fix lintr and change test data files

tools/camera/CAMERA_findAdducts.R

@@ -33,14 +33,17 @@ convertNullString <- function(x) {
   return(x)
 }
 
-# Function to convert string to numeric lists or NA
-convertStringToNumeric <- function(x) {
+# Function to convert string to numeric lists
+convert_psg_list <- function(x) {
+  # Check if x is NULL or has zero length before further processing
+  if (is.null(x) || length(x) == 0) {
+    return(NULL)
+  }
+
   # Force conversion to character
   x <- as.character(x)
 
-  if (x == "NA") {
-    return(NA)
-  } else if (grepl("^[0-9]+$", x)) {
+  if (grepl("^[0-9]+$", x)) {
     # If the string represents a single numeric value
     return(as.numeric(x))
   } else {
@@ -55,7 +58,7 @@ for (arg in names(args)) {
 }
 
 # Convert only the 'psg_list' element in args
-args$psg_list <- convertStringToNumeric(args$psg_list)
+args$psg_list <- convert_psg_list(args$psg_list)
 
 print("Argument types:")
 print(sapply(args, class))

tools/camera/CAMERA_groupFWHM.R

@@ -87,16 +87,11 @@ if (!exists("xdata")) stop("\n\nERROR: The RData doesn't contain any object call
 # Verification of a group step before doing the fillpeaks job.
 if (!hasFeatures(xdata)) stop("You must always do a group step after a retcor. Otherwise it won't work for the groupFWHM step")
 
-# sample = NA  # Automatic selection, particularly useful if you have no specific preference
-# sample = 3 # Single file selection
-# sample = c(1, 2, 5) # Manual selection
-# sample = 1:length(xs@filepaths) # Select all samples
-
 # Convert the xset object to xsAnnotate using CAMERA
 cat("Converting xset object to xsAnnotate...\n")
 xsa <- xsAnnotate(xset, sample = args$sample, nSlaves = as.numeric(args$nSlaves), polarity = args$polarity)
 
-print(paste0("All samples in xset object:", paste(1:length(xset@filepaths), collapse = ", ")))
+print(paste0("All samples in xset object:", paste(seq_along(xset@filepaths), collapse = ", ")))
 print(paste0("Selected samples:", paste(xsa@sample, collapse = ", ")))
 print(paste0("Run in parallel mode (0 = disabled):", paste(xsa@runParallel)))
 print(paste0("Polarity:", xsa@polarity))