new setup unit tests

.github/workflows/check-old.yaml

@@ -50,24 +50,14 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # test all old versions of R >= 3.0, we support them all!
+          # Test all old versions of R >= 3.0, we support them all!
-          # (for R-release and R-devel, see check-current.yaml)
+          # For recent R versions, see check-recent.yaml (r-lib supports the latest 5 major versions)
-          - {os: macOS-latest,   r: '4.1',     allowfail: false}
-          - {os: macOS-latest,   r: '4.0',     allowfail: false}
-          - {os: macOS-latest,   r: '3.6',     allowfail: false}
-          - {os: ubuntu-22.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          # R 3.5 returns a strange GC error when running examples, omit the checks for that
-          # - {os: ubuntu-22.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {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: '4.1',     allowfail: false}
+          
-          - {os: windows-latest, r: '4.0',     allowfail: false}
-          - {os: windows-latest, r: '3.6',     allowfail: false}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

.github/workflows/check-recent.yaml

@@ -38,7 +38,7 @@ on:
     # this is to check that all dependencies are still available (see R/zzz.R)
     - cron:  '0 1 * * *'
 
-name: check-current
+name: check-recent
 
 jobs:
   R-code-check:
@@ -52,15 +52,30 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          # current development version:
           - {os: macOS-latest,   r: 'devel', allowfail: false}
-          - {os: macOS-latest,   r: 'release', allowfail: false}
-          - {os: ubuntu-latest,  r: 'devel',   allowfail: false}
-          - {os: ubuntu-latest,  r: 'release', allowfail: false}
           - {os: windows-latest, r: 'devel', allowfail: false}
-          - {os: windows-latest, r: 'release', allowfail: false}
+          - {os: ubuntu-latest,  r: 'devel', allowfail: false}
+          # current 'release' version:
+          - {os: macOS-latest,   r: '4.2', allowfail: false}
+          - {os: windows-latest, r: '4.2', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.2', allowfail: false}
+          # older versions:
+          - {os: macOS-latest,   r: '4.1', allowfail: false}
+          - {os: windows-latest, r: '4.1', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.1', allowfail: false}
+          
+          - {os: macOS-latest,   r: '4.0', allowfail: false}
+          - {os: windows-latest, r: '4.0', allowfail: false}
+          - {os: ubuntu-latest,  r: '4.0', allowfail: false}
+          
           - {os: macOS-latest,   r: '3.6', allowfail: false}
-          - {os: ubuntu-latest,  r: '3.6',     allowfail: false}
           - {os: windows-latest, r: '3.6', allowfail: false}
+          - {os: ubuntu-latest,  r: '3.6', allowfail: false}
+          
+          - {os: macOS-latest,   r: '3.5', allowfail: false}
+          - {os: windows-latest, r: '3.5', allowfail: false}
+          - {os: ubuntu-latest,  r: '3.5', allowfail: false}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9078
+Version: 1.8.2.9079
 Date: 2023-01-05
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9078
+# AMR 1.8.2.9079
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

inst/tinytest/test-mean_amr_distance.R

@@ -51,13 +51,13 @@ expect_identical(
 )
 
 expect_equal(
-  mean_amr_distance(data.frame(vctr_mic, vctr_rsi, vctr_disk)),
+  mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_rsi, TOB = vctr_disk)),
   c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
   tolerance = 0.00001
 )
 
 expect_equal(
-  mean_amr_distance(data.frame(vctr_mic, vctr_rsi, vctr_disk), 2:3),
+  mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_rsi, TOB = vctr_disk), 2:3),
   c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
   tolerance = 0.00001
 )