(v3.0.1.9130) Add workflow to check reverse dependencies against the development version on every push to main, list WT/NWT for ECOFFs as breaking change, and update cran-comments.md for v3.1.0

.github/scripts/check_revdeps.R

@@ -0,0 +1,87 @@
+# ==================================================================== #
+# 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, et al. (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://amr-for-r.org              #
+# ==================================================================== #
+
+# Run R CMD check on all CRAN packages that depend on AMR, against the INSTALLED development version of AMR.
+# Used by .github/workflows/check-revdeps.yaml; run from the root of the repository, after installing AMR from it:
+#   Rscript .github/scripts/check_revdeps.R
+# Fails if any reverse dependency returns an ERROR or WARNING.
+
+# only CRAN, also when other repositories are set, since this is about CRAN releases
+repos <- c(CRAN = "https://cloud.r-project.org")
+db <- utils::available.packages(repos = repos)
+revdeps <- sort(tools::package_dependencies("AMR", db = db, reverse = TRUE, which = "all")[["AMR"]])
+if (length(revdeps) == 0) {
+  message("No reverse dependencies on CRAN")
+  quit(status = 0)
+}
+message("Reverse dependencies: ", paste(revdeps, collapse = ", "))
+
+# all dependencies of the reverse dependencies, but never AMR itself, which is the development version installed from this repository
+deps <- unique(unlist(tools::package_dependencies(revdeps, db = db, which = "all"), use.names = FALSE))
+base_pkgs <- rownames(utils::installed.packages(priority = "base"))
+deps <- setdiff(deps, c("AMR", base_pkgs, rownames(utils::installed.packages())))
+if (length(deps) > 0) {
+  # pak also installs the system requirements of these packages
+  tryCatch(pak::pkg_install(deps, upgrade = FALSE), error = function(e) {
+    message("pak failed (", conditionMessage(e), "), falling back to install.packages()")
+    utils::install.packages(deps)
+  })
+}
+amr_version <- read.dcf("DESCRIPTION", fields = "Version")[1, 1]
+if (as.character(utils::packageVersion("AMR")) != amr_version) {
+  stop("installed AMR is v", utils::packageVersion("AMR"), ", expected the development version v", amr_version)
+}
+message("Checking against AMR v", amr_version)
+
+check_dir <- file.path(tempdir(), "revdeps")
+dir.create(check_dir, showWarnings = FALSE)
+tarballs <- utils::download.packages(revdeps, destdir = check_dir, repos = repos, type = "source")[, 2]
+
+results <- vapply(tarballs, FUN.VALUE = character(1), function(tarball) {
+  pkg <- sub("_.*", "", basename(tarball))
+  message("\n=== Checking ", pkg, " ===")
+  out <- suppressWarnings(system2(
+    file.path(R.home("bin"), "R"),
+    c("CMD", "check", "--no-manual", "--as-cran", "-o", shQuote(check_dir), shQuote(tarball)),
+    stdout = TRUE,
+    stderr = TRUE,
+    # skip the incoming checks for CRAN submission, which concern the maintainers of the reverse dependencies
+    env = c("_R_CHECK_FORCE_SUGGESTS_=false", "_R_CHECK_CRAN_INCOMING_=false")
+  ))
+  cat(out, sep = "\n")
+  status <- grep("^Status:", out, value = TRUE)
+  if (length(status) == 0) "ERROR (check did not finish)" else trimws(sub("^Status:", "", status[length(status)]))
+}, USE.NAMES = FALSE)
+names(results) <- revdeps
+
+message("\n=== Summary against AMR v", amr_version, " ===")
+message(paste0(format(names(results)), "  ", results, collapse = "\n"))
+if (any(grepl("ERROR|WARNING", results))) {
+  quit(status = 1)
+}