@@ -112,8 +112,9 @@ layout.arc = function (g, target, query)

   target = target[target %in% query]

   V(g)$type = "bridge"

-  V(g)[name %in% query]$type = "query"

-  V(g)[name %in% target]$type = "target"

+  all_name=V(g)$name # could be V(g)[ name %in% query ] but want to avoid "note's" in R CMD check.

+  V(g)[all_name %in% query]$type = "query"

+  V(g)[all_name %in% target]$type = "target"

   g_con = g

   n_left = character()

@@ -123,9 +124,11 @@ layout.arc = function (g, target, query)

     n_left = setdiff(V(g)$name,V(g_con)$name)

   }

-  set = list(target = target, bridge=V(g_con)[type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

-  for(q in V(g_con)[type == "query"]$name) {

-    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[name %in% target])

+  all_type=V(g_con)$type

+  all_name=V(g_con)$name

+  set = list(target = target, bridge=V(g_con)[all_type == "bridge"]$name, query1 = character(), query2 = character(), query3 = character(), left=n_left)

+  for(q in V(g_con)[all_type == "query"]$name) {

+    sp = get.all.shortest.paths(g_con,from=V(g_con)[q],to=V(g_con)[all_name %in% target])

     #print(sp)

     sp_min = min(sapply(sp$res,length))

     #print(sp_min)