# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # 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/ # # ==================================================================== # # This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0. on: push: branches: - premaster - master pull_request: branches: - master schedule: # run a schedule everyday at 1 AM. # this is to check that all dependencies are still available (see R/zzz.R) - cron: '0 1 * * *' name: R-code-check 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: # these are the developmental version of R - we allow those tests to fail - {os: macOS-latest, r: 'devel', allowfail: false} - {os: windows-latest, r: 'devel', allowfail: false} - {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # test all systems against all released versions of R >= 3.0, we support them all! - {os: macOS-latest, r: '4.1', allowfail: false} - {os: windows-latest, r: '4.1', allowfail: false} - {os: ubuntu-20.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '4.0', allowfail: false} - {os: windows-latest, r: '4.0', allowfail: false} - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.6', allowfail: false} - {os: windows-latest, r: '3.6', allowfail: false} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.5', allowfail: false} - {os: windows-latest, r: '3.5', allowfail: false} - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.4', allowfail: false} - {os: windows-latest, r: '3.4', allowfail: false} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.3', allowfail: false} - {os: windows-latest, r: '3.3', allowfail: false} - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: macOS-latest, r: '3.2', allowfail: false} - {os: windows-latest, r: '3.2', allowfail: false} - {os: ubuntu-20.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: macOS-latest, r: '3.1', allowfail: false} # - {os: windows-latest, r: '3.1', allowfail: false} - {os: ubuntu-20.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # - {os: macOS-latest, r: '3.0', allowfail: false} # - {os: windows-latest, r: '3.0', allowfail: false} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} R_REPOSITORIES: "https://cran.rstudio.com" steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@v1 with: r-version: ${{ matrix.config.r }} - name: Install Linux dependencies if: runner.os == 'Linux' # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11 run: | sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev - name: Query dependencies # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates run: | writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle") shell: Rscript {0} - name: Restore cached R packages # this step will add the step 'Post Restore cached R packages' on a succesful run uses: actions/cache@v2 with: path: ${{ env.R_LIBS_USER }} key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4 - name: Unpack AMR and install R dependencies if: always() run: | tar -xf data-raw/AMR_latest.tar.gz Rscript -e "source('data-raw/_install_deps.R')" shell: bash - 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: Only keep vignettes on release version - name: Remove vignettes # if: matrix.config.r != 'release' if: always() # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite run: | rm -rf AMR/vignettes Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')" rm AMR/DESCRIPTION mv AMR/DESCRIPTION2 AMR/DESCRIPTION shell: bash - name: Run R CMD check if: always() 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 # during 'R CMD check', R_LIBS_USER will be overwritten, so: R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} R_RUN_TINYTEST: true run: | R CMD check --no-manual --run-donttest --run-dontrun AMR shell: bash - name: Show unit tests output if: always() run: | find . -name 'tinytest.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload artifacts if: always() uses: actions/upload-artifact@v2 with: name: artifacts-r-${{ matrix.config.r }}-${{ matrix.config.os }} path: AMR.Rcheck