{"id":6071,"date":"2017-06-10T09:32:48","date_gmt":"2017-06-10T14:32:48","guid":{"rendered":"https:\/\/rud.is\/b\/?p=6071"},"modified":"2018-03-10T07:54:26","modified_gmt":"2018-03-10T12:54:26","slug":"engaging-the-tidyverse-clean-slate-protocol","status":"publish","type":"post","link":"https:\/\/rud.is\/b\/2017\/06\/10\/engaging-the-tidyverse-clean-slate-protocol\/","title":{"rendered":"Engaging the tidyverse Clean Slate Protocol"},"content":{"rendered":"<p><a href=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/06\/CSP.png?ssl=1\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" data-attachment-id=\"6072\" data-permalink=\"https:\/\/rud.is\/b\/2017\/06\/10\/engaging-the-tidyverse-clean-slate-protocol\/csp\/\" data-orig-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/06\/CSP.png?fit=1000%2C416&amp;ssl=1\" data-orig-size=\"1000,416\" data-comments-opened=\"1\" data-image-meta=\"{&quot;aperture&quot;:&quot;0&quot;,&quot;credit&quot;:&quot;&quot;,&quot;camera&quot;:&quot;&quot;,&quot;caption&quot;:&quot;&quot;,&quot;created_timestamp&quot;:&quot;0&quot;,&quot;copyright&quot;:&quot;&quot;,&quot;focal_length&quot;:&quot;0&quot;,&quot;iso&quot;:&quot;0&quot;,&quot;shutter_speed&quot;:&quot;0&quot;,&quot;title&quot;:&quot;&quot;,&quot;orientation&quot;:&quot;0&quot;}\" data-image-title=\"CSP\" data-image-description=\"\" data-image-caption=\"\" data-large-file=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/06\/CSP.png?fit=510%2C212&amp;ssl=1\" src=\"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2017\/06\/CSP.png?resize=510%2C212&#038;ssl=1\" alt=\"\" width=\"510\" height=\"212\" class=\"aligncenter size-full wp-image-6072\" \/><\/a><\/p>\n<p>I caught the 0.7.0 release of <code>dplyr<\/code> on my home CRAN server early Friday morning and immediately set out to install it since I&#8217;m eager to finish up my <code>sergeant<\/code> package and get it on CRAN. &#8220;Tidyverse&#8221; upgrades aren&#8217;t trivial for me as I tinker quite a bit with the tidyverse and create packages that depend on various components. The <code>sergeant<\/code> package provides &#8212; amongst other things &#8212; a <code>dplyr<\/code> back-end for Apache Drill, so it has more tidyverse tendrils than other bits of code I maintain.<\/p>\n<p>macOS binaries weren&#8217;t available yet (it generally takes 24-48 hrs for that) so I did an <code>install.packages(\"dplyr\", type=\"source\")<\/code> and was immediately hit with gcc 7 compilation errors. This seemed odd, but switching back to <code>clang<\/code> worked fine.<\/p>\n<p>I, then, proceeded to run chunks in an Rmd I&#8217;m working on and hit &#8220;Encoding&#8221; errors on <code>mutate()<\/code> calls. Not having time to debug further I reverted to 0.5.0 of <code>dplyr<\/code> and went about my day and promised the tidyverse maintainers that I&#8217;d work on a reproducible example after work.<\/p>\n<p>I made R data files from the data frames that were tossing errors and extracted &amp; tweaked a code snippet that  consistently generated the error and created a rocker container on one of my linux boxes to validate that this was an error and a cross-platform one. The rocker container used a full fresh-from-source copy of the tidyverse including <code>dplyr<\/code> 0.7.0. The code worked and no error was generated, so I immediately suspected package rot on my main dev macOS box.<\/p>\n<p>Now, my situation is complicated by an insanely hasty migration to macOS 10.13\u03b21 (I refuse to use the Apple macOS catchy names anymore since the most recent one is just silly) and a move to the gcc 7 toolchain (initially prompted to both get <code>rJava<\/code> working nicely and reproduce some CRAN noted errors with some packages). Further complications were also created by many invocations of <code>install_github()<\/code> of various packages regularly overwriting bits of the tidyverse over the past few weeks since the R 3.4.0 release. In other words, the integrity of the &#8220;tidyverse&#8221; was in serious question on my system and it was time for the <a href=\"http:\/\/marvelcinematicuniverse.wikia.com\/wiki\/Clean_Slate_Protocol\">Clean Slate Protocol<\/a>.<\/p>\n<p>Rather than itemize package versions and surgically nipping and tucking, I opted to use <code>packrat<\/code> to get to my desired end-state of a full-integrity tidyverse install. There are many ways to do this. Feel free to &#8220;one-up&#8221; me and show your l33t method in the comments. This one will likely be accessible to most &#8212; if not all &#8212; R users.<\/p>\n<p>I started a new RStudio project in a new session and told it to use <code>packrat<\/code>. In the new project console, I did <code>install.packages(\"tidyverse\", type=\"source\")<\/code> and let it go for many minutes. I, then, navigated to the packrat subdirectory where the 3.4 package binaries are housed (just follow the project <code>packrat<\/code> tree down to the R version directory) and moved all 51 packages (yes, 51 O_o) to the main R library path (which you can figure out by running <code>.libPaths()<\/code> in any non-<code>packrat<\/code>-maintained project).<\/p>\n<p>After doing that, I fired up the originally failing Rmd and everything worked fine. ?<\/p>\n<p>I don&#8217;t do the Clean Slate Protocol too often (we all get to for new R dot-releases) but it came in handy this time. If you run into errors when trying to get the new <code>dplyr<\/code> working, you may benefit from the Clean Slate Protocol as well.<\/p>\n<p>If you haven&#8217;t seen the changes in 0.6.0\/0.7.0 you should <a href=\"https:\/\/blog.rstudio.com\/2017\/04\/13\/dplyr-0-6-0-coming-soon\/\">check them out<\/a> and give it a go.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>I caught the 0.7.0 release of dplyr on my home CRAN server early Friday morning and immediately set out to install it since I&#8217;m eager to finish up my sergeant package and get it on CRAN. &#8220;Tidyverse&#8221; upgrades aren&#8217;t trivial for me as I tinker quite a bit with the tidyverse and create packages that [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":6072,"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":[779,780,91,797],"tags":[810],"class_list":["post-6071","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-dplyr","category-macos","category-r","category-tidyverse","tag-post"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Engaging the tidyverse Clean Slate Protocol - 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\/2017\/06\/10\/engaging-the-tidyverse-clean-slate-protocol\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Engaging the tidyverse Clean Slate Protocol - rud.is\" \/>\n<meta property=\"og:description\" content=\"I caught the 0.7.0 release of dplyr on my home CRAN server early Friday morning and immediately set out to install it since I&#8217;m eager to finish up my sergeant package and get it on CRAN. &#8220;Tidyverse&#8221; 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I've also wrapped a few goodies into the dplyr custom functions that work with Drill and if you\u2026","rel":"","context":"In &quot;Apache Drill&quot;","block_context":{"text":"Apache Drill","link":"https:\/\/rud.is\/b\/category\/apache-drill\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10834,"url":"https:\/\/rud.is\/b\/2018\/05\/29\/the-fix-is-in-finding-infix-functions-inside-contributed-r-package-utilities-files\/","url_meta":{"origin":6071,"position":3},"title":"The Fix Is In: Finding infix functions inside contributed R package &#8220;utilities&#8221; files","author":"hrbrmstr","date":"2018-05-29","format":false,"excerpt":"Regular readers will recall the \"utility belt\" post from back in April of this year. This is a follow-up to a request made asking for a list of all the % infix functions in those files. We're going to: collect up all of the sources parse them find all the\u2026","rel":"","context":"In &quot;R&quot;","block_context":{"text":"R","link":"https:\/\/rud.is\/b\/category\/r\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":4753,"url":"https:\/\/rud.is\/b\/2016\/12\/20\/sergeant-a-r-boot-camp-for-apache-drill\/","url_meta":{"origin":6071,"position":4},"title":"sergeant : An R Boot Camp for Apache Drill","author":"hrbrmstr","date":"2016-12-20","format":false,"excerpt":"I recently mentioned that I've been working on a development version of an Apache Drill R package called sergeant. Here's a lifted \"TLDR\" on Drill: Drill supports a variety of NoSQL databases and file systems, including HBase, MongoDB, MapR-DB, HDFS, MapR-FS, Amazon S3, Azure Blob Storage, Google Cloud Storage, Swift,\u2026","rel":"","context":"In &quot;Apache Drill&quot;","block_context":{"text":"Apache Drill","link":"https:\/\/rud.is\/b\/category\/apache-drill\/"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":12138,"url":"https:\/\/rud.is\/b\/2019\/04\/10\/lost-in-sql-translation-charting-dbplyr-mapped-sql-function-support-across-all-backends\/","url_meta":{"origin":6071,"position":5},"title":"Lost In [SQL] Translation: Charting d[b]plyr Mapped SQL Function Support Across All Backends","author":"hrbrmstr","date":"2019-04-10","format":false,"excerpt":"Like more posts than I care to admit, this one starts innocently enough with a tweet by @gshotwell: Is there a reference document somewhere of which dplyr commands work on various database backends? #rstats\u2014 Gordon Shotwell (@gshotwell) April 9, 2019 Since I use at least 4 different d[b]plyr backends every\u2026","rel":"","context":"In &quot;dplyr&quot;","block_context":{"text":"dplyr","link":"https:\/\/rud.is\/b\/category\/dplyr\/"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2019\/04\/backend-heatmap.jpg?fit=1200%2C659&ssl=1&resize=350%2C200","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2019\/04\/backend-heatmap.jpg?fit=1200%2C659&ssl=1&resize=350%2C200 1x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2019\/04\/backend-heatmap.jpg?fit=1200%2C659&ssl=1&resize=525%2C300 1.5x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2019\/04\/backend-heatmap.jpg?fit=1200%2C659&ssl=1&resize=700%2C400 2x, https:\/\/i0.wp.com\/rud.is\/b\/wp-content\/uploads\/2019\/04\/backend-heatmap.jpg?fit=1200%2C659&ssl=1&resize=1050%2C600 3x"},"classes":[]}],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/6071","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/comments?post=6071"}],"version-history":[{"count":0,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/posts\/6071\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/media\/6072"}],"wp:attachment":[{"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/media?parent=6071"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/categories?post=6071"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/rud.is\/b\/wp-json\/wp\/v2\/tags?post=6071"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}