From f203928f7ed4963cc964ae6cb01e7c4f37abb83b Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Wed, 19 Oct 2022 06:59:36 +0200
Subject: [PATCH] coercion fixes

---
 DESCRIPTION             | 4 ++--
 NEWS.md                 | 2 +-
 R/mo.R                  | 2 +-
 inst/tinytest/test-ab.R | 4 ++--
 inst/tinytest/test-mo.R | 2 +-
 5 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3b9a92a4..a8e4f70f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9020
-Date: 2022-10-18
+Version: 1.8.2.9021
+Date: 2022-10-19
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
     data analysis and to work with microbial and antimicrobial properties by
diff --git a/NEWS.md b/NEWS.md
index c55f1685..b870a4ff 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9020
+# AMR 1.8.2.9021
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
diff --git a/R/mo.R b/R/mo.R
index 96735673..7d7646d0 100755
--- a/R/mo.R
+++ b/R/mo.R
@@ -440,7 +440,7 @@ as.mo <- function(x,
 
   # All unknowns ----
   out[is.na(out) & !is.na(x)] <- "UNKNOWN"
-  AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & x != "UNKNOWN" & !is.na(x)])
+  AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !x %in% c("UNKNOWN", "con") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
   if (length(AMR_env$mo_failures) > 0) {
     warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.")
   }
diff --git a/inst/tinytest/test-ab.R b/inst/tinytest/test-ab.R
index e755012a..8181f8f2 100755
--- a/inst/tinytest/test-ab.R
+++ b/inst/tinytest/test-ab.R
@@ -51,7 +51,6 @@ expect_stdout(print(data.frame(a = as.ab("amox"))))
 
 expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
 expect_warning(as.ab("UNKNOWN"))
-expect_warning(as.ab(""))
 
 expect_stdout(print(as.ab("amox")))
 
@@ -75,7 +74,7 @@ expect_equal(
   c("MEM", "AMC")
 )
 
-expect_message(as.ab("cipro mero"))
+expect_warning(as.ab("cipro mero"))
 
 # based on Levenshtein distance
 expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
@@ -86,6 +85,7 @@ expect_inherits(x[1], "ab")
 expect_inherits(x[[1]], "ab")
 expect_inherits(c(x[1], x[9]), "ab")
 expect_inherits(unique(x[1], x[9]), "ab")
+expect_inherits(rep(x[1], x[9]), "ab")
 expect_warning(x[1] <- "invalid code")
 expect_warning(x[[1]] <- "invalid code")
 expect_warning(c(x[1], "test"))
diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R
index 1a76745c..4a3b2f1f 100644
--- a/inst/tinytest/test-mo.R
+++ b/inst/tinytest/test-mo.R
@@ -283,7 +283,7 @@ expect_equal(
 )
 
 # no viruses
-expect_equal(as.mo("Virus"), as.mo("UNKNOWN"))
+expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
 
 # summary
 expect_equal(length(summary(example_isolates$mo)), 6)