Modify DESCRIPTION and fix couple of BiocCheck issues

ccb-hms · Apr 14, 2024 · 215b6ee · 215b6ee
1 parent f88d2a7
commit 215b6ee
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Showing 5 changed files with 21 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,7 +32,9 @@ Imports:
     scater,
     SummarizedExperiment,
     BiocGenerics,
-    S4Vectors
+    S4Vectors,
+    stats,
+    utils
 Suggests:
     AUCell,
     BiocStyle,
@@ -44,10 +46,12 @@ Suggests:
     scran,
     scRNAseq,
     SingleR,
-    celldex
+    celldex,
+    testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
 biocView: SingleCell, Software
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
+Config/testthat/edition: 3
diff --git a/R/calculatePairwiseDistancesAndPlotDensity.R b/R/calculatePairwiseDistancesAndPlotDensity.R
@@ -154,10 +154,10 @@ calculatePairwiseDistancesAndPlotDensity <-
     ## Extract the distances or correlations for the different pairwise comparisons
     num_query_cells <- nrow(query_mat)
     num_ref_cells <- nrow(ref_mat)
-    dist_query_query <- dist_matrix[1:num_query_cells, 1:num_query_cells]
+    dist_query_query <- dist_matrix[seq_len(num_query_cells), seq_len(num_query_cells)]
     dist_ref_ref <- dist_matrix[(num_query_cells + 1):(num_query_cells + num_ref_cells), 
                               (num_query_cells + 1):(num_query_cells + num_ref_cells)]
-    dist_query_ref <- dist_matrix[1:num_query_cells,
+    dist_query_ref <- dist_matrix[seq_len(num_query_cells),
                                   (num_query_cells + 1):(num_query_cells + num_ref_cells)]
 
     ## Create data frame for plotting

diff --git a/R/outlierDetection.R b/R/outlierDetection.R
@@ -116,5 +116,5 @@ calculateOutlierScore <- function(sce,
 
     S4Vectors::metadata(sce)$isotree_model <- isotree_res$model
 
-    return(sce)
+    sce
 }
diff --git a/R/visualizeCellTypeMDS.R b/R/visualizeCellTypeMDS.R
@@ -97,7 +97,6 @@
 #'                             mdata = mdata, 
 #'                             cell_type_colors = cell_type_colors, 
 #'                             legend_order = legend_order)
-#' print(plot)
 #'
 #' @importFrom stats cmdscale cor
 #' @importFrom ggplot2 ggplot scale_color_manual guides guide_legend

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(scDiagnostics)
+
+test_check("scDiagnostics")
-Original file line number
+Diff line change
@@ Expand Up / @@ -116,5 +116,5 @@ calculateOutlierScore <- function(sce, @@
         S4Vectors::metadata(sce)$isotree_model <- isotree_res$model
-        return(sce)
+        sce
     }