From 835cf7c32d978e3791589254339cf08552a33136 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Sun, 18 Sep 2022 14:00:29 +0200
Subject: [PATCH] fixes

---
 DESCRIPTION                       |  2 +-
 NEWS.md                           |  2 +-
 R/aa_helper_functions.R           |  4 ----
 inst/tinytest/test-_misc.R        | 11 ++++++-----
 inst/tinytest/test-eucast_rules.R |  2 +-
 tests/tinytest.R                  |  9 +++++++++
 6 files changed, 18 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 582660a77..7cc70be3c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9052
+Version: 1.8.1.9055
 Date: 2022-09-18
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 3b92a2851..8ae49a755 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.1.9052
+# AMR 1.8.1.9055
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 7aed7d40a..96753438e 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -1489,8 +1489,4 @@ if (getRversion() < "4.0.0") {
   }
 }
 
-# for tinytest unit tests, that call AMR:::xxx():
-strrep <- strrep
-
-
 # nolint end
diff --git a/inst/tinytest/test-_misc.R b/inst/tinytest/test-_misc.R
index ff5115893..03e1b85e1 100755
--- a/inst/tinytest/test-_misc.R
+++ b/inst/tinytest/test-_misc.R
@@ -31,11 +31,12 @@ expect_equal(AMR:::percentage(0.1234), "12.3%")
 expect_equal(AMR:::percentage(0.0054), "0.5%")
 expect_equal(AMR:::percentage(0.0055), "0.6%")
 
-expect_equal(AMR:::strrep("A", 5), "AAAAA")
-expect_equal(AMR:::strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
-expect_equal(AMR:::trimws(" test "), "test")
-expect_equal(AMR:::trimws(" test ", "l"), "test ")
-expect_equal(AMR:::trimws(" test ", "r"), " test")
+# test functions on all R versions -  R < 3.3 did not contain these
+expect_equal(strrep("A", 5), "AAAAA")
+expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
+expect_equal(trimws(" test "), "test")
+expect_equal(trimws(" test ", "l"), "test ")
+expect_equal(trimws(" test ", "r"), " test")
 
 expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX")))
 expect_warning(AMR:::generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
diff --git a/inst/tinytest/test-eucast_rules.R b/inst/tinytest/test-eucast_rules.R
index 36692152b..a0c4de339 100755
--- a/inst/tinytest/test-eucast_rules.R
+++ b/inst/tinytest/test-eucast_rules.R
@@ -36,7 +36,7 @@ expect_equal(
   )
 )
 MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
-MOs_mentioned <- sort(AMR:::trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
+MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))
 MOs_test <- suppressWarnings(suppressMessages(mo_name(MOs_mentioned)))
 expect_true(length(MOs_mentioned[MOs_test != MOs_mentioned]) == 0)
 
diff --git a/tests/tinytest.R b/tests/tinytest.R
index fed6c0e18..27c122a96 100644
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@@ -23,13 +23,22 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #
 
+# we use {tinytest} instead of {testthat} because it does not rely on recent R versions - we want to test on R >= 3.0.
+
 # test only on GitHub Actions and at home - not on CRAN as tests are lengthy
 if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
   # env var 'R_LIBS_USER' got 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)) {
     library(AMR)
+    # set language
     set_AMR_locale("English")
+    # get trimws() and strrep() if on old R
+    if (getRversion() < "3.3.0") {
+      trimws <- AMR:::trimws
+      strrep <- AMR:::strrep
+    }
+    # start the unit tests
     out <- test_package("AMR",
       testdir = ifelse(dir.exists("inst/tinytest"),
         "inst/tinytest",