new workflow files

.github/workflows/check-pr.yaml

@@ -0,0 +1,78 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Data Analysis for R                   #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2022 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
+# ==================================================================== #
+
+on:
+  pull_request:
+    # run in each PR in this repo
+    branches: '**'
+
+name: R-code-check-PR
+
+jobs:
+  R-code-check-PR:
+    runs-on: ${{ matrix.config.os }}
+
+    continue-on-error: ${{ matrix.config.allowfail }}
+
+    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'devel',   allowfail: true}
+          - {os: macOS-latest,   r: 'release', allowfail: false}
+          - {os: ubuntu-latest,  r: 'devel',   allowfail: true}
+          - {os: ubuntu-latest,  r: 'release', allowfail: false}
+          - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: 'release', allowfail: false}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          # use RStudio Package Manager to quickly install packages
+          use-public-rspm: true      
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        env:
+          _R_CHECK_LENGTH_1_CONDITION_: verbose
+          _R_CHECK_LENGTH_1_LOGIC2_: verbose
+          # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+          R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+          R_RUN_TINYTEST: true

.github/workflows/check.yaml

@@ -48,6 +48,7 @@ jobs:
         config:
           # test all systems against all released versions of R >= 3.0, we support them all!
           - {os: macOS-latest,   r: 'devel',   allowfail: true}
+          - {os: macOS-latest,   r: '4.2',     allowfail: false}
           - {os: macOS-latest,   r: '4.1',     allowfail: false}
           - {os: macOS-latest,   r: '4.0',     allowfail: false}
           - {os: macOS-latest,   r: '3.6',     allowfail: false}
@@ -63,6 +64,7 @@ jobs:
           - {os: ubuntu-22.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: '4.2',     allowfail: false}
           - {os: windows-latest, r: '4.1',     allowfail: false}
           - {os: windows-latest, r: '4.0',     allowfail: false}
           - {os: windows-latest, r: '3.6',     allowfail: false}
@@ -72,7 +74,7 @@ jobs:
       R_REPOSITORIES: "https://cran.rstudio.com"
     
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/codecovr.yaml

@@ -25,12 +25,9 @@
 
 on:
   push:
-    branches:
+    branches: '**'
-      - development
-      - main
   pull_request:
-    branches:
+    branches: '**'
-      - main
 
 name: code-coverage
 
@@ -40,7 +37,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/lintr.yaml

@@ -25,12 +25,9 @@
 
 on:
   push:
-    branches:
+    branches: '**'
-      - development
-      - main
   pull_request:
-    branches:
+    branches: '**'
-      - main
 
 name: lintr
 
@@ -40,7 +37,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9029
+Version: 1.8.1.9030
 Date: 2022-08-26
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9029
+# AMR 1.8.1.9030
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.