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# ==================================================================== #
# 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:
- development
- main
pull_request:
branches:
- main
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:
# test all systems against all released versions of R >= 3.0, we support them all!
- {os: macOS-latest, r: 'devel', allowfail: true}
- {os: macOS-latest, r: '4.1', allowfail: false}
- {os: macOS-latest, r: '4.0', allowfail: false}
- {os: macOS-latest, r: '3.6', allowfail: false}
- {os: macOS-latest, r: '3.5', allowfail: false}
- {os: macOS-latest, r: '3.4', allowfail: false}
- {os: macOS-latest, r: '3.3', allowfail: false}
- {os: macOS-latest, r: '3.2', allowfail: false}
- {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '4.1', 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: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-20.04, r: '3.1', allowfail: false, 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: windows-latest, r: 'devel', allowfail: true}
- {os: windows-latest, r: '4.1', allowfail: false}
- {os: windows-latest, r: '4.0', allowfail: false}
- {os: windows-latest, r: '3.6', allowfail: false}
- {os: windows-latest, r: '3.5', allowfail: false}
- {os: windows-latest, r: '3.4', allowfail: false}
- {os: windows-latest, r: '3.3', allowfail: false}
- {os: windows-latest, r: '3.2', allowfail: false}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
RSPM: ${{ matrix.config.rspm }}
R_REPOSITORIES: "https://cran.rstudio.com"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
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
steps:
- uses: actions/checkout@v2
- uses: r-lib/actions/setup-pandoc@v1
- uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- uses: r-lib/actions/setup-r-dependencies@v1
with:
extra-packages: rcmdcheck
- name: Show session info
if: always()
run: |
options(width = 100)
utils::sessionInfo()
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- uses: r-lib/actions/check-r-package@v1
- name: Show unit tests output
if: always()
run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- name: Upload check results
if: always()
uses: actions/upload-artifact@main
with:
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
path: check