Start addressing the return NULL issue detected by BiocCheck at https…

…://github.com/LieberInstitute/visiumStitched/actions/runs/10063194884/job/27822951014#step:24:86

Co-authored-by: Nick Eagles <[email protected]>

R/array_coord_utils.R

@@ -9,7 +9,7 @@
 #' @param coords A \code{tibble} containing 'array_row' and 'array_col' columns
 #' calculated internally by \code{add_array_coords()}
 #'
-#' @return NULL
+#' @return It returns `NULL` if all tests were correct.
 #'
 #' @author Nicholas J. Eagles
 #' @keywords internal
@@ -45,6 +45,7 @@
     if (any((coords$array_row == 0) & (coords$array_col == 0))) {
         stop("Internal bug: the invalid array coordinate (0, 0) exists after fitting")
     }
+    return(insivible(NULL))
 }
 
 #' Return array coordinates fit to nearest spot with associated error

R/prep_fiji_coords.R

@@ -14,7 +14,8 @@
 #' the output pixel coordinates CSVs. Provided the parent exists, \code{out_dir}
 #' will be created if necessary.
 #'
-#' @return NULL
+#' @return This function returns `character()` with the file paths to the
+#' `tissue_positions.csv` files it created.
 #'
 #' @import xml2
 #' @importFrom stringr str_replace_all str_detect

R/prep_fiji_image.R

@@ -17,7 +17,8 @@
 #' pixels) of the larger dimension of the output image(s), considered to be "low
 #' resolution".
 #'
-#' @return NULL
+#' @return This function returns `character()` with the file paths to the
+#' `tissue_lowres_image.png` and `scalefactors_json.json` files it created.
 #'
 #' @importFrom imager load.image resize save.image
 #' @importFrom rjson fromJSON toJSON

R/spe_to_seurat.R

@@ -16,7 +16,7 @@
 #' @param verbose A logical(1) vector. If true, print status updates about the
 #' conversion process
 #'
-#' @return A \code{Seurat} object
+#' @return A \code{Seurat} object.
 #'
 #' @export
 #' @author Nicholas J. Eagles