diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index cbdc6067..2d49ae61 100644 --- a/.github/workflows/check.yaml +++ b/.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 diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml index 6dd0afaa..51c0205f 100644 --- a/.github/workflows/codecovr.yaml +++ b/.github/workflows/codecovr.yaml @@ -26,11 +26,11 @@ on: push: branches: - - premaster - - master + - development + - main pull_request: branches: - - master + - main name: code-coverage diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index eb42cd50..ed1acee1 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -26,11 +26,11 @@ on: push: branches: - - premaster - - master + - development + - main pull_request: branches: - - master + - main name: lintr diff --git a/DESCRIPTION b/DESCRIPTION index 00695030..bc50c7af 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index 30cbbd0b..f32b55f6 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9041 +# `AMR` 1.7.1.9043 ## Last updated: 29 September 2021 ### Breaking changes diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index fc4f27c6..0e736f6e 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 0ff18c37..9b7bd9e3 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9041 + 1.7.1.9043 diff --git a/docs/news/index.html b/docs/news/index.html index 7aee29e5..046695b3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9041 + 1.7.1.9043 @@ -240,9 +240,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9041

+
+

+ Unreleased AMR 1.7.1.9043

Last updated: 29 September 2021