(v2.1.1.9094) fix antibiotics #342
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # ==================================================================== # | |
| # 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, et al. (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: ubuntu-latest, r: '3.6', allowfail: false} | |
| # - {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 |