Skip tests/examples when packages in Suggest section are not installed

R/FilteredData.R

@@ -52,7 +52,7 @@
 #' isolate(datasets$get_filter_state())
 #' isolate(datasets$get_call("iris"))
 #' isolate(datasets$get_call("mtcars"))
-#'
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' ### set_filter_state
 #'
 #' utils::data(miniACC, package = "MultiAssayExperiment")

R/FilteredDataset-utils.R

@@ -40,6 +40,7 @@
 #'   shinyApp(ui, server)
 #' }
 #'
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' # MAEFilteredDataset example
 #' library(MultiAssayExperiment)
 #' data(miniACC)

R/FilteredDatasetMAE.R

@@ -2,7 +2,7 @@
 
 #' @title `MAEFilteredDataset` `R6` class
 #' @keywords internal
-#' @examples
+#' @examplesIf requireNamespace("MultiAssayExperiment")
 #' # use non-exported function from teal.slice
 #' MAEFilteredDataset <- getFromNamespace("MAEFilteredDataset", "teal.slice")
 #'

R/filter_panel_api.R

@@ -23,18 +23,53 @@
 #' @seealso [`teal_slice`]
 #'
 #' @examples
-#' library(MultiAssayExperiment)
-#' data(miniACC)
-#'
 #' datasets <- init_filtered_data(
 #'   x = list(
 #'     iris = list(dataset = iris),
-#'     mae = list(dataset = miniACC)
+#'     mtcars = list(dataset = mtcars)
 #'   )
 #' )
 #' fs <- teal_slices(
 #'   teal_slice(dataname = "iris", varname = "Species", selected = c("setosa", "versicolor")),
 #'   teal_slice(dataname = "iris", varname = "Sepal.Length", selected = c(5.1, 6.4)),
+#'   teal_slice(dataname = "mtcars", varname = "gear", selected = c(4, 5)),
+#'   teal_slice(dataname = "mtcars", varname = "carb", selected = c(4, 10))
+#' )
+#'
+#' # set initial filter state
+#' set_filter_state(datasets, filter = fs)
+#'
+#' # get filter state
+#' get_filter_state(datasets)
+#'
+#' # modify filter state
+#' set_filter_state(
+#'   datasets,
+#'   teal_slices(
+#'     teal_slice(dataname = "iris", varname = "Species", selected = "setosa", keep_na = TRUE)
+#'   )
+#' )
+#'
+#' # remove specific filters
+#' remove_filter_state(
+#'   datasets,
+#'   teal_slices(
+#'     teal_slice(dataname = "iris", varname = "Species"),
+#'     teal_slice(dataname = "mtcars", varname = "gear"),
+#'     teal_slice(dataname = "mtcars", varname = "carb")
+#'   )
+#' )
+#'
+#' # remove all states
+#' clear_filter_states(datasets)
+#' @examplesIf requireNamespace("MultiAssayExperiment")
+#'
+#' # Requires MultiAssayExperiment from Bioconductor
+#' library(MultiAssayExperiment)
+#' data(miniACC)
+#'
+#' datasets <- init_filtered_data(x = list(mae = list(dataset = miniAcc)))
+#' fs <- teal_slices(
 #'   teal_slice(
 #'     dataname = "mae", varname = "years_to_birth", selected = c(30, 50),
 #'     keep_na = TRUE, keep_inf = FALSE
@@ -63,15 +98,14 @@
 #' set_filter_state(
 #'   datasets,
 #'   teal_slices(
-#'     teal_slice(dataname = "iris", varname = "Species", selected = "setosa", keep_na = TRUE)
+#'     teal_slice(dataname = "mae", varname = "years_to_birth", selected = c(40, 60))
 #'   )
 #' )
 #'
 #' # remove specific filters
 #' remove_filter_state(
 #'   datasets,
 #'   teal_slices(
-#'     teal_slice(dataname = "iris", varname = "Species"),
 #'     teal_slice(dataname = "mae", varname = "years_to_birth"),
 #'     teal_slice(dataname = "mae", varname = "vital_status")
 #'   )

tests/testthat/test-FilteredData.R

@@ -1,5 +1,6 @@
 # initialize ----
 testthat::test_that("constructor accepts all types of datasets", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
 
   testthat::expect_no_error(FilteredData$new(list("logical" = c(TRUE, FALSE))))
@@ -718,6 +719,8 @@ testthat::test_that("srv_active - clicking remove_all button clears filters", {
 
 # get_filter_count
 testthat::test_that("get_filter_count properly tallies active filter states", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   test_class <- R6::R6Class(
     classname = "test_class",
     inherit = FilteredData,
@@ -753,6 +756,8 @@ testthat::test_that("get_filter_count properly tallies active filter states for
       }
     )
   )
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   datasets <- test_class$new(
     list(
       iris = list(dataset = iris),

tests/testthat/test-MAEFilterStates.R

@@ -1,7 +1,7 @@
-utils::data(miniACC, package = "MultiAssayExperiment")
-
 # initialize ----
 testthat::test_that("constructor accepts a MultiAssayExperiment", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   testthat::expect_no_error(
     MAEFilterStates$new(data = miniACC, dataname = "miniACC")
   )
@@ -13,6 +13,8 @@ testthat::test_that("constructor accepts a MultiAssayExperiment", {
 
 # get_filter_state ----
 testthat::test_that("get_filter_state returns `teal_slices` with include_varname by default and count_type=none", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   filter_states <- MAEFilterStates$new(data = miniACC, dataname = "miniACC")
   fs <- teal_slices(
     count_type = "none",
@@ -27,6 +29,8 @@ testthat::test_that("get_filter_state returns `teal_slices` with include_varname
 
 # get_call ----
 testthat::test_that("get_call returns subsetByColData call with varnames prefixed by dataname$", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
+  utils::data(miniACC, package = "MultiAssayExperiment")
   filter_states <- MAEFilterStates$new(data = miniACC, dataname = "miniacc")
   filter_states$set_filter_state(
     teal_slices(

tests/testthat/test-MAEFilteredDataset.R

@@ -1,5 +1,6 @@
 # initialize ----
 testthat::test_that("constructor accepts a MultiAssayExperiment object", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   testthat::expect_no_error(MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC"))
   testthat::expect_error(
@@ -13,6 +14,7 @@ testthat::test_that("constructor accepts a MultiAssayExperiment object", {
 })
 
 testthat::test_that("filter_states list is initialized with names of experiments", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   testfd <- R6::R6Class(
     "testfd",
     inherit = MAEFilteredDataset,
@@ -30,6 +32,7 @@ testthat::test_that("filter_states list is initialized with names of experiments
 
 # format ---
 testthat::test_that("format returns properly formatted string", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -59,6 +62,7 @@ testthat::test_that("format returns properly formatted string", {
 
 # print ---
 testthat::test_that("print returns properly formatted string", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -88,13 +92,15 @@ testthat::test_that("print returns properly formatted string", {
 
 # get_call ----
 testthat::test_that("get_call returns NULL when no filter applied", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC")
   get_call_output <- shiny::isolate(filtered_dataset$get_call())
   testthat::expect_null(get_call_output)
 })
 
 testthat::test_that("get_call returns a call with applying filter", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -131,6 +137,7 @@ testthat::test_that("get_call returns a call with applying filter", {
 
 # get_filter_overview ----
 testthat::test_that("get_filter_overview_info returns overview matrix for MAEFilteredDataset without filtering", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniACC")
   testthat::expect_equal(
@@ -146,6 +153,7 @@ testthat::test_that("get_filter_overview_info returns overview matrix for MAEFil
 })
 
 testthat::test_that("get_filter_overview_info returns overview matrix for MAEFilteredDataset with filtering", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(
@@ -177,6 +185,7 @@ testthat::test_that("get_filter_overview_info returns overview matrix for MAEFil
 testthat::test_that(
   "MAEFilteredDataset$set_filter_state sets filters in `FilterStates` specified by `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -217,6 +226,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$set_filter_state only acceps `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- list(
@@ -236,6 +246,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$get_filter_state returns list identical to input",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -268,6 +279,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$remove_filter_state removes desired filter",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -297,6 +309,7 @@ testthat::test_that(
 testthat::test_that(
   "MAEFilteredDataset$remove_filter_state only accepts `teal_slices",
   code = {
+    testthat::skip_if_not_installed("MultiAssayExperiment")
     utils::data(miniACC, package = "MultiAssayExperiment")
     dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
     fs <- teal_slices(
@@ -318,6 +331,7 @@ testthat::test_that(
 
 # UI actions ----
 testthat::test_that("remove_filters button removes all filters", {
+  testthat::skip_if_not_installed("MultiAssayExperiment")
   utils::data(miniACC, package = "MultiAssayExperiment")
   filtered_dataset <- MAEFilteredDataset$new(dataset = miniACC, dataname = "miniacc")
   fs <- teal_slices(