(v0.8.0.9005) fix unit tests

R/globals.R

@@ -52,6 +52,7 @@ globalVariables(c(".",
                   "Last name",
                   "lookup",
                   "mdr",
+                  "MDRO",
                   "median",
                   "microorganisms",
                   "microorganisms.codes",

R/mdro.R

@@ -461,7 +461,7 @@ mdro <- function(x,
     left_join_microorganisms(by = col_mo) %>%
     # add unconfirmed to where genus is available
     mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_),
-           row_number = 1:nrow(x)) %>% 
+           row_number = seq_len(nrow(x))) %>% 
     # transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...)
     as.data.frame(stringsAsFactors = FALSE)
   

R/mo.R

@@ -241,7 +241,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
       pull(mo)
     
     # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
-    # set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history))
     
   } else {
     # will be checked for mo class in validation and uses exec_as.mo internally if necessary
@@ -636,7 +635,6 @@ exec_as.mo <- function(x,
         x[i] <- found[1L]
         if (initial_search == TRUE) {
           # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname)
-          # set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
         }
         next
       }