v2.1.1 #2
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| # ==================================================================== # | |
| # TITLE: # | |
| # AMR: An R Package for Working with Antimicrobial Resistance Data # | |
| # # | |
| # SOURCE CODE: # | |
| # https://github.com/msberends/AMR # | |
| # # | |
| # PLEASE CITE THIS SOFTWARE AS: # | |
| # Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C # | |
| # (2022). AMR: An R Package for Working with Antimicrobial Resistance # | |
| # Data. Journal of Statistical Software, 104(3), 1-31. # | |
| # https://doi.org/10.18637/jss.v104.i03 # | |
| # # | |
| # Developed at the University of Groningen and the University Medical # | |
| # Center Groningen in The Netherlands, in collaboration with many # | |
| # colleagues from around the world, see our website. # | |
| # # | |
| # This R package is free software; you can freely use and distribute # | |
| # it for both personal and commercial purposes under the terms of the # | |
| # GNU General Public License version 2.0 (GNU GPL-2), as published by # | |
| # the Free Software Foundation. # | |
| # We created this package for both routine data analysis and academic # | |
| # research and it was publicly released in the hope that it will be # | |
| # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # | |
| # # | |
| # Visit our website for the full manual and a complete tutorial about # | |
| # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # | |
| # ==================================================================== # | |
| on: | |
| push: | |
| # only run after a git push on any branch in this repo | |
| branches: '**' | |
| name: check-old | |
| jobs: | |
| R-code-check: | |
| runs-on: ${{ matrix.config.os }} | |
| continue-on-error: ${{ matrix.config.allowfail }} | |
| name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # Test all old versions of R >= 3.0, we support them all! | |
| # For these old versions, dependencies and vignettes will not be checked. | |
| # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases). | |
| # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8 | |
| - {os: ubuntu-latest, r: '3.4', allowfail: false} | |
| - {os: ubuntu-latest, r: '3.3', allowfail: false} | |
| - {os: ubuntu-latest, r: '3.2', allowfail: false} | |
| - {os: ubuntu-latest, r: '3.1', allowfail: false} | |
| - {os: ubuntu-latest, r: '3.0', allowfail: false} | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install tinytest from CRAN | |
| run: | | |
| install.packages("tinytest", repos = "https://cran.r-project.org") | |
| shell: Rscript {0} | |
| - name: Show session info | |
| if: always() | |
| run: | | |
| options(width = 100) | |
| utils::sessionInfo() | |
| as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] | |
| shell: Rscript {0} | |
| - name: Remove vignettes | |
| if: always() # matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2' || matrix.config.r == '3.3' | |
| # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R <= 3.3 as writeLines() cannot overwrite | |
| run: | | |
| rm -rf vignettes | |
| Rscript -e "writeLines(readLines('DESCRIPTION')[!grepl('VignetteBuilder', readLines('DESCRIPTION'))], 'DESCRIPTION2')" | |
| rm DESCRIPTION | |
| mv DESCRIPTION2 DESCRIPTION | |
| shell: bash | |
| - name: Run R CMD check | |
| if: always() | |
| env: | |
| # see https://rstudio.github.io/r-manuals/r-ints/Tools.html for an overview | |
| _R_CHECK_CRAN_INCOMING_: false | |
| _R_CHECK_DEPENDS_ONLY_: true | |
| _R_CHECK_LENGTH_1_CONDITION_: verbose | |
| _R_CHECK_LENGTH_1_LOGIC2_: verbose | |
| # no check for old R versions - these packages require higher R versions | |
| _R_CHECK_RD_XREFS_: false | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| R_CHECK_CONSTANTS: 5 | |
| R_JIT_STRATEGY: 3 | |
| # during 'R CMD check', R_LIBS_USER will be overwritten, so: | |
| R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} | |
| # this is a required value to run the unit tests: | |
| R_RUN_TINYTEST: true | |
| run: | | |
| cd .. | |
| R CMD build AMR | |
| R CMD check --as-cran --no-manual --run-donttest --run-dontrun AMR_*.tar.gz | |
| shell: bash | |
| - name: Show tinytest output | |
| if: always() | |
| run: | | |
| cd ../AMR.Rcheck | |
| find . -name 'tinytest.Rout*' -exec cat '{}' \; || true | |
| shell: bash |