From 3a5e20c11a8d75b033d4a44260baba1f3324b4ab Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Fri, 23 Sep 2022 16:40:17 +0200
Subject: [PATCH] fixes

---
 DESCRIPTION                      |  2 +-
 NEWS.md                          |  2 +-
 R/aa_helper_functions.R          |  2 +-
 inst/tinytest/test-mo_property.R | 11 ++++++-----
 tests/tinytest.R                 |  2 +-
 5 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1f530136..f25023b4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9066
+Version: 1.8.1.9067
 Date: 2022-09-23
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 554b4ea4..878c2b02 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.1.9066
+# AMR 1.8.1.9067
 
 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 d18f2093..e3ea4501 100755
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -1466,7 +1466,7 @@ if (getRversion() < "3.3.0") {
   }
 }
 
-if (getRversion() < "3.4.2") {
+if (getRversion() < "3.5.0") {
   isFALSE <- function(x) {
     is.logical(x) && length(x) == 1L && !is.na(x) && !x
   }
diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R
index b5118733..438bea66 100644
--- a/inst/tinytest/test-mo_property.R
+++ b/inst/tinytest/test-mo_property.R
@@ -25,7 +25,7 @@
 
 expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
 expect_equal(mo_kingdom("Escherichia coli"), mo_domain("Escherichia coli"))
-expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
+expect_equal(mo_phylum("Escherichia coli"), "Pseudomonadota")
 expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
 expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
 expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
@@ -64,7 +64,7 @@ expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
 expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
 expect_equal(mo_year("Escherichia coli"), 1919)
 
-expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
+expect_true(mo_url("Candida albicans") %like% "gbif.org")
 expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
 
 # test integrity
@@ -84,11 +84,12 @@ expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
 expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
 
 expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
-dutch <- mo_name(microorganisms$fullname, language = "nl") # should be transformable to English again
-expect_identical(mo_name(dutch, language = NULL), microorganisms$fullname) # gigantic test - will run ALL names
+dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase")], language = "nl") # should be transformable to English again
+expect_identical(mo_name(dutch, language = NULL),
+                 microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase")]) # gigantic test - will run ALL names
 
 # manual property function
-expect_error(mo_property("Escherichia coli", property = c("tsn", "fullname")))
+expect_error(mo_property("Escherichia coli", property = c("genus", "fullname")))
 expect_error(mo_property("Escherichia coli", property = "UNKNOWN"))
 expect_identical(
   mo_property("Escherichia coli", property = "fullname"),
diff --git a/tests/tinytest.R b/tests/tinytest.R
index ac9fd997..8e5ae6d1 100644
--- a/tests/tinytest.R
+++ b/tests/tinytest.R
@@ -49,7 +49,7 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
       strrep <- AMR:::strrep
       trimws <- AMR:::trimws
     }
-    if (getRversion() < "3.4.2") {
+    if (getRversion() < "3.5.0") {
       isFALSE <- AMR:::isFALSE
     }
     if (getRversion() < "3.6.0") {