EVOLUTION-MANAGER

Edit File: littler-examples.html

<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang xml:lang>
<head>
 <meta charset="utf-8" />
 <meta name="generator" content="pandoc" />
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
 <meta name="author" content="Dirk Eddelbuettel" />
 <title>Littler Examples</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
 span.underline{text-decoration: underline;}
 div.column{display: inline-block; vertical-align: top; width: 50%;}
 div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
 ul.task-list{list-style: none;}
 pre > code.sourceCode { white-space: pre; position: relative; }
 pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
 pre > code.sourceCode > span:empty { height: 1.2em; }
 .sourceCode { overflow: visible; }
 code.sourceCode > span { color: inherit; text-decoration: inherit; }
 div.sourceCode { margin: 1em 0; }
 pre.sourceCode { margin: 0; }
 @media screen {
 div.sourceCode { overflow: auto; }
 }
 @media print {
 pre > code.sourceCode { white-space: pre-wrap; }
 pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
 }
 pre.numberSource code
 { counter-reset: source-line 0; }
 pre.numberSource code > span
 { position: relative; left: -4em; counter-increment: source-line; }
 pre.numberSource code > span > a:first-child::before
 { content: counter(source-line);
 position: relative; left: -1em; text-align: right; vertical-align: baseline;
 border: none; display: inline-block;
 -webkit-touch-callout: none; -webkit-user-select: none;
 -khtml-user-select: none; -moz-user-select: none;
 -ms-user-select: none; user-select: none;
 padding: 0 4px; width: 4em;
 color: #aaaaaa;
 }
 pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
 div.sourceCode
 { }
 @media screen {
 pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
 }
 code span.al { color: #ff0000; font-weight: bold; } /* Alert */
 code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
 code span.at { color: #7d9029; } /* Attribute */
 code span.bn { color: #40a070; } /* BaseN */
 code span.bu { color: #008000; } /* BuiltIn */
 code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
 code span.ch { color: #4070a0; } /* Char */
 code span.cn { color: #880000; } /* Constant */
 code span.co { color: #60a0b0; font-style: italic; } /* Comment */
 code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
 code span.do { color: #ba2121; font-style: italic; } /* Documentation */
 code span.dt { color: #902000; } /* DataType */
 code span.dv { color: #40a070; } /* DecVal */
 code span.er { color: #ff0000; font-weight: bold; } /* Error */
 code span.ex { } /* Extension */
 code span.fl { color: #40a070; } /* Float */
 code span.fu { color: #06287e; } /* Function */
 code span.im { color: #008000; font-weight: bold; } /* Import */
 code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
 code span.kw { color: #007020; font-weight: bold; } /* Keyword */
 code span.op { color: #666666; } /* Operator */
 code span.ot { color: #007020; } /* Other */
 code span.pp { color: #bc7a00; } /* Preprocessor */
 code span.sc { color: #4070a0; } /* SpecialChar */
 code span.ss { color: #bb6688; } /* SpecialString */
 code span.st { color: #4070a0; } /* String */
 code span.va { color: #19177c; } /* Variable */
 code span.vs { color: #4070a0; } /* VerbatimString */
 code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
 .display.math{display: block; text-align: center; margin: 0.5rem auto;}
 </style>
 <style type="text/css">
body {
max-width: 50rem;
margin-left: auto;
margin-right: auto;
font-family: system-ui;
}

code {
padding: 2px;
border-radius: unset;
}

pre {
background-color: unset;
border: solid #aaa 1px;
padding: 8px;
}
pre.numberSource {
margin: 0;
padding-left: 0;
}
div.sourceCode {
overflow: visible;
}
pre, pre.sourceCode {
overflow-x: auto;
}
pre>code {
white-space: pre;
overflow: visible;
background-color: unset;
padding: 0;
}
pre.sourceCode.numberSource {
overflow-x: visible;
}
pre.sourceCode.numberSource>code {
white-space: pre-wrap
}
pre.sourceCode.numberSource>code>span {
left: 8px;
text-indent: -4.6em;
}

.chunk-summary {
text-align: right;
}
.chunk-summary+pre,
.chunk-summary+div.sourceCode {
margin-top: 2px;
}

nav > ul {
border: .0625rem solid #444;
border-radius: 4px;
margin: 5px;
padding: 5px;
}
nav ul {
list-style-type: none;
padding-inline-start: 1rem;
}
nav ul li {
padding: 0;
}
nav ul ul {
margin-top: 0;
margin-bottom: 0;
padding-top: 0;
padding-bottom: 0;
}
nav code {
background-color: unset;
color: unset;
}
</style>
</head>
<body>
<header id="title-block-header">
<h1 class="title">Littler Examples</h1>
Dirk Eddelbuettel
Originally written 2015-10-28; Updated 2017-12-10,
2018-05-24, 2019-01-06, 2019-06-09 and 2020-06-16
</header>

<h2 id="overview">Overview</h2>
We show and discuss a few of the files included in the
<code>inst/examples/</code> source directory of <a href="http://dirk.eddelbuettel.com/code/littler.html">littler</a> (which
becomes the <code>examples/</code> directory once installed). In a few
cases we remove comment lines to keep things more concise on this page.
We use <code>$</code> to denote a shell (i.e. terminal)
prompt.
Note that some systems (such as macOS) cannot install littler as
<code>r</code> (as lower-case and upper-case are by default the same;
not a great idea). And for example the <code>zsh</code> has
<code>r</code> as a builtin so you would have to use
<code>/usr/bin/r</code>. See the <a href="littler-faq.html">littler
FAQ</a> for more.
<h2 id="simple-direct-command-line-use">Simple Direct Command-line
Use</h2>
<a href="http://dirk.eddelbuettel.com/code/littler.html">littler</a>
can be used directly on the command-line just like, say,
<code>bc</code>, easily consuming standard input from a pipe:
<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>$ echo &#39;cat(pi^2,&quot;\n&quot;)&#39; | r
<a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>9.869604</code></pre></div>
Equivalently, commands that are to be evaluated can be given on the
command-line
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>$ r -e &#39;cat(pi^2, &quot;\n&quot;)&#39;
<a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>9.869604</code></pre></div>
But unlike bc(1), GNU R has a vast number of statistical functions.
For example, we can quickly compute a <code>summary()</code> and show a
stem-and-leaf plot for file sizes in a given directory via
<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>$ ls -l /boot | awk &#39;BEGIN {print &quot;size&quot;} !/^total/ {print $5}&#39; | \
<a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> r -de &quot;print(summary(X[,1])); stem(X[,1])&quot;</code></pre></div>
which produces something like
<pre><code> Min. 1st Qu. Median Mean 3rd Qu. Max.
 13 512 110100 486900 768400 4735000

The decimal point is 6 digit(s) to the right of the |

0 | 0000001122222279222
 2 | 79444
 4 | 71888
 6 | 
 8 | 
 10 | 
 12 | 
 14 | 8
 16 | 4
 18 | 
 20 | 333</code></pre>
(Note that some systems may not have <code>/boot</code> in which case
you can try <code>/sbin</code> or another directory.)
As we saw in the preceding example, the program can also be shortened
like using the new <code>-d</code> option which reads from stdin and
assigns to a <code>data.frame</code> named <code>X</code>.
And, last but not least, this (somewhat unwieldy) expression can be
stored in a helper script (where we now switch to using an explicit
<code>readLines()</code> on <code>stdin</code>):
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/env r
<a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>
<a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>fsizes &lt;- as.integer(readLines(file(&quot;stdin&quot;)))
<a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>print(summary(fsizes))
<a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>stem(fsizes)</code></pre></div>
(where calling <code>#!/usr/bin/env</code> is a trick from Python
which allows one to forget whether r is installed in
<code>/usr/bin/r</code>, <code>/usr/local/bin/r</code>,
<code>~/bin/r</code>, …).
<h2 id="install.r-direct-cran-installation">install.r: Direct CRAN
Installation</h2>
This is one of my favourite <a href="http://dirk.eddelbuettel.com/code/littler.html">littler</a>
scripts which I use frequently to install packages off <a href="https://cran.r-project.org">CRAN</a>.
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/env r
<a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>
<a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>if (is.null(argv) | length(argv)&lt;1) {
<a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> cat(&quot;Usage: installr.r pkg1 [pkg2 pkg3 ...]\n&quot;)
<a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> q()
<a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb6-7" aria-hidden="true" tabindex="-1"></a>
<a href="#cb6-8" aria-hidden="true" tabindex="-1"></a>## adjust as necessary, see help(&#39;download.packages&#39;)
<a href="#cb6-9" aria-hidden="true" tabindex="-1"></a>repos &lt;- &quot;https://cran.rstudio.com&quot; 
<a href="#cb6-10" aria-hidden="true" tabindex="-1"></a>
<a href="#cb6-11" aria-hidden="true" tabindex="-1"></a>## this makes sense on Debian where no packages touch /usr/local
<a href="#cb6-12" aria-hidden="true" tabindex="-1"></a>lib.loc &lt;- &quot;/usr/local/lib/R/site-library&quot;
<a href="#cb6-13" aria-hidden="true" tabindex="-1"></a>
<a href="#cb6-14" aria-hidden="true" tabindex="-1"></a>install.packages(argv, lib.loc, repos)</code></pre></div>
I invoke it all the time with one, two or more packages to install
(or reinstall).
<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>$ install.r digest RcppCNPy</code></pre></div>
It conveniently installs all dependencies, and uses the chosen target
directory, all while keeping my R prompt (or prompts with multiple
sessions) free to do other things. Also, if used with
<code>options(&quot;Ncpu&quot;)</code> set, then (remote CRAN) packages will be
installed in parallel.
<h2 id="install2.r-with-cmdline-parsing">install2.r: With Cmdline
Parsing</h2>
Thanks to the fabulous <a href="https://github.com/edwindj/docopt.R">docopt</a> package, we also
have a variant <code>install2.r</code> with optional settings of repo
and location. It was first installed with <a href="http://dirk.eddelbuettel.com/blog/2014/10/19/">littler 0.2.1</a>.
The current (i.e., 0.3.3 as of this writing) version is more
featureful and longer and included to keep this brief. Some usage
examples are
<div class="sourceCode" id="cb8"><pre class="sourceCode sh"><code class="sourceCode bash"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>$ install2.r -l /tmp/lib Rcpp BH # install into given library
<a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>$ install2.r -- --with-keep.source drat # keep the source
<a href="#cb8-3" aria-hidden="true" tabindex="-1"></a>$ install2.r -- --data-compress=bzip2 stringdist # prefer bz2 compression</code></pre></div>
Another very useful option is <code>-n N</code> or
<code>--ncpus N</code> which will parallelize the installation across
<code>N</code> processes. This can be set automagically by setting
<code>options(&quot;Ncpus&quot;)</code>.
<h3 id="installing-from-sources">Installing From Sources</h3>
Starting with version 0.2.2, <code>install.r</code> and
<code>install2.r</code> now recognise installable source files. So one
can also do this:
<div class="sourceCode" id="cb9"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>$ install.r digest_0.6.8.tar.gz</code></pre></div>
and the local source file will the installed via a call to
<code>R CMD INSTALL</code>.
<h2 id="check.r-simple-checker">check.r: Simple Checker</h2>
A related use case is to check packages via <code>check.r</code>.
This script runs <code>R CMD check</code>, but also installs package
dependencies first as tests may have dependencies not yet satisfied on
the test machine. It offers a number of options:
<div class="sourceCode" id="cb10"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a>$ check.r -h
<a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>Usage: check.r [-h] [-x] [--as-cran] [--repo REPO] [--install-deps] [--install-kitchen] [--deb-pkgs PKGS...] [--use-sudo] [--library LIB] [--setwd DIR] [TARGZ ...]
<a href="#cb10-3" aria-hidden="true" tabindex="-1"></a>
<a href="#cb10-4" aria-hidden="true" tabindex="-1"></a>-a --as-cran customization similar to CRAN&#39;s incoming [default: FALSE]
<a href="#cb10-5" aria-hidden="true" tabindex="-1"></a>-r --repo REPO repository to use, or NULL for file [default: https://cran.rstudio.com]
<a href="#cb10-6" aria-hidden="true" tabindex="-1"></a>-i --install-deps also install packages along with their dependencies [default: FALSE]
<a href="#cb10-7" aria-hidden="true" tabindex="-1"></a>-k --install-kitchen even install packages &#39;kitchen sink&#39;-style up to suggests [default: FALSE]
<a href="#cb10-8" aria-hidden="true" tabindex="-1"></a>-l --library LIB when installing use this library [default: /usr/local/lib/R/site-library]
<a href="#cb10-9" aria-hidden="true" tabindex="-1"></a>-s --setwd DIR change to this directoru before undertaking the test [default: ]
<a href="#cb10-10" aria-hidden="true" tabindex="-1"></a>-d --deb-pkgs PKGS also install binary .deb packages with their dependencies [default: FALSE]
<a href="#cb10-11" aria-hidden="true" tabindex="-1"></a>-u --use-sudo use sudo when installing .deb packages [default: TRUE]
<a href="#cb10-12" aria-hidden="true" tabindex="-1"></a>-h --help show this help text
<a href="#cb10-13" aria-hidden="true" tabindex="-1"></a>-x --usage show help and short example usage
<a href="#cb10-14" aria-hidden="true" tabindex="-1"></a>$</code></pre></div>
<h2 id="rcc.r-r-cmd-check-wrapper">rcc.r: R CMD check wrapper</h2>
The script <code>rcc.r</code> will also check a source tarball, and
offers another set of options:
<div class="sourceCode" id="cb11"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>$ rcc.r -h
<a href="#cb11-2" aria-hidden="true" tabindex="-1"></a>Usage: rcc.r [-h] [-x] [-c] [-f] [-q] [--args ARGS] [--libpath LIBP] [--repos REPO] [PATH...]
<a href="#cb11-3" aria-hidden="true" tabindex="-1"></a>
<a href="#cb11-4" aria-hidden="true" tabindex="-1"></a>-c --as-cran should &#39;--as-cran&#39; be added to ARGS [default: FALSE]
<a href="#cb11-5" aria-hidden="true" tabindex="-1"></a>-a --args ARGS additional arguments to be passed to &#39;R CMD CHECK&#39; [default: ]
<a href="#cb11-6" aria-hidden="true" tabindex="-1"></a>-l --libpath LIBP additional library path to be used by &#39;R CMD CHECK&#39; [default: ]
<a href="#cb11-7" aria-hidden="true" tabindex="-1"></a>-r --repos REPO additional repositories to be used by &#39;R CMD CHECK&#39; [default: ]
<a href="#cb11-8" aria-hidden="true" tabindex="-1"></a>-f --fast should vignettes and manuals be skipped [default: FALSE]
<a href="#cb11-9" aria-hidden="true" tabindex="-1"></a>-q --quiet should &#39;rcmdcheck&#39; be called qietly [default: FALSE]
<a href="#cb11-10" aria-hidden="true" tabindex="-1"></a>-h --help show this help text
<a href="#cb11-11" aria-hidden="true" tabindex="-1"></a>-x --usage show help and short example usage
<a href="#cb11-12" aria-hidden="true" tabindex="-1"></a>$</code></pre></div>
<h2 id="build.r-building-packages">build.r: Building Packages</h2>
A related script is <code>build.r</code> which I often use inside a
source repository to quickly build a source tarball. Like
<code>rcc.r</code>, it has a switch <code>-f</code> or
<code>--fast</code> to omit building of vignettes.
<div class="sourceCode" id="cb12"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>$ build.r # without argument works on current directory
<a href="#cb12-2" aria-hidden="true" tabindex="-1"></a>$ build.r digest/ # with directory argument builds tar.gz from repo in directory</code></pre></div>
<h2 id="installgithub.r-github-install">installGithub.r: GitHub
install</h2>
Installation directly from <a href="https://github.com">GitHub</a> is
also popular. Here is an example:
<div class="sourceCode" id="cb13"><pre class="sourceCode bash"><code class="sourceCode bash"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>$ installGithub.r RcppCore/RcppEigen </code></pre></div>
Installing from github is supported via the following helper
script:
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/env r
<a href="#cb14-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb14-3" aria-hidden="true" tabindex="-1"></a># A simple example to install one or more packages from GitHub
<a href="#cb14-4" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb14-5" aria-hidden="true" tabindex="-1"></a># Copyright (C) 2014 - 2015 Carl Boettiger and Dirk Eddelbuettel
<a href="#cb14-6" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb14-7" aria-hidden="true" tabindex="-1"></a># Released under GPL (&gt;= 2)
<a href="#cb14-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-9" aria-hidden="true" tabindex="-1"></a>## load docopt and remotes (or devtools) from CRAN
<a href="#cb14-10" aria-hidden="true" tabindex="-1"></a>suppressMessages(library(docopt)) # we need docopt (&gt;= 0.3) as on CRAN
<a href="#cb14-11" aria-hidden="true" tabindex="-1"></a>suppressMessages(library(remotes)) # can use devtools as a fallback
<a href="#cb14-12" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-13" aria-hidden="true" tabindex="-1"></a>## configuration for docopt
<a href="#cb14-14" aria-hidden="true" tabindex="-1"></a>doc &lt;- &quot;Usage: installGithub.r [-h] [-d DEPS] REPOS...
<a href="#cb14-15" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-16" aria-hidden="true" tabindex="-1"></a>-d --deps DEPS Install suggested dependencies as well? [default: NA]
<a href="#cb14-17" aria-hidden="true" tabindex="-1"></a>-h --help show this help text
<a href="#cb14-18" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-19" aria-hidden="true" tabindex="-1"></a>where REPOS... is one or more GitHub repositories.
<a href="#cb14-20" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-21" aria-hidden="true" tabindex="-1"></a>Examples:
<a href="#cb14-22" aria-hidden="true" tabindex="-1"></a> installGithub.r RcppCore/RcppEigen 
<a href="#cb14-23" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-24" aria-hidden="true" tabindex="-1"></a>installGithub.r is part of littler which brings &#39;r&#39; to the command-line.
<a href="#cb14-25" aria-hidden="true" tabindex="-1"></a>See http://dirk.eddelbuettel.com/code/littler.html for more information.
<a href="#cb14-26" aria-hidden="true" tabindex="-1"></a>&quot;
<a href="#cb14-27" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-28" aria-hidden="true" tabindex="-1"></a>## docopt parsing
<a href="#cb14-29" aria-hidden="true" tabindex="-1"></a>opt &lt;- docopt(doc)
<a href="#cb14-30" aria-hidden="true" tabindex="-1"></a>if (opt$deps == &quot;TRUE&quot; || opt$deps == &quot;FALSE&quot;) {
<a href="#cb14-31" aria-hidden="true" tabindex="-1"></a> opt$deps &lt;- as.logical(opt$deps)
<a href="#cb14-32" aria-hidden="true" tabindex="-1"></a>} else if (opt$deps == &quot;NA&quot;) {
<a href="#cb14-33" aria-hidden="true" tabindex="-1"></a> opt$deps &lt;- NA
<a href="#cb14-34" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb14-35" aria-hidden="true" tabindex="-1"></a>
<a href="#cb14-36" aria-hidden="true" tabindex="-1"></a>invisible(sapply(opt$REPOS, function(r) install_github(r, dependencies = opt$deps)))</code></pre></div>
<h2 id="update.r-cran-package-update">update.r: CRAN package update</h2>
One of the scripts I use the most (interactively) is
<code>update.r</code> which updates installed packages. An earlier
version looked like the following example, the current version is a
little longer and has more features:
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/env r 
<a href="#cb15-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb15-3" aria-hidden="true" tabindex="-1"></a># a simple example to update packages in /usr/local/lib/R/site-library
<a href="#cb15-4" aria-hidden="true" tabindex="-1"></a># parameters are easily adjustable
<a href="#cb15-5" aria-hidden="true" tabindex="-1"></a>
<a href="#cb15-6" aria-hidden="true" tabindex="-1"></a>## adjust as necessary, see help(&#39;download.packages&#39;)
<a href="#cb15-7" aria-hidden="true" tabindex="-1"></a>repos &lt;- &quot;https://cloud.r-project.org&quot; 
<a href="#cb15-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb15-9" aria-hidden="true" tabindex="-1"></a>## this makes sense on Debian where no package touch /usr/local
<a href="#cb15-10" aria-hidden="true" tabindex="-1"></a>lib.loc &lt;- &quot;/usr/local/lib/R/site-library&quot;
<a href="#cb15-11" aria-hidden="true" tabindex="-1"></a>
<a href="#cb15-12" aria-hidden="true" tabindex="-1"></a>## r use requires non-interactive use
<a href="#cb15-13" aria-hidden="true" tabindex="-1"></a>update.packages(repos=repos, ask=FALSE, lib.loc=lib.loc)</code></pre></div>
As above, it has my preferred mirror and library location
hard-wired.
Another very useful option is <code>-n N</code> or
<code>--ncpus N</code> which will parallelize the upgrade across
<code>N</code> processes. This can be set automagically by setting
<code>options(Ncpus)</code>.
<h2 id="knit.r-calling-knitr">knit.r: Calling knitr</h2>
Here is another convenience script, <code>knit.r</code>, which
knits a given file after testing the file actually exists.
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/r
<a href="#cb16-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb16-3" aria-hidden="true" tabindex="-1"></a># Simple helper script for knitr
<a href="#cb16-4" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb16-5" aria-hidden="true" tabindex="-1"></a># Dirk Eddelbuettel, May 2013
<a href="#cb16-6" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb16-7" aria-hidden="true" tabindex="-1"></a># GPL-2 or later
<a href="#cb16-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb16-9" aria-hidden="true" tabindex="-1"></a>if (is.null(argv)) {
<a href="#cb16-10" aria-hidden="true" tabindex="-1"></a> cat(&quot;Need an argument FILE.Rnw\n&quot;)
<a href="#cb16-11" aria-hidden="true" tabindex="-1"></a> q(status=-1)
<a href="#cb16-12" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb16-13" aria-hidden="true" tabindex="-1"></a>
<a href="#cb16-14" aria-hidden="true" tabindex="-1"></a>
<a href="#cb16-15" aria-hidden="true" tabindex="-1"></a>file &lt;- argv[1]
<a href="#cb16-16" aria-hidden="true" tabindex="-1"></a>if (!file.exists(file)) {
<a href="#cb16-17" aria-hidden="true" tabindex="-1"></a> cat(&quot;File not found: &quot;, file, &quot;\n&quot;)
<a href="#cb16-18" aria-hidden="true" tabindex="-1"></a> q(status=-1)
<a href="#cb16-19" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb16-20" aria-hidden="true" tabindex="-1"></a>
<a href="#cb16-21" aria-hidden="true" tabindex="-1"></a>require(knitr)
<a href="#cb16-22" aria-hidden="true" tabindex="-1"></a>knit2pdf(file)</code></pre></div>
<h2 id="roxy.r-running-roxygen">roxy.r: Running roxygen</h2>
Similar to the previous example, the script <code>roxy.r</code> one
uses roxygen to extract documentation from R files – either in the
current directory, or in the given directory or directories.
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/r
<a href="#cb17-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb17-3" aria-hidden="true" tabindex="-1"></a># Simple helper script for roxygen2::roxygenize() 
<a href="#cb17-4" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb17-5" aria-hidden="true" tabindex="-1"></a># Dirk Eddelbuettel, August 2013
<a href="#cb17-6" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb17-7" aria-hidden="true" tabindex="-1"></a># GPL-2 or later
<a href="#cb17-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb17-9" aria-hidden="true" tabindex="-1"></a>## load roxygen
<a href="#cb17-10" aria-hidden="true" tabindex="-1"></a>library(roxygen2)
<a href="#cb17-11" aria-hidden="true" tabindex="-1"></a>
<a href="#cb17-12" aria-hidden="true" tabindex="-1"></a>## check all command-line arguments (if any are given) for directory status
<a href="#cb17-13" aria-hidden="true" tabindex="-1"></a>argv &lt;- Filter(function(x) file.info(x)$is.dir, argv)
<a href="#cb17-14" aria-hidden="true" tabindex="-1"></a>
<a href="#cb17-15" aria-hidden="true" tabindex="-1"></a>## loop over all argument, with fallback of the current directory, and
<a href="#cb17-16" aria-hidden="true" tabindex="-1"></a>## call compileAttributes() on the given directory
<a href="#cb17-17" aria-hidden="true" tabindex="-1"></a>sapply(ifelse(length(argv) &gt; 0, argv, &quot;.&quot;), FUN=roxygenize, roclets=&quot;rd&quot;)</code></pre></div>
<h2 id="compattr.r-compiling-attributes">compAttr.r: Compiling
Attributes</h2>
The next script, <code>compAttr.</code>, can be used with <a href="http://dirk.eddelbuettel.com/code/rcpp.html">Rcpp</a>, and
particularly is powerful Attributes feature, in order to
auto-generate helper code. It is similar to the preceding script, but
invokes <code>compileAttributes()</code> instead.
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/r
<a href="#cb18-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb18-3" aria-hidden="true" tabindex="-1"></a># Simple helper script for compileAttributes() 
<a href="#cb18-4" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb18-5" aria-hidden="true" tabindex="-1"></a># Dirk Eddelbuettel, July 2014
<a href="#cb18-6" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb18-7" aria-hidden="true" tabindex="-1"></a># GPL-2 or later
<a href="#cb18-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb18-9" aria-hidden="true" tabindex="-1"></a>## load Rcpp
<a href="#cb18-10" aria-hidden="true" tabindex="-1"></a>suppressMessages(library(Rcpp))
<a href="#cb18-11" aria-hidden="true" tabindex="-1"></a>
<a href="#cb18-12" aria-hidden="true" tabindex="-1"></a>## check all command-line arguments (if any are given) for directory status
<a href="#cb18-13" aria-hidden="true" tabindex="-1"></a>argv &lt;- Filter(function(x) file.info(x)$is.dir, argv)
<a href="#cb18-14" aria-hidden="true" tabindex="-1"></a>
<a href="#cb18-15" aria-hidden="true" tabindex="-1"></a>## loop over all argument, with fallback of the current directory, and
<a href="#cb18-16" aria-hidden="true" tabindex="-1"></a>## call compileAttributes() on the given directory
<a href="#cb18-17" aria-hidden="true" tabindex="-1"></a>sapply(ifelse(length(argv) &gt; 0, argv, &quot;.&quot;), compileAttributes)</code></pre></div>
<h2 id="render.r-render-markdown">render.r: Render Markdown</h2>
The <code>render.r</code> script generalizes the earlier
<code>knit.r</code> to convert Markdown into its designated output.
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a>#!/usr/bin/env r
<a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb19-3" aria-hidden="true" tabindex="-1"></a># Another example to run a shiny app
<a href="#cb19-4" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb19-5" aria-hidden="true" tabindex="-1"></a># Copyright (C) 2016 Dirk Eddelbuettel
<a href="#cb19-6" aria-hidden="true" tabindex="-1"></a>#
<a href="#cb19-7" aria-hidden="true" tabindex="-1"></a># Released under GPL (&gt;= 2)
<a href="#cb19-8" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-9" aria-hidden="true" tabindex="-1"></a>suppressMessages(library(docopt)) # we need docopt (&gt;= 0.3) as on CRAN
<a href="#cb19-10" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-11" aria-hidden="true" tabindex="-1"></a>## configuration for docopt
<a href="#cb19-12" aria-hidden="true" tabindex="-1"></a>doc &lt;- &quot;Usage: render.r [-h] [-x] [FILES...]
<a href="#cb19-13" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-14" aria-hidden="true" tabindex="-1"></a>-h --help show this help text
<a href="#cb19-15" aria-hidden="true" tabindex="-1"></a>-x --usage show help and short example usage&quot;
<a href="#cb19-16" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-17" aria-hidden="true" tabindex="-1"></a>opt &lt;- docopt(doc) # docopt parsing
<a href="#cb19-18" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-19" aria-hidden="true" tabindex="-1"></a>if (opt$usage) {
<a href="#cb19-20" aria-hidden="true" tabindex="-1"></a> cat(doc, &quot;\n\n&quot;)
<a href="#cb19-21" aria-hidden="true" tabindex="-1"></a> cat(&quot;Examples:
<a href="#cb19-22" aria-hidden="true" tabindex="-1"></a> render.r foo.Rmd bar.Rmd # convert two given files
<a href="#cb19-23" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-24" aria-hidden="true" tabindex="-1"></a>render.r is part of littler which brings &#39;r&#39; to the command-line.
<a href="#cb19-25" aria-hidden="true" tabindex="-1"></a>See http://dirk.eddelbuettel.com/code/littler.html for more information.\n&quot;)
<a href="#cb19-26" aria-hidden="true" tabindex="-1"></a> q(&quot;no&quot;)
<a href="#cb19-27" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb19-28" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-29" aria-hidden="true" tabindex="-1"></a>library(rmarkdown)
<a href="#cb19-30" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-31" aria-hidden="true" tabindex="-1"></a>## helper function 
<a href="#cb19-32" aria-hidden="true" tabindex="-1"></a>renderArg &lt;- function(p) {
<a href="#cb19-33" aria-hidden="true" tabindex="-1"></a> if (!file.exists(p)) stop(&quot;No file &#39;&quot;, p, &quot;&#39; found. Aborting.&quot;, call.=FALSE)
<a href="#cb19-34" aria-hidden="true" tabindex="-1"></a> render(p)
<a href="#cb19-35" aria-hidden="true" tabindex="-1"></a>}
<a href="#cb19-36" aria-hidden="true" tabindex="-1"></a>
<a href="#cb19-37" aria-hidden="true" tabindex="-1"></a>## render files using helper function 
<a href="#cb19-38" aria-hidden="true" tabindex="-1"></a>sapply(opt$FILES, renderArg)</code></pre></div>
</body>
</html>