diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 07053e51..724f0d53 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -23,16 +23,14 @@
# 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
+ - development
+ - main
pull_request:
branches:
- - master
+ - main
schedule:
# run a schedule everyday at 1 AM.
# this is to check that all dependencies are still available (see R/zzz.R)
@@ -81,45 +79,35 @@ jobs:
- {os: windows-latest, r: '3.2', allowfail: false}
env:
- R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ 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: ${{ matrix.config.http-user-agent }}
+ use-public-rspm: true
- - name: Install Linux dependencies
- if: runner.os == 'Linux'
- # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
- # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
- # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11
- run: |
- sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev
-
- - name: Query dependencies
- # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates
- run: |
- writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$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
+ - uses: r-lib/actions/setup-r-dependencies@v1
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
-
+ extra-packages: rcmdcheck
+
- name: Show session info
if: always()
run: |
@@ -127,31 +115,17 @@ jobs:
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
+
+ - uses: r-lib/actions/check-r-package@v1
- name: Show unit tests output
if: always()
- run: |
- find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
+ run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- - name: Upload artifacts
+ - name: Upload check results
if: always()
- uses: actions/upload-artifact@v2
+ uses: actions/upload-artifact@main
with:
name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts
- path: AMR.Rcheck
+ path: check
diff --git a/.github/workflows/check.yaml.old b/.github/workflows/check.yaml.old
new file mode 100644
index 00000000..07053e51
--- /dev/null
+++ b/.github/workflows/check.yaml.old
@@ -0,0 +1,157 @@
+# ==================================================================== #
+# 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:
+ # 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
diff --git a/DESCRIPTION b/DESCRIPTION
index 759f8514..00695030 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.7.1.9040
+Version: 1.7.1.9041
Date: 2021-09-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 1a0568d4..30cbbd0b 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9040
+# `AMR` 1.7.1.9041
## Last updated: 29 September 2021
### Breaking changes
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index aa1d7515..fc4f27c6 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R
index 68882353..a49e2511 100644
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@@ -31,7 +31,10 @@ pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
unlist(strsplit(unlist(packageDescription("AMR",
fields = c("Suggests", "Enhances", "LinkingTo"))),
split = ", ?")))
+pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
+cat("################################################\n")
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
+cat("################################################\n")
if (.Platform$OS.type != "unix") {
# no compiling on Windows here
@@ -52,6 +55,16 @@ for (i in seq_len(length(to_install))) {
# message = function(m) invisible(),
warning = function(w) message(w$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)
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index d97b3ebb..0ff18c37 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -44,7 +44,7 @@
AMR (for R)
- 1.7.1.9040
+ 1.7.1.9041
diff --git a/docs/news/index.html b/docs/news/index.html
index 6c61d3a7..7aee29e5 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -92,7 +92,7 @@
AMR (for R)
- 1.7.1.9040
+ 1.7.1.9041
@@ -240,9 +240,9 @@
Source: NEWS.md
-
-
+
+
Last updated: 29 September 2021
diff --git a/git_premaster.sh b/git_development.sh
similarity index 93%
rename from git_premaster.sh
rename to git_development.sh
index 48b645a7..9f7bd22c 100755
--- a/git_premaster.sh
+++ b/git_development.sh
@@ -24,26 +24,26 @@
# ==================================================================== #
########################################################################
-# `git_premaster.sh` takes 3 parameters: #
+# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
-# To push new commits to the premaster branch, run: #
-# bash git_premaster.sh "commit message" #
+# To push new commits to the development branch, run: #
+# bash git_development.sh "commit message" #
# 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 #
# #
# 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: #
# 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
@@ -56,8 +56,8 @@ else
lazy=$2
fi
-# be sure to be on premaster branch
-git checkout premaster --quiet
+# be sure to be on development branch
+git checkout development --quiet
echo "••••••••••••••••••••••••••••••••••••••••••••"
echo "• Updating package date and version number •"
@@ -127,7 +127,7 @@ echo "••••••••••••••••••••"
echo "• Building package •"
echo "••••••••••••••••••••"
echo "• Building 'data-raw/AMR_latest.tar.gz'..."
-Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)"
+Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)"
rm data-raw/AMR_latest.tar.gz
mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz
@@ -193,7 +193,7 @@ git add .
git commit -a -m "(v${new_version}) $1" --quiet
git push --quiet
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 "•••••••••"
diff --git a/git_merge.sh b/git_merge.sh
index f0c04c46..340bf74a 100755
--- a/git_merge.sh
+++ b/git_merge.sh
@@ -24,44 +24,44 @@
# ==================================================================== #
########################################################################
-# `git_premaster.sh` takes 3 parameters: #
+# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
-# To push new commits to the premaster branch, run: #
-# bash git_premaster.sh "commit message" #
+# To push new commits to the development branch, run: #
+# bash git_development.sh "commit message" #
# 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 #
# #
# 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: #
# 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
# git stash --quiet
-# go to master
-git checkout master --quiet
-echo "• changed branch to master"
+# go to main
+git checkout main --quiet
+echo "• changed branch to main"
-# import everything from premaster
-git merge premaster --quiet
+# import everything from development
+git merge development --quiet
# and send it to git
git push --quiet
-echo "• pushed changes to master"
+echo "• pushed changes to main"
-# return to premaster
-git checkout premaster --quiet
-echo "• changed branch back to premaster"
+# return to development
+git checkout development --quiet
+echo "• changed branch back to development"
git status --short
echo
diff --git a/git_siteonly.sh b/git_siteonly.sh
index b060753f..c1dabab7 100755
--- a/git_siteonly.sh
+++ b/git_siteonly.sh
@@ -24,35 +24,35 @@
# ==================================================================== #
########################################################################
-# `git_premaster.sh` takes 3 parameters: #
+# `git_development.sh` takes 3 parameters: #
# 1. Commit message (character) [mandatory] #
# 2. Lazy website generation (logical), with TRUE only changed #
# files will be processed [defaults to TRUE] #
# 3. Version number to be used in DESCRIPTION and NEWS.md #
# [defaults to current tag and last commit number + 9000] #
# #
-# To push new commits to the premaster branch, run: #
-# bash git_premaster.sh "commit message" #
+# To push new commits to the development branch, run: #
+# bash git_development.sh "commit message" #
# 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 #
# #
# 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: #
# 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 "• Uploading to master branch •"
-echo "••••••••••••••••••••••••••••••"
-git checkout master
-git merge premaster
+echo "••••••••••••••••••••••••••••"
+echo "• Uploading to main branch •"
+echo "••••••••••••••••••••••••••••"
+git checkout main
+git merge development
git push --quiet
-git checkout premaster
+git checkout development