unit tests

.github/workflows/check-old.yaml

@@ -47,7 +47,9 @@ jobs:
       matrix:
         config:
           # Test all old versions of R >= 3.0, we support them all!
-          # For recent R versions, see check-recent.yaml (r-lib supports the latest 5 major R versions)
+          # For these old versions, dependencies will not be installed and checked.
+          # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R versions).
+          - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
@@ -67,26 +69,10 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install Linux dependencies
+      - name: Install tinytest
-        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,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 libxml2-dev libcurl4-openssl-dev
+          install.packages("tinytest")
-
+        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: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v5
-
-      - name: Install R dependencies
-        if: always()
-        run: |
-          Rscript -e "source('data-raw/_install_deps.R')"
-        shell: bash
 
       - name: Show session info
         if: always()
@@ -135,11 +121,3 @@ jobs:
           cd ../AMR.Rcheck
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload artifacts
-        if: always()
-        continue-on-error: true
-        uses: actions/upload-artifact@v3
-        with:
-          name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
-          path: ${{ github.workspace }}.Rcheck

.github/workflows/check-recent.yaml

@@ -66,8 +66,7 @@ jobs:
           - {os: ubuntu-latest, r: '4.1', allowfail: false}
           - {os: ubuntu-latest, r: '4.0', allowfail: false}
           - {os: ubuntu-latest, r: '3.6', allowfail: false}
-          - {os: ubuntu-latest, r: '3.5', allowfail: false}
+          - {os: ubuntu-latest, r: '3.5', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
-          - {os: ubuntu-latest, r: '3.4', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9082
+Version: 1.8.2.9083
 Date: 2023-01-06
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9082
+# AMR 1.8.2.9083
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 

data-raw/_install_deps.R

@@ -1,95 +0,0 @@
-# ==================================================================== #
-# TITLE                                                                #
-# AMR: An R Package for Working with Antimicrobial Resistance Data     #
-#                                                                      #
-# SOURCE                                                               #
-# https://github.com/msberends/AMR                                     #
-#                                                                      #
-# CITE 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.                 #
-# doi: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/   #
-# ==================================================================== #
-
-# some old R instances have trouble installing tinytest, so we ship it too
-install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
-install.packages(getwd(), repos = NULL, type = "source")
-
-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$OS.type != "unix") {
-  # no compiling on Windows here
-  options(install.packages.compile.from.source = FALSE)
-}
-
-to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
-if (length(to_install) == 0) {
-  message("\nNothing to install\n")
-}
-for (i in seq_len(length(to_install))) {
-  cat("Installing package", to_install[i], "\n")
-  tryCatch(install.packages(to_install[i],
-    type = "source",
-    repos = "https://cran.rstudio.com/",
-    dependencies = c("Depends", "Imports", "LinkingTo"),
-    quiet = FALSE
-  ),
-  # message = function(m) invisible(),
-  warning = function(w) message(w$message),
-  error = function(e) message(e$message)
-  )
-  if (.Platform$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 <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
-if (length(to_update) == 0) {
-  message("\nNothing to update\n")
-}
-for (i in seq_len(length(to_update))) {
-  cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
-  tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
-    # message = function(m) invisible(),
-    warning = function(w) message(w$message),
-    error = function(e) message(e$message)
-  )
-  cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
-}