Fixed issues with testthat and examples failing CRAN checks

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: dietr
-Version: 1.1.6
+Version: 1.1.6-1
 Date: 2025-1-12
 Title: Diet Estimated Trophic Levels
 Authors@R: person(given = c("Samuel", "R."),

NEWS.md

@@ -1,4 +1,4 @@
-dietr 1.1.6
+dietr 1.1.6-1
 ============
 
 ## Minor changes

R/ConvertFishbaseDiet.R

@@ -8,12 +8,13 @@
 #' versions you could specify species names or numbers and only return those of interest, the only function options in the current version
 #' are specifying a server. As such, if the function is run, it will return all diet data on the site, requiring users to subset out 
 #' those of interest for them. We have implemented in this function a way to join the tables for use as well as filter based on life history stage (if necessary).
-#' @examples 
+#' @examplesIf interactive() 
 #' \donttest{
-#' #Convert Fishbase Diet Data
-#' my.diets <- ConvertFishbaseDiet(ExcludeStage=NULL)
 #' #Convert Fishbase Diet Data and exclude juvenile and larval records
-#' my.diets <- ConvertFishbaseDiet(ExcludeStage=c("recruits/juv.","larvae"))
+#' my.diets <- try(ConvertFishbaseDiet(ExcludeStage=c("recruits/juv.","larvae")))
+#'   if (!"try-error" %in% class(my.diets)){
+#'     my.diets
+#'  }
 #' }
 #' @author Samuel Borstein
 #' @export

R/ConvertFishbaseFood.R

@@ -4,12 +4,15 @@
 #' @return a list of length two, with two data frames. One containing the re-formatted food item data and one containing the Taxonomy with species names.
 #' @details This converts the data frame produced by rfishbase fooditem function into a usable format for dietr.
 #' @author Samuel Borstein
-#' @examples
+#' @examplesIf interactive()
 #' \donttest{
 #' #Get rfishbase food item data for a few species
-#' my.food <- as.data.frame(rfishbase::fooditems(c("Lutjanus apodus","Epinephelus itajara")))
+#' my.food <- try(as.data.frame(rfishbase::fooditems(c("Lutjanus apodus","Epinephelus itajara"))))
+#' if (!"try-error" %in% class(my.food)) {
 #' #use the ConvertFishbaseFood function to format it for dietr and exclude recruits/juveniles
 #' cleaned.food <- ConvertFishbaseFood(FishBaseFood=my.food, ExcludeStage=c("larvae","recruits/juv."))
+#' cleaned.food
+#' }
 #' }
 #' @export
 

R/DietTroph.R

@@ -17,7 +17,7 @@
 #' While FishBase data obtained from rfishbase can be used, users can also upload their own data for
 #' use in with function (see vignette for a tutorial). 
 #' @author Samuel Borstein
-#' @examples
+#' @examplesIf interactive()
 #' \donttest{
 #' ###EXAMPLE USING RAW DATA FROM Magalhaes et al., 2015###
 #' data(Herichthys)#load data

R/FoodTroph.R

@@ -18,7 +18,7 @@
 #' the SE which they also refer to as the omnivory index. Alternatively, users can select the Sims option, in which case the SE is estimated based on the estimated TL of the n number
 #' of subsampling routines.Users can also select "Both" if they would like to calculate both types of SE.
 #' @author Samuel Borstein
-#' @examples 
+#' @examplesIf interactive() 
 #' \donttest{
 #' #Get some food item data from rfishbase
 #' my.food <- rfishbase::fooditems(c("Lutjanus apodus","Epinephelus itajara"))

tests/testthat/test_FoodTroph.R

@@ -2,6 +2,7 @@
 #Test obtains food item data from FishBase database and calcultes the trophic level of the record
 #Tests that the calculated trophic level is what we expect it to be
 test_that("FoodTroph function works", {
+  skip_on_cran()
   test.food <- try(rfishbase::fooditems("Plectropomus maculatus"),silent = TRUE)#get food items from database
   if ("try-error"%in%class(test.food)) {
     skip("could not connect to remote database")