From dec29d70ce6357fea4ae7bcf1647d973ac349f19 Mon Sep 17 00:00:00 2001
From: David Schoch <david@schochastics.net>
Date: Fri, 4 Sep 2026 13:07:09 +0200
Subject: [PATCH] perf: batch-construct vertex sequence lists via
 create_vs_list()

Functions returning many vertex sequences used
`lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))`, which
re-read the graph reference, graph id and name source from `verts` on
every object. Add `create_vs_list(graph, idx_list)`, which hoists all of
that per-graph work out of the loop and builds each sequence with a
single `attributes<-`, so per-object cost drops to an integer coercion,
a name subset and one attribute set.

The `VERTEXSET_LIST` OUTCONV template in tools/stimulus/types-RR.yaml now
emits `create_vs_list(graph, res)`; the generated R/aaa-*.R files are
updated to match (27 sites), along with the hand-written call sites in
cliques.R, cohesive.blocks.R, components.R, conversion.R, interface.R,
paths.R and structural-properties.R (10 sites). `unsafe_create_vs()`
stays as the single-object form.

Beyond the speedup this gives the construction loop a single named entry
point, so it can later be moved wholesale (e.g. into C) without touching
any call site.

Edge sequences are left as-is: simple_es_index() already propagates the
shared weak reference from a single E(graph), so unsafe_create_es() does
not pay the per-object cost. An es batch form remains a follow-up.

max_cliques(sample_gnp(200, 0.16)) on a named graph: ~7.8ms -> ~5.6ms.
Output, names, NA handling and graph recovery are unchanged.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
---
 R/aaa-cliques.R              | 18 ++++++++--------
 R/aaa-cycles.R               |  2 +-
 R/aaa-flows.R                |  6 +++---
 R/aaa-graphlets.R            |  4 ++--
 R/aaa-isomorphism.R          |  2 +-
 R/aaa-paths.R                | 14 ++++++------
 R/aaa-separators.R           |  4 ++--
 R/aaa-structural.R           |  4 ++--
 R/cliques.R                  |  4 ++--
 R/cohesive.blocks.R          |  7 +-----
 R/components.R               |  7 +-----
 R/conversion.R               |  2 +-
 R/interface.R                |  2 +-
 R/iterators.R                | 41 ++++++++++++++++++++++++++++++++++++
 R/paths.R                    |  2 +-
 R/structural-properties.R    | 16 +++-----------
 tools/stimulus/types-RR.yaml |  2 +-
 17 files changed, 79 insertions(+), 58 deletions(-)

diff --git a/R/aaa-cliques.R b/R/aaa-cliques.R
index 83f6472fdf4..42bcaf53a44 100644
--- a/R/aaa-cliques.R
+++ b/R/aaa-cliques.R
@@ -107,7 +107,7 @@ cliques_impl <- function(
     max
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -163,7 +163,7 @@ largest_cliques_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -303,7 +303,7 @@ maximal_cliques_impl <- function(
     max_size
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -338,7 +338,7 @@ maximal_cliques_subset_impl <- function(
     max_size
   )
   if (igraph_opt("return.vs.es")) {
-    res$res <- lapply(res$res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$res <- create_vs_list(graph, res$res)
   }
   if (!details) {
     res <- res$res
@@ -383,7 +383,7 @@ independent_vertex_sets_impl <- function(
     max_size
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -420,7 +420,7 @@ largest_independent_vertex_sets_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -438,7 +438,7 @@ maximal_independent_vertex_sets_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -468,7 +468,7 @@ largest_weighted_cliques_impl <- function(
     vertex_weights
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -531,7 +531,7 @@ weighted_cliques_impl <- function(
     maximal
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
diff --git a/R/aaa-cycles.R b/R/aaa-cycles.R
index f7671c6bde0..c97622ce2f7 100644
--- a/R/aaa-cycles.R
+++ b/R/aaa-cycles.R
@@ -380,7 +380,7 @@ simple_cycles_impl <- function(
     max_cycle_length
   )
   if (igraph_opt("return.vs.es")) {
-    res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vertices <- create_vs_list(graph, res$vertices)
   }
   if (igraph_opt("return.vs.es")) {
     res$edges <- lapply(res$edges, unsafe_create_es, graph = graph, es = E(graph))
diff --git a/R/aaa-flows.R b/R/aaa-flows.R
index 44f5b8faf0a..e01723400b3 100644
--- a/R/aaa-flows.R
+++ b/R/aaa-flows.R
@@ -17,7 +17,7 @@ cohesive_blocks_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res$blocks <- lapply(res$blocks, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$blocks <- create_vs_list(graph, res$blocks)
   }
   class(res) <- "cohesiveBlocks"
   res
@@ -176,7 +176,7 @@ all_st_cuts_impl <- function(
     res$cuts <- lapply(res$cuts, unsafe_create_es, graph = graph, es = E(graph))
   }
   if (igraph_opt("return.vs.es")) {
-    res$partition1s <- lapply(res$partition1s, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$partition1s <- create_vs_list(graph, res$partition1s)
   }
   res
 }
@@ -225,7 +225,7 @@ all_st_mincuts_impl <- function(
     res$cuts <- lapply(res$cuts, unsafe_create_es, graph = graph, es = E(graph))
   }
   if (igraph_opt("return.vs.es")) {
-    res$partition1s <- lapply(res$partition1s, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$partition1s <- create_vs_list(graph, res$partition1s)
   }
   res
 }
diff --git a/R/aaa-graphlets.R b/R/aaa-graphlets.R
index e9604885b0c..2a156b1c273 100644
--- a/R/aaa-graphlets.R
+++ b/R/aaa-graphlets.R
@@ -26,7 +26,7 @@ graphlets_candidate_basis_impl <- function(
     weights
   )
   if (igraph_opt("return.vs.es")) {
-    res$cliques <- lapply(res$cliques, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$cliques <- create_vs_list(graph, res$cliques)
   }
   res
 }
@@ -57,7 +57,7 @@ graphlets_impl <- function(
     niter
   )
   if (igraph_opt("return.vs.es")) {
-    res$cliques <- lapply(res$cliques, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$cliques <- create_vs_list(graph, res$cliques)
   }
   res
 }
diff --git a/R/aaa-isomorphism.R b/R/aaa-isomorphism.R
index 343419a9d95..af52bd6da37 100644
--- a/R/aaa-isomorphism.R
+++ b/R/aaa-isomorphism.R
@@ -174,7 +174,7 @@ automorphism_group_impl <- function(
     sh
   )
   if (igraph_opt("return.vs.es")) {
-    res$generators <- lapply(res$generators, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$generators <- create_vs_list(graph, res$generators)
   }
   if (!details) {
     res <- res$generators
diff --git a/R/aaa-paths.R b/R/aaa-paths.R
index 35daacbeb2d..95a29f097c4 100644
--- a/R/aaa-paths.R
+++ b/R/aaa-paths.R
@@ -784,7 +784,7 @@ get_all_shortest_paths_dijkstra_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vpaths <- lapply(res$vpaths, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vpaths <- create_vs_list(graph, res$vpaths)
   }
   if (igraph_opt("return.vs.es")) {
     res$epaths <- lapply(res$epaths, unsafe_create_es, graph = graph, es = E(graph))
@@ -826,7 +826,7 @@ get_all_shortest_paths_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vpaths <- lapply(res$vpaths, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vpaths <- create_vs_list(graph, res$vpaths)
   }
   if (igraph_opt("return.vs.es")) {
     res$epaths <- lapply(res$epaths, unsafe_create_es, graph = graph, es = E(graph))
@@ -931,7 +931,7 @@ get_k_shortest_paths_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vpaths <- lapply(res$vpaths, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vpaths <- create_vs_list(graph, res$vpaths)
   }
   if (igraph_opt("return.vs.es")) {
     res$epaths <- lapply(res$epaths, unsafe_create_es, graph = graph, es = E(graph))
@@ -1206,7 +1206,7 @@ get_shortest_paths_bellman_ford_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vertices <- create_vs_list(graph, res$vertices)
   }
   if (igraph_opt("return.vs.es")) {
     res$edges <- lapply(res$edges, unsafe_create_es, graph = graph, es = E(graph))
@@ -1258,7 +1258,7 @@ get_shortest_paths_dijkstra_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vertices <- create_vs_list(graph, res$vertices)
   }
   if (igraph_opt("return.vs.es")) {
     res$edges <- lapply(res$edges, unsafe_create_es, graph = graph, es = E(graph))
@@ -1300,7 +1300,7 @@ get_shortest_paths_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vertices <- create_vs_list(graph, res$vertices)
   }
   if (igraph_opt("return.vs.es")) {
     res$edges <- lapply(res$edges, unsafe_create_es, graph = graph, es = E(graph))
@@ -1453,7 +1453,7 @@ get_widest_paths_impl <- function(
     mode
   )
   if (igraph_opt("return.vs.es")) {
-    res$vertices <- lapply(res$vertices, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$vertices <- create_vs_list(graph, res$vertices)
   }
   if (igraph_opt("return.vs.es")) {
     res$edges <- lapply(res$edges, unsafe_create_es, graph = graph, es = E(graph))
diff --git a/R/aaa-separators.R b/R/aaa-separators.R
index ef97067ea63..5705728e6a8 100644
--- a/R/aaa-separators.R
+++ b/R/aaa-separators.R
@@ -14,7 +14,7 @@ all_minimal_st_separators_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
@@ -86,7 +86,7 @@ minimum_size_separators_impl <- function(
     graph
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
diff --git a/R/aaa-structural.R b/R/aaa-structural.R
index de9543e847b..e8adb9454ad 100644
--- a/R/aaa-structural.R
+++ b/R/aaa-structural.R
@@ -336,7 +336,7 @@ biconnected_components_impl <- function(
     res$component_edges <- lapply(res$component_edges, unsafe_create_es, graph = graph, es = E(graph))
   }
   if (igraph_opt("return.vs.es")) {
-    res$components <- lapply(res$components, unsafe_create_vs, graph = graph, verts = V(graph))
+    res$components <- create_vs_list(graph, res$components)
   }
   if (igraph_opt("return.vs.es")) {
     res$articulation_points <- create_vs(graph, res$articulation_points)
@@ -1290,7 +1290,7 @@ neighborhood_impl <- function(
     mindist
   )
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
diff --git a/R/cliques.R b/R/cliques.R
index 29fefbe4a65..35b4fc32c51 100644
--- a/R/cliques.R
+++ b/R/cliques.R
@@ -358,7 +358,7 @@ max_cliques <- function(
     res <- lapply(res, function(x) x + 1)
 
     if (igraph_opt("return.vs.es")) {
-      res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+      res <- create_vs_list(graph, res)
     }
 
     res
@@ -749,7 +749,7 @@ ivs <- function(graph, min = NULL, max = NULL) {
   res <- lapply(res, `+`, 1)
 
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
 
   res
diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R
index 18eef59d2ef..5812a07f3b2 100644
--- a/R/cohesive.blocks.R
+++ b/R/cohesive.blocks.R
@@ -402,12 +402,7 @@ cohesive_blocks <- function(
     res$labels <- V(graph)$name
   }
   if (igraph_opt("return.vs.es")) {
-    res$blocks <- lapply(
-      res$blocks,
-      unsafe_create_vs,
-      graph = graph,
-      verts = V(graph)
-    )
+    res$blocks <- create_vs_list(graph, res$blocks)
   }
 
   res$vcount <- vcount(graph)
diff --git a/R/components.R b/R/components.R
index e1ef087a952..13484c4c8b7 100644
--- a/R/components.R
+++ b/R/components.R
@@ -386,12 +386,7 @@ biconnected_components <- function(graph) {
     res$component.edges <- res$component_edges
   }
   if (igraph_opt("return.vs.es")) {
-    res$components <- lapply(
-      res$components,
-      unsafe_create_vs,
-      graph = graph,
-      verts = V(graph)
-    )
+    res$components <- create_vs_list(graph, res$components)
   }
   if (igraph_opt("return.vs.es")) {
     res$articulation_points <- create_vs(graph, res$articulation_points)
diff --git a/R/conversion.R b/R/conversion.R
index 61791722a72..9bdfe3bf858 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -926,7 +926,7 @@ as_adj_list <- function(
   res <- .Call(Rx_igraph_get_adjlist, graph, mode, loops, multiple)
   res <- lapply(res, `+`, 1)
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   if (is_named(graph)) {
     names(res) <- V(graph)$name
diff --git a/R/interface.R b/R/interface.R
index 59ce5d4178e..a3422e2283f 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -849,7 +849,7 @@ adjacent_vertices <- function(
   res <- lapply(res, `+`, 1)
 
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
 
   if (is_named(graph)) {
diff --git a/R/iterators.R b/R/iterators.R
index 70781b467ba..a03ce0427ef 100644
--- a/R/iterators.R
+++ b/R/iterators.R
@@ -330,6 +330,47 @@ unsafe_create_vs <- function(graph, idx, verts = NULL) {
   res
 }
 
+# Build a list of vertex sequences from a list of vertex-ID vectors.
+#
+# This is the batch form of `unsafe_create_vs()` and replaces the
+# `lapply(idx_list, unsafe_create_vs, graph = graph, verts = V(graph))`
+# pattern. All the per-graph work -- `V(graph)`, the shared weak reference,
+# the graph id and the vertex-name source -- is hoisted out of the loop, so
+# each sequence costs one `as.integer()`, one name subset and one
+# `attributes<-` instead of a closure call that re-reads all of it.
+#
+# Having a single named entry point for "turn this list of ID vectors into a
+# list of vertex sequences" also means the construction loop can be moved
+# wholesale (e.g. into C) without touching any of the ~37 call sites.
+create_vs_list <- function(graph, idx_list) {
+  verts <- V(graph)
+  vs_env <- attr(verts, "env")
+  vs_graph <- attr(verts, "graph")
+  vertex_names <- attr(verts, "names")
+  if (is.null(vertex_names)) {
+    lapply(idx_list, function(idx) {
+      res <- as.integer(idx)
+      attributes(res) <- list(
+        class = "igraph.vs",
+        env = vs_env,
+        graph = vs_graph
+      )
+      res
+    })
+  } else {
+    lapply(idx_list, function(idx) {
+      res <- as.integer(idx)
+      attributes(res) <- list(
+        names = vertex_names[res],
+        class = "igraph.vs",
+        env = vs_env,
+        graph = vs_graph
+      )
+      res
+    })
+  }
+}
+
 # Internal function to quickly convert integer vectors to igraph.es
 # for use after C code, when NA and bounds checking is unnecessary
 # Also allows us to construct V(graph) outside the function call in
diff --git a/R/paths.R b/R/paths.R
index 5ee7971e8ed..64994396f6e 100644
--- a/R/paths.R
+++ b/R/paths.R
@@ -173,7 +173,7 @@ all_simple_paths <- function(
   res <- get.all.simple.paths.pp(res)
 
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
   res
 }
diff --git a/R/structural-properties.R b/R/structural-properties.R
index c2970ebc5a9..44785f57350 100644
--- a/R/structural-properties.R
+++ b/R/structural-properties.R
@@ -1708,12 +1708,7 @@ shortest_paths <- function(
 
   if (igraph_opt("return.vs.es")) {
     if (!is.null(res$vpath)) {
-      res$vpath <- lapply(
-        res$vpath,
-        unsafe_create_vs,
-        graph = graph,
-        verts = V(graph)
-      )
+      res$vpath <- create_vs_list(graph, res$vpath)
     }
     if (!is.null(res$epath)) {
       res$epath <- lapply(
@@ -1821,12 +1816,7 @@ all_shortest_paths <- function(
   }
 
   if (igraph_opt("return.vs.es")) {
-    res$vpaths <- lapply(
-      res$vpaths,
-      unsafe_create_vs,
-      graph = graph,
-      verts = V(graph)
-    )
+    res$vpaths <- create_vs_list(graph, res$vpaths)
   }
 
   # Transitional, eventually, remove $res
@@ -2948,7 +2938,7 @@ ego <- function(
   res <- lapply(res, function(x) x + 1)
 
   if (igraph_opt("return.vs.es")) {
-    res <- lapply(res, unsafe_create_vs, graph = graph, verts = V(graph))
+    res <- create_vs_list(graph, res)
   }
 
   res
diff --git a/tools/stimulus/types-RR.yaml b/tools/stimulus/types-RR.yaml
index bfb5ca69ed8..3c9ac878978 100644
--- a/tools/stimulus/types-RR.yaml
+++ b/tools/stimulus/types-RR.yaml
@@ -472,7 +472,7 @@ VERTEXSET_LIST:
     OUTCONV:
         OUT: |-
             if (igraph_opt("return.vs.es")) {
-              %I% <- lapply(%I%, unsafe_create_vs, graph = %I1%, verts = V(%I1%))
+              %I% <- create_vs_list(%I1%, %I%)
             }
 
 EDGESET_LIST: