mirror of https://github.com/msberends/AMR.git
123 lines
5.2 KiB
YAML
123 lines
5.2 KiB
YAML
# ==================================================================== #
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# TITLE: #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# only run after a git push on any branch in this repo
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branches: '**'
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name: check-old
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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 old versions of R >= 3.0, we support them all!
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# For these old versions, dependencies and vignettes will not be checked.
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# For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
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- {os: windows-latest, r: '3.5', allowfail: true}
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- {os: ubuntu-latest, r: '3.4', allowfail: false}
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- {os: ubuntu-latest, r: '3.3', allowfail: false}
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- {os: ubuntu-latest, r: '3.2', allowfail: false}
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- {os: ubuntu-latest, r: '3.1', allowfail: false}
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- {os: ubuntu-latest, r: '3.0', allowfail: false}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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steps:
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Install tinytest from CRAN
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run: |
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install.packages("tinytest", repos = "https://cran.r-project.org")
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shell: Rscript {0}
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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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- name: Remove vignettes
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if: always() # matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3'
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# writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite
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run: |
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rm -rf vignettes
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Rscript -e "writeLines(readLines('DESCRIPTION')[!grepl('VignetteBuilder', readLines('DESCRIPTION'))], 'DESCRIPTION2')"
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rm DESCRIPTION
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mv DESCRIPTION2 DESCRIPTION
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shell: bash
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- name: Run R CMD check
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if: always()
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env:
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# see https://rstudio.github.io/r-manuals/r-ints/Tools.html for an overview
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_R_CHECK_CRAN_INCOMING_: 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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# no check for old R versions - these packages require higher R versions
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_R_CHECK_RD_XREFS_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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R_CHECK_CONSTANTS: 5
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R_JIT_STRATEGY: 3
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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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# this is a required value to run the unit tests:
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R_RUN_TINYTEST: true
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run: |
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cd ..
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R CMD build AMR
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R CMD check --as-cran --no-manual --run-donttest --run-dontrun AMR_*.tar.gz
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shell: bash
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- name: Show tinytest output
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if: always()
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run: |
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cd ../AMR.Rcheck
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find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
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shell: bash
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