diff --git a/.github/workflows/check-old.yaml b/.github/workflows/check-old.yaml index 58548c46..cef86728 100644 --- a/.github/workflows/check-old.yaml +++ b/.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! - # (for R-release and R-devel, see check-current.yaml) - - {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"} + # Test all old versions of R >= 3.0, we support them all! + # For recent R versions, see check-recent.yaml (r-lib supports the latest 5 major versions) - {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 }} diff --git a/.github/workflows/check-current.yaml b/.github/workflows/check-recent.yaml similarity index 72% rename from .github/workflows/check-current.yaml rename to .github/workflows/check-recent.yaml index 3f1b3715..4d66621c 100644 --- a/.github/workflows/check-current.yaml +++ b/.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: - - {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: macOS-latest, r: '3.6', allowfail: false} - - {os: ubuntu-latest, r: '3.6', allowfail: false} - - {os: windows-latest, r: '3.6', allowfail: false} + # current development version: + - {os: macOS-latest, r: 'devel', allowfail: false} + - {os: windows-latest, r: 'devel', 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: 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 }} diff --git a/DESCRIPTION b/DESCRIPTION index fcd410fc..436db19b 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index 24ebfaa2..14a5837d 100755 --- a/NEWS.md +++ b/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!)* diff --git a/inst/tinytest/test-mean_amr_distance.R b/inst/tinytest/test-mean_amr_distance.R index cdbf91fd..0a7290f6 100644 --- a/inst/tinytest/test-mean_amr_distance.R +++ b/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 )