omnideconv · pre-commit-ci · Jul 6, 2026 · Jul 6, 2026 · Jul 6, 2026
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9015
+    rev: v0.4.3.9026
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -14,7 +14,6 @@ Description: SimBu can be used to simulate bulk RNA-seq datasets with known cell
 License: GPL-3 + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE) 
-RoxygenNote: 7.3.3
 Imports: 
     basilisk,
     BiocParallel,
@@ -46,3 +45,4 @@ VignetteBuilder: knitr
 Config/testthat/edition: 3
 StagedInstall: no
 biocViews: Software, RNASeq, SingleCell
+Config/roxygen2/version: 8.0.0
diff --git a/R/dataset.R b/R/dataset.R
@@ -151,8 +151,6 @@ generate_summarized_experiment <- function(annotation, count_matrix, tpm_matrix,
 }
 
 
-
-
 #' Build \link[SummarizedExperiment]{SummarizedExperiment} using local annotation and count matrix R objects
 #'
 #' @param annotation (mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix

diff --git a/R/simulator.R b/R/simulator.R
@@ -837,7 +837,6 @@ merge_simulations <- function(simulation_list) {
 }
 
 
-
 #' Create scaling vector from custom or pre-defined scaling factor
 #'
 #' @param data dataset

diff --git a/man/SimBu.Rd b/man/SimBu.Rd
diff --git a/tests/testthat/test_simulator.R b/tests/testthat/test_simulator.R
@@ -76,8 +76,6 @@ test_that("test different scaling factor calculations + mRNA bias removal from c
 })
 
 
-
-
 test_that("test census", {
   tpm <- Matrix::Matrix(matrix(rpois(3e5, 5), ncol = 300), sparse = TRUE)
   tpm <- Matrix::t(1e6 * Matrix::t(tpm) / Matrix::colSums(tpm))
-Original file line number
+Diff line change
@@ Expand Up @@
     }
     #' Build \link[SummarizedExperiment]{SummarizedExperiment} using local annotation and count matrix R objects
     #'
     #' @param annotation (mandatory) dataframe; needs columns 'ID' and 'cell_type'; 'ID' needs to be equal with cell_names in count_matrix
@@ Expand Down @@