Resolve more comments

Author: stitam

R/chembl.R

@@ -232,7 +232,7 @@ chembl_files <- function(version = "latest") {
 #'   - version: character; database version to use in "offline" mode (default
 #'     "latest").
 #' @param verbose logical; should a verbose output be printed on the console?
-#' @param ... addition arguments, only used for internal testing.
+#' @param ... additional arguments, only used for internal testing.
 #' @return The function returns a list of lists, where each element of the list
 #' contains a list of respective query results. If `tidy = TRUE` results are
 #' simplified, if possible.
@@ -274,7 +274,7 @@ chembl_files <- function(version = "latest") {
 #' chembl_query(
 #'   "CHEMBL266429",
 #'   resource = "compound_structural_alert",
-#'   options = list(tidy = FALSE)
+#'   options = chembl_options(tidy = FALSE)
 #' )
 #'
 #' # Resource: compound_record - requires compound record ID
@@ -294,7 +294,7 @@ chembl_files <- function(version = "latest") {
 #' # By default, the function will use 70 as similarity threshold
 #' chembl_query(
 #'   "CC(=O)Oc1ccccc1C(=O)O", resource = "similarity",
-#'   options = list(similarity = 70)
+#'   options = chembl_options(similarity = 70)
 #' )
 #'
 #' # Resource: substructure - requires compound SMILES

R/chembl_offline.R

@@ -864,6 +864,12 @@ chembl_compare_service <- function(
 #' @return A list with the comparison status and any unique elements found in
 #' either input.
 #' @noRd
+#' @examples
+#' \dontrun{
+#' ws <- chembl_query("CHEMBL1082", resource = "molecule")
+#' off <- chembl_query("CHEMBL1082", resource = "molecule", mode = "offline")
+#' compare_service_lists(ws$CHEMBL1082, off$CHEMBL1082)
+#' }
 compare_service_lists <- function(ws, offline) {
   ws_na <- length(ws) == 1 && is.na(ws)
   offline_na <- length(offline) == 1 && is.na(offline)
@@ -904,8 +910,10 @@ compare_service_lists <- function(ws, offline) {
     if (is.atomic(ws_elem)) {
       if (!identical(ws_elem, off_elem)) {
         stop(sprintf(
-          "Atomic element '%s' differs between webservice and offline.\n",
-          "Webservice value: %s\nOffline value: %s",
+          paste0(
+            "Atomic element '%s' differs between webservice and offline.\n",
+            "Webservice value: %s\nOffline value: %s"
+          ),
           n,
           paste0(utils::capture.output(print(ws_elem)), collapse = "\n"),
           paste0(utils::capture.output(print(off_elem)), collapse = "\n")
@@ -926,12 +934,12 @@ compare_service_lists <- function(ws, offline) {
     } else {
       stop(sprintf("Element '%s' should be either atomic or a data frame.", n))
     }
-    return(list(
-      status = "OK",
-      ws_extra = ws_unique_element,
-      offline_extra = offline_unique_element
-    ))
   }
+  return(list(
+    status = "OK",
+    ws_extra = ws_unique_element,
+    offline_extra = offline_unique_element
+  ))
 }
 
 #' Compare Two Named Lists of Atomic Elements