(v1.6.0.9026) new unit test flow

.github/workflows/check.yaml

@@ -102,12 +102,13 @@ jobs:
         shell: Rscript {0}
         
       - 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: Cache R packages
-        if: runner.os != 'Windows'
+        if: runner.os != 'Windows' && matrix.config.r != '3.0'
         # && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
         uses: actions/cache@v1
         with:
@@ -145,7 +146,8 @@ jobs:
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
-          R CMD check AMR -no-manual -as-cran
+          rm -rf AMR/vignettes
+          R CMD check AMR
         shell: bash
         
       - name: Run R CMD check on Linux and macOS
@@ -158,12 +160,15 @@ jobs:
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
+          rm -rf AMR/vignettes
           R CMD check AMR --no-manual --as-cran
         shell: bash
 
       - name: Show testthat output
         if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        run: |
+          ls -lh
+          find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload check results

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9025
+Version: 1.6.0.9026
 Date: 2021-05-13
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9025
+# `AMR` 1.6.0.9026
 ## <small>Last updated: 13 May 2021</small>
 
 ### New

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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
       </span>
     </div>
 

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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609023" class="section level1">
+    <div id="amr-1609026" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9023">
+<h1 class="page-header" data-toc-text="1.6.0.9026">
-<a href="#amr-1609023" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9023</h1>
+<a href="#amr-1609026" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9026</h1>
 <div id="last-updated-13-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-13-may-2021" class="anchor"></a><small>Last updated: 13 May 2021</small>
@@ -262,7 +262,7 @@
 <li>The documentation of the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/key_antimicrobials.html">key_antimicrobials()</a></code> functions has been completely rewritten.</li>
 </ul>
 </li>
-<li>Added <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
+<li>Added <code>ggplot()</code> method for <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>
 </li>
 </ul>
 </div>
@@ -348,7 +348,7 @@
 <span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
 </li>
 <li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
-<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
+<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
 <li>
 <p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@@ -405,7 +405,7 @@
 <li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
 <li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
 <li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
-<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
+<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
 </ul>
 </li>
 <li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>

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: 2021-05-13T17:31Z
+last_built: 2021-05-13T19:15Z
 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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</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">1.6.0.9023</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9026</span>
       </span>
     </div>
 

tests/testthat/test-atc_online.R

@@ -27,6 +27,7 @@ context("atc_online.R")
 
 test_that("atc_online works", {
   skip_on_cran()
+  skip_if_not_installed("curl")
   skip_if_not(curl::has_internet())
   
   expect_gte(length(atc_online_groups(ab_atc("AMX"))), 1)