# ==================================================================== # # 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/ # # ==================================================================== # on: push: branches: - premaster - master pull_request: branches: - master schedule: # run a schedule everyday at 3 AM. # this is to check that all dependencies are still available (see R/zzz.R) - cron: '0 3 * * *' 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: - {os: macOS-latest, r: 'devel', allowfail: true} - {os: macOS-latest, r: 'release', allowfail: false} - {os: macOS-latest, r: 'oldrel', allowfail: false} - {os: windows-latest, r: 'devel', allowfail: false} - {os: windows-latest, r: 'release', allowfail: false} - {os: windows-latest, r: 'oldrel', allowfail: false} - {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} steps: - uses: actions/checkout@v2 - uses: r-lib/actions/setup-r@master with: r-version: ${{ matrix.config.r }} # - uses: r-lib/actions/setup-pandoc@master # - name: Query dependencies # if: matrix.config.r != '3.0' # run: | # saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) # shell: Rscript {0} - 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 a quite new R version run: | sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev - name: Cache R packages # if: runner.os != 'Windows' uses: actions/cache@v1 with: path: ${{ env.R_LIBS_USER }} key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-20 restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-20 - name: Update AMR package dependencies run: | install.packages("data-raw/AMR_latest.tar.gz") source("data-raw/_install_deps.R") shell: Rscript {0} - name: Session info run: | options(width = 100) utils::sessionInfo() as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - name: Run R CMD check on Windows if: runner.os == 'Windows' 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 R_LIBS_USER: ${{ env.R_LIBS_USER }} R_TINYTEST: true run: | tar -xf data-raw/AMR_latest.tar.gz rm -rf AMR/vignettes R CMD check AMR shell: bash - name: Run R CMD check on Linux and macOS if: runner.os != 'Windows' 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 R_LIBS_USER: ${{ env.R_LIBS_USER }} R_TINYTEST: true run: | tar -xf data-raw/AMR_latest.tar.gz rm -rf AMR/vignettes R CMD check AMR --no-manual --no-vignettes shell: bash - name: Show unit tests output if: always() run: | find . -name 'tinytest.Rout*' -exec cat '{}' \; || true shell: bash - name: Upload check results if: failure() uses: actions/upload-artifact@master with: name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results path: AMR.Rcheck