fix for R <= 3.3

.github/workflows/check.yaml

@@ -135,6 +135,7 @@ jobs:
           R_RUN_TINYTEST: true
         run: |
           cd ..
+          ls -lh
           R CMD build AMR
           R CMD check --no-manual --run-donttest --run-dontrun AMR_*.tar.gz
         shell: bash
@@ -142,6 +143,8 @@ jobs:
       - name: Show unit tests output
         if: always()
         run: |
+          ls -lh
+          cd AMR
           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
         shell: bash
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9039
+Version: 1.8.1.9040
 Date: 2022-08-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9039
+# AMR 1.8.1.9040
 
 ### New
 * EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.

R/aa_helper_functions.R

@@ -651,7 +651,7 @@ dataset_UTF8_to_ASCII <- function(df) {
       df[, i] <- col
     }
   }
-  tibble::as_tibble(df)
+  import_fn("as_tibble", "tibble")(df)
 }
 
 # for eucast_rules() and mdro(), creates markdown output with URLs and names

inst/tinytest/test-data.R

@@ -53,11 +53,13 @@ expect_false(any(is.na(as.disk(rsi_translation[which(rsi_translation$method == "
 # antibiotic names must always be coercible to their original AB code
 expect_identical(as.ab(antibiotics$name), antibiotics$ab)
 
-# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
-datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
-for (i in seq_len(length(datasets))) {
-  dataset <- get(datasets[i], envir = asNamespace("AMR"))
-  expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
+if (AMR:::pkg_is_available("tibble", also_load = FALSE)) {
+  # there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
+  datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
+  for (i in seq_len(length(datasets))) {
+    dataset <- get(datasets[i], envir = asNamespace("AMR"))
+    expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
+  }
 }
 
 df <- AMR:::MO_lookup