(v1.4.0.9057) GH actions update

.github/workflows/check.yaml

@@ -117,9 +117,8 @@ jobs:
           brew install mariadb-connector-c
 
       - name: Install dependencies
-        if: always()
         run: |
-          utils::install.packages(strsplit(utils::packageDescription("AMR")$Suggests, ",\n")[[1]])
+          utils::update.packages(ask = FALSE)
         shell: Rscript {0}
 
       - name: Session info
@@ -151,10 +150,14 @@ jobs:
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
+        
+      - name: Install packages to check for new deps
+        run: |
+          R CMD INSTALL data-raw/AMR_*.tar.gz
 
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.4.0.9056
+Version: 1.4.0.9057
-Date: 2021-01-03
+Date: 2021-01-04
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.4.0.9056
+# AMR 1.4.0.9057
-## <small>Last updated:  3 January 2021</small>
+## <small>Last updated:  4 January 2021</small>
 ### New
 * Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
   ```r

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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</span>
       </span>
     </div>
 
@@ -236,13 +236,13 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1409056" class="section level1">
+    <div id="amr-1409057" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0.9056">
+<h1 class="page-header" data-toc-text="1.4.0.9057">
-<a href="#amr-1409056" class="anchor"></a>AMR 1.4.0.9056<small> Unreleased </small>
+<a href="#amr-1409057" class="anchor"></a>AMR 1.4.0.9057<small> Unreleased </small>
 </h1>
-<div id="last-updated-3-january-2021" class="section level2">
+<div id="last-updated-4-january-2021" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-3-january-2021" class="anchor"></a><small>Last updated: 3 January 2021</small>
+<a href="#last-updated-4-january-2021" class="anchor"></a><small>Last updated: 4 January 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: 2021-01-03T22:35Z
+last_built: 2021-01-04T08:49Z
 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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</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">1.4.0.9056</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9057</span>
       </span>
     </div>