{"id":3732,"date":"2015-10-22T08:29:17","date_gmt":"2015-10-22T13:29:17","guid":{"rendered":"http:\/\/rud.is\/b\/?p=3732"},"modified":"2019-12-16T13:34:49","modified_gmt":"2019-12-16T18:34:49","slug":"installing-r-on-os-x-100-homebrew-edition","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2015\/10\/22\/installing-r-on-os-x-100-homebrew-edition\/","title":{"rendered":"Installing R on OS X &#8211; &#8220;100% Homebrew Edition&#8221;"},"content":{"rendered":"<p>In <a href=\"https:\/\/rud.is\/b\/2015\/10\/20\/installing-r-on-os-x\/\">a previous post<\/a> I provided &#8220;mouse-heavy&#8221; instructions for getting R running on your Mac. A few of the comments suggested that an &#8220;all Homebrew&#8221; solution may be preferable for some folks. Now, there are issues with this since getting &#8220;support&#8221; for what <em>may be<\/em> R issues will be very difficult on the official mailing lists as you&#8217;ll immediately be told to &#8220;use the official distribution&#8221; by some stalwart R folks (this happens on StackOverflow and other forums as well). However, if you have a thick skin and can be somewhat self-sustaining, Homebrew is a superb alternative to setting up your R environment (and other things) on your OS X system.<\/p>\n<h3>What is &#8216;Homebrew&#8217;?<\/h3>\n<p><a href=\"https:\/\/brew.sh\/\">Homebrew<\/a> is the <em>&#8220;missing package manager for OS X&#8221;<\/em>. It&#8217;s similar to <code>apt<\/code>, <code>yum<\/code> and other package managers on linux\/BSD that enable you to install open source (and other types of) packages without having to do the download\u2192unarchive\u2192compile\u2192curse\u2192google\u2192compile\u2192curse\u2192google some more\u2192compile\u2192smile\u2192test\u2192install dance manually. <a href=\"https:\/\/www.macports.org\/\">MacPorts<\/a> is another third-party package manager for OS X, but I use Homebrew, so you get Homebrew examples here.<\/p>\n<p>Homebrew&#8217;s inventory of packages comes from github repositories that contain &#8220;Formulas&#8221; for where to get package components and how to (literally) <code>make<\/code> them work on OS X. Here&#8217;s a small-ish example (some Formula are fairly long\/involved\/complex) of a Homebrew Formula for the <code>cowsay<\/code> utility (what, you don&#8217;t like to have ASCII animals give you handy messages?):<\/p>\n<pre><code class=\"language-ruby\">class Cowsay &lt; Formula\n  desc \"Configurable talking characters in ASCII art\"\n  homepage \"https:\/\/web.archive.org\/web\/20120225123719\/http:\/\/www.nog.net\/~tony\/warez\/cowsay.shtml\"\n  url \"http:\/\/ftp.acc.umu.se\/mirror\/cdimage\/snapshot\/Debian\/pool\/main\/c\/cowsay\/cowsay_3.03.orig.tar.gz\"\n  sha256 \"0b8672a7ac2b51183780db72618b42af8ec1ce02f6c05fe612510b650540b2af\"\n\n  bottle do\n    cellar :any_skip_relocation\n    revision 1\n    sha256 \"c041ce7fbf41fd89bf620ae848e3b36fe1e69ab3e2dfca18bc2f2e79cfe8063a\" =&gt; :el_capitan\n    sha256 \"ffacfb987481394174267fd987dea52607825e3542d1ea3d0b7aa4ccf7ea5cc5\" =&gt; :yosemite\n    sha256 \"12c41b969af30817a4dc7ec25572fe1b707b9d4dcb46d8cc06d22264594219c1\" =&gt; :mavericks\n  end\n\n  # Official download is 404:\n  # url \"http:\/\/www.nog.net\/~tony\/warez\/cowsay-3.03.tar.gz\"\n\n  def install\n    system \"\/bin\/sh\", \"install.sh\", prefix\n    mv prefix\/\"man\", share\n  end\n\n  test do\n    output = shell_output(\"#{bin}\/cowsay moo\")\n    assert output.include?(\"moo\")  # bubble\n    assert output.include?(\"^__^\") # cow\n  end\nend\n<\/code><\/pre>\n<p>It has:<\/p>\n<ul>\n<li>a description of what the package is<\/li>\n<li>the official location of the program\/libraries &#8220;home&#8221;<\/li>\n<li>where the main URL of the contents of the program\/library is<\/li>\n<li>weird hex strings to help the Homebrew ecosystem now pwn you<\/li>\n<li>instructions for how to install (with optional patching of problematic code on particular setups)<\/li>\n<li>test\/validation instructions<\/li>\n<\/ul>\n<p>(You can\/should overlook the fact they use icky Ruby for this whole thing.)<\/p>\n<p>There are <em>thousands<\/em> of Formula in the main Homebrew repository and you can &#8220;tap&#8221; other (<a href=\"https:\/\/github.com\/Homebrew\/homebrew-science\/\">properly organized<\/a>) GitHub repositories for other (usually task-specific) formula. We&#8217;ll need to do this for R.<\/p>\n<p>Finally, the Homebrew community has also come up with the notion of <span class=\"removed_link\" title=\"http:\/\/caskroom.io\/\">Casks<\/span> where actual binary OS X programs (and other things) can be installed. We&#8217;ll use this as well for some ancillary components.<\/p>\n<p>Apart from the ease of initial setup, the truly compelling part of using Homebrew is that all it takes to update components\/libraries is to do a:<\/p>\n<pre lang=\"bash\">brew update && brew upgrade<\/pre>\n<p>from a Terminal prompt. You should get into the habit of issuing those commands daily<i>-ish<\/i>.<\/p>\n<p>Yes, you will need to become comfortable in the Terminal (or, preferably, <a href=\"https:\/\/www.iterm2.com\/\">iTerm 2<\/a>) to use the Homebrew ecosystem (though there are <a href=\"https:\/\/www.cakebrew.com\/\">some efforts<\/a> to make this more GUI-user friendly).<\/p>\n<h3>Using Homebrew to Create &#038; Maintain Your R Installation<\/h3>\n<p>I won&#8217;t provide much (if any) color commentary to the commands below. Suffice it to say that in a few short lines of a script, you&#8217;ll end up having:<\/p>\n<ul>\n<li>R (with <code>gfortran<\/code> and the vast majority of required support libraries for many packages)<\/li>\n<li>Oracle Java (a later step in the sequence ensures R knows about your Java install)<\/li>\n<li>X11 (XQuartz)<\/li>\n<li>MacTex<\/li>\n<li>RStudio<\/li>\n<li>extra SVG, XML, curl, geo-munging and C++ support libraries<\/li>\n<li>A cool font for RStudio (<a href=\"https:\/\/github.com\/tonsky\/FiraCode\">FiraCode<\/a>, though that&#8217;s not necessary)<\/li>\n<li>iTerm 2 (optional)<\/li>\n<li>GitUp git gui (optional)<\/li>\n<\/ul>\n<p>If it&#8217;s your first time using Homebrew you&#8217;ll need to do this:<\/p>\n<pre><code class=\"language-ruby\">ruby -e \"$(curl -fsSL https:\/\/raw.githubusercontent.com\/Homebrew\/install\/master\/install)\"\n<\/code><\/pre>\n<blockquote><p>\n  NOTE that I&#8217;m generally against piping output of <code>curl<\/code> to run raw on your system without validation, so you <em>can<\/em> download <a href=\"https:\/\/raw.githubusercontent.com\/Homebrew\/install\/master\/install\">https:\/\/raw.githubusercontent.com\/Homebrew\/install\/master\/install<\/a> and verify it (or ask a security friend to verify it), but you&#8217;ll be trusting the Homebrew ecosystem to not pwn your system for the rest of your time using it, so as long as you trust that <em>I<\/em> gave you the proper URL to get to the installer, cut\/paste away.\n<\/p><\/blockquote>\n<p>Once Homebrew is setup I&#8217;d recommend copying and pasting each line (below) one-by-one to get familiar with Homebrew operations and messaging.<\/p>\n<p>This can be a pretty scary experience if you&#8217;re not used to the command-line, so drop a note in the comments or on Twitter (target @hrbrmstr and use the <code>#rstats<\/code> <code>#homebrew<\/code> tags) if some things go awry or get confusing and I&#8217;ll try to help as much as I can.<\/p>\n<pre><code class=\"language-bash\">brew tap caskroom\/cask\nbrew install brew-cask\n\nbrew install Caskroom\/cask\/xquartz\nbrew cask install java\n\nbrew tap homebrew\/science\nbrew install R --with-openblas # added --with-openblas based on a spiffy comment by Lincoln Mullen\n\nbrew install Caskroom\/cask\/rstudio\n\n\n# For latex:\nbrew cask install mactex\n\n# OR YOU CAN DO\nbrew install gnupg\nbrew cask install basictex # suggested by @noamross\n# plus the following, provided by Kras.Pten\n# read why here: http:\/\/rud.is\/b\/2015\/10\/22\/installing-r-on-os-x-100-homebrew-edition\/#comment-10603\nsudo tlmgr update \u2013-self \nsudo tlmgr update \u2013-all \nsudo tlmgr install titling framed inconsolata\n\n# DO NOT DO BOTH!\n\nbrew install libsvg curl libxml2 gdal geos boost\n\nR CMD javareconf JAVA_CPPFLAGS=-I\/System\/Library\/Frameworks\/JavaVM.framework\/Headers\n\nbrew tap caskroom\/fonts\nbrew cask install font-fira-code\nbrew cask install iterm2\nbrew cask install gitup           # if you want a GUI for git stuff (h\/t @jennybryan)\n<\/code><\/pre>\n<p>That&#8217;s quite a bit less clicking\/typing from what was required in the previous post.<\/p>\n<h3>Fin<\/h3>\n<p>I validated that <em>entire<\/em> configuration on a completely fresh installation of El Capitan (OS X 10.11) in a VM. At the end, I had a fully-functioning data-science setup. Hopefully, you will as well.<\/p>\n<p>If you have suggestions for other Homebrew things to add to make a good &#8220;data science OS X setup&#8221;, drop a note in the comments!<\/p>\n<h3>P.S.<\/h3>\n<p>Once you have a full Homebrew &amp; &#8220;Cask&#8221; setup, the way to keep up-to-date with everything is more like:<\/p>\n<pre lang=\"bash\">brew update && brew upgrade brew-cask && brew cleanup && brew cask cleanup<\/pre>\n<p>but an complete &#8220;how to use Homebrew&#8221; guide is beyond the scope of this post.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In a previous post I provided &#8220;mouse-heavy&#8221; instructions for getting R running on your Mac. A few of the comments suggested that an &#8220;all Homebrew&#8221; solution may be preferable for some folks. Now, there are issues with this since getting &#8220;support&#8221; for what may be R issues will be very difficult on the official mailing [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":3750,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":3,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":""},"categories":[12,91],"tags":[810],"class_list":["post-3732","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-os-x","category-r","tag-post"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Installing R on OS X - &quot;100% Homebrew Edition&quot; - rud.is<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/rud.is\/b\/2015\/10\/22\/installing-r-on-os-x-100-homebrew-edition\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Installing R on OS X - &quot;100% Homebrew Edition&quot; - rud.is\" \/>\n<meta property=\"og:description\" content=\"In a previous post I provided &#8220;mouse-heavy&#8221; instructions for getting R running on your Mac. 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Keying off\u2026","rel":"","context":"In &quot;homebrew&quot;","block_context":{"text":"homebrew","link":"https:\/\/rud.is\/b\/category\/homebrew\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3709,"url":"https:\/\/rud.is\/b\/2015\/10\/20\/installing-r-on-os-x\/","url_meta":{"origin":3732,"position":2},"title":"Installing R on OS X","author":"hrbrmstr","date":"2015-10-20","format":false,"excerpt":"NOTE: The comments are a must read for this. Some excellent additional advice and \"gotchas\" by some super-helpful readers. I was in a conversation with an academic colleague (wicked smart dude) and the subject of installing R came up (NOTE: this will happen to you, too, if you ever have\u2026","rel":"","context":"In &quot;OS X&quot;","block_context":{"text":"OS X","link":"https:\/\/rud.is\/b\/category\/os-x\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":12945,"url":"https:\/\/rud.is\/b\/2021\/02\/07\/fully-native-m1-apple-silicon-r-setup\/","url_meta":{"origin":3732,"position":3},"title":"Fully Native M1\/Apple Silicon R Setup","author":"hrbrmstr","date":"2021-02-07","format":false,"excerpt":"Presented without much commentary since I stopped once {ggrepel} and {graphlayouts} failed (RStudio doesn't support it yet, either, which I knew). The following steps will get you a fully working and STUPID FAST fully native ARM64 M1\/Apple Silicon R setup with {tidyverse} and {rJava}. 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