(v1.6.0.9040) unit tests

.github/workflows/check.yaml

@@ -89,18 +89,10 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
 
-      # - uses: r-lib/actions/setup-pandoc@master
-      
-      # - name: Query dependencies
-      #   if: matrix.config.r != '3.0'
-      #   run: |
-      #     saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-      #   shell: Rscript {0}
-
       - name: Install Linux dependencies
         if: runner.os == 'Linux'
         # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
@@ -108,7 +100,8 @@ jobs:
         run: |
           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
 
-      - name: Cache R packages
+      - name: Restore cached R packages
+        # this step will add the step 'Post Restore cached R packages' on a succesful run
         if: runner.os != 'Windows'
         uses: actions/cache@v1
         with:
@@ -122,7 +115,7 @@ jobs:
           source("data-raw/_install_deps.R")
         shell: Rscript {0}
         
-      - name: Session info
+      - name: Show session info
         run: |
           options(width = 100)
           utils::sessionInfo()
@@ -137,8 +130,9 @@ jobs:
           _R_CHECK_DEPENDS_ONLY_: true
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
-          R_LIBS_USER: ${{ env.R_LIBS_USER }}
-          R_TINYTEST: true
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
           rm -rf AMR/vignettes
@@ -153,8 +147,9 @@ jobs:
           _R_CHECK_DEPENDS_ONLY_: true
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
-          R_LIBS_USER: ${{ env.R_LIBS_USER }}
-          R_TINYTEST: true
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
           rm -rf AMR/vignettes
@@ -167,9 +162,9 @@ jobs:
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
+      - name: Upload artifacts
+        if: always()
+        uses: actions/upload-artifact@v2
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
           path: AMR.Rcheck

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.6.0.9038
-Date: 2021-05-15
+Version: 1.6.0.9040
+Date: 2021-05-16
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 
@@ -57,7 +57,7 @@ Suggests:
     skimr,
     tidyr,
     tinytest,
-    xml2, 
+    xml2
 VignetteBuilder: knitr,rmarkdown
 URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
 BugReports: https://github.com/msberends/AMR/issues

NEWS.md

@@ -1,5 +1,5 @@
-# `AMR` 1.6.0.9035
-## <small>Last updated: 15 May 2021</small>
+# `AMR` 1.6.0.9040
+## <small>Last updated: 16 May 2021</small>
 
 ### New
 * Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`

data-raw/_install_deps.R

@@ -43,5 +43,3 @@ for (i in seq_len(length(to_update))) {
            warning = function(w) message(w$message),
            error = function(e) message(e$message))
 }
-
-# saveRDS(to_update, ".github/depends.Rds", version = 2)

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/articles/datasets.html

@@ -39,7 +39,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9011</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 
@@ -47,14 +47,14 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="../index.html">
-    <span class="fa fa-home"></span>
+    <span class="fas fa-home"></span>
      
     Home
   </a>
 </li>
 <li class="dropdown">
   <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
-    <span class="fa fa-question-circle"></span>
+    <span class="fas fa-question-circle"></span>
      
     How to
      
@@ -63,77 +63,77 @@
   <ul class="dropdown-menu" role="menu">
 <li>
       <a href="../articles/AMR.html">
-        <span class="fa fa-directions"></span>
+        <span class="fas fa-directions"></span>
          
         Conduct AMR analysis
       </a>
     </li>
     <li>
       <a href="../articles/resistance_predict.html">
-        <span class="fa fa-dice"></span>
+        <span class="fas fa-dice"></span>
          
         Predict antimicrobial resistance
       </a>
     </li>
     <li>
       <a href="../articles/datasets.html">
-        <span class="fa fa-database"></span>
+        <span class="fas fa-database"></span>
          
         Data sets for download / own use
       </a>
     </li>
     <li>
       <a href="../articles/PCA.html">
-        <span class="fa fa-compress"></span>
+        <span class="fas fa-compress"></span>
          
         Conduct principal component analysis for AMR
       </a>
     </li>
     <li>
       <a href="../articles/MDR.html">
-        <span class="fa fa-skull-crossbones"></span>
+        <span class="fas fa-skull-crossbones"></span>
          
         Determine multi-drug resistance (MDR)
       </a>
     </li>
     <li>
       <a href="../articles/WHONET.html">
-        <span class="fa fa-globe-americas"></span>
+        <span class="fas fa-globe-americas"></span>
          
         Work with WHONET data
       </a>
     </li>
     <li>
       <a href="../articles/SPSS.html">
-        <span class="fa fa-file-upload"></span>
+        <span class="fas fa-file-upload"></span>
          
         Import data from SPSS/SAS/Stata
       </a>
     </li>
     <li>
       <a href="../articles/EUCAST.html">
-        <span class="fa fa-exchange-alt"></span>
+        <span class="fas fa-exchange-alt"></span>
          
         Apply EUCAST rules
       </a>
     </li>
     <li>
       <a href="../reference/mo_property.html">
-        <span class="fa fa-bug"></span>
+        <span class="fas fa-bug"></span>
          
         Get properties of a microorganism
       </a>
     </li>
     <li>
       <a href="../reference/ab_property.html">
-        <span class="fa fa-capsules"></span>
+        <span class="fas fa-capsules"></span>
          
         Get properties of an antibiotic
       </a>
     </li>
     <li>
       <a href="../articles/benchmarks.html">
-        <span class="fa fa-shipping-fast"></span>
+        <span class="fas fa-shipping-fast"></span>
          
         Other: benchmarks
       </a>
@@ -142,21 +142,21 @@
 </li>
 <li>
   <a href="../reference/index.html">
-    <span class="fa fa-book-open"></span>
+    <span class="fas fa-book-open"></span>
      
     Manual
   </a>
 </li>
 <li>
   <a href="../authors.html">
-    <span class="fa fa-users"></span>
+    <span class="fas fa-users"></span>
      
     Authors
   </a>
 </li>
 <li>
   <a href="../news/index.html">
-    <span class="far fa far fa-newspaper"></span>
+    <span class="far fa-newspaper"></span>
      
     Changelog
   </a>
@@ -165,14 +165,14 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://github.com/msberends/AMR">
-    <span class="fab fa fab fa-github"></span>
+    <span class="fab fa-github"></span>
      
     Source Code
   </a>
 </li>
 <li>
   <a href="../survey.html">
-    <span class="fa fa-clipboard-list"></span>
+    <span class="fas fa-clipboard-list"></span>
      
     Survey
   </a>
@@ -187,13 +187,12 @@
 
       
 
-      </header><link href="datasets_files/anchor-sections-1.0/anchor-sections.css" rel="stylesheet">
-<script src="datasets_files/anchor-sections-1.0/anchor-sections.js"></script><div class="row">
+      </header><script src="datasets_files/header-attrs-2.7/header-attrs.js"></script><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1 data-toc-skip>Data sets for download / own use</h1>
             
-            <h4 class="date">27 April 2021</h4>
+            <h4 class="date">16 May 2021</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="hidden name"><code>datasets.Rmd</code></div>
@@ -212,7 +211,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
 <p>A data set with 70,026 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 11 March 2021 20:59:32 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
@@ -433,7 +432,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <p>A data set with 14,100 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
 <p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
 <p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
+<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
@@ -498,7 +497,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
 <p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>atc</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 4 May 2021 13:38:27 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
@@ -666,7 +665,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
@@ -793,7 +792,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
 <p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
@@ -1008,7 +1007,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
 <p>A data set with 20,486 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 5 March 2021 09:46:55 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/rsi_translation.rds">R file</a> (34 kB)<br>
@@ -1138,7 +1137,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
 <a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
 <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 27 April 2021 08:12:46 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/master/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 
@@ -236,12 +236,12 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609031" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9031">
-<a href="#amr-1609031" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9031</h1>
-<div id="last-updated-15-may-2021" class="section level2">
+    <div id="amr-1609040" class="section level1">
+<h1 class="page-header" data-toc-text="1.6.0.9040">
+<a href="#amr-1609040" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9040</h1>
+<div id="last-updated-16-may-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-15-may-2021" class="anchor"></a><small>Last updated: 15 May 2021</small>
+<a href="#last-updated-16-may-2021" class="anchor"></a><small>Last updated: 16 May 2021</small>
 </h2>
 <div id="new" class="section level3">
 <h3 class="hasAnchor">

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-15T19:35Z
+last_built: 2021-05-16T07:24Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9031</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9040</span>
       </span>
     </div>
 

git_premaster.sh

@@ -134,6 +134,8 @@ echo "•••••••••••••••••"
 echo "• Building site •"
 echo "•••••••••••••••••"
 Rscript -e "suppressMessages(pkgdown::build_site(lazy = $lazy, examples = FALSE))"
+# always rebuild datasets vignette 
+Rscript -e "pkgdown::build_article('datasets', lazy = FALSE, quiet = TRUE)"
 # add the survey page
 Rscript -e "source('data-raw/create_survey_page.R')"
 echo

inst/tinytest/test-join_microorganisms.R

@@ -24,12 +24,12 @@
 # ==================================================================== #
 
 unjoined <- example_isolates
-inner <- example_isolates %>% inner_join_microorganisms()
-left <- example_isolates %>% left_join_microorganisms()
-semi <- example_isolates %>% semi_join_microorganisms()
-anti <- example_isolates %>% anti_join_microorganisms()
-suppressWarnings(right <- example_isolates %>% right_join_microorganisms())
-suppressWarnings(full <- example_isolates %>% full_join_microorganisms())
+inner <- inner_join_microorganisms(example_isolates)
+left <- left_join_microorganisms(example_isolates)
+semi <- semi_join_microorganisms(example_isolates)
+anti <- anti_join_microorganisms(example_isolates)
+suppressWarnings(right <- right_join_microorganisms(example_isolates))
+suppressWarnings(full <- full_join_microorganisms(example_isolates))
 
 expect_true(ncol(unjoined) < ncol(inner))
 expect_true(nrow(unjoined) == nrow(inner))

tests/tinytest.R

@@ -24,11 +24,10 @@
 # ==================================================================== #
 
 # test only on GitHub Actions and at home - not on CRAN as tests are lengthy
-if (identical(Sys.getenv("R_TINYTEST"), "true")) {
-  print(Sys.getenv("R_LIBS_USER"))
-  .libPaths(c("/Users/runner/work/_temp/Library", .libPaths()))
+if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
+  # env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
+  .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
   print(.libPaths())
-  print(as.data.frame(utils::installed.packages())[, "Version", drop = FALSE])
   library(tinytest)
   library(AMR)
   test_package("AMR")