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131 lines
6.2 KiB
131 lines
6.2 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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# # |
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# SOURCE # |
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# https://github.com/msberends/AMR # |
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# # |
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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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# # |
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# This R package is free software; you can freely use and distribute # |
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# it for both personal and commercial purposes under the terms of the # |
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# GNU General Public License version 2.0 (GNU GPL-2), as published by # |
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# the Free Software Foundation. # |
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# We created this package for both routine data analysis and academic # |
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# research and it was publicly released in the hope that it will be # |
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # |
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# # |
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# Visit our website for the full manual and a complete tutorial about # |
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # |
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# ==================================================================== # |
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on: |
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push: |
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branches: |
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- development |
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- main |
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pull_request: |
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branches: |
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- main |
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schedule: |
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# run a schedule everyday at 1 AM. |
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# this is to check that all dependencies are still available (see R/zzz.R) |
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- cron: '0 1 * * *' |
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name: R-code-check |
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jobs: |
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R-code-check: |
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runs-on: ${{ matrix.config.os }} |
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continue-on-error: ${{ matrix.config.allowfail }} |
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name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}) |
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strategy: |
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fail-fast: false |
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matrix: |
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config: |
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# test all systems against all released versions of R >= 3.0, we support them all! |
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- {os: macOS-latest, r: 'devel', allowfail: true} |
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- {os: macOS-latest, r: '4.1', allowfail: false} |
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- {os: macOS-latest, r: '4.0', allowfail: false} |
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- {os: macOS-latest, r: '3.6', allowfail: false} |
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- {os: macOS-latest, r: '3.5', allowfail: false} |
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- {os: macOS-latest, r: '3.4', allowfail: false} |
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- {os: macOS-latest, r: '3.3', allowfail: false} |
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- {os: macOS-latest, r: '3.2', allowfail: false} |
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- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} |
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- {os: windows-latest, r: 'devel', allowfail: true} |
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- {os: windows-latest, r: '4.1', allowfail: false} |
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- {os: windows-latest, r: '4.0', allowfail: false} |
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- {os: windows-latest, r: '3.6', allowfail: false} |
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- {os: windows-latest, r: '3.5', allowfail: false} |
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- {os: windows-latest, r: '3.4', allowfail: false} |
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- {os: windows-latest, r: '3.3', allowfail: false} |
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- {os: windows-latest, r: '3.2', allowfail: false} |
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env: |
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: false |
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RSPM: ${{ matrix.config.rspm }} |
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R_REPOSITORIES: "https://cran.rstudio.com" |
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} |
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R_KEEP_PKG_SOURCE: yes |
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R_CHECK_CRAN_INCOMING_: false |
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R_CHECK_FORCE_SUGGESTS_: false |
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R_CHECK_DEPENDS_ONLY_: true |
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R_CHECK_LENGTH_1_CONDITION_: verbose |
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R_CHECK_LENGTH_1_LOGIC2_: verbose |
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# during 'R CMD check', R_LIBS_USER will be overwritten, so: |
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} |
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R_RUN_TINYTEST: true |
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steps: |
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- uses: actions/checkout@v2 |
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- uses: r-lib/actions/setup-pandoc@v1 |
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- uses: r-lib/actions/setup-r@v1 |
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with: |
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r-version: ${{ matrix.config.r }} |
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http-user-agent: ${{ matrix.config.http-user-agent }} |
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use-public-rspm: true |
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- uses: r-lib/actions/setup-r-dependencies@v1 |
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with: |
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extra-packages: rcmdcheck |
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- name: Show session info |
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if: always() |
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run: | |
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options(width = 100) |
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utils::sessionInfo() |
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] |
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shell: Rscript {0} |
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- uses: r-lib/actions/check-r-package@v1 |
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- name: Show unit tests output |
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if: always() |
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run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true |
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shell: bash |
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- name: Upload check results |
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if: always() |
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uses: actions/upload-artifact@main |
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with: |
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name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts |
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path: check
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