mirror of https://github.com/msberends/AMR.git
124 lines
5.3 KiB
YAML
124 lines
5.3 KiB
YAML
# ==================================================================== #
|
|
# 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, Sinha BNM, Albers CJ, Glasner C #
|
|
# (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
|