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Platform-notes-1"></a> <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> <p>Older versions of this manual contain notes on platforms such as HP-UX, IRIX, Alpha/OSF1 (for R < 2.10.0, and support has since been removed for all of these) and AIX (for R < = 3.5.x) for which we have had no recent reports. </p> <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 have used (often in included software under <samp>src/extra</samp>) </p><div class="example"> <pre class="example">AIX: _AIX Cygwin: __CYGWIN__ FreeBSD: __FreeBSD__ HP-UX: __hpux__, __hpux IRIX: sgi, __sgi Linux: __linux__ macOS: __APPLE__ NetBSD: __NetBSD__ OpenBSD: __OpenBSD__ Solaris: __sun, sun Windows: _WIN32, _WIN64 </pre></div> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#X11-issues" accesskey="1">X11 issues</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Linux" accesskey="2">Linux</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#macOS" accesskey="3">macOS</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Solaris" accesskey="4">Solaris</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#FreeBSD" accesskey="5">FreeBSD</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#OpenBSD" accesskey="6">OpenBSD</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Cygwin" accesskey="7">Cygwin</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#New-platforms" accesskey="8">New platforms</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="X11-issues"></a> <div class="header"> <p> Next: <a href="#Linux" accesskey="n" rel="next">Linux</a>, Previous: <a href="#Platform-notes" accesskey="p" rel="previous">Platform notes</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="X11-issues-1"></a> <h3 class="section">C.1 X11 issues</h3> <p>The ‘<samp>X11()</samp>’ graphics device is the one started automatically on Unix-alikes (except most macOS builds) 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> <p>The ‘modern’ version of the ‘<samp>X11()</samp>’ device is based on ‘<samp>cairo</samp>’ graphics and (in most implementations) uses ‘<samp>fontconfig</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>X11()</samp>’ discussed in the rest of this section. </p> <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 name="DOCF70" href="#FOOT70"><sup>70</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 </p><div class="example"> <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></div> <p>and you need to ensure that the ‘<samp>-100dpi</samp>’ versions are installed and on the X11 font path (check via <code>xset -q</code>). The ‘<samp>X11()</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> <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 </p> <div class="example"> <pre class="example">"-adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*" </pre></div> <p>If you are using a single-byte encoding, for example ISO 8859-2 in Eastern Europe or KOI8-R in Russian, use <code>xlsfonts</code> 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>xorg-x11-fonts-ISO8859-2-75dpi</samp>’ and ‘<samp>xorg-x11-fonts-cyrillic</samp>’ shown in the listing above. </p> <p>Multi-byte encodings (most commonly UTF-8) are even more complicated. There are few fonts in ‘<samp>iso10646-1</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>XLC_LOCALE</samp>’ directory (typically <samp>/usr/share/X11/locale</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>ja_JP.UTF-8</samp>’ but not when running in ‘<samp>en_GB.UTF-8</samp>’ on the same machine (although on some systems many UTF-8 X11 locales are aliased to ‘<samp>en_US.UTF-8</samp>’ which covers several character sets, e.g. ISO 8859-1 (Western European), JISX0208 (Kanji), KSC5601 (Korean), GB2312 (Chinese Han) and JISX0201 (Kana)). </p> <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>fonts</samp> directory or elsewhere, for example, </p> <div class="example"> <pre class="example">/usr/share/fonts/default/Type1 /usr/share/fonts/ja/TrueType </pre></div> <hr> <a name="Linux"></a> <div class="header"> <p> Next: <a href="#macOS" accesskey="n" rel="next">macOS</a>, Previous: <a href="#X11-issues" accesskey="p" rel="previous">X11 issues</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Linux-1"></a> <h3 class="section">C.2 Linux</h3> <a name="index-Linux-1"></a> <p>Linux is the main development platform for R, so compilation from the sources is normally straightforward with the most common compilers and libraries.<a name="DOCF71" href="#FOOT71"><sup>71</sup></a> </p> <p>Recall 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>-devel</samp>’ or ‘<samp>-dev</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>readline</samp>’ is missing add the developer package. (On most systems you will also need ‘<samp>ncurses</samp>’ and its developer package, although these should be dependencies of the ‘<samp>readline</samp>’ package(s).) You should expect to see in the <code>configure</code> summary </p> <div class="example"> <pre class="example"> Interfaces supported: X11, tcltk External libraries: readline, curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU </pre></div> <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>R-help</samp>’ archives will normally reveal what is needed. </p> <p>It seems that ‘<samp>ix86</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>x86_64</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> <p>The default optimization settings chosen for <code>CFLAGS</code> etc are conservative. It is likely that using <samp>-mtune</samp> will result in significant performance improvements on recent CPUs: one possibility is to add <samp>-mtune=native</samp> for the best possible performance on the machine on which R is being installed. It is also possible to increase the optimization levels to <samp>-O3</samp>: however for many versions of the compilers this has caused problems in at least one <acronym>CRAN</acronym> package. </p> <p>For platforms with both 64- and 32-bit support, it is likely that </p> <div class="example"> <pre class="example">LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib" </pre></div> <p>is appropriate since most (but not all) software installs its 64-bit libraries in <samp>/usr/local/lib64</samp>. To build a 32-bit version of R on ‘<samp>x86_64</samp>’ with Fedora 28 we used </p> <div class="example"> <pre class="example">CC="gcc -m32" CXX="g++ -m32" FC="gfortran -m32" OBJC=${CC} LDFLAGS="-L/usr/local/lib" LIBnn=lib </pre></div> <p>Note the use of ‘<samp>LIBnn</samp>’: ‘<samp>x86_64</samp>’ Fedora installs its 64-bit software in <samp>/usr/lib64</samp> and 32-bit software in <samp>/usr/lib</samp>. Linking will skip over inappropriate binaries, but for example the 32-bit Tcl/Tk configure scripts are in <samp>/usr/lib</samp>. It may also be necessary to set the <code>pkg-config</code> path, e.g. by </p> <div class="example"> <pre class="example">export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig </pre></div> <p>The 32-bit system <code>libcurl</code> did not work with the system CA certificates: this is worked around in R’s test suite. </p> <p>64-bit versions on Linux are built with support for files > 2Gb, and 32-bit versions will be if possible unless <samp>--disable-largefile</samp> is specified. </p> <p>Note that 32-bit <code>glibc</code> currently<a name="DOCF72" href="#FOOT72"><sup>72</sup></a> uses a 32-bit <code>time_t</code> type, so to pass all the date-time checks needs R built with flag <samp>--with-internal-tzcode</samp>. </p> <p>To build a 64-bit version of R on ‘<samp>ppc64</samp>’ (also known as ‘<samp>powerpc64</samp>’) with <code>gcc</code> 4.1.1, Ei-ji Nakama used </p> <div class="example"> <pre class="example">CC="gcc -m64" CXX="gxx -m64" FC="gfortran -m64" CFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" FFLAGS="-mminimal-toc -fno-optimize-sibling-calls -g -O2" </pre></div> <p>the additional flags being needed to resolve problems linking against <samp>libnmath.a</samp> and when linking R as a shared library. </p> <p>The setting of the macro ‘<samp>SAFE_FFLAGS</samp>’ may need some help. It should not need additional flags on platforms other than ‘<samp>68000</samp>’ (not likely to be encountered) and ‘<samp>ix86</samp>’. For the latter, if the Fortran compiler is GNU (<code>gfortran</code> or possibly <code>g77</code>) the flags </p><div class="example"> <pre class="example">-msse2 -mfpmath=sse </pre></div> <p>are added: earlier versions of R added <samp>-ffloat-store</samp> and this might still be needed if a ‘<samp>ix86</samp>’ CPU is encountered without SSE2 support. Note that it is a <em>replacement</em> for ‘<samp>FFLAGS</samp>’, so should include all the flags in that macro (except perhaps the optimization level). </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Clang" accesskey="1">Clang</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Intel-compilers" accesskey="2">Intel compilers</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Clang"></a> <div class="header"> <p> Next: <a href="#Intel-compilers" accesskey="n" rel="next">Intel compilers</a>, Previous: <a href="#Linux" accesskey="p" rel="previous">Linux</a>, Up: <a href="#Linux" accesskey="u" rel="up">Linux</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Clang-1"></a> <h4 class="subsection">C.2.1 Clang</h4> <p>R has been built with Linux ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’ C and C++ compilers (<a href="http://clang.llvm.org">http://clang.llvm.org</a>) based on the Clang front-ends, invoked by <code>CC=clang CXX=clang++</code>, together with <code>gfortran</code>. These take very similar options to the corresponding GCC compilers. </p> <p>This has to be used in conjunction with a Fortran compiler: the <code>configure</code> code will remove <samp>-lgcc</samp> from <code>FLIBS</code>, which is needed for some versions of <code>gfortran</code>. </p> <p>The current out-of-the-box default for <code>clang++</code> is to use the C++ runtime from the installed <code>g++</code>. Using the runtime from the <code>libc++</code> project (<a href="http://libcxx.llvm.org/">http://libcxx.llvm.org/</a>, Fedora RPM <code>libcxx-devel</code>) <em>via</em> <samp>-stdlib=libc++</samp> has also been tested. </p> <p>Recent versions have (optional when built) OpenMP support.<a name="DOCF73" href="#FOOT73"><sup>73</sup></a> </p> <p>There is a project called <code>flang</code> (<a href="https://github.com/flang-compiler/flang">https://github.com/flang-compiler/flang</a>)) to develop a Fortran compiler similar to clang but based on the Portland Group’s front end. This needs something like </p><div class="example"> <pre class="example">FC=/usr/local/flang/bin/flang LDFLAGS="-L/usr/local/flang/lib -L/usr/local/lib64" </pre></div> <p>Note that <code>flang</code> accepts all the flags which <code>clang</code> does (the driver is a modified version of <code>clang</code>, and <code>flang</code> is a symbolic link to <code>clang</code>), but does not implement all of them for Fortran compilation: it also accepts most PGI-style flags such as <samp>-mp</samp> for OpenMP. It currently produces few diagnostics even with <samp>-Wall -pedantic</samp>. </p> <p><code>flang</code>’s Fortran runtime is compiled against OpenMP and it seems this conflicts with using OpenMP in R. So it may be necessary to disable the latter by configuring R using <samp>--disable-openmp</samp>. </p> <p>It is not clear what architectures <code>flang</code> intends to support: our experiments were done on ‘<samp>x86_64</samp>’. At the time of writing binary ‘releases’ were available for that platform (called by them ‘<samp>x86</samp>’) and ‘<samp>ppc64le</samp>’. </p> <hr> <a name="Intel-compilers"></a> <div class="header"> <p> Previous: <a href="#Clang" accesskey="p" rel="previous">Clang</a>, Up: <a href="#Linux" accesskey="u" rel="up">Linux</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Intel-compilers-1"></a> <h4 class="subsection">C.2.2 Intel compilers</h4> <p>Intel compilers have been used under ‘<samp>ix86</samp>’ and ‘<samp>x86_64</samp>’ Linux. Brian Ripley used version 9.0 of the compilers for ‘<samp>x86_64</samp>’ on Fedora Core 5 with </p> <div class="example"> <pre class="example">CC=icc CFLAGS="-g -O3 -wd188 -ip -mp" FC=ifort FLAGS="-g -O3 -mp" CXX=icpc CXXFLAGS="-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$IFC_LIBS -L/usr/local/lib64" SHLIB_CXXLD=icpc </pre></div> <p>It may be necessary to use <code>CC="icc -std=c99"</code> or <code>CC="icc -c99"</code> for C99-compliance. The flag <samp>-wd188</samp> suppresses a large number of warnings about the enumeration type ‘<samp>Rboolean</samp>’. Because the Intel C compiler sets ‘<samp>__GNUC__</samp>’ without complete emulation of <code>gcc</code>, we suggest adding <code>CPPFLAGS=-no-gcc</code>. </p> <p>To maintain correct <acronym>IEC</acronym> 60559 arithmetic you most likely need add flags to <code>CFLAGS</code>, <code>FFLAGS</code>, <code>FCFLAGS</code> and <code>CXXFLAGS</code> such as <samp>-mp</samp> (shown above) or <samp>-fp-model precise -fp-model source</samp>, depending on the compiler version. </p> <p>Others have reported success with versions 10.x and 11.x. Bjørn-Helge Mevik reported success with version 2015.3 of the compilers, using (for a SandyBridge CPU on Centos 6.x) </p> <div class="example"> <pre class="example">fast="-fp-model precise -ip -O3 -opt-mem-layout-trans=3 -xHost -mavx" CC=icc CFLAGS="$fast -wd188" FC=ifort FFLAGS="$fast" CXX=icpc CXXFLAGS="$fast" </pre></div> <p>It is possible that 32-builds need to force the use of SSE2 instructions in <code>SAFE_FFLAGS</code>, e.g. by </p><div class="example"> <pre class="example">SAFE_FFLAGS=-axsse2 </pre></div> <hr> <a name="macOS"></a> <div class="header"> <p> Next: <a href="#Solaris" accesskey="n" rel="next">Solaris</a>, Previous: <a href="#Linux" accesskey="p" rel="previous">Linux</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="macOS-2"></a> <h3 class="section">C.3 macOS</h3> <a name="index-macOS-2"></a> <p>(‘macOS’ was known as ‘OS X’ from 2012–2016.) </p> <p>The instructions here are for ‘<samp>x86_64</samp>’ builds on 10.11 (El Capitan) or later. R can in principle be built for 10.6 and later, although this is little tested and it may be necessary to install later versions of software such as <code>libcurl</code>. </p> <p>To build R you need Apple’s ‘Command Line Tools’: these can be (re-)installed by <code>xcode-select --install</code>. (If you have a fresh OS installation, running e.g. <code>make</code> in a terminal will offer the installation of the command-line tools. If you have installed Xcode, this provides the command-line tools. The tools will need to be reinstalled when macOS is upgraded, as upgrading partially removes them.) For macOS 10.14 (‘Mojave’) an additional step is needed to install the headers to <samp>/usr/include</samp>: from a Terminal run </p><div class="example"> <pre class="example">sudo installer -pkg \ /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg \ -target / </pre></div> <p>(This will need to be re-run if the OS decides to update the Command Line Tools.) Alternatively, change the include path <em>via</em> </p><div class="example"> <pre class="example">CPPFLAGS="-isystem /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include" </pre></div> <p>Which is said to be going to be needed for future versions of macOS. (The location of the SDK, which could change, can be found by running <code>xcrun -show-sdk-path</code>. It is likely that the compilers included in the Command Line Tools will find the headers under the SDK without this additional step, but other versions of <code>clang</code> will not.) </p> <p>You need GNU <code>readline</code>. That and other binary components are available from <a href="https://mac.R-project.org/libs">https://mac.R-project.org/libs</a>: you will need <code>pcre</code> and <code>xz</code> (for <code>libzma</code>) as recent macOS versions provide libraries but not headers for these (and the system <code>pcre</code> is too old at 8.02 for versions up to Sierra, although High Sierra had 8.40). </p> <p>An X sub-system is required unless configuring using <samp>--without-x</samp>: see <a href="https://xquartz.macosforge.org/">https://xquartz.macosforge.org/</a>. R’s <code>configure</code> script can be told to look for <code>X11</code> in <code>XQuartz</code>’s main location of <samp>/opt/X11</samp>, e.g. by </p><div class="example"> <pre class="example">--x-includes=/opt/X11/include --x-libraries=/opt/X11/lib </pre></div> <p>although linked versions under <samp>/usr/X11</samp> will be found. </p> <p>To use the <code>quartz()</code> graphics device you need to configure with <samp>--with-aqua</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 command-line-R data editor/viewer and one version of Tcl/Tk. (This option needs an Objective-C compiler<a name="DOCF74" href="#FOOT74"><sup>74</sup></a> which can compile the source code of <code>quartz()</code>.) </p> <p>Use <samp>--without-aqua</samp> if you want a standard Unix-alike build: apart from disabling <code>quartz()</code> and the ability to use the build with <small>R.APP</small>, it also changes the default location of the personal library (see <code>?.libPaths</code>). </p> <p>Various compilers can be used. One could use </p> <div class="example"> <pre class="example">CC=clang CXX=clang++ FC=/usr/local/gfortran/bin/gfortran OBJC=clang CFLAGS='-Wal -g -O2' CXXFLAGS='-Wall -g -O2' OBJCFLAGS='-Wall -g -O2' FFLAGS='-Wall -g -O2 -mtune=generic' </pre></div> <p>with <code>clang</code> and <code>clang++</code> from the ‘Command Line Tools’ and the Fortran compiler from one of the packages described in the next paragraph. </p> <p>There are installers<a name="DOCF75" href="#FOOT75"><sup>75</sup></a> for Fortran compilers for El Capitan, Sierra and Mojave at <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases/download/6.1/gfortran-6.1-ElCapitan.dmg">https://github.com/fxcoudert/gfortran-for-macOS/releases/download/6.1/gfortran-6.1-ElCapitan.dmg</a>, <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases/download/6.3/gfortran-6.3-Sierra.dmg">https://github.com/fxcoudert/gfortran-for-macOS/releases/download/6.3/gfortran-6.3-Sierra.dmg</a> and <a href="https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg">https://github.com/fxcoudert/gfortran-for-macOS/releases/download/8.2/gfortran-8.2-Mojave.dmg</a>. (An Apple package for 6.1 is also available at <a href="https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg">https://cran.r-project.org/bin/macosx/tools/gfortran-6.1.pkg</a>.) One way to use these builds with a binary distribution of R is to have a <samp>~/.R/Makevars</samp> file similar to (El Capitan) </p><div class="example"> <pre class="example">FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm </pre></div> <p>or (Sierra or High Sierra) </p><div class="example"> <pre class="example">FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm </pre></div> <p>or (Mojave) </p><div class="example"> <pre class="example">FC = /usr/local/gfortran/bin/gfortran FLIBS = -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm </pre></div> <p>(with lines broken here for legibility). </p> <p>Current <acronym>CRAN</acronym> binary distributions use the build of <code>clang</code> 6.0.0 contained in <a href="https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg">https://cran.r-project.org/bin/macosx/tools/clang-6.0.0.pkg</a>. Other recent distributions of <code>clang</code> are often available from <a href="http://llvm.org/releases/">http://llvm.org/releases/</a>: for example at the time of writing<a name="DOCF76" href="#FOOT76"><sup>76</sup></a> of 6.0.1, 7.0.0 and 8.0.0. In particular, all of these include support for OpenMP which Apple builds of <code>clang</code> do not. Suppose one of these distributions is installed under <samp>/usr/local/clang6</samp>. Then R could be configured by something like </p><div class="example"> <pre class="example">./configure --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib \ PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig \ DYLD_FALLBACK_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib </pre></div> <p>with <samp>config.site</samp> containing </p><div class="example"> <pre class="example">CC=/usr/local/clang6/bin/clang OBJC=$CC FC=/usr/local/gfortran/bin/gfortran CXX=/usr/local/clang6/bin/clang++ LDFLAGS="-L/usr/local/clang6/lib -L/usr/local/lib" R_LD_LIBRARY_PATH=/usr/local/clang6/lib:/usr/local/lib </pre></div> <p>The care to specify library paths is to ensure that the OpenMP runtime library, here <samp>/usr/local/clang6/lib/libomp.dylib</samp>, is found when needed. If this works, you should see the line </p><div class="example"> <pre class="example">checking whether OpenMP SIMD reduction is supported... yes </pre></div> <p>in the <code>configure</code> output. Also, ‘<samp>R_LD_LIBRARY_PATH</samp>’ needs to be set to find the latest version of the C++ run-time libraries rather than the system ones. </p> <p>Pre-compiled versions of many of the <a href="#Useful-libraries-and-programs">Useful libraries and programs</a> are available from <a href="https://mac.R-project.org/libs/">https://mac.R-project.org/libs/</a>. You will most likely want at least <code>jpeg</code> and <code>tiff</code>. The <code>pkg-config</code> utility is not provided by Apple and used for the installation from source of many packages: it will also be used if present when configuring the <code>X11()</code> and bitmap devices. </p> <p>Support for <code>cairo</code> (without <code>Pango</code>) can be enabled if <code>pkg-config</code> and XQuartz are available. Make sure the XQuartz’s <code>pkg-config</code> files are found first on the configuration path: for example by setting </p><div class="example"> <pre class="example">export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig </pre></div> <p>or appending that variable to the <code>configure</code> command. </p> <a name="index-BLAS-library-1"></a> <a name="index-LAPACK-library-1"></a> <p>The <code>Accelerate</code> library<a name="DOCF77" href="#FOOT77"><sup>77</sup></a> can be used <em>via</em> the configuration options </p> <div class="example"> <pre class="example">--with-blas="-framework Accelerate" </pre></div> <p>to provide potentially higher-performance versions of the <acronym>BLAS</acronym> and LAPACK routines.<a name="DOCF78" href="#FOOT78"><sup>78</sup></a> This also includes a full LAPACK which can be used <em>via</em> <samp>--with-lapack</samp>: however, the version of LAPACK it contains is currently seriously old (‘<samp>3.2.1</samp>’ in macOS 10.13.6). </p> <p>In recent versions of macOS, threading in Accelerate is controlled by ‘Grand Central Dispatch’ and is said not to need user control. </p> <p>Looking at the top of <samp>/Library/Frameworks/R.framework/Resources/etc/Makeconf</samp> will show the compilers and configuration options used for the <acronym>CRAN</acronym> binary package for R: at the time of writing the non-default options </p><div class="example"> <pre class="example">--enable-memory-profiling --enable-R-framework --x-libraries=/opt/X11/lib </pre></div> <p>were used. </p> <p>Configure option <samp>--with-internal-tzcode</samp> is the default on macOS, as the system implementation of time zones does not work correctly for times before 1902 or after 2037 (despite using a 64-bit <code>time_t</code>). </p> <p>The TeX implementation used by the developers is MacTeX (<a href="https://www.tug.org/mactex/">https://www.tug.org/mactex/</a>): the full installation is about 5GB, but a smaller version (‘Basic TeX’) is available at <a href="https://www.tug.org/mactex/morepackages.html">https://www.tug.org/mactex/morepackages.html</a> to which you will need to add some packages, e.g. for the 2018 version we needed to add<a name="DOCF79" href="#FOOT79"><sup>79</sup></a> <strong>cm-super</strong>, <strong>helvetic</strong>, <strong>inconsolata</strong> and <strong>texinfo</strong> which brought this to about 310MB. ‘<samp>TeX Live Utility</samp>’ (available <em>via</em> the MacTeX front page) provides a graphical means to manage TeX packages. </p> <p>One macOS quirk is that the default path has <samp>/usr/local/bin</samp> after <samp>/usr/bin</samp>, contrary to common practice on Unix-alikes. This means that if you install tools from the sources they will by default be installed under <samp>/usr/local</samp> and not supersede the system versions. </p> <p>If you upgrade your OS you should re-install the ‘Command Line Tools’ and may need to re-install XQuartz and Java (this has been needed for some upgrades but not others). </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#Tcl_002fTk-headers-and-libraries" accesskey="1">Tcl/Tk headers and libraries</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Java-_0028macOS_0029" accesskey="2">Java (macOS)</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Frameworks" accesskey="3">Frameworks</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Building-R_002eapp" accesskey="4">Building R.app</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="Tcl_002fTk-headers-and-libraries"></a> <div class="header"> <p> Next: <a href="#Java-_0028macOS_0029" accesskey="n" rel="next">Java (macOS)</a>, Previous: <a href="#macOS" accesskey="p" rel="previous">macOS</a>, Up: <a href="#macOS" accesskey="u" rel="up">macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Tcl_002fTk-headers-and-libraries-1"></a> <h4 class="subsection">C.3.1 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 <small>R.APP</small> 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 and available as separate <code>tcl</code> and <code>tk</code> components from <a href="https://mac.R-project.org/libs/">https://mac.R-project.org/libs/</a>. This may need <code>configure</code> options </p><div class="example"> <pre class="example">-with-tcltk=/usr/local/lib </pre></div> <p>or </p><div class="example"> <pre class="example">--with-tcl-config=/usr/local/lib/tclConfig.sh --with-tk-config=/usr/local/lib/tkConfig.sh </pre></div> <p>Note that this requires a matching XQuartz installation. </p> <p>There is also a native (‘Aqua’) version of Tcl/Tk which produces widgets in the native macOS style: this will not work with <small>R.APP</small> because of conflicts over the macOS menu, but for those only using command-line R this provides a much more intuitive interface to Tk for experienced Mac users. Most versions of macOS come with Aqua Tcl/Tk libraries, but these are not at all recent versions of Tcl/Tk (8.5.9 in Sierra, which is not even the latest patched version in that series). It is better to install Tcl/Tk 8.6.x from the sources or a binary distribution from <a href="https://www.activestate.com/activetcl/downloads">https://www.activestate.com/activetcl/downloads</a>. Configure R with </p><div class="example"> <pre class="example">--with-tcl-config=/Library/Frameworks/Tcl.framework/tclConfig.sh --with-tk-config=/Library/Frameworks/Tk.framework/tkConfig.sh </pre></div> <p>If you need to find out which distribution of Tk is in use at run time, use </p><div class="example"> <pre class="example">library(tcltk) tclvalue(.Tcl("tk windowingsystem")) # "x11" or "aqua" </pre></div> <hr> <a name="Java-_0028macOS_0029"></a> <div class="header"> <p> Next: <a href="#Frameworks" accesskey="n" rel="next">Frameworks</a>, Previous: <a href="#Tcl_002fTk-headers-and-libraries" accesskey="p" rel="previous">Tcl/Tk headers and libraries</a>, Up: <a href="#macOS" accesskey="u" rel="up">macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Java"></a> <h4 class="subsection">C.3.2 Java</h4> <p>The situation with Java support on macOS is messy,<a name="DOCF80" href="#FOOT80"><sup>80</sup></a> and distribution of Java for all platforms changed in 2018. </p> <p>macOS no longer comes with an installed Java runtime (JRE), and a macOS upgrade may remove one if already installed: it is intended to be installed at first use. Check if a JRE is installed by running <code>java -version</code> in a <code>Terminal</code> window: if Java is not installed<a name="DOCF81" href="#FOOT81"><sup>81</sup></a> this should prompt you to install it. You can also install directly a recent Java from Oracle (currently from <a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">http://www.oracle.com/technetwork/java/javase/downloads/index.html</a>). Builds of OpenJDK may also be available, e.g. from <a href="http://jdk.java.net/">http://jdk.java.net/</a>. We recommend you install a version with long-term support, e.g. 8 or 11 (but not 9, 10 or 12 which have/had a 6-month lifetime). </p> <p>Binary distributions of R are built against a specific version (e.g. 9) of Java so <code>sudo R CMD javareconf</code> will likely be needed before using Java-using packages. </p> <p>To see what compatible versions of Java are currently installed, run <code>/usr/libexec/java_home -V -a x86_64</code>. If needed, set the environment variable <code>JAVA_HOME</code> to choose between these, both when R is built from the sources and when <code>R CMD javareconf</code> is run. </p> <p>Configuring and building R both looks for a JRE and for support for compiling JNI programs (used by packages <a href="https://CRAN.R-project.org/package=rJava"><strong>rJava</strong></a> and <a href="https://CRAN.R-project.org/package=JavaGD"><strong>JavaGD</strong></a>); the latter requires a JDK (Java SDK) and not just a JRE<a name="DOCF82" href="#FOOT82"><sup>82</sup></a>. </p> <p>The build process tries to fathom out what JRE/JDK to use, but it may need some help, e.g. by setting <code>JAVA_HOME</code>. A JDK can be specified explicitly by something like </p><div class="example"> <pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin" JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/lib/server" JAVA_LIBS="-L/${JAVA_HOME}/lib/server -ljvm" </pre></div> <p>or </p><div class="example"> <pre class="example">JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_191.jdk/Contents/Home JAVA_CPPFLAGS="-I/${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></div> <p>in <samp>config.site</samp>. </p> <p>To use the builds of OpenJDK (tarballs) from <a href="http://jdk.java.net/">http://jdk.java.net/</a>, set <code>JAVA_HOME</code>: </p><div class="example"> <pre class="example">JAVA_HOME=<var>/path/to/JDK</var>/jdk-11.jdk/Contents/Home </pre></div> <p>where <samp><var>/path/to/JDK</var></samp> is wherever the distribution tarball was unpacked. </p> <p>Note that it is necessary to set the environment variable <code>NOAWT</code> to <code>1</code> to install many of the Java-using packages. </p> <hr> <a name="Frameworks"></a> <div class="header"> <p> Next: <a href="#Building-R_002eapp" accesskey="n" rel="next">Building R.app</a>, Previous: <a href="#Java-_0028macOS_0029" accesskey="p" rel="previous">Java (macOS)</a>, Up: <a href="#macOS" accesskey="u" rel="up">macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Frameworks-1"></a> <h4 class="subsection">C.3.3 Frameworks</h4> <p>The <acronym>CRAN</acronym> build of R is installed as a framework, which is selected by the option </p> <div class="example"> <pre class="example">./configure --enable-R-framework </pre></div> <p>(This is intended to be used with an Apple toolchain: others may not support frameworks correctly but those from <code>llvm.org</code> do.) </p> <p>It is only needed if you want to build R for use with the <small>R.APP</small> console, and implies <samp>--enable-R-shlib</samp> to build R as a dynamic library. This option configures R to be built and installed as a framework called <samp>R.framework</samp>. The default installation path for <samp>R.framework</samp> is <samp>/Library/Frameworks</samp> but this can be changed at configure time by specifying the flag <samp>--enable-R-framework[=<var>DIR</var>]</samp> (or <samp>--prefix</samp>) or at install time <em>via</em> </p> <div class="example"> <pre class="example">make prefix=/where/you/want/R.framework/to/go install </pre></div> <p>Note that installation as a framework is non-standard (especially to a non-standard location) and Unix utilities may not support it (e.g. the <code>pkg-config</code> file <samp>libR.pc</samp> will be put somewhere unknown to <code>pkg-config</code>). </p> <hr> <a name="Building-R_002eapp"></a> <div class="header"> <p> Previous: <a href="#Frameworks" accesskey="p" rel="previous">Frameworks</a>, Up: <a href="#macOS" accesskey="u" rel="up">macOS</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Building-R_002eapp-1"></a> <h4 class="subsection">C.3.4 Building R.app</h4> <p>Note that building the <small>R.APP</small> GUI console is a separate project, using Xcode. Before compiling <small>R.APP</small> make sure the current version of R is installed in <samp>/Library/Frameworks/R.framework</samp> and working at the command-line (this can be a binary install). </p> <p>The current sources can be checked out by </p><div class="example"> <pre class="example">svn co https://svn.r-project.org/R-packages/trunk/Mac-GUI </pre></div> <p>and built by loading the <code>R.xcodeproj</code> project (select the <code>R</code> target and a suitable configuration), or from the command-line by e.g. </p><div class="example"> <pre class="example">xcodebuild -target R -configuration Release </pre></div> <p>See also the <samp>INSTALL</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> <p><small>R.APP</small> does not need to be installed in any specific way. Building <small>R.APP</small> results in the <small>R.APP</small> bundle which appears as one R icon. This application bundle can be run anywhere and it is customary to place it in the <samp>/Applications</samp> folder. </p> <hr> <a name="Solaris"></a> <div class="header"> <p> Next: <a href="#FreeBSD" accesskey="n" rel="next">FreeBSD</a>, Previous: <a href="#macOS" accesskey="p" rel="previous">macOS</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Solaris-1"></a> <h3 class="section">C.4 Solaris</h3> <a name="index-Solaris"></a> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#g_t64_002dbit-builds" accesskey="1">64-bit builds</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Using-gcc" accesskey="2">Using gcc</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <p>R has been built successfully on Solaris 10 using the (zero cost) Oracle Developer Studio<a name="DOCF83" href="#FOOT83"><sup>83</sup></a> compilers: there has also been success with <code>gcc</code>/<code>gfortran</code>. (Recent Sun machines are AMD Opterons or Intel Xeons (‘<samp>amd64</samp>’) rather than ‘<samp>x86</samp>’, but 32-bit ‘<samp>x86</samp>’ executables are the default.) How these compilers identify themselves is slightly confusing: commands <code>CC -V</code> with Developer Studio 12.5 and 12.6 report as versions 5.14 and 5.15. We will only consider Developer Studio versions 12.5 (May 2016) and 12.6 (July 2017): instructions for 12.3 can be found in versions of this manual for R 3.3.x. </p> <p>There have been few reports on Solaris 11, with no known extra issues. </p> <p>Solaris was last tested on Sparc machines in June 2017. </p> <p>The Solaris versions of several of the tools needed to build R (e.g. <code>make</code>, <code>ar</code> and <code>ld</code>) are in <samp>/usr/ccs/bin</samp>, so if using those tools ensure this is in your path. A version of the preferred <acronym>GNU</acronym> <code>tar</code> is (if installed) in <samp>/usr/sfw/bin</samp>. It may be necessary to avoid the tools in <samp>/usr/ucb</samp>: POSIX-compliant versions of some tools can be found in <samp>/usr/xpg4/bin</samp> and <samp>/usr/xpg6/bin</samp>. </p> <p>A large selection of Open Source software can be installed from <a href="https://www.opencsw.org">https://www.opencsw.org</a>, by default installed under <samp>/opt/csw</samp>. Solaris 10 ships with <code>bzlib</code> version 1.0.6 (sufficient) but <code>zlib</code> version 1.2.3 (too old): OpenCSW has 1.2.8. (Note from 2019: updating of OpenCSW has slowed or stopped.) </p> <p>At least when compiling with Oracle compilers, Solaris uses far more stack space than other platforms. This makes it desirable to build PCRE with the option <samp>--disable-stack-for-recursion</samp>: the OpenCSW distribution was at the time of writing. </p> <p>The Oracle compilers are unusual in not including <samp>/usr/local/include</samp> in the default include search path: R’s default <code>CPPFLAGS=-I/usr/local/include</code> remedies this. If you rely on OpenCSW software you may need <code>CPPFLAGS=-I/opt/csw/include</code> (or both). </p> <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> <p>The native <code>make</code> suffices to build R but a number of packages require <acronym>GNU</acronym> <code>make</code> (some without declaring it as ‘<samp>SystemRequirements</samp>’ in the <samp>DESCRIPTION</samp> file). </p> <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 the <code>configure</code> option <samp>--disable-long-double</samp> can be used for faster but less accurate computations. </p> <p>The Solaris time-zone conversion services seem to be unreliable pre-1916 in Europe (when daylight-savings time was first introduced): most often reporting in the non-existent DST variant. Using <code>configure</code> option <samp>--with-internal-tzcode</samp> is recommended, and required if you find time-zone abbreviations being given odd values (as has been seen on 64-bit builds without it). </p> <p>When using the Oracle compilers do <em>not</em> specify <samp>-fast</samp>, as this disables <acronym>IEEE</acronym> arithmetic and <code>make check</code> will fail. </p> <p>A little juggling of paths was needed to ensure <acronym>GNU</acronym> <code>libiconv</code> (in <samp>/usr/local</samp>) was used rather than the Solaris <code>iconv</code>: </p> <div class="example"> <pre class="example">CC="cc -xc99" CFLAGS="-O -xlibmieee" FC=f95 FFLAGS=-O CXX=CC CXXSTD="-std=c++11 -library=stdcpp,CrunG3" CXX98STD="-compat=g -library=stdcpp,CrunG3" CXX11STD="-std=c++11 -library=stdcpp,CrunG3" CXX14STD="-std=c++14 -library=stdcpp,CrunG3" CXXFLAGS=-O R_LD_LIBRARY_PATH="/opt/developerstudio12.6/lib:/usr/local/lib:/opt/csw/lib" </pre></div> <p>The Oracle 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>-xlibmieee</samp> to ensure this. </p> <p>A peculiarity of some versions of the Fortran compiler has been that when asked to link a shared object they did not link against all the Fortran 9x runtime libraries, hence </p><div class="example"> <pre class="example">FCLIBS_XTRA="-lfsu /opt/developerstudio12.6/lib/libfui.so.2" </pre></div> <p>has been needed. </p> <p>Using <code>-xlibmil</code> in <code>CFLAGS</code> or <code>-xlibmil</code> in <code>FFLAGS</code>/<code>FCFLAGS</code> allows more system mathematical functions to be inlined. </p> <p>On ‘<samp>x86</samp>’ you will get marginally higher performance <em>via</em> </p> <div class="example"> <pre class="example">CFLAGS="-xO5 -xlibmieee -xlibmil -nofstore -xtarget=native" FFLAGS="-xO5 -libmil -nofstore -xtarget=native" CXXFLAGS="-xO5 -xlibmil -nofstore -xtarget=native" SAFE_FFLAGS="-O -libmil -fstore -xtarget=native" </pre></div> <p>but the use of <code>-nofstore</code> can be less numerically stable, and some packages have in the past failed to compile at optimization level 5. </p> <p>The Oracle compilers provide several implementations of the C++ standards which select both the set of headers and a C++ runtime library. One of those is selected by the <samp>-library</samp> flag, which as it is needed for both compiling and linking is best specified as part of the compiler or standard. Current R expects a C++11 compiler, for which the choice given above is the only possibility. For C++98 there are several with </p> <div class="example"> <pre class="example">CXX98=CC CXX98STD="-compat=g -library=stdcpp,CrunG3" </pre></div> <p>being the most compatible with C++11 compilation. Another possibility (commonly used for earlier versions of R) would be </p> <div class="example"> <pre class="example">CXX98="CC -library=stlport4" </pre></div> <p>Although version 12.5 accepts the flag <samp>-std=c++14</samp>, it did not pass <code>configure</code>’s conformance tests: version 12.6 did. </p> <a name="index-BLAS-library-2"></a> <a name="index-LAPACK-library-2"></a> <p>The performance library <code>sunperf</code> is available for use with the Oracle compilers. If selected as a <acronym>BLAS</acronym>, it must also be selected as LAPACK <em>via</em> </p> <div class="example"> <pre class="example">./configure --with-blas='-library=sunperf' --with-lapack </pre></div> <p>This has often given test failures in the past, in several different places.<a name="DOCF84" href="#FOOT84"><sup>84</sup></a> </p> <p>Parsing very complex R expressions needs a lot of stack space when the Oracle compilers are used: several packages require the stack increased to at least 20MB. </p> <p>Some people have reported that the Solaris <code>libintl</code> needs to be avoided, for example by using <samp>--disable-nls</samp> or <samp>--with-included-gettext</samp> or using <code>libintl</code> from OpenCSW. (On the other hand, there have been many successful installs which automatically detected <code>libintl</code> from OpenCSW or selected the included <code>gettext</code>.) </p> <p>It has been reported that some Solaris installations need </p> <div class="example"> <pre class="example">INTERNET_LIBS="-lsocket -lnsl" </pre></div> <p>on the <code>configure</code> command line or in file <samp>config.site</samp>; however, there have been many successful installs without this. </p> <hr> <a name="g_t64_002dbit-builds"></a> <div class="header"> <p> Next: <a href="#Using-gcc" accesskey="n" rel="next">Using gcc</a>, Previous: <a href="#Solaris" accesskey="p" rel="previous">Solaris</a>, Up: <a href="#Solaris" accesskey="u" rel="up">Solaris</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="g_t64_002dbit-builds-1"></a> <h4 class="subsection">C.4.1 64-bit builds</h4> <p>On both ‘<samp>x86</samp>’ and ‘<samp>Sparc</samp>’ platforms the compilers default to 32-bit code. </p> <p>For a 64-bit target add <samp>-m64</samp> to the compiler macros and use something like <code>LDFLAGS=-L/usr/local/lib/amd64</code> or <code>LDFLAGS=-L/usr/local/lib/sparcv9</code> as appropriate (and other 64-bit library directories if used, e.g. <code>-L/opt/csw/lib/amd64</code>). It will also be necessary to point <code>pkg-config</code> at the 64-bit directories, e.g. by something like </p> <div class="example"> <pre class="example">PKG_CONFIG_PATH= /usr/local/lib/amd64/pkgconfig:/opt/csw/lib/64/pkgconfig:/usr/lib/64/pkgconfig </pre></div> <p>and to specify a 64-bit Java VM by e.g. </p> <div class="example"> <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></div> <hr> <a name="Using-gcc"></a> <div class="header"> <p> Previous: <a href="#g_t64_002dbit-builds" accesskey="p" rel="previous">64-bit builds</a>, Up: <a href="#Solaris" accesskey="u" rel="up">Solaris</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Using-gcc-1"></a> <h4 class="subsection">C.4.2 Using gcc</h4> <p>If using <code>gcc</code>, ensure that the compiler was compiled for the version of Solaris in use. (This can be ascertained from <code>gcc -v</code>.) <code>gcc</code> makes modified versions of some header files, and several reports of problems were due to using <code>gcc</code> compiled on one version of Solaris on a later version. Note that this can even apply to OS patches: some 2016 patches to Solaris 10 changed its C header files in way incompatible<a name="DOCF85" href="#FOOT85"><sup>85</sup></a> with the modified versions included with OpenCSW’s binary distribution. </p> <p>The notes here are for <code>gcc</code> set up to use the Solaris linker: it can also be set up to use GNU <code>ld</code>, but that has not been tested. The tests were for compilers from the OpenCSW repository: Solaris systems often come with much older compilers installed under <samp>/usr/sfw/bin</samp>. One of <samp>-m32</samp> or <samp>-m64</samp> will be the default and could be omitted, but it is not easy to find out which. (For OpenCSW it is <samp>-m32</samp>.) </p> <p>Compilation for an ‘<samp>x86</samp>’ target with <code>gcc</code> 5.2.0 needed </p> <div class="example"> <pre class="example">CC="gcc -m32" CPPFLAGS="-I/opt/csw/include -I/usr/local/include" FC="gfortran -m32" CXX="g++ -m32" LDFLAGS="-L/opt/csw/lib -L/usr/local/lib" </pre></div> <p>For an ‘<samp>amd64</samp>’ target we used </p> <div class="example"> <pre class="example">CC="gcc -m64" CPPFLAGS="-I/opt/csw/include -I/usr/local/include" FC="gfortran -m64" CXX="g++ -m64" LDFLAGS="-L/opt/csw/lib/amd64 -L/usr/local/lib/amd64" </pre></div> <p>Note that paths such as <samp>/opt/csw/lib</samp>, <samp>/usr/local/lib/amd64</samp> and <samp>/opt/csw/lib/amd64</samp> may need to be in the <a name="index-LD_005fLIBRARY_005fPATH-3"></a> <code>LD_LIBRARY_PATH</code> during configuration. </p> <hr> <a name="FreeBSD"></a> <div class="header"> <p> Next: <a href="#OpenBSD" accesskey="n" rel="next">OpenBSD</a>, Previous: <a href="#Solaris" accesskey="p" rel="previous">Solaris</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="FreeBSD-1"></a> <h3 class="section">C.5 FreeBSD</h3> <a name="index-FreeBSD"></a> <p>There have been few recent reports on FreeBSD: there is a ‘port’ at <a href="https://www.freebsd.org/ports/math.html">https://www.freebsd.org/ports/math.html</a>. Recent versions of FreeBSD use Clang and the <code>libc++</code> C++ headers and runtime, but the ‘port’ is configured to use GCC. </p> <p>Use of ICU for collation and the <code>configure</code> option <samp>--with-internal-tzcode</samp> are desirable workarounds. </p> <hr> <a name="OpenBSD"></a> <div class="header"> <p> Next: <a href="#Cygwin" accesskey="n" rel="next">Cygwin</a>, Previous: <a href="#FreeBSD" accesskey="p" rel="previous">FreeBSD</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="OpenBSD-1"></a> <h3 class="section">C.6 OpenBSD</h3> <a name="index-OpenBSD"></a> <p>Ingo Feinerer installed R version 3.2.2 on OpenBSD 5.8 arch ‘<samp>amd64</samp>’ (their name for ‘<samp>x86_64</samp>’). Details of the build (and patches applied) are at <a href="http://cvsweb.openbsd.org/cgi-bin/cvsweb/ports/math/R/">http://cvsweb.openbsd.org/cgi-bin/cvsweb/ports/math/R/</a>. (Downgrading the <code>zlib</code> requirement to 1.2.3 is against the advice of the R developers.) </p> <hr> <a name="Cygwin"></a> <div class="header"> <p> Next: <a href="#New-platforms" accesskey="n" rel="next">New platforms</a>, Previous: <a href="#OpenBSD" accesskey="p" rel="previous">OpenBSD</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Cygwin-1"></a> <h3 class="section">C.7 Cygwin</h3> <p>The 32-bit version never worked well enough to pass R’s <code>make check</code>, and residual support from earlier experiments was removed in R 3.3.0. </p> <p>The 64-bit version was never unsupported. </p> <hr> <a name="New-platforms"></a> <div class="header"> <p> Previous: <a href="#Cygwin" accesskey="p" rel="previous">Cygwin</a>, Up: <a href="#Platform-notes" accesskey="u" rel="up">Platform notes</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="New-platforms-1"></a> <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> <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>ix86</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>-ieee_with_inexact</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>config.site</samp> which resides in the top level directory. </p> <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>-fast</samp> on the Oracle compilers has caused R’s <code>NaN</code> to be set incorrectly, and <code>gcc</code>’s <samp>-ffast-math</samp> and <code>clang</code>’s <samp>-Ofast</samp> have given incorrect results. </p> <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 <code>xmkmf</code>), 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 <code>cc</code> and <code>ld</code> usually reveals the correct incantation. Once you know the recipe you can modify the file <samp>config.site</samp> (following the instructions therein) so that the build will use these options. </p> <p>It seems that <code>gcc</code> 3.4.x and later on ‘<samp>ix86</samp>’ Linux defeat attempts by the LAPACK code to avoid computations entirely in extended-precision registers, so file <samp>src/modules/lapack/dlamc.f</samp> may need to be compiled without optimization or with additional flags. Set the configure variable <code>SAFE_FFLAGS</code> to the flags to be used for this file. </p> <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> <p>If you are having trouble getting R to work on your platform please feel free to use the ‘<samp>R-devel</samp>’ mailing list to ask questions. We have had a fair amount of practice at porting R to new platforms <small class="enddots">...</small> </p> <hr> <a name="The-Windows-toolset"></a> <div class="header"> <p> Next: <a href="#Function-and-variable-index" accesskey="n" rel="next">Function and variable index</a>, Previous: <a href="#Platform-notes" accesskey="p" rel="previous">Platform notes</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="The-Windows-toolset-1"></a> <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="https://CRAN.R-project.org/bin/windows/Rtools/">https://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> <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 name="DOCF86" href="#FOOT86"><sup>86</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> <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> <p>We have collected most of the necessary tools (unfortunately not all, due to license or size limitations) into an executable installer named <samp>Rtools*.exe</samp>, available from <a href="https://CRAN.R-project.org/bin/windows/Rtools/">https://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> <p>You will need the following items to build R and packages. See the subsections below for detailed descriptions. </p><ul> <li> The command line tools (in <samp>Rtools*.exe</samp>) </li><li> The MinGW-w64 32/64-bit toolchain to compile C, Fortran and C++. </li></ul> <p>For installing simple source packages containing data or R source but no compiled code, none of these are needed. </p> <p>A complete build of R including PDF manuals, and producing the installer will also need the following: </p><ul> <li> LaTeX </li><li> The Inno Setup installer </li><li> (optional) <code>qpdf</code> </li></ul> <a name="index-PATH-2"></a> <p>It is important to set your <code>PATH</code> properly. The installer <samp>Rtools*.exe</samp> optionally sets the path to components that it installs. </p> <p>Your <code>PATH</code> may include <samp>.</samp> first, then the <samp>bin</samp> directories of the tools 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> <p>For example for a 32-bit build, all on one line, </p> <div class="example"> <pre class="example">PATH=c:\Rtools\bin;c:\MiKTeX\miktex\bin; c:\R\R-3.2\bin\i386;c:\windows;c:\windows\system32 </pre></div> <p>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 name="DOCF87" href="#FOOT87"><sup>87</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> <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. </p> <table summary="" class="menu" border="0" cellspacing="0"> <tr><td align="left" valign="top">• <a href="#LaTeX" accesskey="1">LaTeX</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#The-Inno-Setup-installer" accesskey="2">The Inno Setup installer</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#The-command-line-tools" accesskey="3">The command line tools</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#The-MinGW_002dw64-toolchain" accesskey="4">The MinGW-w64 toolchain</a>:</td><td> </td><td align="left" valign="top"> </td></tr> <tr><td align="left" valign="top">• <a href="#Useful-additional-programs" accesskey="5">Useful additional programs</a>:</td><td> </td><td align="left" valign="top"> </td></tr> </table> <hr> <a name="LaTeX"></a> <div class="header"> <p> Next: <a href="#The-Inno-Setup-installer" accesskey="n" rel="next">The Inno Setup installer</a>, Previous: <a href="#The-Windows-toolset" accesskey="p" rel="previous">The Windows toolset</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="LaTeX-1"></a> <h3 class="section">D.1 LaTeX</h3> <p>The ‘<samp>MiKTeX</samp>’ (<a href="http://www.miktex.org/">http://www.miktex.org/</a>) distribution of LaTeX includes a suitable port of <code>pdftex</code>. This can be set up to install extra packages ‘on the fly’, which is the simplest way to use it (and the default). The ‘basic’ version of ‘<samp>MiKTeX</samp>’ almost suffices: when last checked packages </p> <div class="example"> <pre class="example">epsf inconsolata mptopdf url </pre></div> <p>needed to be added (on the fly or <em>via</em> the ‘<samp>MiKTeX</samp>’ Package Manager) to install R. In any case ensure that the <strong>inconsolata</strong> package is installed—you can check with the ‘<samp>MiKTeX</samp>’ Package Manager. </p> <p>The <samp>Rtools*.exe</samp> installer does <em>not</em> include any version of LaTeX. </p> <p>It is also possible to use the TeX Live distribution from <a href="https://www.tug.org/texlive/">https://www.tug.org/texlive/</a>. </p> <a name="index-R_005fRD4PDF-2"></a> <p>Please read <a href="#Making-the-manuals">Making the manuals</a> about how to make <samp>fullrefman.pdf</samp> and set the environment variable <code>R_RD4PDF</code> suitably; ensure you have the required fonts installed or that ‘<samp>MiKTeX</samp>’ is set up to install LaTeX packages on first use. </p> <hr> <a name="The-Inno-Setup-installer"></a> <div class="header"> <p> Next: <a href="#The-command-line-tools" accesskey="n" rel="next">The command line tools</a>, Previous: <a href="#LaTeX" accesskey="p" rel="previous">LaTeX</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="The-Inno-Setup-installer-1"></a> <h3 class="section">D.2 The Inno Setup installer</h3> <p>To make the installer package (<samp>R-3.6.0-win.exe</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>Rtools*.exe</samp>. </p> <p>Copy file <samp>src/gnuwin32/MkRules.dist</samp> to <samp>src/gnuwin32/MkRules.local</samp> and edit it to set <code>ISDIR</code> to the location where Inno Setup was installed. </p> <hr> <a name="The-command-line-tools"></a> <div class="header"> <p> Next: <a href="#The-MinGW_002dw64-toolchain" accesskey="n" rel="next">The MinGW-w64 toolchain</a>, Previous: <a href="#The-Inno-Setup-installer" accesskey="p" rel="previous">The Inno Setup installer</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="The-command-line-tools-1"></a> <h3 class="section">D.3 The command line tools</h3> <p>This item is installed by the <samp>Rtools*.exe</samp> installer. </p> <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="https://www.cygwin.com/">https://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>Rtools*.exe</samp>. </p> <p><strong>Beware</strong>: ‘Native’ ports of make are <strong>not</strong> suitable (including those called ‘MinGW make’ at the MinGW SourceForge site and <code>mingw32-make</code> 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"></a> <p>You may need to set the environment variable <code>CYGWIN</code> to a value including ‘<samp>nodosfilewarning</samp>’ to suppress messages about Windows-style paths. </p> <hr> <a name="The-MinGW_002dw64-toolchain"></a> <div class="header"> <p> Next: <a href="#Useful-additional-programs" accesskey="n" rel="next">Useful additional programs</a>, Previous: <a href="#The-command-line-tools" accesskey="p" rel="previous">The command line tools</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="The-MinGW_002dw64-toolchain-1"></a> <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> <p>The preferred toolchain is part of <code>Rtools*.exe</code>: this uses a version of <code>gcc 4.9.3</code> and version rt_v3 of the MinGW-w64 project’s runtime. </p> <p>This toolchain does not use <em>multilib</em>: separate front-ends are used for 32-bit and 64-bit compilation. These compilers need to be specified in <code>BINPREF</code> and <code>BINPREF64</code> make variables as described previously at the end of <a href="#Windows-packages">Windows packages</a>. </p> <p>To select a 32-bit or 64-bit build of R, set the options in <samp>MkRules.local</samp> appropriately (following the comments in the file). </p> <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="https://www.stats.ox.ac.uk/pub/Rtools/multilib/">https://www.stats.ox.ac.uk/pub/Rtools/multilib/</a>. Users developing packages with <a href="https://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="https://CRAN.R-project.org/package=Rcpp"><strong>Rcpp</strong></a> from its sources yourself. </p> <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. </p> <hr> <a name="Useful-additional-programs"></a> <div class="header"> <p> Previous: <a href="#The-MinGW_002dw64-toolchain" accesskey="p" rel="previous">The MinGW-w64 toolchain</a>, Up: <a href="#The-Windows-toolset" accesskey="u" rel="up">The Windows toolset</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Useful-additional-programs-1"></a> <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>MkRules.local</samp>. </p> <p>Developers of packages will find some of the ‘goodies’ at <a href="https://www.stats.ox.ac.uk/pub/Rtools/goodies">https://www.stats.ox.ac.uk/pub/Rtools/goodies</a> useful. </p> <p>There is a version of the <code>file</code> command that identifies the type of files, and is used by <code>Rcmd check</code> if available. The binary distribution is included in <samp>Rtools*.exe</samp>. </p> <p>The file <samp>xzutils.zip</samp> contains the program <code>xz</code> which can be used to (de)compress files with that form of compression. </p> <hr> <a name="Function-and-variable-index"></a> <div class="header"> <p> Next: <a href="#Concept-index" accesskey="n" rel="next">Concept index</a>, Previous: <a href="#The-Windows-toolset" accesskey="p" rel="previous">The Windows toolset</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Function-and-variable-index-1"></a> <h2 class="unnumbered">Function and variable index</h2> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a> </td></tr></table> <table summary="" class="index-vr" border="0"> <tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Function-and-variable-index_vr_letter-C">C</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-configure"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-configure-1"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-configure-2"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-configure-3"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-configure-4"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Configuration-variables">Configuration variables</a></td></tr> <tr><td></td><td valign="top"><a href="#index-configure-5"><code>configure</code></a>:</td><td> </td><td valign="top"><a href="#Using-make">Using make</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Function-and-variable-index_vr_letter-I">I</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-install_002epackages"><code>install.packages</code></a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Function-and-variable-index_vr_letter-M">M</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-make"><code>make</code></a>:</td><td> </td><td valign="top"><a href="#Using-make">Using make</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Function-and-variable-index_vr_letter-R">R</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-remove_002epackages"><code>remove.packages</code></a>:</td><td> </td><td valign="top"><a href="#Removing-packages">Removing packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fHOME"><code>R_HOME</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Function-and-variable-index_vr_letter-U">U</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-update_002epackages"><code>update.packages</code></a>:</td><td> </td><td valign="top"><a href="#Updating-packages">Updating packages</a></td></tr> <tr><td colspan="4"> <hr></td></tr> </table> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Function-and-variable-index_vr_letter-C"><b>C</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-I"><b>I</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-M"><b>M</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-R"><b>R</b></a> <a class="summary-letter" href="#Function-and-variable-index_vr_letter-U"><b>U</b></a> </td></tr></table> <hr> <a name="Concept-index"></a> <div class="header"> <p> Next: <a href="#Environment-variable-index" accesskey="n" rel="next">Environment variable index</a>, Previous: <a href="#Function-and-variable-index" accesskey="p" rel="previous">Function and variable index</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Concept-index-1"></a> <h2 class="unnumbered">Concept index</h2> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a> </td></tr></table> <table summary="" class="index-cp" border="0"> <tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-B">B</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-BLAS-library">BLAS library</a>:</td><td> </td><td valign="top"><a href="#Linear-algebra">Linear algebra</a></td></tr> <tr><td></td><td valign="top"><a href="#index-BLAS-library-1">BLAS library</a>:</td><td> </td><td valign="top"><a href="#macOS">macOS</a></td></tr> <tr><td></td><td valign="top"><a href="#index-BLAS-library-2">BLAS library</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-F">F</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Fortran">Fortran</a>:</td><td> </td><td valign="top"><a href="#Using-Fortran">Using Fortran</a></td></tr> <tr><td></td><td valign="top"><a href="#index-FreeBSD">FreeBSD</a>:</td><td> </td><td valign="top"><a href="#FreeBSD">FreeBSD</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-I">I</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Installation">Installation</a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Installing-under-Unix_002dalikes">Installing under Unix-alikes</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Installing-under-Windows">Installing under Windows</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Windows">Installing R under Windows</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Internationalization">Internationalization</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-L">L</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-LAPACK-library">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#LAPACK">LAPACK</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LAPACK-library-1">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#macOS">macOS</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LAPACK-library-2">LAPACK library</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Libraries">Libraries</a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Libraries_002c-managing">Libraries, managing</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Libraries_002c-site">Libraries, site</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Libraries_002c-user">Libraries, user</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Linux">Linux</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Linux-1">Linux</a>:</td><td> </td><td valign="top"><a href="#Linux">Linux</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Locale">Locale</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Locale-1">Locale</a>:</td><td> </td><td valign="top"><a href="#Locales">Locales</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Localization">Localization</a>:</td><td> </td><td valign="top"><a href="#Internationalization">Internationalization</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-M">M</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-macOS">macOS</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-Unix_002dalikes">Installing R under Unix-alikes</a></td></tr> <tr><td></td><td valign="top"><a href="#index-macOS-1">macOS</a>:</td><td> </td><td valign="top"><a href="#Installing-R-under-macOS">Installing R under macOS</a></td></tr> <tr><td></td><td valign="top"><a href="#index-macOS-2">macOS</a>:</td><td> </td><td valign="top"><a href="#macOS">macOS</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Manuals">Manuals</a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Manuals_002c-installing">Manuals, installing</a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-O">O</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Obtaining-R">Obtaining R</a>:</td><td> </td><td valign="top"><a href="#Obtaining-R">Obtaining R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-OpenBSD">OpenBSD</a>:</td><td> </td><td valign="top"><a href="#OpenBSD">OpenBSD</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-P">P</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Packages">Packages</a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Packages_002c-default">Packages, default</a>:</td><td> </td><td valign="top"><a href="#Default-packages">Default packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Packages_002c-installing">Packages, installing</a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Packages_002c-removing">Packages, removing</a>:</td><td> </td><td valign="top"><a href="#Removing-packages">Removing packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Packages_002c-updating">Packages, updating</a>:</td><td> </td><td valign="top"><a href="#Updating-packages">Updating packages</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-R">R</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Repositories">Repositories</a>:</td><td> </td><td valign="top"><a href="#Setting-up-a-package-repository">Setting up a package repository</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-S">S</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Site-libraries">Site libraries</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Solaris">Solaris</a>:</td><td> </td><td valign="top"><a href="#Solaris">Solaris</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Sources-for-R">Sources for R</a>:</td><td> </td><td valign="top"><a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Subversion">Subversion</a>:</td><td> </td><td valign="top"><a href="#Using-Subversion-and-rsync">Using Subversion and rsync</a></td></tr> <tr><td></td><td valign="top"><a href="#index-Subversion-1">Subversion</a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-U">U</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-User-libraries">User libraries</a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-V">V</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-Vignettes">Vignettes</a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Concept-index_cp_letter-W">W</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-winCairo_002edll">winCairo.dll</a>:</td><td> </td><td valign="top"><a href="#Building-the-cairo-devices-files">Building the cairo devices files</a></td></tr> <tr><td colspan="4"> <hr></td></tr> </table> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Concept-index_cp_letter-B"><b>B</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-F"><b>F</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-I"><b>I</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-L"><b>L</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-M"><b>M</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-O"><b>O</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-P"><b>P</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-R"><b>R</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-S"><b>S</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-U"><b>U</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-V"><b>V</b></a> <a class="summary-letter" href="#Concept-index_cp_letter-W"><b>W</b></a> </td></tr></table> <hr> <a name="Environment-variable-index"></a> <div class="header"> <p> Previous: <a href="#Concept-index" accesskey="p" rel="previous">Concept index</a>, Up: <a href="#Top" accesskey="u" rel="up">Top</a> [<a href="#SEC_Contents" title="Table of contents" rel="contents">Contents</a>][<a href="#Function-and-variable-index" title="Index" rel="index">Index</a>]</p> </div> <a name="Environment-variable-index-1"></a> <h2 class="unnumbered">Environment variable index</h2> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Environment-variable-index_en_letter-B"><b>B</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-C"><b>C</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-D"><b>D</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-J"><b>J</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-L"><b>L</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-P"><b>P</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-R"><b>R</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-T"><b>T</b></a> </td></tr></table> <table summary="" class="index-en" border="0"> <tr><td></td><th align="left">Index Entry</th><td> </td><th align="left"> Section</th></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-B">B</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-BINPREF"><code>BINPREF</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-BINPREF64"><code>BINPREF64</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-BLAS_005fLIBS"><code>BLAS_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#BLAS">BLAS</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-C">C</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-CONFIG_005fSITE"><code>CONFIG_SITE</code></a>:</td><td> </td><td valign="top"><a href="#Configuration-variables">Configuration variables</a></td></tr> <tr><td></td><td valign="top"><a href="#index-CYGWIN"><code>CYGWIN</code></a>:</td><td> </td><td valign="top"><a href="#The-command-line-tools">The command line tools</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-D">D</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-DESTDIR"><code>DESTDIR</code></a>:</td><td> </td><td valign="top"><a href="#Installation">Installation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-DESTDIR-1"><code>DESTDIR</code></a>:</td><td> </td><td valign="top"><a href="#Unix_002dalike-standalone">Unix-alike standalone</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-J">J</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-JAVA_005fHOME"><code>JAVA_HOME</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-L">L</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-LANG"><code>LANG</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LANGUAGE"><code>LANGUAGE</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LANGUAGE-1"><code>LANGUAGE</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LAPACK_005fLIBS"><code>LAPACK_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#LAPACK">LAPACK</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LC_005fALL"><code>LC_ALL</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LC_005fCOLLATE"><code>LC_COLLATE</code></a>:</td><td> </td><td valign="top"><a href="#Testing-a-Unix_002dalike-Installation">Testing a Unix-alike Installation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LC_005fMESSAGES"><code>LC_MESSAGES</code></a>:</td><td> </td><td valign="top"><a href="#Localization-of-messages">Localization of messages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Unix_002dalike-standalone">Unix-alike standalone</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-1"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-Fortran">Using Fortran</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-2"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Compile-and-load-flags">Compile and load flags</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LD_005fLIBRARY_005fPATH-3"><code>LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-gcc">Using gcc</a></td></tr> <tr><td></td><td valign="top"><a href="#index-LOCAL_005fSOFT"><code>LOCAL_SOFT</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-P">P</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-PAPERSIZE"><code>PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Setting-paper-size">Setting paper size</a></td></tr> <tr><td></td><td valign="top"><a href="#index-PATH"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-PATH-1"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#Using-Fortran">Using Fortran</a></td></tr> <tr><td></td><td valign="top"><a href="#index-PATH-2"><code>PATH</code></a>:</td><td> </td><td valign="top"><a href="#The-Windows-toolset">The Windows toolset</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-R">R</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fARCH"><code>R_ARCH</code></a>:</td><td> </td><td valign="top"><a href="#Sub_002darchitectures">Sub-architectures</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fARCH-1"><code>R_ARCH</code></a>:</td><td> </td><td valign="top"><a href="#Sub_002darchitectures">Sub-architectures</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fBROWSER"><code>R_BROWSER</code></a>:</td><td> </td><td valign="top"><a href="#Setting-the-browsers">Setting the browsers</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fDEFAULT_005fPACKAGES"><code>R_DEFAULT_PACKAGES</code></a>:</td><td> </td><td valign="top"><a href="#Default-packages">Default packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fDISABLE_005fHTTPD"><code>R_DISABLE_HTTPD</code></a>:</td><td> </td><td valign="top"><a href="#Help-options">Help options</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fGSCMD"><code>R_GSCMD</code></a>:</td><td> </td><td valign="top"><a href="#Useful-libraries-and-programs">Useful libraries and programs</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fINSTALL_005fTAR"><code>R_INSTALL_TAR</code></a>:</td><td> </td><td valign="top"><a href="#Windows-packages">Windows packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH"><code>R_JAVA_LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fJAVA_005fLD_005fLIBRARY_005fPATH-1"><code>R_JAVA_LD_LIBRARY_PATH</code></a>:</td><td> </td><td valign="top"><a href="#Java-support">Java support</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fLIBS"><code>R_LIBS</code></a>:</td><td> </td><td valign="top"><a href="#Add_002don-packages">Add-on packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fLIBS_005fSITE"><code>R_LIBS_SITE</code></a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fLIBS_005fUSER"><code>R_LIBS_USER</code></a>:</td><td> </td><td valign="top"><a href="#Managing-libraries">Managing libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-1"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-2"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Setting-paper-size">Setting paper size</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fPAPERSIZE-3"><code>R_PAPERSIZE</code></a>:</td><td> </td><td valign="top"><a href="#Making-manuals">Making manuals</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fPDFVIEWER"><code>R_PDFVIEWER</code></a>:</td><td> </td><td valign="top"><a href="#Setting-the-browsers">Setting the browsers</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#Making-the-manuals">Making the manuals</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF-1"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#Making-manuals">Making manuals</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fRD4PDF-2"><code>R_RD4PDF</code></a>:</td><td> </td><td valign="top"><a href="#LaTeX">LaTeX</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fSCRIPT_005fDEFAULT_005fPACKAGES"><code>R_SCRIPT_DEFAULT_PACKAGES</code></a>:</td><td> </td><td valign="top"><a href="#Default-packages">Default packages</a></td></tr> <tr><td></td><td valign="top"><a href="#index-R_005fUSER"><code>R_USER</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td colspan="4"> <hr></td></tr> <tr><th><a name="Environment-variable-index_en_letter-T">T</a></th><td></td><td></td></tr> <tr><td></td><td valign="top"><a href="#index-TAR"><code>TAR</code></a>:</td><td> </td><td valign="top"><a href="#Essential-programs-and-libraries">Essential programs and libraries</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TAR_005fOPTIONS"><code>TAR_OPTIONS</code></a>:</td><td> </td><td valign="top"><a href="#Getting-and-unpacking-the-sources">Getting and unpacking the sources</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TAR_005fOPTIONS-1"><code>TAR_OPTIONS</code></a>:</td><td> </td><td valign="top"><a href="#Getting-the-source-files">Getting the source files</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TEMP"><code>TEMP</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMP"><code>TMP</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMPDIR"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Simple-compilation">Simple compilation</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMPDIR-1"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Building-the-core-files">Building the core files</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMPDIR-2"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMPDIR-3"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Running-R">Running R</a></td></tr> <tr><td></td><td valign="top"><a href="#index-TMPDIR-4"><code>TMPDIR</code></a>:</td><td> </td><td valign="top"><a href="#Installing-packages">Installing packages</a></td></tr> <tr><td colspan="4"> <hr></td></tr> </table> <table summary=""><tr><th valign="top">Jump to: </th><td><a class="summary-letter" href="#Environment-variable-index_en_letter-B"><b>B</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-C"><b>C</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-D"><b>D</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-J"><b>J</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-L"><b>L</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-P"><b>P</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-R"><b>R</b></a> <a class="summary-letter" href="#Environment-variable-index_en_letter-T"><b>T</b></a> </td></tr></table> <div class="footnote"> <hr> <h4 class="footnotes-heading">Footnotes</h4> <h3><a name="FOOT1" href="#DOCF1">(1)</a></h3> <p>e.g. <acronym>GNU</acronym> <code>tar</code> version 1.15 or later, or that from the ‘<samp>libarchive</samp>’ (as used on macOS versions 10.6 and later) or ‘Heirloom Toolchest’ distributions.</p> <h3><a name="FOOT2" href="#DOCF2">(2)</a></h3> <p>for some Subversion clients ‘<samp>http:</samp>’ may appear to work, but requires continual redirection.</p> <h3><a name="FOOT3" href="#DOCF3">(3)</a></h3> <p>Most aspects will work with paths containing spaces, but external software used by R, e.g. <code>texi2dvi</code> version <code>4.8</code>, may not.</p> <h3><a name="FOOT4" href="#DOCF4">(4)</a></h3> <p>which use <samp>lib</samp> rather than <samp>lib64</samp> for their primary 64-bit library directories.</p> <h3><a name="FOOT5" href="#DOCF5">(5)</a></h3> <p>Instructions on how to install the latest version are at <a href="https://www.ctan.org/tex-archive/fonts/inconsolata/">https://www.ctan.org/tex-archive/fonts/inconsolata/</a>.</p> <h3><a name="FOOT6" href="#DOCF6">(6)</a></h3> <p>on a Unix-alike, ‘<samp>inconsolata</samp>’ is omitted if not found by <code>configure</code>.</p> <h3><a name="FOOT7" href="#DOCF7">(7)</a></h3> <p>This will be needed if more than one sub-architecture is to be installed.</p> <h3><a name="FOOT8" href="#DOCF8">(8)</a></h3> <p>with possible values ‘<samp>i386</samp>’, ‘<samp>x64</samp>’, ‘<samp>32</samp>’ and ‘<samp>64</samp>’.</p> <h3><a name="FOOT9" href="#DOCF9">(9)</a></h3> <p>mainly on RedHat and Fedora, whose layout is described here.</p> <h3><a name="FOOT10" href="#DOCF10">(10)</a></h3> <p>How to prepare such a directory is described in file <samp>src/extra/tzone/Notes</samp> in the R sources.</p> <h3><a name="FOOT11" href="#DOCF11">(11)</a></h3> <p>for example, <samp>-fopenmp</samp>, <samp>-xopenmp</samp> or <samp>-qopenmp</samp>. This includes for <code>clang</code> and the Intel and Oracle compilers.</p> <h3><a name="FOOT12" href="#DOCF12">(12)</a></h3> <p>This does not necessarily disable <em>use</em> of OpenMP – the <code>configure</code> code allows for platforms where OpenMP is used without a flag. For the <code>flang</code> compiler in late 2017, the Fortran runtime always used OpenMP.</p> <h3><a name="FOOT13" href="#DOCF13">(13)</a></h3> <p>Currently this is a valid option for <code>g++</code> 5 and later and 2016 versions of the Intel and Solaris compilers. For earlier versions of <code>g++</code> one could try <samp>-std=c++1y</samp>.</p> <h3><a name="FOOT14" href="#DOCF14">(14)</a></h3> <p>This is true for earlier versions of <code>g++</code> such as 4.2.1, and also for earlier versions of the Solaris compiler <code>CC</code>.</p> <h3><a name="FOOT15" href="#DOCF15">(15)</a></h3> <p>Currently only GCC and <code>clang++</code> versions 6 and later.</p> <h3><a name="FOOT16" href="#DOCF16">(16)</a></h3> <p>For when features were supported, see <a href="https://gcc.gnu.org/projects/cxx-status.html#cxx11">https://gcc.gnu.org/projects/cxx-status.html#cxx11</a>.</p> <h3><a name="FOOT17" href="#DOCF17">(17)</a></h3> <p>Suitable distributions include Strawberry Perl, <a href="http://strawberryperl.com/">http://strawberryperl.com/</a> and ActivePerl, <a href="https://www.activestate.com/activeperl">https://www.activestate.com/activeperl</a>.</p> <h3><a name="FOOT18" href="#DOCF18">(18)</a></h3> <p>The installer as puts links to <code>R</code> and <code>Rscript</code> in <samp>/usr/local/bin</samp>. If these are missing, you can run directly the copies in <samp>/Library/Frameworks/R.framework/Resources/</samp>.</p> <h3><a name="FOOT19" href="#DOCF19">(19)</a></h3> <p>The framework for R 3.3.x was named <code>org.r-project.R.mavericks.fw.pkg</code>: use <code>pkgutil --pkgs | grep org.r-project</code> to check for earlier versions of R.</p> <h3><a name="FOOT20" href="#DOCF20">(20)</a></h3> <p>More precisely, of the Apple package of the same name: this means that installing a package for 3.3.x does not remove an installation for 3.4.x or later.</p> <h3><a name="FOOT21" href="#DOCF21">(21)</a></h3> <p>unless they were excluded in the build.</p> <h3><a name="FOOT22" href="#DOCF22">(22)</a></h3> <p>its binding is locked once the startup files have been read, so users cannot easily change it.</p> <h3><a name="FOOT23" href="#DOCF23">(23)</a></h3> <p>If a proxy needs to be set, see <code>?download.file</code>.</p> <h3><a name="FOOT24" href="#DOCF24">(24)</a></h3> <p>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>tools:::.install_packages</samp> for the list. It can also be specified in the package’s <samp>DESCRIPTION</samp> file.</p> <h3><a name="FOOT25" href="#DOCF25">(25)</a></h3> <p>or by adding it in a file such as <samp>etc/i386/Makevars.site</samp>, which does not exist by default.</p> <h3><a name="FOOT26" href="#DOCF26">(26)</a></h3> <p>Note that capitalization and version may differ from the Open Source project.</p> <h3><a name="FOOT27" href="#DOCF27">(27)</a></h3> <p>using a path containing spaces is likely to cause problems</p> <h3><a name="FOOT28" href="#DOCF28">(28)</a></h3> <p>They need to have been created using <samp>-headerpad_max_install_names</samp>, which is the default for an R package.</p> <h3><a name="FOOT29" href="#DOCF29">(29)</a></h3> <p>‘X/Open Portability Guide’, which has had several versions.</p> <h3><a name="FOOT30" href="#DOCF30">(30)</a></h3> <p>On some systems setting <code>LC_ALL</code> or <code>LC_MESSAGES</code> to ‘<samp>C</samp>’ disables <code>LANGUAGE</code>.</p> <h3><a name="FOOT31" href="#DOCF31">(31)</a></h3> <p>If you try changing from French to Russian except in a UTF-8 locale, you will most likely find messages change to English.</p> <h3><a name="FOOT32" href="#DOCF32">(32)</a></h3> <p>the language written in England: some people living in the USA appropriate this name for their language.</p> <h3><a name="FOOT33" href="#DOCF33">(33)</a></h3> <p>with Americanisms.</p> <h3><a name="FOOT34" href="#DOCF34">(34)</a></h3> <p>also known as <acronym>IEEE</acronym> 754</p> <h3><a name="FOOT35" href="#DOCF35">(35)</a></h3> <p>at least when storing quantities: the on-FPU precision is allowed to vary</p> <h3><a name="FOOT36" href="#DOCF36">(36)</a></h3> <p>e.g. Bessel, beta and gamma functions</p> <h3><a name="FOOT37" href="#DOCF37">(37)</a></h3> <p>including copying <samp>MkRules.dist</samp> to <samp>MkRule.local</samp> and selecting the architecture.</p> <h3><a name="FOOT38" href="#DOCF38">(38)</a></h3> <p>also known as <acronym>IEEE</acronym> 754</p> <h3><a name="FOOT39" href="#DOCF39">(39)</a></h3> <p>Note that C11 compilers need not be C99-compliant: R requires support for <code>double complex</code> and variable-length arrays which are optional in C11 but is mandatory in C99.</p> <h3><a name="FOOT40" href="#DOCF40">(40)</a></h3> <p>Examples are <samp>-std=gnu99</samp>, <samp>-std=c99</samp> and <samp>-c99</samp>.</p> <h3><a name="FOOT41" href="#DOCF41">(41)</a></h3> <p><samp>-std=c99</samp> excludes POSIX functionality, but <samp>config.h</samp> will turn on all <acronym>GNU</acronym> extensions to include the POSIX functionality for R itself: this does not apply to badly-written packages. The default mode for GCC 5.1 and later is <samp>-std=gnu11</samp>, which currently includes the optional features R needs.</p> <h3><a name="FOOT42" href="#DOCF42">(42)</a></h3> <p>However, it is possible to break the default behaviour of <code>glibc</code> by re-specifying the <code>gconv</code> modules to be loaded.</p> <h3><a name="FOOT43" href="#DOCF43">(43)</a></h3> <p>specifically, the C99 functionality of headers <samp>wchar.h</samp> and <samp>wctype.h</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> <h3><a name="FOOT44" href="#DOCF44">(44)</a></h3> <p>including <code>expm1</code>, <code>hypot</code>, <code>log1p</code>, <code>nearbyint</code> and <code>va_copy</code>.</p> <h3><a name="FOOT45" href="#DOCF45">(45)</a></h3> <p>including <code>opendir</code>, <code>readdir</code>, <code>closedir</code>, <code>popen</code>, <code>stat</code>, <code>glob</code>, <code>access</code>, <code>getcwd</code> and <code>chdir</code> system calls, <code>select</code> on a Unix-alike, and either <code>putenv</code> or <code>setenv</code>.</p> <h3><a name="FOOT46" href="#DOCF46">(46)</a></h3> <p>such as <code>realpath</code>, <code>symlink</code>.</p> <h3><a name="FOOT47" href="#DOCF47">(47)</a></h3> <p>most often distributed as part of <code>xz</code>: possible names in Linux distributions include <code>xz-devel</code>/<code>xz-libs</code> and <code>liblzma-dev</code>.</p> <h3><a name="FOOT48" href="#DOCF48">(48)</a></h3> <p>sometimes known as PCRE1, and not PCRE2 which started at version 10.0.</p> <h3><a name="FOOT49" href="#DOCF49">(49)</a></h3> <p>but not a major version greater than 7 should there ever be one: the major version has been 7 since 2000.</p> <h3><a name="FOOT50" href="#DOCF50">(50)</a></h3> <p>for example to specify static linking with a build which has both shared and static libraries.</p> <h3><a name="FOOT51" href="#DOCF51">(51)</a></h3> <p>Such as <acronym>GNU</acronym> <code>tar</code> 1.15 or later, <code>bsdtar</code> (from <a href="https://github.com/libarchive/libarchive/">https://github.com/libarchive/libarchive/</a>, as used as <code>tar</code> by FreeBSD and macOS 10.6 and later) or <code>tar</code> from the Heirloom Toolchest (<a href="http://heirloom.sourceforge.net/tools.html">http://heirloom.sourceforge.net/tools.html</a>), although the latter does not support <code>xz</code> compression.</p> <h3><a name="FOOT52" href="#DOCF52">(52)</a></h3> <p><code>texi2dvi</code> is normally a shell script. Some versions (including that from <strong>texinfo</strong> 5.2 and 6.0) need to be run under <code>bash</code> rather than a Bourne shell, especially on Solaris. Some of the issues which have been observed with broken versions of <code>texi2dvi</code> can be circumvented by setting the environment variable <code>R_TEXI2DVICMD</code> to the value <code>emulation</code>.</p> <h3><a name="FOOT53" href="#DOCF53">(53)</a></h3> <p>If necessary the path to <code>pkg-config</code> can be specified by setting <code>PKG_CONFIG</code> in <samp>config.site</samp>, on the <code>configure</code> command line or in the environment.</p> <h3><a name="FOOT54" href="#DOCF54">(54)</a></h3> <p>also known as <code>ttf-mscorefonts-installer</code> in the Debian/Ubuntu world: see also <a href="https://en.wikipedia.org/wiki/Core_fonts_for_the_Web">https://en.wikipedia.org/wiki/Core_fonts_for_the_Web</a>.</p> <h3><a name="FOOT55" href="#DOCF55">(55)</a></h3> <p><code>ttf-liberation</code> in Debian/Ubuntu.</p> <h3><a name="FOOT56" href="#DOCF56">(56)</a></h3> <p>This is the default as from <code>glibc</code> 2.26 and has been confirmed for Fedora 28, which does not mention this on its <code>man</code> pages.</p> <h3><a name="FOOT57" href="#DOCF57">(57)</a></h3> <p>R uses <samp>rpc/xdr.h</samp> but that includes <samp>netconfig.h</samp> from the top <samp>tirpc</samp> directory.</p> <h3><a name="FOOT58" href="#DOCF58">(58)</a></h3> <p>This is true even for the ‘Aqua’ version of Tk on macOS, but distributions of that include a copy of the X11 files needed.</p> <h3><a name="FOOT59" href="#DOCF59">(59)</a></h3> <p>The search includes OpenBLAS, ATLAS and a generic <samp>libblas</samp>, plus some platform-specific choices (see below).</p> <h3><a name="FOOT60" href="#DOCF60">(60)</a></h3> <p>Using the Oracle Developer Studio <code>cc</code> and <code>f95</code> compilers</p> <h3><a name="FOOT61" href="#DOCF61">(61)</a></h3> <p>There were others for earlier versions of ATLAS, and are for non-Intel architectures. The only way to see exactly which CPUs the distributed libraries have been tuned for is to read the <samp>atlas.spec</samp> file: at the time of writing ‘<samp>HAMMER64SSE3</samp>’ and ‘<samp>Corei264AVX</samp>’ for ‘<samp>x86_64</samp>’ Fedora.</p> <h3><a name="FOOT62" href="#DOCF62">(62)</a></h3> <p><a href="http://math-atlas.sourceforge.net/atlas_install/">http://math-atlas.sourceforge.net/atlas_install/</a></p> <h3><a name="FOOT63" href="#DOCF63">(63)</a></h3> <p><a href="http://math-atlas.sourceforge.net/faq.html#tnum">http://math-atlas.sourceforge.net/faq.html#tnum</a></p> <h3><a name="FOOT64" href="#DOCF64">(64)</a></h3> <p>(and more, e.g. for 64-bit ints and static versions).</p> <h3><a name="FOOT65" href="#DOCF65">(65)</a></h3> <p>The issue for macOS has been the use of double-complex routines.</p> <h3><a name="FOOT66" href="#DOCF66">(66)</a></h3> <p>We have measured 15–20% on ‘<samp>i686</samp>’ Linux and around 10% on ‘<samp>x86_64</samp>’ Linux.</p> <h3><a name="FOOT67" href="#DOCF67">(67)</a></h3> <p>We believe that versions 3.4.0 to 3.13.0 are compatible.</p> <h3><a name="FOOT68" href="#DOCF68">(68)</a></h3> <p>at the time of revision of this para in late 2018, <strong>autoconf-2.69</strong> from 2012 and <strong>automake-1.16.1</strong> from 2018.</p> <h3><a name="FOOT69" href="#DOCF69">(69)</a></h3> <p>The links there have proved difficult to access, in which case either point an FTP client at <a href="ftp://www.eecs.harvard.edu/pub/nr/">ftp://www.eecs.harvard.edu/pub/nr/</a> or grab the copy made available at <a href="http://developer.r-project.org/noweb-2.11b.tgz">http://developer.r-project.org/noweb-2.11b.tgz</a>.</p> <h3><a name="FOOT70" href="#DOCF70">(70)</a></h3> <p>for example, <code>X11 font at size 14 could not be loaded</code>.</p> <h3><a name="FOOT71" href="#DOCF71">(71)</a></h3> <p>For example, <code>glibc</code>: other C libraries such as <code>musl</code> have been used but are not routinely tested.</p> <h3><a name="FOOT72" href="#DOCF72">(72)</a></h3> <p>This has been announced to change in version 2.29, having been postponed from 2.28.</p> <h3><a name="FOOT73" href="#DOCF73">(73)</a></h3> <p>This also needs the OpenMP runtime which has sometimes been distributed separately.</p> <h3><a name="FOOT74" href="#DOCF74">(74)</a></h3> <p>These days that is defined by Apple’s implementation of <code>clang</code>, so it is strongly recommended to use that.</p> <h3><a name="FOOT75" href="#DOCF75">(75)</a></h3> <p>Some of these are unsigned packages: to install them you may need to right-click and select <code>Open with -> Installer</code>.</p> <h3><a name="FOOT76" href="#DOCF76">(76)</a></h3> <p>It is unstated what the minimum OS requirement is for these: the distribution of 5.0.0 required Sierra or later.</p> <h3><a name="FOOT77" href="#DOCF77">(77)</a></h3> <p><a href="https://developer.apple.com/documentation/accelerate">https://developer.apple.com/documentation/accelerate</a>.</p> <h3><a name="FOOT78" href="#DOCF78">(78)</a></h3> <p>It was reported that for some non-Apple toolchains <code>CPPFLAGS</code> needed to contain <code>-D__ACCELERATE__</code>: not needed for <code>clang</code> 6.0.0, though.</p> <h3><a name="FOOT79" href="#DOCF79">(79)</a></h3> <p>E.g. <em>via</em> <code>tlmgr install cm-super helvetic inconsolata texinfo</code> .</p> <h3><a name="FOOT80" href="#DOCF80">(80)</a></h3> <p>For more details see <a href="http://www.macstrategy.com/article.php?3">http://www.macstrategy.com/article.php?3</a>.</p> <h3><a name="FOOT81" href="#DOCF81">(81)</a></h3> <p>In the unlikely event that the version reported does not start with <code>1.8.0</code>, <code>9</code>, <code>10</code> or <code>11</code> you need to update your Java.</p> <h3><a name="FOOT82" href="#DOCF82">(82)</a></h3> <p>As from Java 11, there is no separate client JRE distribution.</p> <h3><a name="FOOT83" href="#DOCF83">(83)</a></h3> <p>Oracle Solaris Studio prior to 2016, and previously Sun Studio.</p> <h3><a name="FOOT84" href="#DOCF84">(84)</a></h3> <p>When last checked it failed in <samp>tests/reg-BLAS.R</samp>, and on some builds, including for ‘<samp>amd64</samp>’, it failed in <code>example(eigen)</code>.</p> <h3><a name="FOOT85" href="#DOCF85">(85)</a></h3> <p>In particular, header <samp>cmath</samp> in C++11 mode includes <samp>math.h</samp> and <samp>iso/math_c99.h</samp> and <code>gcc</code> had ‘fixed’ an earlier version of the latter.</p> <h3><a name="FOOT86" href="#DOCF86">(86)</a></h3> <p>For example, the Cygwin version of <code>make 3.81</code> fails to work correctly.</p> <h3><a name="FOOT87" href="#DOCF87">(87)</a></h3> <p>such as <code>sort</code>, <code>find</code> and perhaps <code>make</code>.</p> </div> <hr> </body> </html>