use base namespace to save RDS file:

- otherwise this throws an error on R 4.4.2 (Bioc 3.20)
BIMSBbioinfo · Nov 14, 2024 · 1794453 · 1794453
1 parent 4ed2fb5
commit 1794453
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diff --git a/scripts/convert_loom_to_Seurat.R b/scripts/convert_loom_to_Seurat.R
@@ -53,7 +53,7 @@ convert_loom_to_seurat = function(
         seu = ScaleData(object = seu)
 
     seu@meta.data$CellID = colnames(seu)
-    saveRDS(seu, outfile)
+    base::saveRDS(seu, outfile)
 }
 
 

diff --git a/scripts/convert_loom_to_singleCellExperiment.R b/scripts/convert_loom_to_singleCellExperiment.R
@@ -142,7 +142,7 @@ loomToSingleCellExperiment = function(
   sce = loom2sce(path = loom_file)
 
   outname = str_replace(outfile,'.RDS','')
-  saveRDS(object = sce, file = paste0(outname, '.raw.RDS'))
+  base::saveRDS(object = sce, file = paste0(outname, '.raw.RDS'))
   #4.1.1 Subset the sce object, remove cells that don't exist in the metaDataFile
 
 
@@ -186,7 +186,7 @@ loomToSingleCellExperiment = function(
     "scale" = scaled_counts
   )
 
-  saveRDS(object = sce, file = paste0(outname, '.intermediate.RDS'))
+  base::saveRDS(object = sce, file = paste0(outname, '.intermediate.RDS'))
 
 
   # 4.8 Map gene ids to gene names and update rowData
@@ -197,7 +197,7 @@ loomToSingleCellExperiment = function(
   rowData(sce)$gene_name = gtf[match(rowData(sce)$gene_id, gtf$gene_id),]$gene_name
 
   #5 save SingleCellExperiment object in .RDS format
-  saveRDS(object = sce, file = outfile)
+  base::saveRDS(object = sce, file = outfile)
 
 }