(v3.0.1.9114) Fix errors without cli and on R 3.0, and make the tinytest pipeline actually run the unit tests

Package:
- stop_() called cli::ansi_has_hyperlink_support() before checking that cli is available, so without cli every error became "there is no package called 'cli'"
- interpretive_rules() failed on R 3.0 for guidelines without AmpC rules (assignment to zero rows)
- Guard the ggplot2 example of wisca_plot()

CI:
- check-old: R 3.0 could not install tinytest over HTTPS, so no unit tests ran; install it with curl, and fail when tinytest is missing or any test fails
- tinytest shim: record expectations in the test file environment, support skips and errors per test_that() block, add missing testthat equivalents, source helper files
- Add R 4.0 (oldrel-6) to check-old, and oldrel-5 to check-recent

.github/workflows/check-current-testthat.yaml

@@ -53,7 +53,7 @@ jobs:
           if [ "${{ github.event_name }}" = "pull_request" ]; then
             echo 'matrix={"config":[{"os":"ubuntu-latest","r":"release","allowfail":false}]}' >> "$GITHUB_OUTPUT"
           else
-            echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false}]}' >> "$GITHUB_OUTPUT"
+            echo 'matrix={"config":[{"os":"windows-latest","r":"devel","allowfail":false},{"os":"ubuntu-latest","r":"devel","allowfail":false,"http-user-agent":"release"},{"os":"macOS-latest","r":"release","allowfail":true},{"os":"windows-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"release","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-1","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-2","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-3","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-4","allowfail":false},{"os":"ubuntu-latest","r":"oldrel-5","allowfail":false}]}' >> "$GITHUB_OUTPUT"
           fi
 
   R-code-check:

.github/workflows/check-old-tinytest.yaml

@@ -48,7 +48,9 @@ jobs:
         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).
+          # For recent R versions, see check-current-testthat.yaml (r-lib and tidyverse support the latest 5 major R releases).
+          # R 4.0 (oldrel-6) is tested here, since current testthat and its dependencies cannot be installed on it.
+          - {os: ubuntu-latest, r: '4.0', allowfail: false}
           # - {os: ubuntu-latest, r: '3.6', allowfail: false}
           # - {os: windows-latest, r: '3.5', allowfail: false} # always fails, horrible with UTF-8
           # - {os: ubuntu-latest, r: '3.4', allowfail: false}  # 3.1-3.4 now always fails with Error in grep(warn_re, lines, invert = TRUE, value = TRUE) attempt to set index 46/46 in SET_STRING_ELT
@@ -76,15 +78,17 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install suggested pkgs (and tinytest) from CRAN
+      - name: Install tinytest from CRAN
+        # R < 3.2 cannot download over HTTPS, so install.packages() fails silently on CRAN;
+        # download the source with curl instead (suggested packages require much newer R versions anyway)
         run: |
-          desc_lines <- readLines('DESCRIPTION')
-          suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:|  )", readLines('DESCRIPTION'))]
-          suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
-          suggests <- gsub("[ ,]", "", suggests)
-          pkgs <- unique(c(suggests, "tinytest"))
-          for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
-        shell: Rscript {0}
+          set -euo pipefail
+          mkdir -p "$R_LIBS_USER"
+          pkg=$(curl -sSL https://cran.r-project.org/src/contrib/ | grep -oE 'tinytest_[0-9.-]+\.tar\.gz' | head -1)
+          curl -sSLo "/tmp/$pkg" "https://cran.r-project.org/src/contrib/$pkg"
+          R CMD INSTALL -l "$R_LIBS_USER" "/tmp/$pkg"
+          Rscript -e "library(tinytest, lib.loc = Sys.getenv('R_LIBS_USER'))"
+        shell: bash
 
       - name: Show session info
         if: always()

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9113
+Version: 3.0.1.9114
 Date: 2026-10-10
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9113
+# AMR 3.0.1.9114
 
 Planned as v3.1.0, mid October 2026.
 

R/aa_helper_functions.R

@@ -650,10 +650,10 @@ stop_ <- function(...,
   }
   # prevent errors with single opening curly brackets, we don't evaluate cli's/glue's {} in AMR anyway
   msg <- gsub("\\{(?!\\.)", "", msg, perl = TRUE)
-  if (!cli::ansi_has_hyperlink_support()) {
-    msg <- simplify_help_markup(msg)
-  }
   if (has_cli_rlang()) {
+    if (!cli::ansi_has_hyperlink_support()) {
+      msg <- simplify_help_markup(msg)
+    }
     if (isTRUE(call)) {
       call_obj <- sys.call(-1)
     } else if (!isFALSE(call)) {

R/antibiogram.R

@@ -214,7 +214,9 @@
 #'   syndromic_group = "ward"
 #' )
 #' out
-#' wisca_plot(out)
+#' if (requireNamespace("ggplot2")) {
+#'   wisca_plot(out)
+#' }
 #'
 #' # stratified using grouped tibbles (e.g. by age and gender)
 #' if (requireNamespace("dplyr")) {

R/interpretive_rules.R

@@ -663,8 +663,10 @@ interpretive_rules <- function(x,
     if (isTRUE(ampc_cephalosporin_resistance)) {
       ampc_cephalosporin_resistance <- "R"
     }
-    if (!is.null(interpretive_rules_df$reference.rule)) {
-      interpretive_rules_df[which(interpretive_rules_df$reference.rule %like% "ampc"), "to_value"] <- as.character(ampc_cephalosporin_resistance)
+    # old R versions (at least 3.0) give an error when assigning to no rows of a data.frame without rows
+    ampc_rows <- if (is.null(interpretive_rules_df$reference.rule)) integer(0) else which(interpretive_rules_df$reference.rule %like% "ampc")
+    if (length(ampc_rows) > 0) {
+      interpretive_rules_df[ampc_rows, "to_value"] <- as.character(ampc_cephalosporin_resistance)
     }
   }
 

man/antibiogram.Rd

@@ -313,7 +313,9 @@ out <- wisca(example_isolates,
   syndromic_group = "ward"
 )
 out
-wisca_plot(out)
+if (requireNamespace("ggplot2")) {
+  wisca_plot(out)
+}
 
 # stratified using grouped tibbles (e.g. by age and gender)
 if (requireNamespace("dplyr")) {

tests/testthat/helper-microorganisms.R

@@ -98,7 +98,7 @@ mo_repository_root <- function() {
   NULL
 }
 skip_if_no_mo_repository <- function() {
-  testthat::skip_if(is.null(mo_repository_root()), "Source repository not available (data-raw/ does not ship with the package)")
+  skip_if(is.null(mo_repository_root()), "Source repository not available (data-raw/ does not ship with the package)")
 }
 
 # names without a rank suffix, e.g. "Kapabacteria {class}" and "Nitrospira (class)" are both the class

tests/testthat/test-_deprecated.R

@@ -37,7 +37,7 @@ test_that("test-_deprecated.R", {
     # deprecated custom_interpretive_rules() still works and emits a warning
     expect_warning(
       x_old <- custom_eucast_rules(AMC == "R" ~ aminopenicillins == "R"),
-      regexp = "custom_eucast_rules"
+      "custom_eucast_rules"
     )
     expect_inherits(x_old, "custom_interpretive_rules")
   }

tests/testthat/test-_misc.R

@@ -62,8 +62,10 @@ test_that("test-misc.R", {
   check_df <- function(check_element, return_val = 0) {
     is_right <<- FALSE
     for (env in sys.frames()) {
-      if (!is.null(env[[check_element]]) && is.data.frame(env[[check_element]])) {
-        is_right <<- all(colnames(example_isolates) %in% colnames(env[[check_element]]))
+      # in R < 4.2, reading a promise that is still being evaluated (such as `x` in tibble's `[`) gives an error
+      val <- tryCatch(env[[check_element]], error = function(e) NULL)
+      if (!is.null(val) && is.data.frame(val)) {
+        is_right <<- all(colnames(example_isolates) %in% colnames(val))
       }
     }
     return_val

tests/testthat/test-interpretive_rules.R

@@ -242,9 +242,10 @@ test_that("test-interpretive_rules.R", {
     tolerance = 0.5
   )
 
-  # clsi_rules() no longer errors (returns data unchanged until CLSI rows are added)
+  # clsi_rules() no longer errors (returns data unchanged until CLSI rows are added);
+  # without the tibble package, a plain data.frame is returned
   expect_identical(
     suppressWarnings(clsi_rules(example_isolates, info = FALSE)),
-    example_isolates
+    if (AMR:::pkg_is_available("tibble")) example_isolates else as.data.frame(example_isolates, stringsAsFactors = FALSE)
   )
 })

tests/tinytest.R.old

@@ -34,16 +34,30 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
   # env var 'R_LIBS_USER' gets overwritten during 'R CMD check' in GitHub Actions, so:
   .libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
   
-  if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
+  if (!AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
+    stop("R_RUN_TINYTEST is 'true', but the tinytest package could not be loaded, so no unit tests were run")
+  } else {
     
     # load the package
     library(AMR)
     
+    # testthat equivalents; tinytest only records expectations that are called from the environment
+    # of a test file, so these call the expectations found there (via `env`) instead of tinytest::
     test_that <- function(desc, code) {
-      code
+      env <- parent.frame()
+      tryCatch(code,
+        skip_test = function(s) invisible(NULL),
+        error = function(e) get("expect_true", envir = env)(FALSE, info = paste0("Error in '", desc, "': ", conditionMessage(e)))
+      )
+    }
+    skip_if <- function(condition, message = "") {
+      if (isTRUE(condition)) stop(structure(class = c("skip_test", "condition"), list(message = message, call = NULL)))
     }
-    expect_output <- tinytest::expect_stdout
     skip_on_cran <- function() invisible(NULL)
+    expect_output <- function(...) get("expect_stdout", envir = parent.frame())(...)
+    expect_named <- function(object, expected, ...) get("expect_identical", envir = parent.frame())(names(object), expected, ...)
+    expect_setequal <- function(object, expected, ...) get("expect_true", envir = parent.frame())(setequal(object, expected), ...)
+    expect_lte <- function(object, expected, ...) get("expect_true", envir = parent.frame())(isTRUE(all(object <= expected)), ...)
     
     # set language
     set_AMR_locale("English")
@@ -75,17 +89,26 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
       `%||%` <- AMR:::`%||%`
     }
 
+    testdir <- ifelse(dir.exists("inst/testthat"), "inst/testthat", "testthat")
+    # helper files are sourced by testthat, but not by tinytest; helper-functions.R only contains expect_inherits(), which tinytest has itself
+    helpers <- list.files(system.file(testdir, package = "AMR"), pattern = "^helper.*[.]R$", full.names = TRUE)
+    for (helper in helpers[basename(helpers) != "helper-functions.R"]) {
+      source(helper)
+    }
+
     suppressMessages(
       out <- test_package("AMR",
-                          testdir = ifelse(dir.exists("inst/testthat"),
-                                           "inst/testthat",
-                                           "testthat"
-                          ),
+                          testdir = testdir,
                           verbose = FALSE,
                           color = FALSE
       )
     )
     cat("\n\nSUMMARY:\n")
     print(summary(out))
+    if (!all_pass(out)) {
+      cat("\n\nFAILURES:\n")
+      print(out, passes = FALSE, limit = 100)
+      stop("Unit tests failed, see above")
+    }
   }
 }