From e5e6d2200d475a3202d18c9d10bfb329a75b0126 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <berendsms@gmail.com>
Date: Tue, 18 Oct 2022 22:53:38 +0200
Subject: [PATCH] fix add manual ab

---
 .github/workflows/check-devel.yaml   |  4 ++++
 .github/workflows/check-release.yaml |  2 +-
 DESCRIPTION                          |  4 ++--
 NEWS.md                              |  2 +-
 R/add_custom_antimicrobials.R        | 10 ++++++++--
 inst/tinytest/test-zzz.R             |  4 +++-
 6 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/check-devel.yaml b/.github/workflows/check-devel.yaml
index d878223c..994c511b 100644
--- a/.github/workflows/check-devel.yaml
+++ b/.github/workflows/check-devel.yaml
@@ -33,6 +33,10 @@ on:
     branches: '**'
   push:
     branches: '**'
+  schedule:
+    # run a schedule everyday at 1 AM.
+    # this is to check that all dependencies are still available (see R/zzz.R)
+    cron:  '0 1 * * *'
 
 name: check-devel
 
diff --git a/.github/workflows/check-release.yaml b/.github/workflows/check-release.yaml
index e004ffb3..43a68f7a 100644
--- a/.github/workflows/check-release.yaml
+++ b/.github/workflows/check-release.yaml
@@ -34,7 +34,7 @@ on:
   schedule:
     # run a schedule everyday at 1 AM.
     # this is to check that all dependencies are still available (see R/zzz.R)
-    - cron:  '0 1 * * *'
+    cron:  '0 1 * * *'
 
 name: check-release
 
diff --git a/DESCRIPTION b/DESCRIPTION
index 825704e8..22908e7f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.8.2.9018
-Date: 2022-10-15
+Version: 1.8.2.9019
+Date: 2022-10-18
 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 b09db9ba..33bebca7 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9018
+# AMR 1.8.2.9019
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 
diff --git a/R/add_custom_antimicrobials.R b/R/add_custom_antimicrobials.R
index db9f2145..2a915d11 100644
--- a/R/add_custom_antimicrobials.R
+++ b/R/add_custom_antimicrobials.R
@@ -112,13 +112,19 @@ add_custom_antimicrobials <- function(x) {
   AMR_env$custom_ab_codes <- c(AMR_env$custom_ab_codes, x$ab)
   class(AMR_env$AB_lookup$ab) <- "character"
 
-  bind_rows <- import_fn("bind_rowtts", "dplyr", error_on_fail = FALSE)
+  bind_rows <- import_fn("bind_rows", "dplyr", error_on_fail = FALSE)
   if (is.null(bind_rows)) {
     # do the binding in base R
     new_df <- AMR_env$AB_lookup[0, , drop = FALSE][seq_len(NROW(x)), , drop = FALSE]
     rownames(new_df) <- NULL
+    list_cols <- vapply(FUN.VALUE = logical(1), new_df, is.list)
+    for (l in which(list_cols)) {
+      # prevent binding NULLs in lists, replace with NA
+      new_df[, l] <- as.list(NA_character_)
+    }
     for (col in colnames(x)) {
-      new_df[, col] <- x[, col, drop = TRUE]
+      # assign new values
+      new_df[, col] <-  x[, col, drop = TRUE]
     }
     AMR_env$AB_lookup <- unique(rbind(AMR_env$AB_lookup, new_df))
   } else {
diff --git a/inst/tinytest/test-zzz.R b/inst/tinytest/test-zzz.R
index 47d5490c..6d98315e 100644
--- a/inst/tinytest/test-zzz.R
+++ b/inst/tinytest/test-zzz.R
@@ -34,6 +34,7 @@
 import_functions <- c(
   "%chin%" = "data.table",
   "anti_join" = "dplyr",
+  "bind_rows" = "dplyr",
   "chmatch" = "data.table",
   "cur_column" = "dplyr",
   "full_join" = "dplyr",
@@ -54,8 +55,8 @@ import_functions <- c(
   "semi_join" = "dplyr",
   "showQuestion" = "rstudioapi"
 )
-# functions that are called directly
 
+# functions that are called directly with ::
 call_functions <- c(
   # cleaner
   "freq.default" = "cleaner",
@@ -104,6 +105,7 @@ extended_functions <- c(
   "get_skimmers" = "skimr",
   "type_sum" = "tibble",
   "vec_cast" = "vctrs",
+  "vec_math" = "vctrs",
   "vec_ptype2" = "vctrs"
 )