pass BiocCheck again

.Rbuildignore

@@ -16,4 +16,4 @@
 ^doc$
 ^Meta$
 ^codecov\.yml$
-^.vscode
+^.vscode

R/example.R

@@ -8,25 +8,26 @@
 #' @importFrom SingleCellExperiment SingleCellExperiment
 #' @importFrom stats rpois
 #' @importFrom S4Vectors DataFrame
+#' @importFrom withr with_seed
 #' @return A SingleCellExperiment object
 #' @examples
 #' sce <- sce_example()
 #' sce
 #' @export
-sce_example <- function(){
-    # Set seed for reproducibility (optional)
-    set.seed(42)
+sce_example <- function(seed = 42){
     # generate example data with two "batches"
-    counts_mat <- cbind(
-        matrix(rpois(300 * 300, lambda = 5),
-            nrow = 300,
-            dimnames = list(paste0("gene", 1:300), paste0("cell", 1:300))
-        ),
-        matrix(rpois(300 * 300, lambda = 3),
-            nrow = 300,
-            dimnames = list(paste0("gene", 1:300), paste0("cell", 301:600))
+    withr::with_seed(seed, {
+        counts_mat <- cbind(
+            matrix(rpois(300 * 300, lambda = 5),
+                nrow = 300,
+                dimnames = list(paste0("gene", 1:300), paste0("cell", 1:300))
+            ),
+            matrix(rpois(300 * 300, lambda = 3),
+                nrow = 300,
+                dimnames = list(paste0("gene", 1:300), paste0("cell", 301:600))
+            )
         )
-    )
+    })
     # add metadata
     batch <- rep(c("batch1", "batch2"), each = 300)
     dataset <- rep(c("dataset1", "dataset2", "dataset1", "dataset2"), each = 150)

R/objects.R

@@ -561,6 +561,7 @@ setGeneric(
 #' @import checkmate
 #' @importFrom SingleCellExperiment colData
 #' @keywords internal
+#' @noRd
 .get_meta_data <- function(object) {
   if (checkmate::test_class(object, "Seurat")) {
     return(object[[]])