`, etc.) that has more than one element. Defaults to 1 (for ``).
- getTopLevel: function($scope) {
- for (var i = 1; i <= 6; i++) {
- var $headings = this.findOrFilter($scope, 'h' + i);
- if ($headings.length > 1) {
- return i;
- }
- }
-
- return 1;
- },
-
- // returns the elements for the top level, and the next below it
- getHeadings: function($scope, topLevel) {
- var topSelector = 'h' + topLevel;
-
- var secondaryLevel = topLevel + 1;
- var secondarySelector = 'h' + secondaryLevel;
-
- return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
- },
-
- getNavLevel: function(el) {
- return parseInt(el.tagName.charAt(1), 10);
- },
-
- populateNav: function($topContext, topLevel, $headings) {
- var $context = $topContext;
- var $prevNav;
-
- var helpers = this;
- $headings.each(function(i, el) {
- var $newNav = helpers.generateNavItem(el);
- var navLevel = helpers.getNavLevel(el);
-
- // determine the proper $context
- if (navLevel === topLevel) {
- // use top level
- $context = $topContext;
- } else if ($prevNav && $context === $topContext) {
- // create a new level of the tree and switch to it
- $context = helpers.createChildNavList($prevNav);
- } // else use the current $context
-
- $context.append($newNav);
-
- $prevNav = $newNav;
- });
- },
-
- parseOps: function(arg) {
- var opts;
- if (arg.jquery) {
- opts = {
- $nav: arg
- };
- } else {
- opts = arg;
- }
- opts.$scope = opts.$scope || $(document.body);
- return opts;
- }
- },
-
- // accepts a jQuery object, or an options object
- init: function(opts) {
- opts = this.helpers.parseOps(opts);
-
- // ensure that the data attribute is in place for styling
- opts.$nav.attr('data-toggle', 'toc');
-
- var $topContext = this.helpers.createChildNavList(opts.$nav);
- var topLevel = this.helpers.getTopLevel(opts.$scope);
- var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
- this.helpers.populateNav($topContext, topLevel, $headings);
- }
- };
-
- $(function() {
- $('nav[data-toggle="toc"]').each(function(i, el) {
- var $nav = $(el);
- Toc.init($nav);
- });
- });
-})();
diff --git a/docs/docsearch.css b/docs/docsearch.css
deleted file mode 100644
index e5f1fe1..0000000
--- a/docs/docsearch.css
+++ /dev/null
@@ -1,148 +0,0 @@
-/* Docsearch -------------------------------------------------------------- */
-/*
- Source: https://github.com/algolia/docsearch/
- License: MIT
-*/
-
-.algolia-autocomplete {
- display: block;
- -webkit-box-flex: 1;
- -ms-flex: 1;
- flex: 1
-}
-
-.algolia-autocomplete .ds-dropdown-menu {
- width: 100%;
- min-width: none;
- max-width: none;
- padding: .75rem 0;
- background-color: #fff;
- background-clip: padding-box;
- border: 1px solid rgba(0, 0, 0, .1);
- box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
-}
-
-@media (min-width:768px) {
- .algolia-autocomplete .ds-dropdown-menu {
- width: 175%
- }
-}
-
-.algolia-autocomplete .ds-dropdown-menu::before {
- display: none
-}
-
-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
- padding: 0;
- background-color: rgb(255,255,255);
- border: 0;
- max-height: 80vh;
-}
-
-.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
- margin-top: 0
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion {
- padding: 0;
- overflow: visible
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
- padding: .125rem 1rem;
- margin-top: 0;
- font-size: 1.3em;
- font-weight: 500;
- color: #00008B;
- border-bottom: 0
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
- float: none;
- padding-top: 0
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
- float: none;
- width: auto;
- padding: 0;
- text-align: left
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--content {
- float: none;
- width: auto;
- padding: 0
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
- display: none
-}
-
-.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
- padding-top: .75rem;
- margin-top: .75rem;
- border-top: 1px solid rgba(0, 0, 0, .1)
-}
-
-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
- display: block;
- padding: .1rem 1rem;
- margin-bottom: 0.1;
- font-size: 1.0em;
- font-weight: 400
- /* display: none */
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--title {
- display: block;
- padding: .25rem 1rem;
- margin-bottom: 0;
- font-size: 0.9em;
- font-weight: 400
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text {
- padding: 0 1rem .5rem;
- margin-top: -.25rem;
- font-size: 0.8em;
- font-weight: 400;
- line-height: 1.25
-}
-
-.algolia-autocomplete .algolia-docsearch-footer {
- width: 110px;
- height: 20px;
- z-index: 3;
- margin-top: 10.66667px;
- float: right;
- font-size: 0;
- line-height: 0;
-}
-
-.algolia-autocomplete .algolia-docsearch-footer--logo {
- background-image: url("data:image/svg+xml;utf8,");
- background-repeat: no-repeat;
- background-position: 50%;
- background-size: 100%;
- overflow: hidden;
- text-indent: -9000px;
- width: 100%;
- height: 100%;
- display: block;
- transform: translate(-8px);
-}
-
-.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
- color: #FF8C00;
- background: rgba(232, 189, 54, 0.1)
-}
-
-
-.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
- box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
-}
-
-.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
- background-color: rgba(192, 192, 192, .15)
-}
diff --git a/docs/docsearch.js b/docs/docsearch.js
deleted file mode 100644
index b35504c..0000000
--- a/docs/docsearch.js
+++ /dev/null
@@ -1,85 +0,0 @@
-$(function() {
-
- // register a handler to move the focus to the search bar
- // upon pressing shift + "/" (i.e. "?")
- $(document).on('keydown', function(e) {
- if (e.shiftKey && e.keyCode == 191) {
- e.preventDefault();
- $("#search-input").focus();
- }
- });
-
- $(document).ready(function() {
- // do keyword highlighting
- /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
- var mark = function() {
-
- var referrer = document.URL ;
- var paramKey = "q" ;
-
- if (referrer.indexOf("?") !== -1) {
- var qs = referrer.substr(referrer.indexOf('?') + 1);
- var qs_noanchor = qs.split('#')[0];
- var qsa = qs_noanchor.split('&');
- var keyword = "";
-
- for (var i = 0; i < qsa.length; i++) {
- var currentParam = qsa[i].split('=');
-
- if (currentParam.length !== 2) {
- continue;
- }
-
- if (currentParam[0] == paramKey) {
- keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
- }
- }
-
- if (keyword !== "") {
- $(".contents").unmark({
- done: function() {
- $(".contents").mark(keyword);
- }
- });
- }
- }
- };
-
- mark();
- });
-});
-
-/* Search term highlighting ------------------------------*/
-
-function matchedWords(hit) {
- var words = [];
-
- var hierarchy = hit._highlightResult.hierarchy;
- // loop to fetch from lvl0, lvl1, etc.
- for (var idx in hierarchy) {
- words = words.concat(hierarchy[idx].matchedWords);
- }
-
- var content = hit._highlightResult.content;
- if (content) {
- words = words.concat(content.matchedWords);
- }
-
- // return unique words
- var words_uniq = [...new Set(words)];
- return words_uniq;
-}
-
-function updateHitURL(hit) {
-
- var words = matchedWords(hit);
- var url = "";
-
- if (hit.anchor) {
- url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
- } else {
- url = hit.url + '?q=' + escape(words.join(" "));
- }
-
- return url;
-}
diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png
deleted file mode 100644
index c155b97..0000000
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diff --git a/docs/favicon-32x32.png b/docs/favicon-32x32.png
deleted file mode 100644
index 2366ed9..0000000
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diff --git a/docs/favicon.ico b/docs/favicon.ico
deleted file mode 100644
index e2fd2fe..0000000
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diff --git a/docs/index.html b/docs/index.html
deleted file mode 100644
index 0143519..0000000
--- a/docs/index.html
+++ /dev/null
@@ -1,299 +0,0 @@
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-
-Advice on R Package Building • goodpractice
-
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-
-Advice on R Package Building
-
-Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
-
-
-Installation
-
-You can install the release version from CRAN
-
-install.packages("goodpractice")
-and the development version from GitHub
-
-source("https://install-github.me/MangoTheCat/goodpractice")
-# or
-# install.packages("devtools")
-devtools::install_github("mangothecat/goodpractice")
-
-
-Usage
-
-
-library(goodpractice)
-gp("<my-package>")
-
-
-Example
-
-
-library(goodpractice)
-# use example package contained in the goodpractice package
-pkg_path <- system.file("bad1", package = "goodpractice")
-g <- gp(pkg_path)
-#>
-#> * checking for file ‘/private/var/folders/f3/gr9my1s97r3654cmvzc6dngm0000gn/T/Rtmp6Kts8C/remotesa3ff1315cc49/badpackage/DESCRIPTION’ ... OK
-#> * preparing ‘badpackage’:
-#> * checking DESCRIPTION meta-information ... OK
-#> * checking vignette meta-information ... OK
-#> * checking for LF line-endings in source and make files and shell scripts
-#> * checking for empty or unneeded directories
-#> * building ‘badpackage_1.0.0.tar.gz’
-
-g
-#> ── GP badpackage ───────────────────────────────────────────────────────────────
-#>
-#> It is good practice to
-#>
-#> ✖ not use "Depends" in DESCRIPTION, as it can cause name clashes, and
-#> poor interaction with other packages. Use "Imports" instead.
-#> ✖ omit "Date" in DESCRIPTION. It is not required and it gets invalid
-#> quite often. A build date will be added to the package when you
-#> perform `R CMD build` on it.
-#> ✖ add a "URL" field to DESCRIPTION. It helps users find information
-#> about your package online. If your package does not have a
-#> homepage, add an URL to GitHub, or the CRAN package package page.
-#> ✖ add a "BugReports" field to DESCRIPTION, and point it to a bug
-#> tracker. Many online code hosting services provide bug trackers for
-#> free, https://github.com, https://gitlab.com, etc.
-#> ✖ omit trailing semicolons from code lines. They are not needed and
-#> most R coding standards forbid them
-#>
-#> R/semicolons.R:4:30
-#> R/semicolons.R:5:29
-#> R/semicolons.R:9:38
-#>
-#> ✖ not import packages as a whole, as this can cause name clashes
-#> between the imported packages. Instead, import only the specific
-#> functions you need.
-#> ✖ fix this R CMD check ERROR: VignetteBuilder package not declared:
-#> ‘knitr’ See section ‘The DESCRIPTION file’ in the ‘Writing R
-#> Extensions’ manual.
-#> ✖ avoid 'T' and 'F', as they are just variables which are set to the
-#> logicals 'TRUE' and 'FALSE' by default, but are not reserved words
-#> and hence can be overwritten by the user. Hence, one should always
-#> use 'TRUE' and 'FALSE' for the logicals.
-#>
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> ... and 4 more lines
-#>
-#> ────────────────────────────────────────────────────────────────────────────────
-
-# show all available checks
-# all_checks()
-
-# run only a specific check
-g_url <- gp(pkg_path, checks = "description_url")
-g_url
-#> ── GP badpackage ───────────────────────────────────────────────────────────────
-#>
-#> It is good practice to
-#>
-#> ✖ add a "URL" field to DESCRIPTION. It helps users find information
-#> about your package online. If your package does not have a
-#> homepage, add an URL to GitHub, or the CRAN package package page.
-#> ────────────────────────────────────────────────────────────────────────────────
-
-# which checks were carried out?
-checks(g_url)
-#> [1] "description_url"
-
-# which checks failed?
-failed_checks(g)
-#> [1] "no_description_depends"
-#> [2] "no_description_date"
-#> [3] "description_url"
-#> [4] "description_bugreports"
-#> [5] "lintr_trailing_semicolon_linter"
-#> [6] "no_import_package_as_a_whole"
-#> [7] "rcmdcheck_package_dependencies_present"
-#> [8] "truefalse_not_tf"
-
-# show the first 5 checks carried out and their results
-results(g)[1:5,]
-#> check result
-#> 1 covr NA
-#> 2 cyclocomp TRUE
-#> 3 no_description_depends FALSE
-#> 4 no_description_date FALSE
-#> 5 description_url FALSE
-
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diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
deleted file mode 100644
index 1c16271..0000000
--- a/docs/jquery.sticky-kit.min.js
+++ /dev/null
@@ -1,11 +0,0 @@
-/* Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | */
-/*
- Source: https://github.com/leafo/sticky-kit
- License: MIT
-*/
-(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
-if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b(""))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
-u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),eb&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}),
-a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize",
-y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n
-
-
diff --git a/docs/logo.png b/docs/logo.png
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diff --git a/docs/news/index.html b/docs/news/index.html
deleted file mode 100644
index 344a4fb..0000000
--- a/docs/news/index.html
+++ /dev/null
@@ -1,112 +0,0 @@
-
-Changelog • goodpractice
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- Changelog
- Source: NEWS.md
-
-
-
-goodpractice 1.0.3
-Additions:
-- Limit for cyclomatic complexity check can be adjusted using the
goodpractice.cyclocomp.limit option, default 50 (#132, @fabian-s).
-- The number of lines printed to the console by each check result can be set using the new
positions_limit parameter into print() - previously it was always 5 lines (#130, @fabian-s).
-- GitHub Actions now used for CI/CD checks (#145), as well as to calculate code coverage with {covr} and build the package site with {pkgdown}.
-
Bugfixes:
-
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diff --git a/docs/pkgdown.css b/docs/pkgdown.css
deleted file mode 100644
index 80ea5b8..0000000
--- a/docs/pkgdown.css
+++ /dev/null
@@ -1,384 +0,0 @@
-/* Sticky footer */
-
-/**
- * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
- * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
- *
- * .Site -> body > .container
- * .Site-content -> body > .container .row
- * .footer -> footer
- *
- * Key idea seems to be to ensure that .container and __all its parents__
- * have height set to 100%
- *
- */
-
-html, body {
- height: 100%;
-}
-
-body {
- position: relative;
-}
-
-body > .container {
- display: flex;
- height: 100%;
- flex-direction: column;
-}
-
-body > .container .row {
- flex: 1 0 auto;
-}
-
-footer {
- margin-top: 45px;
- padding: 35px 0 36px;
- border-top: 1px solid #e5e5e5;
- color: #666;
- display: flex;
- flex-shrink: 0;
-}
-footer p {
- margin-bottom: 0;
-}
-footer div {
- flex: 1;
-}
-footer .pkgdown {
- text-align: right;
-}
-footer p {
- margin-bottom: 0;
-}
-
-img.icon {
- float: right;
-}
-
-/* Ensure in-page images don't run outside their container */
-.contents img {
- max-width: 100%;
- height: auto;
-}
-
-/* Fix bug in bootstrap (only seen in firefox) */
-summary {
- display: list-item;
-}
-
-/* Typographic tweaking ---------------------------------*/
-
-.contents .page-header {
- margin-top: calc(-60px + 1em);
-}
-
-dd {
- margin-left: 3em;
-}
-
-/* Section anchors ---------------------------------*/
-
-a.anchor {
- display: none;
- margin-left: 5px;
- width: 20px;
- height: 20px;
-
- background-image: url(./link.svg);
- background-repeat: no-repeat;
- background-size: 20px 20px;
- background-position: center center;
-}
-
-h1:hover .anchor,
-h2:hover .anchor,
-h3:hover .anchor,
-h4:hover .anchor,
-h5:hover .anchor,
-h6:hover .anchor {
- display: inline-block;
-}
-
-/* Fixes for fixed navbar --------------------------*/
-
-.contents h1, .contents h2, .contents h3, .contents h4 {
- padding-top: 60px;
- margin-top: -40px;
-}
-
-/* Navbar submenu --------------------------*/
-
-.dropdown-submenu {
- position: relative;
-}
-
-.dropdown-submenu>.dropdown-menu {
- top: 0;
- left: 100%;
- margin-top: -6px;
- margin-left: -1px;
- border-radius: 0 6px 6px 6px;
-}
-
-.dropdown-submenu:hover>.dropdown-menu {
- display: block;
-}
-
-.dropdown-submenu>a:after {
- display: block;
- content: " ";
- float: right;
- width: 0;
- height: 0;
- border-color: transparent;
- border-style: solid;
- border-width: 5px 0 5px 5px;
- border-left-color: #cccccc;
- margin-top: 5px;
- margin-right: -10px;
-}
-
-.dropdown-submenu:hover>a:after {
- border-left-color: #ffffff;
-}
-
-.dropdown-submenu.pull-left {
- float: none;
-}
-
-.dropdown-submenu.pull-left>.dropdown-menu {
- left: -100%;
- margin-left: 10px;
- border-radius: 6px 0 6px 6px;
-}
-
-/* Sidebar --------------------------*/
-
-#pkgdown-sidebar {
- margin-top: 30px;
- position: -webkit-sticky;
- position: sticky;
- top: 70px;
-}
-
-#pkgdown-sidebar h2 {
- font-size: 1.5em;
- margin-top: 1em;
-}
-
-#pkgdown-sidebar h2:first-child {
- margin-top: 0;
-}
-
-#pkgdown-sidebar .list-unstyled li {
- margin-bottom: 0.5em;
-}
-
-/* bootstrap-toc tweaks ------------------------------------------------------*/
-
-/* All levels of nav */
-
-nav[data-toggle='toc'] .nav > li > a {
- padding: 4px 20px 4px 6px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
-}
-
-nav[data-toggle='toc'] .nav > li > a:hover,
-nav[data-toggle='toc'] .nav > li > a:focus {
- padding-left: 5px;
- color: inherit;
- border-left: 1px solid #878787;
-}
-
-nav[data-toggle='toc'] .nav > .active > a,
-nav[data-toggle='toc'] .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav > .active:focus > a {
- padding-left: 5px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
- border-left: 2px solid #878787;
-}
-
-/* Nav: second level (shown on .active) */
-
-nav[data-toggle='toc'] .nav .nav {
- display: none; /* Hide by default, but at >768px, show it */
- padding-bottom: 10px;
-}
-
-nav[data-toggle='toc'] .nav .nav > li > a {
- padding-left: 16px;
- font-size: 1.35rem;
-}
-
-nav[data-toggle='toc'] .nav .nav > li > a:hover,
-nav[data-toggle='toc'] .nav .nav > li > a:focus {
- padding-left: 15px;
-}
-
-nav[data-toggle='toc'] .nav .nav > .active > a,
-nav[data-toggle='toc'] .nav .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav .nav > .active:focus > a {
- padding-left: 15px;
- font-weight: 500;
- font-size: 1.35rem;
-}
-
-/* orcid ------------------------------------------------------------------- */
-
-.orcid {
- font-size: 16px;
- color: #A6CE39;
- /* margins are required by official ORCID trademark and display guidelines */
- margin-left:4px;
- margin-right:4px;
- vertical-align: middle;
-}
-
-/* Reference index & topics ----------------------------------------------- */
-
-.ref-index th {font-weight: normal;}
-
-.ref-index td {vertical-align: top; min-width: 100px}
-.ref-index .icon {width: 40px;}
-.ref-index .alias {width: 40%;}
-.ref-index-icons .alias {width: calc(40% - 40px);}
-.ref-index .title {width: 60%;}
-
-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
-
-/* Nice scrolling for wide elements --------------------------------------- */
-
-table {
- display: block;
- overflow: auto;
-}
-
-/* Syntax highlighting ---------------------------------------------------- */
-
-pre, code, pre code {
- background-color: #f8f8f8;
- color: #333;
-}
-pre, pre code {
- white-space: pre-wrap;
- word-break: break-all;
- overflow-wrap: break-word;
-}
-
-pre {
- border: 1px solid #eee;
-}
-
-pre .img, pre .r-plt {
- margin: 5px 0;
-}
-
-pre .img img, pre .r-plt img {
- background-color: #fff;
-}
-
-code a, pre a {
- color: #375f84;
-}
-
-a.sourceLine:hover {
- text-decoration: none;
-}
-
-.fl {color: #1514b5;}
-.fu {color: #000000;} /* function */
-.ch,.st {color: #036a07;} /* string */
-.kw {color: #264D66;} /* keyword */
-.co {color: #888888;} /* comment */
-
-.error {font-weight: bolder;}
-.warning {font-weight: bolder;}
-
-/* Clipboard --------------------------*/
-
-.hasCopyButton {
- position: relative;
-}
-
-.btn-copy-ex {
- position: absolute;
- right: 0;
- top: 0;
- visibility: hidden;
-}
-
-.hasCopyButton:hover button.btn-copy-ex {
- visibility: visible;
-}
-
-/* headroom.js ------------------------ */
-
-.headroom {
- will-change: transform;
- transition: transform 200ms linear;
-}
-.headroom--pinned {
- transform: translateY(0%);
-}
-.headroom--unpinned {
- transform: translateY(-100%);
-}
-
-/* mark.js ----------------------------*/
-
-mark {
- background-color: rgba(255, 255, 51, 0.5);
- border-bottom: 2px solid rgba(255, 153, 51, 0.3);
- padding: 1px;
-}
-
-/* vertical spacing after htmlwidgets */
-.html-widget {
- margin-bottom: 10px;
-}
-
-/* fontawesome ------------------------ */
-
-.fab {
- font-family: "Font Awesome 5 Brands" !important;
-}
-
-/* don't display links in code chunks when printing */
-/* source: https://stackoverflow.com/a/10781533 */
-@media print {
- code a:link:after, code a:visited:after {
- content: "";
- }
-}
-
-/* Section anchors ---------------------------------
- Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
-*/
-
-div.csl-bib-body { }
-div.csl-entry {
- clear: both;
-}
-.hanging-indent div.csl-entry {
- margin-left:2em;
- text-indent:-2em;
-}
-div.csl-left-margin {
- min-width:2em;
- float:left;
-}
-div.csl-right-inline {
- margin-left:2em;
- padding-left:1em;
-}
-div.csl-indent {
- margin-left: 2em;
-}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
deleted file mode 100644
index 6f0eee4..0000000
--- a/docs/pkgdown.js
+++ /dev/null
@@ -1,108 +0,0 @@
-/* http://gregfranko.com/blog/jquery-best-practices/ */
-(function($) {
- $(function() {
-
- $('.navbar-fixed-top').headroom();
-
- $('body').css('padding-top', $('.navbar').height() + 10);
- $(window).resize(function(){
- $('body').css('padding-top', $('.navbar').height() + 10);
- });
-
- $('[data-toggle="tooltip"]').tooltip();
-
- var cur_path = paths(location.pathname);
- var links = $("#navbar ul li a");
- var max_length = -1;
- var pos = -1;
- for (var i = 0; i < links.length; i++) {
- if (links[i].getAttribute("href") === "#")
- continue;
- // Ignore external links
- if (links[i].host !== location.host)
- continue;
-
- var nav_path = paths(links[i].pathname);
-
- var length = prefix_length(nav_path, cur_path);
- if (length > max_length) {
- max_length = length;
- pos = i;
- }
- }
-
- // Add class to parent , and enclosing if in dropdown
- if (pos >= 0) {
- var menu_anchor = $(links[pos]);
- menu_anchor.parent().addClass("active");
- menu_anchor.closest("li.dropdown").addClass("active");
- }
- });
-
- function paths(pathname) {
- var pieces = pathname.split("/");
- pieces.shift(); // always starts with /
-
- var end = pieces[pieces.length - 1];
- if (end === "index.html" || end === "")
- pieces.pop();
- return(pieces);
- }
-
- // Returns -1 if not found
- function prefix_length(needle, haystack) {
- if (needle.length > haystack.length)
- return(-1);
-
- // Special case for length-0 haystack, since for loop won't run
- if (haystack.length === 0) {
- return(needle.length === 0 ? 0 : -1);
- }
-
- for (var i = 0; i < haystack.length; i++) {
- if (needle[i] != haystack[i])
- return(i);
- }
-
- return(haystack.length);
- }
-
- /* Clipboard --------------------------*/
-
- function changeTooltipMessage(element, msg) {
- var tooltipOriginalTitle=element.getAttribute('data-original-title');
- element.setAttribute('data-original-title', msg);
- $(element).tooltip('show');
- element.setAttribute('data-original-title', tooltipOriginalTitle);
- }
-
- if(ClipboardJS.isSupported()) {
- $(document).ready(function() {
- var copyButton = "";
-
- $("div.sourceCode").addClass("hasCopyButton");
-
- // Insert copy buttons:
- $(copyButton).prependTo(".hasCopyButton");
-
- // Initialize tooltips:
- $('.btn-copy-ex').tooltip({container: 'body'});
-
- // Initialize clipboard:
- var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
- text: function(trigger) {
- return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, "");
- }
- });
-
- clipboardBtnCopies.on('success', function(e) {
- changeTooltipMessage(e.trigger, 'Copied!');
- e.clearSelection();
- });
-
- clipboardBtnCopies.on('error', function() {
- changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
- });
- });
- }
-})(window.jQuery || window.$)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
deleted file mode 100644
index 5c07367..0000000
--- a/docs/pkgdown.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-pandoc: 2.14.0.3
-pkgdown: 2.0.3
-pkgdown_sha: ~
-articles:
- custom_checks: custom_checks.html
- goodpractice: goodpractice.html
-last_built: 2022-05-19T10:13Z
-
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
deleted file mode 100644
index 17a3580..0000000
Binary files a/docs/reference/Rplot001.png and /dev/null differ
diff --git a/docs/reference/all_checks.html b/docs/reference/all_checks.html
deleted file mode 100644
index f0c81c5..0000000
--- a/docs/reference/all_checks.html
+++ /dev/null
@@ -1,100 +0,0 @@
-
-List the names of all checks — all_checks • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- List the names of all checks
-
-
-
- all_checks()
-
-
-
- Value
- Character vector of checks
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/checks.html b/docs/reference/checks.html
deleted file mode 100644
index 42496d8..0000000
--- a/docs/reference/checks.html
+++ /dev/null
@@ -1,129 +0,0 @@
-
-List all checks performed — checks • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- List all checks performed
-
-
-
- checks(gp)
-
-
-
- Arguments
- - gp
-gp output.
-
- Value
- Character vector of check names.
-
-
- See also
- Other API:
-failed_checks(),
-results()
-
-
-
- Examples
- path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-checks(g)
-#> [1] "no_description_depends" "no_description_date"
-#> [3] "description_url" "description_bugreports"
-#> [5] "lintr_assignment_linter" "lintr_line_length_linter"
-#> [7] "lintr_trailing_semicolon_linter" "lintr_attach_detach_linter"
-#> [9] "lintr_setwd_linter" "lintr_sapply_linter"
-#> [11] "lintr_library_require_linter" "lintr_seq_linter"
-#> [13] "no_import_package_as_a_whole" "no_export_pattern"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/customization.html b/docs/reference/customization.html
deleted file mode 100644
index 9fecd77..0000000
--- a/docs/reference/customization.html
+++ /dev/null
@@ -1,151 +0,0 @@
-
-Defining custom preparations and checks — customization • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Defining custom preparations and checks
-
-
-
- make_prep(name, func)
-
-make_check(description, check, gp, ...)
-
-
-
- Arguments
- - name
-Name of the preparation function.
- func
-A function that takes two arguments:
-The path to the root directory of the package, and a logical
-argument: quiet. If quiet is true, the preparation function
-may print out diagnostic messages. The output of this function will be
-saved as the " name" entry of state, i.e. of the input for
-the check-functions (see example).
- description
-A description of the check.
- check
-A function that takes the state as an argument.
- gp
-A short description of what is good practice.
- ...
-Further arguments. Most important: A preps argument that
-contains the names of all the preparation functions required for the check.
-
- Functions
-
-make_prep: Create a preparation function
make_check: Create a check function
-
-
- Examples
- # make a preparation function
-url_prep <- make_prep(
- name = "desc",
- func = function(path, quiet) desc::description$new(path)
-)
-# and the corresponding check function
-url_chk <- make_check(
- description = "URL field in DESCRIPTION",
- tags = character(),
- preps = "desc",
- gp = "have a URL field in DESCRIPTION",
- check = function(state) state$desc$has_fields("URL")
-)
-# use together in gp():
-# (note that you have to list the name of your custom check in
-# the checks-argument as well....)
-bad1 <- system.file("bad1", package = "goodpractice")
-res <- gp(bad1, checks = c("url", "no_description_depends"),
- extra_preps = list("desc" = url_prep),
- extra_checks = list("url" = url_chk))
-#> Preparing: desc
-#> Preparing: description
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/default_r_file_pattern.html b/docs/reference/default_r_file_pattern.html
deleted file mode 100644
index efb4880..0000000
--- a/docs/reference/default_r_file_pattern.html
+++ /dev/null
@@ -1,100 +0,0 @@
-
-Default pattern for R files — default_r_file_pattern • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Default pattern for R files
-
-
-
- default_r_file_pattern()
-
-
-
- Value
- Regular expression.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/export_json.html b/docs/reference/export_json.html
deleted file mode 100644
index 0b90b52..0000000
--- a/docs/reference/export_json.html
+++ /dev/null
@@ -1,105 +0,0 @@
-
-Export failed checks to JSON — export_json • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/failed_checks.html b/docs/reference/failed_checks.html
deleted file mode 100644
index 5e9bf91..0000000
--- a/docs/reference/failed_checks.html
+++ /dev/null
@@ -1,125 +0,0 @@
-
-Names of the failed checks — failed_checks • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Names of the failed checks
-
-
-
- failed_checks(gp)
-
-
-
- Arguments
- - gp
-gp output.
-
- Value
- Names of the failed checks.
-
-
-
-
- Examples
- path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-failed_checks(g)
-#> [1] "no_description_depends" "no_description_date"
-#> [3] "description_url" "description_bugreports"
-#> [5] "lintr_trailing_semicolon_linter" "no_import_package_as_a_whole"
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/failed_positions.html b/docs/reference/failed_positions.html
deleted file mode 100644
index 6a5349e..0000000
--- a/docs/reference/failed_positions.html
+++ /dev/null
@@ -1,116 +0,0 @@
-
-Positions of check failures in the source code — failed_positions • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Note that not all checks refer to the source code.
-For these the result will be NULL.
-
-
-
- failed_positions(gp)
-
-
-
- Arguments
- - gp
-gp output.
-
- Value
- A list of lists of positions. See details below.
-
-
- Details
- For the ones that do, the results is a list, one for each failure.
-Since the same check can fail multiple times. A single failure
-is a list with entries: filename, line_number,
-column_number, ranges. ranges is a list of
-pairs of start and end positions for each line involved in the
-check.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/figures/logo.png b/docs/reference/figures/logo.png
deleted file mode 100644
index f2b20c3..0000000
Binary files a/docs/reference/figures/logo.png and /dev/null differ
diff --git a/docs/reference/get_marker.html b/docs/reference/get_marker.html
deleted file mode 100644
index a81ca5d..0000000
--- a/docs/reference/get_marker.html
+++ /dev/null
@@ -1,103 +0,0 @@
-
-Get a marker from the positions of a check — get_marker • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Get a marker from the positions of a check
-
-
-
- get_marker(gp, check)
-
-
-
- Arguments
- - gp
-gp() output
- check
-name of the check to extract
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/goodpractice-package.html b/docs/reference/goodpractice-package.html
deleted file mode 100644
index 20ff96e..0000000
--- a/docs/reference/goodpractice-package.html
+++ /dev/null
@@ -1,113 +0,0 @@
-
-goodpractice: Advice on R Package Building — goodpractice-package • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Give advice about good practices when building R packages. Advice includes
-functions and syntax to avoid, package structure, code complexity, code
-formatting, etc.
-
-
-
-
- See also
- Useful links:
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/gp.html b/docs/reference/gp.html
deleted file mode 100644
index c58dd07..0000000
--- a/docs/reference/gp.html
+++ /dev/null
@@ -1,164 +0,0 @@
-
-Run good practice checks — gp • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- To see the results, just print it to the screen.
-
-
-
- gp(
- path = ".",
- checks = all_checks(),
- extra_preps = NULL,
- extra_checks = NULL,
- quiet = TRUE
-)
-
-
-
- Arguments
- - path
-Path to a package root.
- checks
-Character vector, the checks to run. Defaults to
-all checks. Use all_checks to list all checks.
- extra_preps
-Custom preparation functions. See
-make_prep on creating preparation functions.
- extra_checks
-Custom checks. See make_check on
-creating checks.
- quiet
-Whether to suppress output from the preparation
-functions. Note that not all preparation functions produce output,
-even if this option is set to FALSE.
-
- Value
- A goodpractice object that you can query
-with a simple API. See results to start.
-
-
-
- Examples
- path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-g
-#> -- GP badpackage ---------------------------------------------------------------
-#>
-#> It is good practice to
-#>
-#> <U+2716> not use "Depends" in DESCRIPTION, as it can cause name
-#> clashes, and poor interaction with other packages. Use "Imports"
-#> instead.
-#> <U+2716> omit "Date" in DESCRIPTION. It is not required and it gets
-#> invalid quite often. A build date will be added to the package when
-#> you perform `R CMD build` on it.
-#> <U+2716> add a "URL" field to DESCRIPTION. It helps users find
-#> information about your package online. If your package does not
-#> have a homepage, add an URL to GitHub, or the CRAN package package
-#> page.
-#> <U+2716> add a "BugReports" field to DESCRIPTION, and point it to a
-#> bug tracker. Many online code hosting services provide bug trackers
-#> for free, https://github.com, https://gitlab.com, etc.
-#> <U+2716> omit trailing semicolons from code lines. They are not
-#> needed and most R coding standards forbid them
-#>
-#> R\semicolons.R:4:30
-#> R\semicolons.R:5:29
-#> R\semicolons.R:9:38
-#>
-#> <U+2716> not import packages as a whole, as this can cause name
-#> clashes between the imported packages. Instead, import only the
-#> specific functions you need.
-#> --------------------------------------------------------------------------------
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/index.html b/docs/reference/index.html
deleted file mode 100644
index 10aa1b9..0000000
--- a/docs/reference/index.html
+++ /dev/null
@@ -1,130 +0,0 @@
-
-Function reference • goodpractice
-
-
-
-
-
-
-
-
-
-
- Reference
-
-
-
- All functions
-
-
-
-
-
- List the names of all checks
-
-
- List all checks performed
-
-
- Defining custom preparations and checks
-
-
- Export failed checks to JSON
-
-
- Names of the failed checks
-
-
- Positions of check failures in the source code
-
-
- goodpractice: Advice on R Package Building
-
-
- Run good practice checks
-
-
- Print goodpractice results
-
-
- Return all check results in a data frame
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/make_check.html b/docs/reference/make_check.html
deleted file mode 100644
index 98f6476..0000000
--- a/docs/reference/make_check.html
+++ /dev/null
@@ -1,199 +0,0 @@
-
-
-
-
-
-
-
-
-Create a check function — make_check • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Create a check function
-
-
-
- make_check(description, check, gp, ...)
-
- Arguments
-
-
- description
- A description of the check.
-
- check
- A function that takes the state as an argument.
-
- gp
- A short description of what is good practice.
-
- ...
- Further arguments.
-
-
-
- Examples
- # make a preparation function
-url_prep <- make_prep(
- name = "desc",
- func = function(path, quiet) desc::description$new(path)
-)
-# and the corresponding check function
-url_chk <- make_check(
- description = "URL field in DESCRIPTION",
- tags = character(),
- preps = "desc",
- gp = "have a URL field in DESCRIPTION",
- check = function(state) state$desc$has_fields("URL")
-)
-# use together in gp()
-bad1 <- system.file("bad1", package = "goodpractice")
-res <- gp(bad1, checks = "no_description_depends",
- extra_preps = list("desc" = url_prep),
- extra_checks = list("url" = url_chk))#>
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/make_prep.html b/docs/reference/make_prep.html
deleted file mode 100644
index 679bc6f..0000000
--- a/docs/reference/make_prep.html
+++ /dev/null
@@ -1,194 +0,0 @@
-
-
-
-
-
-
-
-
-Create a preparation function — make_prep • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Create a preparation function
-
-
-
- make_prep(name, func)
-
- Arguments
-
-
- name
- Name of the preparation function.
-
- func
- A function that takes two arguments:
-The path to the root directory of the package, and
-a logical argument: quiet. If quiet is true,
-the preparation function may print out diagnostic messages.
-
-
-
- Examples
- # make a preparation function
-url_prep <- make_prep(
- name = "desc",
- func = function(path, quiet) desc::description$new(path)
-)
-# and the corresponding check function
-url_chk <- make_check(
- description = "URL field in DESCRIPTION",
- tags = character(),
- preps = "desc",
- gp = "have a URL field in DESCRIPTION",
- check = function(state) state$desc$has_fields("URL")
-)
-# use together in gp()
-bad1 <- system.file("bad1", package = "goodpractice")
-res <- gp(bad1, checks = "no_description_depends",
- extra_preps = list("desc" = url_prep),
- extra_checks = list("url" = url_chk))#>
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/make_rcmd_check.html b/docs/reference/make_rcmd_check.html
deleted file mode 100644
index d3b6e81..0000000
--- a/docs/reference/make_rcmd_check.html
+++ /dev/null
@@ -1,119 +0,0 @@
-
-Wrapper on make_check, specific to R CMD check — make_rcmd_check • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Wrapper on make_check, specific to R CMD check
-
-
-
- make_rcmd_check(
- description,
- pattern,
- gp = NULL,
- type = c("warnings", "notes", "errors"),
- tags = NULL,
- preps = NULL,
- ...
-)
-
-
-
- Arguments
- - description
-A description of the check.
- pattern
-The text pattern identifying the check.
- type
-Type of notification, one of "warnings", "notes" or "errors".
- tags
-Tags to be passed on to make_check.
- preps
-Preps to be passed on to make_check.
- ...
-Currently not supported.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/package_collate.html b/docs/reference/package_collate.html
deleted file mode 100644
index 011aaf3..0000000
--- a/docs/reference/package_collate.html
+++ /dev/null
@@ -1,105 +0,0 @@
-
-Collate field from DESCRIPTION — package_collate • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- NULL is returned if there is no such field.
-
-
-
- package_collate(path = ".")
-
-
-
- Arguments
- - path
-Path to the package root.
-
- Value
- Character scalar or NULL.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/prep_expressions.html b/docs/reference/prep_expressions.html
deleted file mode 100644
index 506e039..0000000
--- a/docs/reference/prep_expressions.html
+++ /dev/null
@@ -1,113 +0,0 @@
-
-Extract all closures from a package — prep_expressions • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- The package must be extracted into the working directory, as usual.
-
-
-
- prep_expressions(state, version = NULL, quiet)
-
-
-
- Arguments
- - state
-GP state.
- version
-Currently ignored.
-
- Value
- The modified state, with the closures in a named list.
-
-
- Details
- We can use lintr to extract the functions, but need to use
-our own code (based on similar code in functionMap) to
-get the right collation order.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/print.goodPractice.html b/docs/reference/print.goodPractice.html
deleted file mode 100644
index 8217782..0000000
--- a/docs/reference/print.goodPractice.html
+++ /dev/null
@@ -1,106 +0,0 @@
-
-Print goodpractice results — print.goodPractice • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Print goodpractice results
-
-
-
- # S3 method for goodPractice
-print(x, positions_limit = 5, ...)
-
-
-
- Arguments
- - x
-Object of class goodPractice, as returned by gp().
- positions_limit
-How many positions to print at most.
- ...
-Unused, for compatibility with base::print() generic method.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/r_package_files.html b/docs/reference/r_package_files.html
deleted file mode 100644
index 29fcbe9..0000000
--- a/docs/reference/r_package_files.html
+++ /dev/null
@@ -1,108 +0,0 @@
-
-Get all source files of a package, in the right order — r_package_files • goodpractice
-
-
-
-
-
-
-
-
-
-
- Get all source files of a package, in the right order
- Source: R/prep_expressions.R
- r_package_files.Rd
-
-
-
- It uses the Collate entry in the DESCRIPTION file,
-if there is one. Otherwise the order is alphabetical.
-
-
-
- r_package_files(path)
-
-
-
- Arguments
- - path
-Path to the root of the R package.
-
- Value
- A character vector of (relative) file
-names in the current collation order.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/results.html b/docs/reference/results.html
deleted file mode 100644
index d6b22a1..0000000
--- a/docs/reference/results.html
+++ /dev/null
@@ -1,141 +0,0 @@
-
-Return all check results in a data frame — results • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Return all check results in a data frame
-
-
-
- results(gp)
-
-
-
- Arguments
- - gp
-gp output.
-
- Value
- Data frame, with columns:
-- check
-The name of the check.
- result
-Logical, whether it has failed or not.
-
- See also
- Other API:
-checks(),
-failed_checks()
-
-
-
- Examples
- path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-results(g)
-#> check result
-#> 1 no_description_depends FALSE
-#> 2 no_description_date FALSE
-#> 3 description_url FALSE
-#> 4 description_bugreports FALSE
-#> 5 lintr_assignment_linter TRUE
-#> 6 lintr_line_length_linter TRUE
-#> 7 lintr_trailing_semicolon_linter FALSE
-#> 8 lintr_attach_detach_linter TRUE
-#> 9 lintr_setwd_linter TRUE
-#> 10 lintr_sapply_linter TRUE
-#> 11 lintr_library_require_linter TRUE
-#> 12 lintr_seq_linter TRUE
-#> 13 no_import_package_as_a_whole FALSE
-#> 14 no_export_pattern TRUE
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/reference/seq_linter.html b/docs/reference/seq_linter.html
deleted file mode 100644
index b9f740a..0000000
--- a/docs/reference/seq_linter.html
+++ /dev/null
@@ -1,109 +0,0 @@
-
-Find dangerous 1:x expressions — seq_linter • goodpractice
-
-
-
-
-
-
-
-
-
-
-
-
- Find occurrences of 1:length(x), 1:nrow(x),
-1:ncol(x), 1:NROW(x), 1:NCOL(x) where
-x is an R expression.
-
-
-
- seq_linter(source_file)
-
-
-
- Arguments
- - source_file
-Parse data. Passed from lintr.
-
- Value
- Lint object.
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
deleted file mode 100644
index c932185..0000000
--- a/docs/sitemap.xml
+++ /dev/null
@@ -1,90 +0,0 @@
-
-
-
- /404.html
-
-
- /articles/custom_checks.html
-
-
- /articles/goodpractice.html
-
-
- /articles/index.html
-
-
- /authors.html
-
-
- /index.html
-
-
- /LICENSE-text.html
-
-
- /LICENSE.html
-
-
- /news/index.html
-
-
- /reference/all_checks.html
-
-
- /reference/checks.html
-
-
- /reference/customization.html
-
-
- /reference/default_r_file_pattern.html
-
-
- /reference/export_json.html
-
-
- /reference/failed_checks.html
-
-
- /reference/failed_positions.html
-
-
- /reference/get_marker.html
-
-
- /reference/goodpractice-package.html
-
-
- /reference/gp.html
-
-
- /reference/index.html
-
-
- /reference/make_check.html
-
-
- /reference/make_prep.html
-
-
- /reference/make_rcmd_check.html
-
-
- /reference/package_collate.html
-
-
- /reference/prep_expressions.html
-
-
- /reference/print.goodPractice.html
-
-
- /reference/results.html
-
-
- /reference/r_package_files.html
-
-
- /reference/seq_linter.html
-
-
diff --git a/pkgdown/favicon/apple-touch-icon-120x120.png b/pkgdown/favicon/apple-touch-icon-120x120.png
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-
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diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
deleted file mode 100644
index 1c16271..0000000
--- a/docs/jquery.sticky-kit.min.js
+++ /dev/null
@@ -1,11 +0,0 @@
-/* Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | */
-/*
- Source: https://github.com/leafo/sticky-kit
- License: MIT
-*/
-(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
-if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b(""))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
-u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e
-
-
-
-
-
-
-
-
-
-
-
-
- 
-
-Advice on R Package Building -
-Give advice about good practices when building R packages. Advice includes functions and syntax to avoid, package structure, code complexity, code formatting, etc.
-
-
-
-
-Installation -
-You can install the release version from CRAN
-
-install.packages("goodpractice")and the development version from GitHub
-
-source("https://install-github.me/MangoTheCat/goodpractice")
-# or
-# install.packages("devtools")
-devtools::install_github("mangothecat/goodpractice")
-
-
-Usage -
-
-library(goodpractice)
-gp("<my-package>")
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-Example -
-
-library(goodpractice)
-# use example package contained in the goodpractice package
-pkg_path <- system.file("bad1", package = "goodpractice")
-g <- gp(pkg_path)#>
-#> * checking for file ‘/private/var/folders/f3/gr9my1s97r3654cmvzc6dngm0000gn/T/Rtmp6Kts8C/remotesa3ff1315cc49/badpackage/DESCRIPTION’ ... OK
-#> * preparing ‘badpackage’:
-#> * checking DESCRIPTION meta-information ... OK
-#> * checking vignette meta-information ... OK
-#> * checking for LF line-endings in source and make files and shell scripts
-#> * checking for empty or unneeded directories
-#> * building ‘badpackage_1.0.0.tar.gz’
-g#> ── GP badpackage ───────────────────────────────────────────────────────────────
-#>
-#> It is good practice to
-#>
-#> ✖ not use "Depends" in DESCRIPTION, as it can cause name clashes, and
-#> poor interaction with other packages. Use "Imports" instead.
-#> ✖ omit "Date" in DESCRIPTION. It is not required and it gets invalid
-#> quite often. A build date will be added to the package when you
-#> perform `R CMD build` on it.
-#> ✖ add a "URL" field to DESCRIPTION. It helps users find information
-#> about your package online. If your package does not have a
-#> homepage, add an URL to GitHub, or the CRAN package package page.
-#> ✖ add a "BugReports" field to DESCRIPTION, and point it to a bug
-#> tracker. Many online code hosting services provide bug trackers for
-#> free, https://github.com, https://gitlab.com, etc.
-#> ✖ omit trailing semicolons from code lines. They are not needed and
-#> most R coding standards forbid them
-#>
-#> R/semicolons.R:4:30
-#> R/semicolons.R:5:29
-#> R/semicolons.R:9:38
-#>
-#> ✖ not import packages as a whole, as this can cause name clashes
-#> between the imported packages. Instead, import only the specific
-#> functions you need.
-#> ✖ fix this R CMD check ERROR: VignetteBuilder package not declared:
-#> ‘knitr’ See section ‘The DESCRIPTION file’ in the ‘Writing R
-#> Extensions’ manual.
-#> ✖ avoid 'T' and 'F', as they are just variables which are set to the
-#> logicals 'TRUE' and 'FALSE' by default, but are not reserved words
-#> and hence can be overwritten by the user. Hence, one should always
-#> use 'TRUE' and 'FALSE' for the logicals.
-#>
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> R/tf.R:NA:NA
-#> ... and 4 more lines
-#>
-#> ────────────────────────────────────────────────────────────────────────────────
-# show all available checks
-# all_checks()
-
-# run only a specific check
-g_url <- gp(pkg_path, checks = "description_url")
-g_url#> ── GP badpackage ───────────────────────────────────────────────────────────────
-#>
-#> It is good practice to
-#>
-#> ✖ add a "URL" field to DESCRIPTION. It helps users find information
-#> about your package online. If your package does not have a
-#> homepage, add an URL to GitHub, or the CRAN package package page.
-#> ────────────────────────────────────────────────────────────────────────────────
-# which checks were carried out?
-checks(g_url)#> [1] "description_url"
-# which checks failed?
-failed_checks(g)#> [1] "no_description_depends"
-#> [2] "no_description_date"
-#> [3] "description_url"
-#> [4] "description_bugreports"
-#> [5] "lintr_trailing_semicolon_linter"
-#> [6] "no_import_package_as_a_whole"
-#> [7] "rcmdcheck_package_dependencies_present"
-#> [8] "truefalse_not_tf"
-# show the first 5 checks carried out and their results
-results(g)[1:5,]#> check result
-#> 1 covr NA
-#> 2 cyclocomp TRUE
-#> 3 no_description_depends FALSE
-#> 4 no_description_date FALSE
-#> 5 description_url FALSE
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
deleted file mode 100644
index 80ea5b8..0000000
--- a/docs/pkgdown.css
+++ /dev/null
@@ -1,384 +0,0 @@
-/* Sticky footer */
-
-/**
- * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
- * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
- *
- * .Site -> body > .container
- * .Site-content -> body > .container .row
- * .footer -> footer
- *
- * Key idea seems to be to ensure that .container and __all its parents__
- * have height set to 100%
- *
- */
-
-html, body {
- height: 100%;
-}
-
-body {
- position: relative;
-}
-
-body > .container {
- display: flex;
- height: 100%;
- flex-direction: column;
-}
-
-body > .container .row {
- flex: 1 0 auto;
-}
-
-footer {
- margin-top: 45px;
- padding: 35px 0 36px;
- border-top: 1px solid #e5e5e5;
- color: #666;
- display: flex;
- flex-shrink: 0;
-}
-footer p {
- margin-bottom: 0;
-}
-footer div {
- flex: 1;
-}
-footer .pkgdown {
- text-align: right;
-}
-footer p {
- margin-bottom: 0;
-}
-
-img.icon {
- float: right;
-}
-
-/* Ensure in-page images don't run outside their container */
-.contents img {
- max-width: 100%;
- height: auto;
-}
-
-/* Fix bug in bootstrap (only seen in firefox) */
-summary {
- display: list-item;
-}
-
-/* Typographic tweaking ---------------------------------*/
-
-.contents .page-header {
- margin-top: calc(-60px + 1em);
-}
-
-dd {
- margin-left: 3em;
-}
-
-/* Section anchors ---------------------------------*/
-
-a.anchor {
- display: none;
- margin-left: 5px;
- width: 20px;
- height: 20px;
-
- background-image: url(./link.svg);
- background-repeat: no-repeat;
- background-size: 20px 20px;
- background-position: center center;
-}
-
-h1:hover .anchor,
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- display: inline-block;
-}
-
-/* Fixes for fixed navbar --------------------------*/
-
-.contents h1, .contents h2, .contents h3, .contents h4 {
- padding-top: 60px;
- margin-top: -40px;
-}
-
-/* Navbar submenu --------------------------*/
-
-.dropdown-submenu {
- position: relative;
-}
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-.dropdown-submenu>.dropdown-menu {
- top: 0;
- left: 100%;
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-.dropdown-submenu:hover>.dropdown-menu {
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- float: right;
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- border-color: transparent;
- border-style: solid;
- border-width: 5px 0 5px 5px;
- border-left-color: #cccccc;
- margin-top: 5px;
- margin-right: -10px;
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-.dropdown-submenu.pull-left {
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- left: -100%;
- margin-left: 10px;
- border-radius: 6px 0 6px 6px;
-}
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-#pkgdown-sidebar {
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- position: -webkit-sticky;
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-}
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- font-size: 1.5em;
- margin-top: 1em;
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- margin-top: 0;
-}
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-#pkgdown-sidebar .list-unstyled li {
- margin-bottom: 0.5em;
-}
-
-/* bootstrap-toc tweaks ------------------------------------------------------*/
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- padding: 4px 20px 4px 6px;
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- color: inherit;
-}
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-nav[data-toggle='toc'] .nav > li > a:hover,
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- padding-left: 5px;
- color: inherit;
- border-left: 1px solid #878787;
-}
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-nav[data-toggle='toc'] .nav > .active > a,
-nav[data-toggle='toc'] .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav > .active:focus > a {
- padding-left: 5px;
- font-size: 1.5rem;
- font-weight: 400;
- color: inherit;
- border-left: 2px solid #878787;
-}
-
-/* Nav: second level (shown on .active) */
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-nav[data-toggle='toc'] .nav .nav {
- display: none; /* Hide by default, but at >768px, show it */
- padding-bottom: 10px;
-}
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-nav[data-toggle='toc'] .nav .nav > li > a {
- padding-left: 16px;
- font-size: 1.35rem;
-}
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-nav[data-toggle='toc'] .nav .nav > li > a:hover,
-nav[data-toggle='toc'] .nav .nav > li > a:focus {
- padding-left: 15px;
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-nav[data-toggle='toc'] .nav .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav .nav > .active:focus > a {
- padding-left: 15px;
- font-weight: 500;
- font-size: 1.35rem;
-}
-
-/* orcid ------------------------------------------------------------------- */
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-.orcid {
- font-size: 16px;
- color: #A6CE39;
- /* margins are required by official ORCID trademark and display guidelines */
- margin-left:4px;
- margin-right:4px;
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-}
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-/* Reference index & topics ----------------------------------------------- */
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-.ref-index th {font-weight: normal;}
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-.ref-index td {vertical-align: top; min-width: 100px}
-.ref-index .icon {width: 40px;}
-.ref-index .alias {width: 40%;}
-.ref-index-icons .alias {width: calc(40% - 40px);}
-.ref-index .title {width: 60%;}
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-.ref-arguments th {text-align: right; padding-right: 10px;}
-.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
-.ref-arguments .name {width: 20%;}
-.ref-arguments .desc {width: 80%;}
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- display: block;
- overflow: auto;
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- background-color: #f8f8f8;
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- margin: 5px 0;
-}
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- background-color: #fff;
-}
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-code a, pre a {
- color: #375f84;
-}
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-}
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-.fl {color: #1514b5;}
-.fu {color: #000000;} /* function */
-.ch,.st {color: #036a07;} /* string */
-.kw {color: #264D66;} /* keyword */
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- font-family: "Font Awesome 5 Brands" !important;
-}
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-/* don't display links in code chunks when printing */
-/* source: https://stackoverflow.com/a/10781533 */
-@media print {
- code a:link:after, code a:visited:after {
- content: "";
- }
-}
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-/* Section anchors ---------------------------------
- Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
-*/
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diff --git a/docs/pkgdown.js b/docs/pkgdown.js
deleted file mode 100644
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--- a/docs/pkgdown.js
+++ /dev/null
@@ -1,108 +0,0 @@
-/* http://gregfranko.com/blog/jquery-best-practices/ */
-(function($) {
- $(function() {
-
- $('.navbar-fixed-top').headroom();
-
- $('body').css('padding-top', $('.navbar').height() + 10);
- $(window).resize(function(){
- $('body').css('padding-top', $('.navbar').height() + 10);
- });
-
- $('[data-toggle="tooltip"]').tooltip();
-
- var cur_path = paths(location.pathname);
- var links = $("#navbar ul li a");
- var max_length = -1;
- var pos = -1;
- for (var i = 0; i < links.length; i++) {
- if (links[i].getAttribute("href") === "#")
- continue;
- // Ignore external links
- if (links[i].host !== location.host)
- continue;
-
- var nav_path = paths(links[i].pathname);
-
- var length = prefix_length(nav_path, cur_path);
- if (length > max_length) {
- max_length = length;
- pos = i;
- }
- }
-
- // Add class to parent
-
-
-
-
-
-
-
-
-
-
-
- Changelog
- Source:NEWS.md
-
-
-
-
- goodpractice 1.0.3
-Additions:
-- Limit for cyclomatic complexity check can be adjusted using the
goodpractice.cyclocomp.limitoption, default 50 (#132, @fabian-s).
- - The number of lines printed to the console by each check result can be set using the new
positions_limitparameter intoprint()- previously it was always 5 lines (#130, @fabian-s).
- - GitHub Actions now used for CI/CD checks (#145), as well as to calculate code coverage with {covr} and build the package site with {pkgdown}. -
Bugfixes:
-
-
-
-
-
-
-
-
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-
diff --git a/docs/reference/checks.html b/docs/reference/checks.html
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+++ /dev/null
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-
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-
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-
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- List the names of all checks
-
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-
-
- all_checks()
-
-
- Value
-Character vector of checks
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diff --git a/docs/reference/customization.html b/docs/reference/customization.html
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-
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- List all checks performed
-
-
-
-
- checks(gp)
-
- Arguments
-- gp -
gpoutput.
-
-
- Value
-Character vector of check names.
-
-
-
-
- See also
-Other API:
-failed_checks(),
-results()
-
-
- Examples
-path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-checks(g)
-#> [1] "no_description_depends" "no_description_date"
-#> [3] "description_url" "description_bugreports"
-#> [5] "lintr_assignment_linter" "lintr_line_length_linter"
-#> [7] "lintr_trailing_semicolon_linter" "lintr_attach_detach_linter"
-#> [9] "lintr_setwd_linter" "lintr_sapply_linter"
-#> [11] "lintr_library_require_linter" "lintr_seq_linter"
-#> [13] "no_import_package_as_a_whole" "no_export_pattern"
-
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diff --git a/docs/reference/default_r_file_pattern.html b/docs/reference/default_r_file_pattern.html
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-
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-
-
- Defining custom preparations and checks
-
-
-
-
- make_prep(name, func)
-
-make_check(description, check, gp, ...)
-
- Arguments
-- name -
Name of the preparation function.
-- func -
A function that takes two arguments: -The
pathto the root directory of the package, and a logical -argument:quiet. Ifquietis true, the preparation function -may print out diagnostic messages. The output of this function will be -saved as the "name" entry ofstate, i.e. of the input for -thecheck-functions (see example).
-- description -
A description of the check.
-- check -
A function that takes the
stateas an argument.
-- gp -
A short description of what is good practice.
-- ... -
Further arguments. Most important: A
prepsargument that -contains the names of all the preparation functions required for the check.
-
-
-
- Functions
- -make_prep: Create a preparation function
-make_check: Create a check function
-
-
-
- Examples
-# make a preparation function
-url_prep <- make_prep(
- name = "desc",
- func = function(path, quiet) desc::description$new(path)
-)
-# and the corresponding check function
-url_chk <- make_check(
- description = "URL field in DESCRIPTION",
- tags = character(),
- preps = "desc",
- gp = "have a URL field in DESCRIPTION",
- check = function(state) state$desc$has_fields("URL")
-)
-# use together in gp():
-# (note that you have to list the name of your custom check in
-# the checks-argument as well....)
-bad1 <- system.file("bad1", package = "goodpractice")
-res <- gp(bad1, checks = c("url", "no_description_depends"),
- extra_preps = list("desc" = url_prep),
- extra_checks = list("url" = url_chk))
-#> Preparing: desc
-#> Preparing: description
-
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diff --git a/docs/reference/export_json.html b/docs/reference/export_json.html
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- Default pattern for R files
-
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- Value
-Regular expression.
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diff --git a/docs/reference/failed_checks.html b/docs/reference/failed_checks.html
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diff --git a/docs/reference/failed_positions.html b/docs/reference/failed_positions.html
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- Names of the failed checks
-
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-
-
- failed_checks(gp)
-
- Arguments
-- gp -
gpoutput.
-
-
-
-
- Value
-Names of the failed checks.
-
-
-
- Examples
-path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-failed_checks(g)
-#> [1] "no_description_depends" "no_description_date"
-#> [3] "description_url" "description_bugreports"
-#> [5] "lintr_trailing_semicolon_linter" "no_import_package_as_a_whole"
-
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diff --git a/docs/reference/figures/logo.png b/docs/reference/figures/logo.png
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diff --git a/docs/reference/get_marker.html b/docs/reference/get_marker.html
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-
-
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-
-
-
-
-
-
- Note that not all checks refer to the source code.
-For these the result will be NULL.
-
-
-
- failed_positions(gp)
-
- Arguments
-- gp -
gpoutput.
-
-
- Value
-A list of lists of positions. See details below.
-
-
-
- Details
-For the ones that do, the results is a list, one for each failure.
-Since the same check can fail multiple times. A single failure
-is a list with entries: filename, line_number,
-column_number, ranges. ranges is a list of
-pairs of start and end positions for each line involved in the
-check.
-
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diff --git a/docs/reference/goodpractice-package.html b/docs/reference/goodpractice-package.html
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-
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-
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-
- Get a marker from the positions of a check
-
-
-
-
- get_marker(gp, check)
-
-
- Arguments
-- gp -
gp()output
-- check -
name of the check to extract
-
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diff --git a/docs/reference/gp.html b/docs/reference/gp.html
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@@ -1,164 +0,0 @@
-
-
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-
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-
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-
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-
-
-
-
- Give advice about good practices when building R packages. Advice includes -functions and syntax to avoid, package structure, code complexity, code -formatting, etc.
-
-
-
-
-
- See also
-Useful links:
-
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diff --git a/docs/reference/index.html b/docs/reference/index.html
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-
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-
-
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-
-
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-
-
- To see the results, just print it to the screen.
-
-
-
-
- gp(
- path = ".",
- checks = all_checks(),
- extra_preps = NULL,
- extra_checks = NULL,
- quiet = TRUE
-)
-
- Arguments
-- path -
Path to a package root.
-- checks -
Character vector, the checks to run. Defaults to -all checks. Use
all_checksto list all checks.
-- extra_preps -
Custom preparation functions. See -
make_prepon creating preparation functions.
-- extra_checks -
Custom checks. See
make_checkon -creating checks.
-- quiet -
Whether to suppress output from the preparation -functions. Note that not all preparation functions produce output, -even if this option is set to
FALSE.
-
-
-
- Value
-A goodpractice object that you can query
-with a simple API. See results to start.
-
-
- Examples
-path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-g
-#> -- GP badpackage ---------------------------------------------------------------
-#>
-#> It is good practice to
-#>
-#> <U+2716> not use "Depends" in DESCRIPTION, as it can cause name
-#> clashes, and poor interaction with other packages. Use "Imports"
-#> instead.
-#> <U+2716> omit "Date" in DESCRIPTION. It is not required and it gets
-#> invalid quite often. A build date will be added to the package when
-#> you perform `R CMD build` on it.
-#> <U+2716> add a "URL" field to DESCRIPTION. It helps users find
-#> information about your package online. If your package does not
-#> have a homepage, add an URL to GitHub, or the CRAN package package
-#> page.
-#> <U+2716> add a "BugReports" field to DESCRIPTION, and point it to a
-#> bug tracker. Many online code hosting services provide bug trackers
-#> for free, https://github.com, https://gitlab.com, etc.
-#> <U+2716> omit trailing semicolons from code lines. They are not
-#> needed and most R coding standards forbid them
-#>
-#> R\semicolons.R:4:30
-#> R\semicolons.R:5:29
-#> R\semicolons.R:9:38
-#>
-#> <U+2716> not import packages as a whole, as this can cause name
-#> clashes between the imported packages. Instead, import only the
-#> specific functions you need.
-#> --------------------------------------------------------------------------------
-
-
-
-
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-
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diff --git a/docs/reference/make_check.html b/docs/reference/make_check.html
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- Reference
-
- All functions- - |
- |
|---|---|
| - - | -List the names of all checks |
-
| - - | -List all checks performed |
-
| - - | -Defining custom preparations and checks |
-
| - - | -Export failed checks to JSON |
-
| - - | -Names of the failed checks |
-
| - - | -Positions of check failures in the source code |
-
| - - | -goodpractice: Advice on R Package Building |
-
| - - | -Run good practice checks |
-
| - - | -Print goodpractice results |
-
| - - | -Return all check results in a data frame |
-
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diff --git a/docs/reference/make_prep.html b/docs/reference/make_prep.html
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- -make_check(description, check, gp, ...)- -
Arguments
-| description | -A description of the check. |
-
|---|---|
| check | -A function that takes the |
-
| gp | -A short description of what is good practice. |
-
| ... | -Further arguments. |
-
Examples
--# make a preparation function -url_prep <- make_prep( - name = "desc", - func = function(path, quiet) desc::description$new(path) -) -# and the corresponding check function -url_chk <- make_check( - description = "URL field in DESCRIPTION", - tags = character(), - preps = "desc", - gp = "have a URL field in DESCRIPTION", - check = function(state) state$desc$has_fields("URL") -) -# use together in gp() -bad1 <- system.file("bad1", package = "goodpractice") -res <- gp(bad1, checks = "no_description_depends", - extra_preps = list("desc" = url_prep), - extra_checks = list("url" = url_chk))#>
-
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diff --git a/docs/reference/make_rcmd_check.html b/docs/reference/make_rcmd_check.html
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- Create a preparation function
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-| name | -Name of the preparation function. |
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-The |
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Examples
--# make a preparation function -url_prep <- make_prep( - name = "desc", - func = function(path, quiet) desc::description$new(path) -) -# and the corresponding check function -url_chk <- make_check( - description = "URL field in DESCRIPTION", - tags = character(), - preps = "desc", - gp = "have a URL field in DESCRIPTION", - check = function(state) state$desc$has_fields("URL") -) -# use together in gp() -bad1 <- system.file("bad1", package = "goodpractice") -res <- gp(bad1, checks = "no_description_depends", - extra_preps = list("desc" = url_prep), - extra_checks = list("url" = url_chk))#>
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diff --git a/docs/reference/package_collate.html b/docs/reference/package_collate.html
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- Wrapper on make_check, specific to R CMD check
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- make_rcmd_check(
- description,
- pattern,
- gp = NULL,
- type = c("warnings", "notes", "errors"),
- tags = NULL,
- preps = NULL,
- ...
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- Arguments
-- description -
A description of the check.
-- pattern -
The text pattern identifying the check.
-- type -
Type of notification, one of "warnings", "notes" or "errors".
-- tags -
Tags to be passed on to make_check.
-- preps -
Preps to be passed on to make_check.
-- ... -
Currently not supported.
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diff --git a/docs/reference/prep_expressions.html b/docs/reference/prep_expressions.html
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- NULL is returned if there is no such field.
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- package_collate(path = ".")
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-- path -
Path to the package root.
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-Character scalar or NULL.
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diff --git a/docs/reference/print.goodPractice.html b/docs/reference/print.goodPractice.html
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- The package must be extracted into the working directory, as usual.
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- prep_expressions(state, version = NULL, quiet)
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- Arguments
-- state -
GP state.
-- version -
Currently ignored.
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- Value
-The modified state, with the closures in a named list.
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- Details
-We can use lintr to extract the functions, but need to use -our own code (based on similar code in functionMap) to -get the right collation order.
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diff --git a/docs/reference/r_package_files.html b/docs/reference/r_package_files.html
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- Print goodpractice results
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-print(x, positions_limit = 5, ...)
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- Arguments
-- x -
Object of class
goodPractice, as returned bygp().
-- positions_limit -
How many positions to print at most.
-- ... -
Unused, for compatibility with
base::print()generic method.
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diff --git a/docs/reference/results.html b/docs/reference/results.html
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- Get all source files of a package, in the right order
- Source:R/prep_expressions.R
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-- path -
Path to the root of the R package.
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-A character vector of (relative) file -names in the current collation order.
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diff --git a/docs/reference/seq_linter.html b/docs/reference/seq_linter.html
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- Return all check results in a data frame
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-- gp -
gpoutput.
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-Data frame, with columns:
-- check -
The name of the check.
-- result -
Logical, whether it has failed or not.
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-Other API:
-checks(),
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-path <- system.file("bad1", package = "goodpractice")
-# run a subset of all checks available
-g <- gp(path, checks = all_checks()[3:16])
-#> Preparing: description
-#> Preparing: lintr
-#> Preparing: namespace
-results(g)
-#> check result
-#> 1 no_description_depends FALSE
-#> 2 no_description_date FALSE
-#> 3 description_url FALSE
-#> 4 description_bugreports FALSE
-#> 5 lintr_assignment_linter TRUE
-#> 6 lintr_line_length_linter TRUE
-#> 7 lintr_trailing_semicolon_linter FALSE
-#> 8 lintr_attach_detach_linter TRUE
-#> 9 lintr_setwd_linter TRUE
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-#> 11 lintr_library_require_linter TRUE
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diff --git a/docs/sitemap.xml b/docs/sitemap.xml
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- Find occurrences of 1:length(x), 1:nrow(x),
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- Arguments
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Parse data. Passed from lintr.
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