(v0.7.1.9079) small fixes

R/freq.R

@@ -29,6 +29,7 @@ clean::freq
 #' @export
 #' @noRd
 freq.mo <- function(x, ...) {
+  x <- as.mo(x) # to get the newest mo codes
   x_noNA <- x[!is.na(x)]
   grams <- mo_gramstain(x_noNA, language = NULL)
   freq.default(x = x, ...,

R/globals.R

@@ -46,6 +46,7 @@ globalVariables(c(".",
                   "key_ab_lag",
                   "key_ab_other",
                   "kingdom",
+                  "kingdom_index",
                   "lang",
                   "Last name",
                   "lookup",

R/mo.R

@@ -1721,7 +1721,7 @@ exec_as.mo <- function(x,
     print(mo_renamed())
   }
   
-  if (old_mo_warning == TRUE) {
+  if (old_mo_warning == TRUE & property != "mo") {
     warning("The input contained old microorganism IDs from previous versions of this package. Please use as.mo() on these old codes.\nSUPPORT FOR THIS WILL BE DROPPED IN A FUTURE VERSION.", call. = FALSE)
   }
   

R/mo_history.R

@@ -29,6 +29,7 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
   
   if (base::interactive() | force == TRUE) {
     mo_hist <- read_mo_history(uncertainty_level = uncertainty_level, force = force)
+    warning_new_write <- FALSE
     df <- data.frame(x, mo, stringsAsFactors = FALSE) %>%
       distinct(x, .keep_all = TRUE) %>%
       filter(!is.na(x) & !is.na(mo))
@@ -55,8 +56,9 @@ set_mo_history <- function(x, mo, uncertainty_level, force = FALSE, disable = FA
         # if (tryCatch(nrow(getOption("mo_remembered_results")), error = function(e) 1001) > 1000) {
         #   return(base::invisible())
         # }
-        if (is.null(mo_hist) & interactive()) {
+        if (is.null(mo_hist) & interactive() & warning_new_write == FALSE) {
           message(blue(paste0("NOTE: results are saved to ", mo_history_file(), ".")))
+          warning_new_write <- TRUE
         }
         tryCatch(write.csv(rbind(mo_hist,
                                  data.frame(