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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/ #
# ==================================================================== #
# 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