mirror of https://github.com/msberends/AMR.git
(v1.7.1.9041) new GH actions, branches rename
This commit is contained in:
parent
93a4734b44
commit
e8d3ce05d7
|
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@ -23,16 +23,14 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# ==================================================================== #
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# This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0.
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|
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on:
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on:
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push:
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push:
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branches:
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branches:
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- premaster
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- development
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- master
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- main
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pull_request:
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pull_request:
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branches:
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branches:
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- master
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- main
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||||||
schedule:
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schedule:
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# run a schedule everyday at 1 AM.
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# run a schedule everyday at 1 AM.
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||||||
# this is to check that all dependencies are still available (see R/zzz.R)
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# this is to check that all dependencies are still available (see R/zzz.R)
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@ -81,45 +79,35 @@ jobs:
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- {os: windows-latest, r: '3.2', allowfail: false}
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- {os: windows-latest, r: '3.2', allowfail: false}
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env:
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: false
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RSPM: ${{ matrix.config.rspm }}
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RSPM: ${{ matrix.config.rspm }}
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R_REPOSITORIES: "https://cran.rstudio.com"
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R_REPOSITORIES: "https://cran.rstudio.com"
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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R_CHECK_CRAN_INCOMING_: false
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R_CHECK_FORCE_SUGGESTS_: false
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R_CHECK_DEPENDS_ONLY_: true
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R_CHECK_LENGTH_1_CONDITION_: verbose
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R_CHECK_LENGTH_1_LOGIC2_: verbose
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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steps:
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v2
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- uses: r-lib/actions/setup-pandoc@v1
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- uses: r-lib/actions/setup-r@v1
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- uses: r-lib/actions/setup-r@v1
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with:
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with:
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r-version: ${{ matrix.config.r }}
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- name: Install Linux dependencies
|
- uses: r-lib/actions/setup-r-dependencies@v1
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if: runner.os == 'Linux'
|
|
||||||
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
|
|
||||||
# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
|
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# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
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run: |
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
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- name: Query dependencies
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# this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
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run: |
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writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
|
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with:
|
with:
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path: ${{ env.R_LIBS_USER }}
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extra-packages: rcmdcheck
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4
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- name: Unpack AMR and install R dependencies
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if: always()
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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- name: Show session info
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- name: Show session info
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if: always()
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if: always()
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run: |
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run: |
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@ -127,31 +115,17 @@ jobs:
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utils::sessionInfo()
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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shell: Rscript {0}
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|
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- name: Run R CMD check
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- uses: r-lib/actions/check-r-package@v1
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if: always()
|
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env:
|
|
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
|
|
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_R_CHECK_DEPENDS_ONLY_: true
|
|
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_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
|
|
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run: |
|
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R CMD check --no-manual --run-donttest --run-dontrun AMR
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shell: bash
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|
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|
|
||||||
- name: Show unit tests output
|
- name: Show unit tests output
|
||||||
if: always()
|
if: always()
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run: |
|
run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
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find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
|
|
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shell: bash
|
shell: bash
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|
|
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- name: Upload artifacts
|
- name: Upload check results
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if: always()
|
if: always()
|
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uses: actions/upload-artifact@v2
|
uses: actions/upload-artifact@main
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with:
|
with:
|
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name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
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name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
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path: AMR.Rcheck
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path: check
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@ -0,0 +1,157 @@
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|
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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|
# 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
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||||||
|
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: 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: 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: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
|
||||||
|
path: AMR.Rcheck
|
||||||
|
|
@ -1,5 +1,5 @@
|
||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 1.7.1.9040
|
Version: 1.7.1.9041
|
||||||
Date: 2021-09-29
|
Date: 2021-09-29
|
||||||
Title: Antimicrobial Resistance Data Analysis
|
Title: Antimicrobial Resistance Data Analysis
|
||||||
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
|
||||||
|
|
|
||||||
2
NEWS.md
2
NEWS.md
|
|
@ -1,4 +1,4 @@
|
||||||
# `AMR` 1.7.1.9040
|
# `AMR` 1.7.1.9041
|
||||||
## <small>Last updated: 29 September 2021</small>
|
## <small>Last updated: 29 September 2021</small>
|
||||||
|
|
||||||
### Breaking changes
|
### Breaking changes
|
||||||
|
|
|
||||||
Binary file not shown.
|
|
@ -31,7 +31,10 @@ pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
|
||||||
unlist(strsplit(unlist(packageDescription("AMR",
|
unlist(strsplit(unlist(packageDescription("AMR",
|
||||||
fields = c("Suggests", "Enhances", "LinkingTo"))),
|
fields = c("Suggests", "Enhances", "LinkingTo"))),
|
||||||
split = ", ?")))
|
split = ", ?")))
|
||||||
|
pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
|
||||||
|
cat("################################################\n")
|
||||||
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
|
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
|
||||||
|
cat("################################################\n")
|
||||||
|
|
||||||
if (.Platform$OS.type != "unix") {
|
if (.Platform$OS.type != "unix") {
|
||||||
# no compiling on Windows here
|
# no compiling on Windows here
|
||||||
|
|
@ -52,6 +55,16 @@ for (i in seq_len(length(to_install))) {
|
||||||
# message = function(m) invisible(),
|
# message = function(m) invisible(),
|
||||||
warning = function(w) message(w$message),
|
warning = function(w) message(w$message),
|
||||||
error = function(e) message(e$message))
|
error = function(e) message(e$message))
|
||||||
|
if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
|
||||||
|
tryCatch(install.packages(to_install[i],
|
||||||
|
type = "binary",
|
||||||
|
repos = "https://cran.rstudio.com/",
|
||||||
|
dependencies = c("Depends", "Imports", "LinkingTo"),
|
||||||
|
quiet = FALSE),
|
||||||
|
# message = function(m) invisible(),
|
||||||
|
warning = function(w) message(w$message),
|
||||||
|
error = function(e) message(e$message))
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
|
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
|
||||||
|
|
|
||||||
|
|
@ -44,7 +44,7 @@
|
||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -92,7 +92,7 @@
|
||||||
</button>
|
</button>
|
||||||
<span class="navbar-brand">
|
<span class="navbar-brand">
|
||||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span>
|
||||||
</span>
|
</span>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
|
|
@ -240,9 +240,9 @@
|
||||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div id="amr-1719040" class="section level1">
|
<div id="amr-1719041" class="section level1">
|
||||||
<h1 class="page-header" data-toc-text="1.7.1.9040">
|
<h1 class="page-header" data-toc-text="1.7.1.9041">
|
||||||
<a href="#amr-1719040" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9040</h1>
|
<a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1>
|
||||||
<div id="last-updated-29-september-2021" class="section level2">
|
<div id="last-updated-29-september-2021" class="section level2">
|
||||||
<h2 class="hasAnchor">
|
<h2 class="hasAnchor">
|
||||||
<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>
|
<a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small>
|
||||||
|
|
|
||||||
|
|
@ -24,26 +24,26 @@
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
########################################################################
|
########################################################################
|
||||||
# `git_premaster.sh` takes 3 parameters: #
|
# `git_development.sh` takes 3 parameters: #
|
||||||
# 1. Commit message (character) [mandatory] #
|
# 1. Commit message (character) [mandatory] #
|
||||||
# 2. Lazy website generation (logical), with TRUE only changed #
|
# 2. Lazy website generation (logical), with TRUE only changed #
|
||||||
# files will be processed [defaults to TRUE] #
|
# files will be processed [defaults to TRUE] #
|
||||||
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
||||||
# [defaults to current tag and last commit number + 9000] #
|
# [defaults to current tag and last commit number + 9000] #
|
||||||
# #
|
# #
|
||||||
# To push new commits to the premaster branch, run: #
|
# To push new commits to the development branch, run: #
|
||||||
# bash git_premaster.sh "commit message" #
|
# bash git_development.sh "commit message" #
|
||||||
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
||||||
# #
|
# #
|
||||||
# After successful test checks, merge it to the master branch with: #
|
# After successful test checks, merge it to the main branch with: #
|
||||||
# bash git_merge.sh #
|
# bash git_merge.sh #
|
||||||
# #
|
# #
|
||||||
# To prerelease a new version number, run: #
|
# To prerelease a new version number, run: #
|
||||||
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
|
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
|
||||||
# #
|
# #
|
||||||
# To only update the website, run: #
|
# To only update the website, run: #
|
||||||
# bash git_siteonly.sh #
|
# bash git_siteonly.sh #
|
||||||
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
|
# (which is short for 'bash git_development.sh "website update" FALSE')#
|
||||||
########################################################################
|
########################################################################
|
||||||
|
|
||||||
if [ -z "$1" ]; then
|
if [ -z "$1" ]; then
|
||||||
|
|
@ -56,8 +56,8 @@ else
|
||||||
lazy=$2
|
lazy=$2
|
||||||
fi
|
fi
|
||||||
|
|
||||||
# be sure to be on premaster branch
|
# be sure to be on development branch
|
||||||
git checkout premaster --quiet
|
git checkout development --quiet
|
||||||
|
|
||||||
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
echo "••••••••••••••••••••••••••••••••••••••••••••"
|
||||||
echo "• Updating package date and version number •"
|
echo "• Updating package date and version number •"
|
||||||
|
|
@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
|
||||||
echo "• Building package •"
|
echo "• Building package •"
|
||||||
echo "••••••••••••••••••••"
|
echo "••••••••••••••••••••"
|
||||||
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
|
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
|
||||||
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
|
Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
|
||||||
rm data-raw/AMR_latest.tar.gz
|
rm data-raw/AMR_latest.tar.gz
|
||||||
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
|
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
|
||||||
|
|
||||||
|
|
@ -193,7 +193,7 @@ git add .
|
||||||
git commit -a -m "(v${new_version}) $1" --quiet
|
git commit -a -m "(v${new_version}) $1" --quiet
|
||||||
git push --quiet
|
git push --quiet
|
||||||
echo "Comparison:"
|
echo "Comparison:"
|
||||||
echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline"
|
echo "https://github.com/msberends/AMR/compare/main...development?view=inline"
|
||||||
|
|
||||||
echo
|
echo
|
||||||
echo "•••••••••"
|
echo "•••••••••"
|
||||||
30
git_merge.sh
30
git_merge.sh
|
|
@ -24,44 +24,44 @@
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
########################################################################
|
########################################################################
|
||||||
# `git_premaster.sh` takes 3 parameters: #
|
# `git_development.sh` takes 3 parameters: #
|
||||||
# 1. Commit message (character) [mandatory] #
|
# 1. Commit message (character) [mandatory] #
|
||||||
# 2. Lazy website generation (logical), with TRUE only changed #
|
# 2. Lazy website generation (logical), with TRUE only changed #
|
||||||
# files will be processed [defaults to TRUE] #
|
# files will be processed [defaults to TRUE] #
|
||||||
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
||||||
# [defaults to current tag and last commit number + 9000] #
|
# [defaults to current tag and last commit number + 9000] #
|
||||||
# #
|
# #
|
||||||
# To push new commits to the premaster branch, run: #
|
# To push new commits to the development branch, run: #
|
||||||
# bash git_premaster.sh "commit message" #
|
# bash git_development.sh "commit message" #
|
||||||
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
||||||
# #
|
# #
|
||||||
# After successful test checks, merge it to the master branch with: #
|
# After successful test checks, merge it to the main branch with: #
|
||||||
# bash git_merge.sh #
|
# bash git_merge.sh #
|
||||||
# #
|
# #
|
||||||
# To prerelease a new version number, run: #
|
# To prerelease a new version number, run: #
|
||||||
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
|
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
|
||||||
# #
|
# #
|
||||||
# To only update the website, run: #
|
# To only update the website, run: #
|
||||||
# bash git_siteonly.sh #
|
# bash git_siteonly.sh #
|
||||||
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
|
# (which is short for 'bash git_development.sh "website update" FALSE')#
|
||||||
########################################################################
|
########################################################################
|
||||||
|
|
||||||
# stash current changes
|
# stash current changes
|
||||||
# git stash --quiet
|
# git stash --quiet
|
||||||
|
|
||||||
# go to master
|
# go to main
|
||||||
git checkout master --quiet
|
git checkout main --quiet
|
||||||
echo "• changed branch to master"
|
echo "• changed branch to main"
|
||||||
|
|
||||||
# import everything from premaster
|
# import everything from development
|
||||||
git merge premaster --quiet
|
git merge development --quiet
|
||||||
# and send it to git
|
# and send it to git
|
||||||
git push --quiet
|
git push --quiet
|
||||||
echo "• pushed changes to master"
|
echo "• pushed changes to main"
|
||||||
|
|
||||||
# return to premaster
|
# return to development
|
||||||
git checkout premaster --quiet
|
git checkout development --quiet
|
||||||
echo "• changed branch back to premaster"
|
echo "• changed branch back to development"
|
||||||
git status --short
|
git status --short
|
||||||
echo
|
echo
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -24,35 +24,35 @@
|
||||||
# ==================================================================== #
|
# ==================================================================== #
|
||||||
|
|
||||||
########################################################################
|
########################################################################
|
||||||
# `git_premaster.sh` takes 3 parameters: #
|
# `git_development.sh` takes 3 parameters: #
|
||||||
# 1. Commit message (character) [mandatory] #
|
# 1. Commit message (character) [mandatory] #
|
||||||
# 2. Lazy website generation (logical), with TRUE only changed #
|
# 2. Lazy website generation (logical), with TRUE only changed #
|
||||||
# files will be processed [defaults to TRUE] #
|
# files will be processed [defaults to TRUE] #
|
||||||
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
# 3. Version number to be used in DESCRIPTION and NEWS.md #
|
||||||
# [defaults to current tag and last commit number + 9000] #
|
# [defaults to current tag and last commit number + 9000] #
|
||||||
# #
|
# #
|
||||||
# To push new commits to the premaster branch, run: #
|
# To push new commits to the development branch, run: #
|
||||||
# bash git_premaster.sh "commit message" #
|
# bash git_development.sh "commit message" #
|
||||||
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
# This creates auto version numbering in DESCRIPTION and NEWS.md. #
|
||||||
# #
|
# #
|
||||||
# After successful test checks, merge it to the master branch with: #
|
# After successful test checks, merge it to the main branch with: #
|
||||||
# bash git_merge.sh #
|
# bash git_merge.sh #
|
||||||
# #
|
# #
|
||||||
# To prerelease a new version number, run: #
|
# To prerelease a new version number, run: #
|
||||||
# bash git_premaster.sh "v1.x.x" FALSE "1.x.x" #
|
# bash git_development.sh "v1.x.x" FALSE "1.x.x" #
|
||||||
# #
|
# #
|
||||||
# To only update the website, run: #
|
# To only update the website, run: #
|
||||||
# bash git_siteonly.sh #
|
# bash git_siteonly.sh #
|
||||||
# (which is short for 'bash git_premaster.sh "website update" FALSE') #
|
# (which is short for 'bash git_development.sh "website update" FALSE')#
|
||||||
########################################################################
|
########################################################################
|
||||||
|
|
||||||
bash git_premaster.sh "website update" FALSE
|
bash git_development.sh "website update" FALSE
|
||||||
|
|
||||||
echo
|
echo
|
||||||
echo "••••••••••••••••••••••••••••••"
|
echo "••••••••••••••••••••••••••••"
|
||||||
echo "• Uploading to master branch •"
|
echo "• Uploading to main branch •"
|
||||||
echo "••••••••••••••••••••••••••••••"
|
echo "••••••••••••••••••••••••••••"
|
||||||
git checkout master
|
git checkout main
|
||||||
git merge premaster
|
git merge development
|
||||||
git push --quiet
|
git push --quiet
|
||||||
git checkout premaster
|
git checkout development
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue