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<h3 style="text-align: center;"><strong style="font-size: 130%;">Building R-devel from Source</strong></h3>
<h3 style="text-align: center;"><strong style="font-size: 130%;">macOS 10.13.2</strong></h3>
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<a href="#Prelim">Preliminaries</a> <br>
<a href="#DL">Download and Unpack</a> <br>
<a href="#Config">Configure</a> <br>
<a href="#ConfigOpt">Alt Configure: Optimization and OpenMP</a> <br>
<a href="#BLASLapack">BLAS/Lapack</a> <br>
<a href="#Build">Build and Install</a> <br>
<a href="#Call">Calling R-devel</a>
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<p>This page describes the steps involved in compiling R-devel on a Mac operating system (macOS, formerly known as OS X), with an emphasis on non-standard build configurations that can significantly improve computing performance compared to a standard build.</p>
<hr style="height:2px;border-width:0;background-color:black">
<h3 style="text-align: left;" id="Prelim"><strong style="font-size: 120%;">Preliminaries</strong></h3>
<p>First we need to install some libraries and tools.</p>
<ul>
<li> Get Xcode from the App Store. (The page should look something like <a href="https://itunes.apple.com/us/app/xcode/id497799835?mt=12" target="_blank">this</a>.) The latest version of Xcode should install the <b>command line tools</b> by default.</li>
<ul>
<li>Open a terminal window—search spotlight for 'terminal' if you've never used terminal/bash before—and run:</li>
<pre class="brush: bash;">
clang++ -v</pre>
<li>You should see something similar to</li>
<pre class="brush: bash;">
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin17.3.0
Thread model: posix</pre>
</ul>
<li> Download and install <a href="https://www.xquartz.org/" target="_blank">XQuartz</a>. (A computer restart might be required to complete the installation process.)</li>
<li> Download and install the <a href="http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html" target="_blank">Java SDK</a>. (No need for the 'demos and samples' pack.)</li>
</ul>
<p>Most of the following items are from the <a href="https://r.research.att.com/libs/" target="_blank">R-devel optional library list</a>.</p>
<ul>
<li>Unfortunately, Xcode does not include a Fortran compiler, which we will need. The simplest way to obtain an R-compatible version of <b>gfortran</b> is to open a terminal window and type:</li>
<pre class="brush: bash;">
cd ~/Desktop
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /</pre>
<p>The 'sudo' command will require your system password because we are placing files into areas that are password restricted (/usr/local).</p>
<p><strong>Note:</strong> that you are free to choose a more recent distribution of gfortran, which may be obtained via MacPorts or Homebrew.</p>
<li>We also need pkg-config, xz, and pcre:</li>
<pre class="brush: bash;">
cd ~/Desktop
curl -O http://r.research.att.com/libs/pkgconfig-0.28-darwin.15-x86_64.tar.gz
sudo tar fvxz pkgconfig-0.28-darwin.15-x86_64.tar.gz -C /
curl -O http://r.research.att.com/libs/xz-5.2.3-darwin.15-x86_64.tar.gz
sudo tar fvxz xz-5.2.3-darwin.15-x86_64.tar.gz -C /
curl -O http://r.research.att.com/libs/pcre-8.40-darwin.15-x86_64.tar.gz
sudo tar fvxz pcre-8.40-darwin.15-x86_64.tar.gz -C /</pre>
<li>Finally, for creating images, we need JPEG, PNG, and TIFF libraries:</li>
<pre class="brush: bash;">
cd ~/Desktop
curl -O http://r.research.att.com/libs/jpeg-9-darwin.15-x86_64.tar.gz
sudo tar fvxz jpeg-9-darwin.15-x86_64.tar.gz -C /
curl -O http://r.research.att.com/libs/libpng-1.6.28-darwin.15-x86_64.tar.gz
sudo tar fvxz libpng-1.6.28-darwin.15-x86_64.tar.gz -C /
curl -O http://r.research.att.com/libs/tiff-4.0.7-darwin.15-x86_64.tar.gz
sudo tar fvxz tiff-4.0.7-darwin.15-x86_64.tar.gz -C /</pre>
</ul>
<hr>
<h3 style="text-align: left;" id="DL"><strong style="font-size: 120%;">Download and Unpack</strong></h3>
<p>Create a folder to work in. For example,</p>
<pre class="brush: bash;">
cd ~/Desktop
mkdir R</pre>
<p>Then download and unpack the latest development version of R:</p>
<pre class="brush: bash;">
cd ~/Desktop/R
curl -O ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz
tar -zxvf R-devel.tar.gz</pre>
<p>Alternatively, to obtain R via SVN:</p>
<pre class="brush: bash;">
svn co https://svn.r-project.org/R/trunk/ ~/Desktop/R/trunk
cp -rf ~/Desktop/R/trunk ~/Desktop/R/R-devel # copy to build folder</pre>
<p>Update when needed using</p>
<pre class="brush: bash;">
cd ~/Desktop/R/trunk
svn up</pre>
<hr>
<h3 style="text-align: left;" id="Config"><strong style="font-size: 120%;">Basic Configure</strong></h3>
<p>Open the 'config.site' file in '~/Desktop/R/R-devel' and change the contents to the following (but see the next section for alternative configurations):</p>
<pre class="brush: bash;">
#! /bin/sh
CC=clang
CXX=clang++
F77=gfortran-4.8
FC=$F77
OBJC=clang
CFLAGS="-Wall -mtune=core2 -g -O2"
CXXFLAGS="-Wall -mtune=core2 -g -O2"
OBJCFLAGS="-Wall -mtune=core2 -g -O2"
F77FLAGS="-Wall -g -O2"
FCFLAGS=$F77FLAGS
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
JAVA_HOME="$(/usr/libexec/java_home)"
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"</pre>
<p>Open a terminal window and switch to the R-devel folder:</p>
<pre class="brush: bash;">
cd ~/Desktop/R/R-devel</pre>
<p>Set the pkg-config path as follows:</p>
<pre class="brush: bash;">
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig</pre>
<hr>
<h3 style="text-align: left;" id="ConfigOpt"><strong style="font-size: 120%;">Alternative Configure: Optimization and OpenMP</strong></h3>
<p>It is possible to use an updated version of gfortran while also enabling architecture-specific optimizations such as <a href="https://en.wikipedia.org/wiki/Advanced_Vector_Extensions" target="_blank">Intel's AVX instructions</a>.</p>
<p>If you've installed gcc7 using <a href="https://www.macports.org/" target="_blank">MacPorts</a>, then create a symbolic link to the LLVM assembler in the default install directory:</p>
<pre class="brush: bash;">
cd /opt/local/bin
sudo ln -s /usr/bin/clang</pre>
<p>Then add <code>-Wa,-q</code> to the Fortran flags to use LLVM's (Clang integrated) assembler:</p>
<pre class="brush: bash;">
#! /bin/sh
CC=clang
CXX=clang++
F77=gfortran-mp-7
FC=$F77
OBJC=clang
CFLAGS="-Wall -march=native -g -O3 -ffp-contract=fast"
CXXFLAGS="-Wall -march=native -g -O3 -ffp-contract=fast"
OBJCFLAGS="-Wall -march=native -g -O3"
F77FLAGS="-Wall -march=native -g -O3 -Wa,-q"
FCFLAGS=$F77FLAGS
FFLAGS=$F77FLAGS
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
JAVA_HOME="$(/usr/libexec/java_home)"
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"</pre>
<p>Note: Without the <code>-Wa,-q</code> option, <code>-march=native</code> instructions will result in an unknown symbol error.</p>
<p>To utilise OpenMP features we need to switch from Apple's version of LLVM. Install Clang v6.0 via MacPorts:</p>
<pre class="brush: bash;">
sudo port install clang-6.0</pre>
<p>and modify the config.site file:</p>
<pre class="brush: bash;">
#! /bin/sh
CC=clang-mp-6.0
CXX=clang++-mp-6.0
F77=gfortran-mp-7
FC=$F77
OBJC=clang-mp-6.0
CFLAGS="-Wall -march=native -g -O3 -ffp-contract=fast"
CXXFLAGS="-Wall -march=native -g -O3 -ffp-contract=fast"
OBJCFLAGS="-Wall -march=native -g -O3"
F77FLAGS="-Wall -march=native -g -O3 -Wa,-q"
FCFLAGS=$F77FLAGS
FFLAGS=$F77FLAGS
PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/usr/local/lib/pkgconfig:/usr/lib/pkgconfig
JAVA_HOME="$(/usr/libexec/java_home)"
JAVA_CPPFLAGS="-I/${JAVA_HOME}/include -I/${JAVA_HOME}/include/darwin"
JAVA_LD_LIBRARY_PATH="${JAVA_HOME}/jre/lib/server"
JAVA_LIBS="-L/${JAVA_HOME}/jre/lib/server -ljvm"</pre>
<p><strong>Note:</strong> If you receive a 'library not found for -lomp' error, add a symbolic link to libomp.dylib under /usr/local/lib:</p>
<pre class="brush: bash;">
sudo ln -s /opt/local/lib/libomp/libomp.dylib /usr/local/lib/libomp.dylib</pre>
<hr>
<h3 style="text-align: left;" id="BLASLapack"><strong style="font-size: 120%;">Select a BLAS and Lapack Distribution</strong></h3>
<p>R includes a single-threaded BLAS and Lapack distribution, but we are free to choose an external, multithreaded library.</p>
<p>To link against the Accelerate framework (pre-installed with macOS) run</p>
<pre class="brush: bash;">
./configure --prefix=/Users/${USER}/Desktop/R-devel --without-x --without-internal-tzcode \
--with-blas="-framework Accelerate" --with-lapack \
--enable-R-shlib --enable-memory-profiling
</pre>
<p>If you want to link against the OpenBLAS library run</p>
<pre class="brush: bash;">
./configure --prefix=/Users/${USER}/Desktop/R-devel --without-x --without-internal-tzcode \
--with-blas="-lopenblas" --with-lapack \
--enable-R-shlib --enable-memory-profiling
</pre>
<hr>
<h3 style="text-align: left;" id="Build"><strong style="font-size: 120%;">Build and Install</strong></h3>
<p>To build R-devel, run make:</p>
<pre class="brush: bash;">
cd ~/Desktop/R/R-devel
make</pre>
<p>The build checks are run using:</p>
<pre class="brush: bash;">
make check</pre>
<p>Finally, we need to choose an install location for R-devel; I use <code>/Users/${USER}/Desktop/R-devel</code>; I recommend installing to somewhere that does not require sudo privileges.</p>
<pre class="brush: bash;">
make prefix=/Users/${USER}/Desktop/R-devel install</pre>
<hr>
<h3 style="text-align: left;" id="Call"><strong style="font-size: 120%;">Calling R-devel</strong></h3>
<p>For easy access to R-devel from a terminal window, add the following lines of code to your bash profile:</p>
<pre class="brush: bash;">
alias Rdevel="/where/I/installed/to/bin/R"</pre>
<p>For example,</p>
<pre class="brush: bash;">
alias Rdevel="/Users/${USER}/Desktop/R-devel/bin/R"</pre>
<p>To run R-devel with sudo privileges, you need to add</p>
<pre class="brush: bash;">
alias sudo='sudo '</pre>
<p>To run R-devel from <a href"https://www.rstudio.com/" target="_blank">RStudio</a>, use</p>
<pre class="brush: bash;">
export RSTUDIO_WHICH_R=/where/I/installed/to/bin/R
open -n -a RStudio</pre>
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