(v1.7.1.9043) unit tests

.github/workflows/check.yaml

@@ -84,13 +84,7 @@ jobs:
       R_REPOSITORIES: "https://cran.rstudio.com"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-      R_CHECK_CRAN_INCOMING: false
+      
-      R_CHECK_FORCE_SUGGESTS: false
-      R_CHECK_DEPENDS_ONLY: true
-      R_CHECK_LENGTH_1_CONDITION: verbose
-      R_CHECK_LENGTH_1_LOGIC2: verbose
-      R_RUN_TINYTEST: true
-
     steps:
       - uses: actions/checkout@v2
 
@@ -101,11 +95,18 @@ jobs:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v1
-        with:
-          extra-packages: rcmdcheck
           
+      - name: show file list
+        run: ls -lh
+        shell: bash
+        
+      - name: Install dependencies
+        if: always()
+        run: |
+          install.packages("remotes")
+          remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
+       shell: Rscript {0}
+       
       - name: Show session info
         if: always()
         run: |
@@ -116,10 +117,15 @@ jobs:
 
       - uses: r-lib/actions/check-r-package@v1
         env:
+          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_FORCE_SUGGESTS_: false
+          _R_CHECK_DEPENDS_ONLY_: true
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          R_RUN_TINYTEST: true
           # during 'R CMD check', R_LIBS_USER will be overwritten, so:
           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
       
-
       - name: Show unit tests output
         if: always()
         run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true

.github/workflows/codecovr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: code-coverage
 

.github/workflows/lintr.yaml

@@ -26,11 +26,11 @@
 on:
   push:
     branches:
-      - premaster
+      - development
-      - master
+      - main
   pull_request:
     branches:
-      - master
+      - main
 
 name: lintr
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.7.1.9041
+Version: 1.7.1.9043
 Date: 2021-09-29
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9041
+# `AMR` 1.7.1.9043
 ## <small>Last updated: 29 September 2021</small>
 
 ### Breaking changes

docs/articles/datasets.html

@@ -44,7 +44,7 @@
       </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">1.7.1.9041</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9043</span>
       </span>
     </div>
 

docs/news/index.html

@@ -92,7 +92,7 @@
       </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">1.7.1.9041</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9043</span>
       </span>
     </div>
 
@@ -240,9 +240,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1719041" class="section level1">
+    <div id="amr-1719043" class="section level1">
-<h1 class="page-header" data-toc-text="1.7.1.9041">
+<h1 class="page-header" data-toc-text="1.7.1.9043">
-<a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1>
+<a href="#amr-1719043" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9043</h1>
 <div id="last-updated-29-september-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>