From 63bfda1635cdc367cfdb60c8691661c05a10c5ab Mon Sep 17 00:00:00 2001
From: kollo97 <aaron.kollo@gmail.com>
Date: Wed, 8 Jan 2025 15:03:32 +0100
Subject: [PATCH] pass BiocCheck again

---
 .Rbuildignore            |  2 +-
 R/example.R              | 25 +++++++++++++------------
 R/objects.R              |  1 +
 man/dot-get_meta_data.Rd | 12 ------------
 man/sce_example.Rd       |  2 +-
 5 files changed, 16 insertions(+), 26 deletions(-)
 delete mode 100644 man/dot-get_meta_data.Rd

diff --git a/.Rbuildignore b/.Rbuildignore
index b751679..a6efef0 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -16,4 +16,4 @@
 ^doc$
 ^Meta$
 ^codecov\.yml$
-^.vscode
\ No newline at end of file
+^.vscode
diff --git a/R/example.R b/R/example.R
index df7b027..eba1df1 100644
--- a/R/example.R
+++ b/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)
diff --git a/R/objects.R b/R/objects.R
index f6d544e..8ed48d1 100644
--- a/R/objects.R
+++ b/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[[]])
diff --git a/man/dot-get_meta_data.Rd b/man/dot-get_meta_data.Rd
deleted file mode 100644
index f8780dd..0000000
--- a/man/dot-get_meta_data.Rd
+++ /dev/null
@@ -1,12 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/objects.R
-\name{.get_meta_data}
-\alias{.get_meta_data}
-\title{Internal helper function to get metadata from a Seurat or SCE object}
-\usage{
-.get_meta_data(object)
-}
-\description{
-Internal helper function to get metadata from a Seurat or SCE object
-}
-\keyword{internal}
diff --git a/man/sce_example.Rd b/man/sce_example.Rd
index 858c61f..c4e46a0 100644
--- a/man/sce_example.Rd
+++ b/man/sce_example.Rd
@@ -4,7 +4,7 @@
 \alias{sce_example}
 \title{Generate example SingleCellExperiment object}
 \usage{
-sce_example()
+sce_example(seed = 42)
 }
 \value{
 A SingleCellExperiment object