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<h3>vcfR documentation</h3>
by
<br>
Brian J. Knaus and Niklaus J. Grünwald
</center>
</p>
<div id="header">
<h1 class="title toc-ignore">Compiling vcfR</h1>
</div>
<p>The package vcfR includes compiled code to increase it’s performance.
For Windows and OSX precompiled binaries are available at CRAN and
should always be your first choice. If you do want to compile vcfR
yourself you need to make sure you have cupport for C++11. C++11 is an
extension of C++, similar to how R packages extend the functionality of
R. If you’re having problems compiling it may be good to validate your
system has this functionality. We can test for this functionality by
creating a small C++ function (this is entirely independent of R).</p>
<p>Copy the below code into a text file named
<code>myTest.cpp</code>.</p>
<pre class="r"><code>#include <iostream>
// Originally based on:
// http://stackoverflow.com/a/34681870
int main()
{
// Query OS info
if (system( NULL )){
system("cat /etc/*release");
} else {
std::cout << "Couldn't queru OS" << std::endl;
}
std::cout << std::endl;
// Introduction.
std::cout << "Querying for g++: ";
std::cout << __cplusplus;
std::cout << std::endl;
// Determine support.
if(__cplusplus==201402L){
std::cout << "C++14" << std::endl;
} else if(__cplusplus==201103L){
std::cout << "C++11" << std::endl;
} else if(__cplusplus == 199711L){
std::cout << "C++" << std::endl;
} else {
std::cout << "Unexpected result." << std::endl;
}
return 0;
}</code></pre>
<p>First, let’s compile our program without C++11 support.</p>
<pre class="r"><code>g++ myTest.cpp</code></pre>
<p>And execute.</p>
<pre class="r"><code>./a.out
C++</code></pre>
<p>Now we can compile with C++11 support.</p>
<pre class="r"><code>g++ -std=c++11 myTest.cpp </code></pre>
<pre class="r"><code>./a.out
C++11</code></pre>
<p>Your results should be the same as above. If not, you may not have
C++ support on your system.</p>
<center>
<hr class="style1">
<p>Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.</p>
<p>USDA Agricultural Research Service, Horticultural Crops Research Lab.</p>
</center>
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