diff --git a/.Rbuildignore b/.Rbuildignore
index f6cd805ee96..b79b546771e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -71,3 +71,4 @@
 ^BRANCHES\.md$
 ^scripts$
 ^\.claude$
+^lifecycle-TODO\.md$
diff --git a/R/adjacency.R b/R/adjacency.R
index 65b4eb21411..f1424f964e4 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -17,7 +17,7 @@ graph.adjacency <- function(
   add.rownames = NA
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.adjacency()",
     "graph_from_adjacency_matrix()"
@@ -293,7 +293,7 @@ graph_from_adjacency_matrix <- function(
   ensure_no_na(adjmatrix, "adjacency matrix", mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "graph_from_adjacency_matrix(adjmatrix = 'must be a matrix')"
     )
@@ -302,7 +302,7 @@ graph_from_adjacency_matrix <- function(
 
   if (mode == "undirected") {
     if (!is_symmetric(adjmatrix)) {
-      lifecycle::deprecate_soft(
+      lifecycle::deprecate_warn(
         "1.6.0",
         "graph_from_adjacency_matrix(adjmatrix = 'must be symmetric with mode = \"undirected\"')",
         details = 'Use mode = "max" to achieve the original behavior.'
diff --git a/R/as_phylo.R b/R/as_phylo.R
index c33615d8db4..03e8b21e0a4 100644
--- a/R/as_phylo.R
+++ b/R/as_phylo.R
@@ -10,7 +10,7 @@
 #' @inheritParams ape::as.phylo
 #' @keywords internal
 as_phylo <- function(x, ...) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.5.0",
     "ape::as.phylo()"
   )
diff --git a/R/assortativity.R b/R/assortativity.R
index 5a1b7d2055a..074fa421b35 100644
--- a/R/assortativity.R
+++ b/R/assortativity.R
@@ -15,7 +15,7 @@ assortativity.nominal <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "assortativity.nominal()",
     "assortativity_nominal()"
@@ -40,7 +40,7 @@ assortativity.nominal <- function(
 #' @export
 assortativity.degree <- function(graph, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "assortativity.degree()",
     "assortativity_degree()"
@@ -171,7 +171,7 @@ assortativity <- function(
   types2 = NULL
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(... =)",
       details = "Arguments `values` and `values.in` must be named."
@@ -193,7 +193,7 @@ assortativity <- function(
   }
 
   if (missing(values)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(types1 =)",
       "assortativity(values =)"
@@ -202,7 +202,7 @@ assortativity <- function(
   }
 
   if (!is.null(types2)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "assortativity(types2 =)",
       "assortativity(values.in =)"
diff --git a/R/attributes.R b/R/attributes.R
index 87af8d6b304..1a34d29fc8e 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -10,7 +10,7 @@
 #' @export
 set.vertex.attribute <- function(graph, name, index = V(graph), value) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "set.vertex.attribute()",
     "set_vertex_attr()"
@@ -30,7 +30,7 @@ set.vertex.attribute <- function(graph, name, index = V(graph), value) {
 #' @export
 set.graph.attribute <- function(graph, name, value) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "set.graph.attribute()",
     "set_graph_attr()"
@@ -50,7 +50,7 @@ set.graph.attribute <- function(graph, name, value) {
 #' @export
 set.edge.attribute <- function(graph, name, index = E(graph), value) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "set.edge.attribute()", "set_edge_attr()")
+  lifecycle::deprecate_warn("2.0.0", "set.edge.attribute()", "set_edge_attr()")
   set_edge_attr(graph = graph, name = name, index = index, value = value)
 } # nocov end
 
@@ -66,7 +66,7 @@ set.edge.attribute <- function(graph, name, index = E(graph), value) {
 #' @export
 remove.vertex.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.vertex.attribute()",
     "delete_vertex_attr()"
@@ -86,7 +86,7 @@ remove.vertex.attribute <- function(graph, name) {
 #' @export
 remove.graph.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.graph.attribute()",
     "delete_graph_attr()"
@@ -106,7 +106,7 @@ remove.graph.attribute <- function(graph, name) {
 #' @export
 remove.edge.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "remove.edge.attribute()",
     "delete_edge_attr()"
@@ -126,7 +126,7 @@ remove.edge.attribute <- function(graph, name) {
 #' @export
 list.vertex.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.vertex.attributes()",
     "vertex_attr_names()"
@@ -146,7 +146,7 @@ list.vertex.attributes <- function(graph) {
 #' @export
 list.graph.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.graph.attributes()",
     "graph_attr_names()"
@@ -166,7 +166,7 @@ list.graph.attributes <- function(graph) {
 #' @export
 list.edge.attributes <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "list.edge.attributes()",
     "edge_attr_names()"
@@ -186,7 +186,7 @@ list.edge.attributes <- function(graph) {
 #' @export
 is.weighted <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.weighted()", "is_weighted()")
+  lifecycle::deprecate_warn("2.0.0", "is.weighted()", "is_weighted()")
   is_weighted(graph = graph)
 } # nocov end
 
@@ -202,7 +202,7 @@ is.weighted <- function(graph) {
 #' @export
 is.named <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.named()", "is_named()")
+  lifecycle::deprecate_warn("2.0.0", "is.named()", "is_named()")
   is_named(graph = graph)
 } # nocov end
 
@@ -218,7 +218,7 @@ is.named <- function(graph) {
 #' @export
 is.bipartite <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.bipartite()", "is_bipartite()")
+  lifecycle::deprecate_warn("2.0.0", "is.bipartite()", "is_bipartite()")
   is_bipartite(graph = graph)
 } # nocov end
 
@@ -234,7 +234,7 @@ is.bipartite <- function(graph) {
 #' @export
 get.vertex.attribute <- function(graph, name, index = V(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.vertex.attribute()", "vertex_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.vertex.attribute()", "vertex_attr()")
   vertex_attr(graph = graph, name = name, index = index)
 } # nocov end
 
@@ -250,7 +250,7 @@ get.vertex.attribute <- function(graph, name, index = V(graph)) {
 #' @export
 get.graph.attribute <- function(graph, name) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.graph.attribute()", "graph_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.graph.attribute()", "graph_attr()")
   graph_attr(graph = graph, name = name)
 } # nocov end
 
@@ -266,7 +266,7 @@ get.graph.attribute <- function(graph, name) {
 #' @export
 get.edge.attribute <- function(graph, name, index = E(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.edge.attribute()", "edge_attr()")
+  lifecycle::deprecate_warn("2.0.0", "get.edge.attribute()", "edge_attr()")
   edge_attr(graph = graph, name = name, index = index)
 } # nocov end
 #   IGraph R package
diff --git a/R/basic.R b/R/basic.R
index 47b00f7e071..4769854df36 100644
--- a/R/basic.R
+++ b/R/basic.R
@@ -10,7 +10,7 @@
 #' @export
 is.igraph <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.igraph()", "is_igraph()")
+  lifecycle::deprecate_warn("2.0.0", "is.igraph()", "is_igraph()")
   is_igraph(graph = graph)
 } # nocov end
 #   IGraph R package
@@ -56,19 +56,6 @@ is_igraph <- function(graph) {
   TRUE
 }
 
-#' Incident vertices of some graph edges
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' Use [ends()].
-#' @inheritParams ends
-#' @export
-#' @keywords internal
-get.edge <- function(graph, id) {
-  lifecycle::deprecate_stop("2.1.0", "get.edge()", "ends()")
-}
-
-
 #' Head of the edge(s) in a graph
 #'
 #' For undirected graphs, head and tail is not defined.  In this case
diff --git a/R/bipartite.R b/R/bipartite.R
index 5e640313588..24f2d63ebda 100644
--- a/R/bipartite.R
+++ b/R/bipartite.R
@@ -10,7 +10,7 @@
 #' @export
 bipartite.projection.size <- function(graph, types = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.projection.size()",
     "bipartite_projection_size()"
@@ -37,7 +37,7 @@ bipartite.projection <- function(
   remove.type = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.projection()",
     "bipartite_projection()"
@@ -64,7 +64,7 @@ bipartite.projection <- function(
 #' @export
 bipartite.mapping <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "bipartite.mapping()",
     "bipartite_mapping()"
diff --git a/R/centrality.R b/R/centrality.R
index f239487876f..0cec52a6a44 100644
--- a/R/centrality.R
+++ b/R/centrality.R
@@ -10,7 +10,7 @@
 #' @export
 subgraph.centrality <- function(graph, diag = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "subgraph.centrality()",
     "subgraph_centrality()"
@@ -39,7 +39,7 @@ page.rank <- function(
   options = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "page.rank()", "page_rank()")
+  lifecycle::deprecate_warn("2.0.0", "page.rank()", "page_rank()")
   page_rank(
     graph = graph,
     algo = algo,
@@ -69,7 +69,7 @@ hub.score <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_warn("2.0.0", "hub.score()", "hits_scores()")
+  lifecycle::deprecate_stop("2.0.0", "hub.score()", "hits_scores()")
   hub_score(graph = graph, scale = scale, weights = weights, options = options)
 } # nocov end
 
@@ -90,7 +90,7 @@ authority.score <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_warn("2.0.0", "authority.score()", "hits_scores()")
+  lifecycle::deprecate_stop("2.0.0", "authority.score()", "hits_scores()")
   authority_score(
     graph = graph,
     scale = scale,
@@ -117,7 +117,7 @@ graph.strength <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.strength()", "strength()")
+  lifecycle::deprecate_warn("2.0.0", "graph.strength()", "strength()")
   strength(
     graph = graph,
     vids = vids,
@@ -151,7 +151,7 @@ graph.eigen <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.eigen()", "spectrum()")
+  lifecycle::deprecate_warn("2.0.0", "graph.eigen()", "spectrum()")
   spectrum(
     graph = graph,
     algorithm = algorithm,
@@ -172,7 +172,7 @@ graph.eigen <- function(
 #' @export
 graph.diversity <- function(graph, weights = NULL, vids = V(graph)) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.diversity()", "diversity()")
+  lifecycle::deprecate_warn("2.0.0", "graph.diversity()", "diversity()")
   diversity(graph = graph, weights = weights, vids = vids)
 } # nocov end
 
@@ -194,7 +194,7 @@ evcent <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "evcent()", "eigen_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "evcent()", "eigen_centrality()")
   eigen_centrality(
     graph = graph,
     directed = directed,
@@ -222,7 +222,7 @@ edge.betweenness <- function(
   cutoff = -1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "edge.betweenness()", "edge_betweenness()")
+  lifecycle::deprecate_warn("2.0.0", "edge.betweenness()", "edge_betweenness()")
   edge_betweenness(
     graph = graph,
     e = e,
@@ -252,7 +252,7 @@ bonpow <- function(
   sparse = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "bonpow()", "power_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "bonpow()", "power_centrality()")
   power_centrality(
     graph = graph,
     nodes = nodes,
@@ -285,7 +285,7 @@ alpha.centrality <- function(
   sparse = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "alpha.centrality()", "alpha_centrality()")
+  lifecycle::deprecate_warn("2.0.0", "alpha.centrality()", "alpha_centrality()")
   alpha_centrality(
     graph = graph,
     nodes = nodes,
@@ -336,7 +336,7 @@ estimate_betweenness <- function(
   cutoff,
   weights = NULL
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_betweenness()",
     "betweenness()",
@@ -498,7 +498,7 @@ estimate_edge_betweenness <- function(
   cutoff,
   weights = NULL
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_edge_betweenness()",
     "edge_betweenness()",
@@ -611,7 +611,7 @@ estimate_closeness <- function(
   weights = NULL,
   normalized = FALSE
 ) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "estimate_closeness()",
     "closeness()",
@@ -961,7 +961,7 @@ arpack <- function(
   complex = !sym
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "arpack(options = 'must be a list')",
       details = c(
@@ -1170,7 +1170,7 @@ spectrum <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "spectrum(options = 'must be a list')",
       details = c(
@@ -1299,7 +1299,7 @@ eigen_centrality <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "eigen_centrality(options = 'must be a list')",
       details = c(
@@ -1311,13 +1311,13 @@ eigen_centrality <- function(
 
   if (lifecycle::is_present(scale)) {
     if (isTRUE(scale)) {
-      lifecycle::deprecate_soft(
+      lifecycle::deprecate_warn(
         "2.1.1",
         "eigen_centrality(scale)",
         details = "eigen_centrality() will always behave as if scale=TRUE were used."
       )
     } else {
-      lifecycle::deprecate_warn(
+      lifecycle::deprecate_stop(
         "2.1.1",
         "eigen_centrality(scale = 'always as if TRUE')",
         details = "Normalization is always performed"
@@ -1522,9 +1522,9 @@ authority_score <- function(
   weights = NULL,
   options = arpack_defaults()
 ) {
-  lifecycle::deprecate_soft("2.1.0", "authority_score()", "hits_scores()")
+  lifecycle::deprecate_warn("2.1.0", "authority_score()", "hits_scores()")
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       I("arpack_defaults"),
       "arpack_defaults()",
@@ -1567,9 +1567,9 @@ hub_score <- function(
   weights = NULL,
   options = arpack_defaults()
 ) {
-  lifecycle::deprecate_soft("2.0.3", "hub_score()", "hits_scores()")
+  lifecycle::deprecate_warn("2.0.3", "hub_score()", "hits_scores()")
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       I("arpack_defaults"),
       "arpack_defaults()",
diff --git a/R/centralization.R b/R/centralization.R
index bd6dfb570ef..e0655d7f295 100644
--- a/R/centralization.R
+++ b/R/centralization.R
@@ -10,7 +10,7 @@
 #' @export
 centralize.scores <- function(scores, theoretical.max = 0, normalized = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "centralize.scores()", "centralize()")
+  lifecycle::deprecate_warn("2.0.0", "centralize.scores()", "centralize()")
   centralize(
     scores = scores,
     theoretical.max = theoretical.max,
@@ -35,7 +35,7 @@ centralization.evcent.tmax <- function(
   scale = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.evcent.tmax()",
     "centr_eigen_tmax()"
@@ -66,7 +66,7 @@ centralization.evcent <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "centralization.evcent()", "centr_eigen()")
+  lifecycle::deprecate_warn("2.0.0", "centralization.evcent()", "centr_eigen()")
   centr_eigen(
     graph = graph,
     directed = directed,
@@ -93,7 +93,7 @@ centralization.degree.tmax <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.degree.tmax()",
     "centr_degree_tmax()"
@@ -118,7 +118,7 @@ centralization.degree <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.degree()",
     "centr_degree()"
@@ -147,7 +147,7 @@ centralization.closeness.tmax <- function(
   mode = c("out", "in", "all", "total")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.closeness.tmax()",
     "centr_clo_tmax()"
@@ -171,7 +171,7 @@ centralization.closeness <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.closeness()",
     "centr_clo()"
@@ -195,7 +195,7 @@ centralization.betweenness.tmax <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.betweenness.tmax()",
     "centr_betw_tmax()"
@@ -219,7 +219,7 @@ centralization.betweenness <- function(
   normalized = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "centralization.betweenness()",
     "centr_betw()"
@@ -404,7 +404,7 @@ centr_degree_tmax <- function(
   loops
 ) {
   if (!lifecycle::is_present(loops)) {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       when = "2.0.0",
       what = "centr_degree_tmax(loops = 'must be explicit')",
       details = "The default value (currently `FALSE`) will be dropped in the next release. Add an explicit value for the `loops` argument."
@@ -658,7 +658,7 @@ centr_eigen <- function(
   normalized = TRUE
 ) {
   if (lifecycle::is_present(scale)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "centr_eigen(scale = )",
       details = "The function always behaves as if `scale = TRUE`.
@@ -708,7 +708,7 @@ centr_eigen_tmax <- function(
   scale = deprecated()
 ) {
   if (lifecycle::is_present(scale)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "centr_eigen_tmax(scale = )",
       details = "The function always behaves as if `scale = TRUE`.
diff --git a/R/cliques.R b/R/cliques.R
index 4bd6018334c..9d3ce765399 100644
--- a/R/cliques.R
+++ b/R/cliques.R
@@ -10,7 +10,7 @@
 #' @export
 maximal.independent.vertex.sets <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximal.independent.vertex.sets()",
     "max_ivs()"
@@ -35,7 +35,7 @@ maximal.cliques.count <- function(
   subset = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "maximal.cliques.count()",
     "count_max_cliques()"
@@ -61,7 +61,7 @@ maximal.cliques <- function(
   file = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "maximal.cliques()", "max_cliques()")
+  lifecycle::deprecate_warn("2.0.0", "maximal.cliques()", "max_cliques()")
   max_cliques(graph = graph, min = min, max = max, subset = subset, file = file)
 } # nocov end
 
@@ -77,7 +77,7 @@ maximal.cliques <- function(
 #' @export
 largest.independent.vertex.sets <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "largest.independent.vertex.sets()",
     "largest_ivs()"
@@ -97,7 +97,7 @@ largest.independent.vertex.sets <- function(graph) {
 #' @export
 largest.cliques <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "largest.cliques()", "largest_cliques()")
+  lifecycle::deprecate_warn("2.0.0", "largest.cliques()", "largest_cliques()")
   largest_cliques(graph = graph)
 } # nocov end
 
@@ -113,7 +113,7 @@ largest.cliques <- function(graph) {
 #' @export
 independent.vertex.sets <- function(graph, min = NULL, max = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "independent.vertex.sets()", "ivs()")
+  lifecycle::deprecate_warn("2.0.0", "independent.vertex.sets()", "ivs()")
   ivs(graph = graph, min = min, max = max)
 } # nocov end
 
@@ -129,7 +129,7 @@ independent.vertex.sets <- function(graph, min = NULL, max = NULL) {
 #' @export
 independence.number <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "independence.number()", "ivs_size()")
+  lifecycle::deprecate_warn("2.0.0", "independence.number()", "ivs_size()")
   ivs_size(graph = graph)
 } # nocov end
 
@@ -145,7 +145,7 @@ independence.number <- function(graph) {
 #' @export
 clique.number <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "clique.number()", "clique_num()")
+  lifecycle::deprecate_warn("2.0.0", "clique.number()", "clique_num()")
   clique_num(graph = graph)
 } # nocov end
 #   IGraph R package
@@ -615,7 +615,7 @@ max_ivs <- function(graph) {
 #' @inheritParams max_ivs
 #' @keywords internal
 maximal_ivs <- function(graph) {
-  lifecycle::deprecate_soft("2.1.0", "maximal_ivs()", "max_ivs()")
+  lifecycle::deprecate_warn("2.1.0", "maximal_ivs()", "max_ivs()")
   max_ivs(graph)
 }
 
diff --git a/R/cohesive.blocks.R b/R/cohesive.blocks.R
index 35844360284..202ed43dad8 100644
--- a/R/cohesive.blocks.R
+++ b/R/cohesive.blocks.R
@@ -10,7 +10,7 @@
 #' @export
 exportPajek <- function(blocks, graph, file, project.file = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "exportPajek()", "export_pajek()")
+  lifecycle::deprecate_warn("2.0.0", "exportPajek()", "export_pajek()")
   export_pajek(
     blocks = blocks,
     graph = graph,
@@ -35,7 +35,7 @@ plotHierarchy <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "plotHierarchy()", "plot_hierarchy()")
+  lifecycle::deprecate_warn("2.0.0", "plotHierarchy()", "plot_hierarchy()")
   plot_hierarchy(blocks = blocks, layout = layout, ...)
 } # nocov end
 
@@ -51,7 +51,7 @@ plotHierarchy <- function(
 #' @export
 maxcohesion <- function(blocks) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "maxcohesion()", "max_cohesion()")
+  lifecycle::deprecate_warn("2.0.0", "maxcohesion()", "max_cohesion()")
   max_cohesion(blocks = blocks)
 } # nocov end
 
@@ -68,7 +68,7 @@ maxcohesion <- function(blocks) {
 #' @export
 graph.cohesion <- function(x, ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.cohesion()", "cohesion()")
+  lifecycle::deprecate_warn("2.0.0", "graph.cohesion()", "cohesion()")
   cohesion(x = x, ...)
 } # nocov end
 
@@ -84,7 +84,7 @@ graph.cohesion <- function(x, ...) {
 #' @export
 cohesive.blocks <- function(graph, labels = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cohesive.blocks()", "cohesive_blocks()")
+  lifecycle::deprecate_warn("2.0.0", "cohesive.blocks()", "cohesive_blocks()")
   cohesive_blocks(graph = graph, labels = labels)
 } # nocov end
 
@@ -100,7 +100,7 @@ cohesive.blocks <- function(graph, labels = TRUE) {
 #' @export
 blockGraphs <- function(blocks, graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "blockGraphs()",
     "graphs_from_cohesive_blocks()"
diff --git a/R/community.R b/R/community.R
index 352f534ba11..0d9b8cf3781 100644
--- a/R/community.R
+++ b/R/community.R
@@ -16,7 +16,7 @@ create.communities <- function(
   modularity = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "create.communities()", "make_clusters()")
+  lifecycle::deprecate_warn("2.0.0", "create.communities()", "make_clusters()")
   make_clusters(
     graph = graph,
     membership = membership,
@@ -45,7 +45,7 @@ walktrap.community <- function(
   membership = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "walktrap.community()",
     "cluster_walktrap()"
@@ -85,7 +85,7 @@ spinglass.community <- function(
   gamma.minus = 1.0
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "spinglass.community()",
     "cluster_spinglass()"
@@ -118,7 +118,7 @@ spinglass.community <- function(
 #' @export
 showtrace <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "showtrace()", "show_trace()")
+  lifecycle::deprecate_warn("2.0.0", "showtrace()", "show_trace()")
   show_trace(communities = communities)
 } # nocov end
 
@@ -134,7 +134,7 @@ showtrace <- function(communities) {
 #' @export
 optimal.community <- function(graph, weights = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "optimal.community()", "cluster_optimal()")
+  lifecycle::deprecate_warn("2.0.0", "optimal.community()", "cluster_optimal()")
   cluster_optimal(graph = graph, weights = weights)
 } # nocov end
 
@@ -150,7 +150,7 @@ optimal.community <- function(graph, weights = NULL) {
 #' @export
 multilevel.community <- function(graph, weights = NULL, resolution = 1) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "multilevel.community()",
     "cluster_louvain()"
@@ -176,7 +176,7 @@ mod.matrix <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "mod.matrix()", "modularity_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "mod.matrix()", "modularity_matrix()")
   modularity_matrix(
     graph = graph,
     membership = membership,
@@ -207,7 +207,7 @@ leading.eigenvector.community <- function(
   env = parent.frame()
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "leading.eigenvector.community()",
     "cluster_leading_eigen()"
@@ -243,7 +243,7 @@ label.propagation.community <- function(
   fixed = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "label.propagation.community()",
     "cluster_label_prop()"
@@ -270,7 +270,7 @@ label.propagation.community <- function(
 #' @export
 is.hierarchical <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.hierarchical()", "is_hierarchical()")
+  lifecycle::deprecate_warn("2.0.0", "is.hierarchical()", "is_hierarchical()")
   is_hierarchical(communities = communities)
 } # nocov end
 
@@ -292,7 +292,7 @@ infomap.community <- function(
   modularity = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "infomap.community()", "cluster_infomap()")
+  lifecycle::deprecate_warn("2.0.0", "infomap.community()", "cluster_infomap()")
   cluster_infomap(
     graph = graph,
     e.weights = e.weights,
@@ -320,7 +320,7 @@ fastgreedy.community <- function(
   weights = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "fastgreedy.community()",
     "cluster_fast_greedy()"
@@ -355,7 +355,7 @@ edge.betweenness.community <- function(
   membership = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.betweenness.community()",
     "cluster_edge_betweenness()"
@@ -384,7 +384,7 @@ edge.betweenness.community <- function(
 #' @export
 dendPlot <- function(x, mode = igraph_opt("dend.plot.type"), ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "dendPlot()", "plot_dendrogram()")
+  lifecycle::deprecate_warn("2.0.0", "dendPlot()", "plot_dendrogram()")
   plot_dendrogram(x = x, mode = mode, ...)
 } # nocov end
 
@@ -400,7 +400,7 @@ dendPlot <- function(x, mode = igraph_opt("dend.plot.type"), ...) {
 #' @export
 cutat <- function(communities, no, steps) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cutat()", "cut_at()")
+  lifecycle::deprecate_warn("2.0.0", "cutat()", "cut_at()")
   cut_at(communities = communities, no = no, steps = steps)
 } # nocov end
 
@@ -420,7 +420,7 @@ contract.vertices <- function(
   vertex.attr.comb = igraph_opt("vertex.attr.comb")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "contract.vertices()", "contract()")
+  lifecycle::deprecate_warn("2.0.0", "contract.vertices()", "contract()")
   contract(
     graph = graph,
     mapping = mapping,
@@ -440,7 +440,7 @@ contract.vertices <- function(
 #' @export
 code.length <- function(communities) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "code.length()", "code_len()")
+  lifecycle::deprecate_warn("2.0.0", "code.length()", "code_len()")
   code_len(communities = communities)
 } # nocov end
 #   IGraph R package
@@ -951,7 +951,7 @@ modularity_matrix <- function(
   ensure_igraph(graph)
 
   if (!missing(membership)) {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "modularity_matrix(membership = 'is no longer used')"
     )
@@ -1636,7 +1636,7 @@ cluster_leiden <- function(
   check_dots_empty()
 
   if (lifecycle::is_present(resolution_parameter)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "cluster_leiden(resolution_parameter)",
       "cluster_leiden(resolution)"
@@ -2229,7 +2229,7 @@ cluster_leading_eigen <- function(
   env = parent.frame()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "cluster_leading_eigen(options = 'must be a list')",
       details = c(
@@ -2358,7 +2358,7 @@ cluster_label_prop <- function(
   fixed = NULL
 ) {
   if (...length() > 0) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "cluster_label_prop(... = )",
       details = "Arguments `initial` and `fixed` must be named."
diff --git a/R/components.R b/R/components.R
index fab025773b2..1c0ab7b0a12 100644
--- a/R/components.R
+++ b/R/components.R
@@ -10,7 +10,7 @@
 #' @export
 no.clusters <- function(graph, mode = c("weak", "strong")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "no.clusters()", "count_components()")
+  lifecycle::deprecate_warn("2.0.0", "no.clusters()", "count_components()")
   count_components(graph = graph, mode = mode)
 } # nocov end
 
@@ -31,7 +31,7 @@ decompose.graph <- function(
   min.vertices = 0
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "decompose.graph()", "decompose()")
+  lifecycle::deprecate_warn("2.0.0", "decompose.graph()", "decompose()")
   decompose(
     graph = graph,
     mode = mode,
@@ -57,7 +57,7 @@ cluster.distribution <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "cluster.distribution()",
     "component_distribution()"
@@ -82,7 +82,7 @@ cluster.distribution <- function(
 #' @export
 biconnected.components <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "biconnected.components()",
     "biconnected_components()"
@@ -102,7 +102,7 @@ biconnected.components <- function(graph) {
 #' @export
 articulation.points <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "articulation.points()",
     "articulation_points()"
diff --git a/R/console.R b/R/console.R
index 71defc045a7..ff898e1bfe0 100644
--- a/R/console.R
+++ b/R/console.R
@@ -11,7 +11,7 @@
 #' @export
 igraph.console <- function() {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.console()", "console()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.console()", "console()")
   console()
 } # nocov end
 
diff --git a/R/conversion.R b/R/conversion.R
index 230cd369bd1..0634fb46949 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -10,7 +10,7 @@
 #' @export
 igraph.to.graphNEL <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "igraph.to.graphNEL()", "as_graphnel()")
+  lifecycle::deprecate_warn("2.0.0", "igraph.to.graphNEL()", "as_graphnel()")
   as_graphnel(graph = graph)
 } # nocov end
 
@@ -31,7 +31,7 @@ igraph.from.graphNEL <- function(
   unlist.attrs = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "igraph.from.graphNEL()",
     "graph_from_graphnel()"
@@ -60,7 +60,7 @@ graph.adjlist <- function(
   duplicate = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.adjlist()", "graph_from_adj_list()")
+  lifecycle::deprecate_warn("2.0.0", "graph.adjlist()", "graph_from_adj_list()")
   graph_from_adj_list(adjlist = adjlist, mode = mode, duplicate = duplicate)
 } # nocov end
 
@@ -82,7 +82,7 @@ get.incidence <- function(
   sparse = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "get.incidence()",
     "as_biadjacency_matrix()"
@@ -108,7 +108,7 @@ get.incidence <- function(
 #' @export
 get.edgelist <- function(graph, names = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.edgelist()", "as_edgelist()")
+  lifecycle::deprecate_warn("2.0.0", "get.edgelist()", "as_edgelist()")
   as_edgelist(graph = graph, names = names)
 } # nocov end
 
@@ -124,7 +124,7 @@ get.edgelist <- function(graph, names = TRUE) {
 #' @export
 get.data.frame <- function(x, what = c("edges", "vertices", "both")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.data.frame()", "as_data_frame()")
+  lifecycle::deprecate_warn("2.0.0", "get.data.frame()", "as_data_frame()")
   as_data_frame(x = x, what = what)
 } # nocov end
 
@@ -147,7 +147,7 @@ get.adjacency <- function(
   sparse = igraph_opt("sparsematrices")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjacency()", "as_adjacency_matrix()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjacency()", "as_adjacency_matrix()")
   as_adjacency_matrix(
     graph = graph,
     type = type,
@@ -175,7 +175,7 @@ get.adjlist <- function(
   multiple = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjlist()", "as_adj_list()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjlist()", "as_adj_list()")
   as_adj_list(graph = graph, mode = mode, loops = loops, multiple = multiple)
 } # nocov end
 
@@ -195,7 +195,7 @@ get.adjedgelist <- function(
   loops = c("twice", "once", "ignore")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "get.adjedgelist()", "as_adj_edge_list()")
+  lifecycle::deprecate_warn("2.0.0", "get.adjedgelist()", "as_adj_edge_list()")
   as_adj_edge_list(graph = graph, mode = mode, loops = loops)
 } # nocov end
 #   IGraph R package
@@ -232,7 +232,7 @@ get.adjacency.dense <- function(
 
   if (is.logical(loops)) {
     loops <- ifelse(loops, "once", "ignore")
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.0",
       "get.adjacency.dense(loops = 'must be a character')",
       details = sprintf(
@@ -412,7 +412,7 @@ as_adj <- function(
   names = TRUE,
   sparse = igraph_opt("sparsematrices")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as_adj()", "as_adjacency_matrix()")
+  lifecycle::deprecate_warn("2.1.0", "as_adj()", "as_adjacency_matrix()")
 
   as_adjacency_matrix(
     graph = graph,
@@ -1129,7 +1129,7 @@ as_biadjacency_matrix <- function(
 #' @export
 as_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "as_incidence_matrix()",
     "as_biadjacency_matrix()"
@@ -1367,7 +1367,7 @@ as.directed <- function(
   graph,
   mode = c("mutual", "arbitrary", "random", "acyclic")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as.directed()", "as_directed()")
+  lifecycle::deprecate_warn("2.1.0", "as.directed()", "as_directed()")
   as_directed(graph, mode = mode)
 }
 
@@ -1386,7 +1386,7 @@ as.undirected <- function(
   mode = c("collapse", "each", "mutual"),
   edge.attr.comb = igraph_opt("edge.attr.comb")
 ) {
-  lifecycle::deprecate_soft("2.1.0", "as.undirected()", "as_undirected()")
+  lifecycle::deprecate_warn("2.1.0", "as.undirected()", "as_undirected()")
   as_undirected(graph = graph, mode = mode, edge.attr.comb = edge.attr.comb)
 }
 
@@ -1402,7 +1402,7 @@ as.undirected <- function(
 #' @export
 graph.edgelist <- function(el, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.edgelist()",
     "graph_from_edgelist()"
@@ -1422,7 +1422,7 @@ graph.edgelist <- function(el, directed = TRUE) {
 #' @export
 graph.data.frame <- function(d, directed = TRUE, vertices = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.data.frame()",
     "graph_from_data_frame()"
diff --git a/R/decomposition.R b/R/decomposition.R
index 8c8e92b570c..47df101955e 100644
--- a/R/decomposition.R
+++ b/R/decomposition.R
@@ -16,7 +16,7 @@ is.chordal <- function(
   newgraph = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.chordal()", "is_chordal()")
+  lifecycle::deprecate_warn("2.0.0", "is.chordal()", "is_chordal()")
   is_chordal(
     graph = graph,
     alpha = alpha,
diff --git a/R/degseq.R b/R/degseq.R
index 76a4401822d..918239d17dd 100644
--- a/R/degseq.R
+++ b/R/degseq.R
@@ -14,7 +14,7 @@ is.graphical.degree.sequence <- function(
   allowed.edge.types = c("simple", "loops", "multi", "all")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "is.graphical.degree.sequence()",
     "is_graphical()"
@@ -38,7 +38,7 @@ is.graphical.degree.sequence <- function(
 #' @export
 is.degree.sequence <- function(out.deg, in.deg = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.degree.sequence()", "is_degseq()")
+  lifecycle::deprecate_warn("2.0.0", "is.degree.sequence()", "is_degseq()")
   is_degseq(out.deg = out.deg, in.deg = in.deg)
 } # nocov end
 
diff --git a/R/fit.R b/R/fit.R
index e0849b32a4c..4993d32bc4e 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -17,7 +17,7 @@ power.law.fit <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "power.law.fit()", "fit_power_law()")
+  lifecycle::deprecate_warn("2.0.0", "power.law.fit()", "fit_power_law()")
   fit_power_law(
     x = x,
     xmin = xmin,
diff --git a/R/flow.R b/R/flow.R
index 0609fce12c3..43c3f0bf35c 100644
--- a/R/flow.R
+++ b/R/flow.R
@@ -10,7 +10,7 @@
 #' @export
 vertex.disjoint.paths <- function(graph, source = NULL, target = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "vertex.disjoint.paths()",
     "vertex_disjoint_paths()"
@@ -35,7 +35,7 @@ vertex.connectivity <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "vertex.connectivity()",
     "vertex_connectivity()"
@@ -60,7 +60,7 @@ vertex.connectivity <- function(
 #' @export
 stMincuts <- function(graph, source, target, capacity = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "stMincuts()", "st_min_cuts()")
+  lifecycle::deprecate_warn("2.0.0", "stMincuts()", "st_min_cuts()")
   st_min_cuts(
     graph = graph,
     source = source,
@@ -81,7 +81,7 @@ stMincuts <- function(graph, source, target, capacity = NULL) {
 #' @export
 stCuts <- function(graph, source, target) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "stCuts()", "st_cuts()")
+  lifecycle::deprecate_warn("2.0.0", "stCuts()", "st_cuts()")
   st_cuts(graph = graph, source = source, target = target)
 } # nocov end
 
@@ -97,7 +97,7 @@ stCuts <- function(graph, source, target) {
 #' @export
 minimum.size.separators <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "minimum.size.separators()",
     "min_separators()"
@@ -117,7 +117,7 @@ minimum.size.separators <- function(graph) {
 #' @export
 minimal.st.separators <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "minimal.st.separators()",
     "min_st_separators()"
@@ -137,7 +137,7 @@ minimal.st.separators <- function(graph) {
 #' @export
 is.separator <- function(graph, candidate) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.separator()", "is_separator()")
+  lifecycle::deprecate_warn("2.0.0", "is.separator()", "is_separator()")
   is_separator(graph = graph, candidate = candidate)
 } # nocov end
 
@@ -153,7 +153,7 @@ is.separator <- function(graph, candidate) {
 #' @export
 is.minimal.separator <- function(graph, candidate) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "is.minimal.separator()",
     "is_min_separator()"
@@ -179,7 +179,7 @@ graph.mincut <- function(
   value.only = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.mincut()", "min_cut()")
+  lifecycle::deprecate_warn("2.0.0", "graph.mincut()", "min_cut()")
   min_cut(
     graph = graph,
     source = source,
@@ -201,7 +201,7 @@ graph.mincut <- function(
 #' @export
 graph.maxflow <- function(graph, source, target, capacity = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.maxflow()", "max_flow()")
+  lifecycle::deprecate_warn("2.0.0", "graph.maxflow()", "max_flow()")
   max_flow(graph = graph, source = source, target = target, capacity = capacity)
 } # nocov end
 
@@ -217,7 +217,7 @@ graph.maxflow <- function(graph, source, target, capacity = NULL) {
 #' @export
 graph.adhesion <- function(graph, checks = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.adhesion()", "adhesion()")
+  lifecycle::deprecate_warn("2.0.0", "graph.adhesion()", "adhesion()")
   adhesion(graph = graph, checks = checks)
 } # nocov end
 
@@ -238,7 +238,7 @@ edge.disjoint.paths <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.disjoint.paths()",
     "edge_connectivity()"
@@ -268,7 +268,7 @@ edge.connectivity <- function(
   checks = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "edge.connectivity()",
     "edge_connectivity()"
@@ -293,7 +293,7 @@ edge.connectivity <- function(
 #' @export
 dominator.tree <- function(graph, root, mode = c("out", "in", "all", "total")) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "dominator.tree()", "dominator_tree()")
+  lifecycle::deprecate_warn("2.0.0", "dominator.tree()", "dominator_tree()")
   dominator_tree(graph = graph, root = root, mode = mode)
 } # nocov end
 #   IGraph R package
diff --git a/R/foreign.R b/R/foreign.R
index ebf9280b01d..b493c1fdb83 100644
--- a/R/foreign.R
+++ b/R/foreign.R
@@ -25,7 +25,7 @@ write.graph <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "write.graph()", "write_graph()")
+  lifecycle::deprecate_warn("2.0.0", "write.graph()", "write_graph()")
   write_graph(graph = graph, file = file, format = format, ...)
 } # nocov end
 
@@ -55,7 +55,7 @@ read.graph <- function(
   ...
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "read.graph()", "read_graph()")
+  lifecycle::deprecate_warn("2.0.0", "read.graph()", "read_graph()")
   read_graph(file = file, format = format, ...)
 } # nocov end
 
@@ -81,7 +81,7 @@ graph.graphdb <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graph.graphdb()", "graph_from_graphdb()")
+  lifecycle::deprecate_warn("2.0.0", "graph.graphdb()", "graph_from_graphdb()")
   graph_from_graphdb(
     url = url,
     prefix = prefix,
diff --git a/R/games.R b/R/games.R
index f37cb832403..17d42f7fd94 100644
--- a/R/games.R
+++ b/R/games.R
@@ -17,7 +17,7 @@ watts.strogatz.game <- function(
   multiple = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "watts.strogatz.game()",
     "sample_smallworld()"
@@ -52,7 +52,7 @@ static.power.law.game <- function(
   finite.size.correction = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "static.power.law.game()",
     "sample_fitness_pl()"
@@ -86,7 +86,7 @@ static.fitness.game <- function(
   multiple = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "static.fitness.game()",
     "sample_fitness()"
@@ -118,7 +118,7 @@ sbm.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "sbm.game()", "sample_sbm()")
+  lifecycle::deprecate_warn("2.0.0", "sbm.game()", "sample_sbm()")
   sample_sbm(
     n = n,
     pref.matrix = pref.matrix,
@@ -148,7 +148,7 @@ preference.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "preference.game()", "sample_pref()")
+  lifecycle::deprecate_warn("2.0.0", "preference.game()", "sample_pref()")
   sample_pref(
     nodes = nodes,
     types = types,
@@ -178,7 +178,7 @@ lastcit.game <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "lastcit.game()", "sample_last_cit()")
+  lifecycle::deprecate_warn("2.0.0", "lastcit.game()", "sample_last_cit()")
   sample_last_cit(
     n = n,
     edges = edges,
@@ -200,7 +200,7 @@ lastcit.game <- function(
 #' @export
 k.regular.game <- function(no.of.nodes, k, directed = FALSE, multiple = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "k.regular.game()", "sample_k_regular()")
+  lifecycle::deprecate_warn("2.0.0", "k.regular.game()", "sample_k_regular()")
   sample_k_regular(
     no.of.nodes = no.of.nodes,
     k = k,
@@ -226,7 +226,7 @@ interconnected.islands.game <- function(
   n.inter
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "interconnected.islands.game()",
     "sample_islands()"
@@ -251,7 +251,7 @@ interconnected.islands.game <- function(
 #' @export
 grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "grg.game()", "sample_grg()")
+  lifecycle::deprecate_warn("2.0.0", "grg.game()", "sample_grg()")
   sample_grg(nodes = nodes, radius = radius, torus = torus, coords = coords)
 } # nocov end
 
@@ -267,7 +267,7 @@ grg.game <- function(nodes, radius, torus = FALSE, coords = FALSE) {
 #' @export
 growing.random.game <- function(n, m = 1, directed = TRUE, citation = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "growing.random.game()",
     "sample_growing()"
@@ -293,7 +293,7 @@ forest.fire.game <- function(
   directed = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "forest.fire.game()",
     "sample_forestfire()"
@@ -326,7 +326,7 @@ establishment.game <- function(
   directed = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "establishment.game()", "sample_traits()")
+  lifecycle::deprecate_warn("2.0.0", "establishment.game()", "sample_traits()")
   sample_traits(
     nodes = nodes,
     types = types,
@@ -353,7 +353,7 @@ degree.sequence.game <- function(
   method = c("simple", "vl", "simple.no.multiple", "simple.no.multiple.uniform")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "degree.sequence.game()",
     "sample_degseq()"
@@ -377,7 +377,7 @@ connect.neighborhood <- function(
   mode = c("all", "out", "in", "total")
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "connect.neighborhood()", "connect()")
+  lifecycle::deprecate_warn("2.0.0", "connect.neighborhood()", "connect()")
   connect(graph = graph, order = order, mode = mode)
 } # nocov end
 
@@ -400,7 +400,7 @@ citing.cited.type.game <- function(
   attr = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "citing.cited.type.game()",
     "sample_cit_cit_types()"
@@ -434,7 +434,7 @@ cited.type.game <- function(
   attr = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "cited.type.game()", "sample_cit_types()")
+  lifecycle::deprecate_warn("2.0.0", "cited.type.game()", "sample_cit_types()")
   sample_cit_types(
     n = n,
     edges = edges,
@@ -464,7 +464,7 @@ callaway.traits.game <- function(
   directed = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "callaway.traits.game()",
     "sample_traits_callaway()"
@@ -499,7 +499,7 @@ bipartite.random.game <- function(
   mode = c("out", "in", "all")
 ) {
   # nocov start
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "2.0.0",
     "bipartite.random.game()",
     details = "Use sample_bipartite_gnp() or sample_bipartite_gnm()"
@@ -538,7 +538,7 @@ barabasi.game <- function(
   start.graph = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "barabasi.game()", "sample_pa()")
+  lifecycle::deprecate_warn("2.0.0", "barabasi.game()", "sample_pa()")
   sample_pa(
     n = n,
     power = power,
@@ -576,7 +576,7 @@ ba.game <- function(
   start.graph = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "ba.game()", "sample_pa()")
+  lifecycle::deprecate_warn("2.0.0", "ba.game()", "sample_pa()")
   sample_pa(
     n = n,
     power = power,
@@ -609,7 +609,7 @@ asymmetric.preference.game <- function(
   loops = FALSE
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "asymmetric.preference.game()",
     "sample_asym_pref()"
@@ -650,7 +650,7 @@ aging.barabasi.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.barabasi.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.barabasi.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -696,7 +696,7 @@ aging.ba.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.ba.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.ba.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -742,7 +742,7 @@ aging.prefatt.game <- function(
   time.window = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "aging.prefatt.game()", "sample_pa_age()")
+  lifecycle::deprecate_warn("2.0.0", "aging.prefatt.game()", "sample_pa_age()")
   sample_pa_age(
     n = n,
     pa.exp = pa.exp,
@@ -1158,10 +1158,10 @@ erdos.renyi.game <- function(
   type <- igraph_match_arg(type)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft("0.8.0", "erdos.renyi.game()", "sample_gnp()")
+    lifecycle::deprecate_warn("0.8.0", "erdos.renyi.game()", "sample_gnp()")
     sample_gnp(n = n, p = p.or.m, directed = directed, loops = loops)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft("0.8.0", "erdos.renyi.game()", "sample_gnm()")
+    lifecycle::deprecate_warn("0.8.0", "erdos.renyi.game()", "sample_gnm()")
     sample_gnm(n = n, m = p.or.m, directed = directed, loops = loops)
   }
 }
@@ -1178,10 +1178,10 @@ random.graph.game <- function(
   type <- igraph_match_arg(type)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft("0.8.0", "random.graph.game()", "sample_gnp()")
+    lifecycle::deprecate_warn("0.8.0", "random.graph.game()", "sample_gnp()")
     sample_gnp(n = n, p = p.or.m, directed = directed, loops = loops)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft("0.8.0", "random.graph.game()", "sample_gnm()")
+    lifecycle::deprecate_warn("0.8.0", "random.graph.game()", "sample_gnm()")
     sample_gnm(n = n, m = p.or.m, directed = directed, loops = loops)
   }
 }
@@ -1388,7 +1388,7 @@ sample_degseq <- function(
   )
 
   if (method == "simple") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be configuration instead of simple')"
     )
@@ -1396,7 +1396,7 @@ sample_degseq <- function(
   }
 
   if (method == "simple.no.multiple") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be fast.heur.simple instead of simple.no.multiple')"
     )
@@ -1404,7 +1404,7 @@ sample_degseq <- function(
   }
 
   if (method == "simple.no.multiple.uniform") {
-    lifecycle::deprecate_warn(
+    lifecycle::deprecate_stop(
       "2.1.0",
       "sample_degseq(method = 'must be configuration.simple instead of simple.no.multiple.uniform')"
     )
@@ -2474,14 +2474,14 @@ sample_bipartite <- function(
   mode <- igraph_match_arg(mode)
 
   if (type == "gnp") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "sample_bipartite()",
       "sample_bipartite_gnp()"
     )
     sample_bipartite_gnp(n1, n2, p, directed = directed, mode = mode)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.2.0",
       "sample_bipartite()",
       "sample_bipartite_gnm()"
@@ -2497,14 +2497,14 @@ sample_bipartite <- function(
 #' @export
 bipartite <- function(..., type = NULL) {
   if (is.null(type) || type == "gnp") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.3",
       "bipartite()",
       "bipartite_gnp()"
     )
     bipartite_gnp(...)
   } else if (type == "gnm") {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.1.3",
       "bipartite()",
       "bipartite_gnm()"
diff --git a/R/glet.R b/R/glet.R
index 252b227cfe8..8122a59f55f 100644
--- a/R/glet.R
+++ b/R/glet.R
@@ -16,7 +16,7 @@ graphlets.project <- function(
   Mu = rep(1, length(cliques))
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "graphlets.project()", "graphlet_proj()")
+  lifecycle::deprecate_warn("2.0.0", "graphlets.project()", "graphlet_proj()")
   graphlet_proj(
     graph = graph,
     weights = weights,
@@ -38,7 +38,7 @@ graphlets.project <- function(
 #' @export
 graphlets.candidate.basis <- function(graph, weights = NULL) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graphlets.candidate.basis()",
     "graphlet_basis()"
diff --git a/R/hrg.R b/R/hrg.R
index b8eb3c4a860..83f65d16c7d 100644
--- a/R/hrg.R
+++ b/R/hrg.R
@@ -16,7 +16,7 @@ hrg.predict <- function(
   num.bins = 25
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.predict()", "predict_edges()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.predict()", "predict_edges()")
   predict_edges(
     graph = graph,
     hrg = hrg,
@@ -38,7 +38,7 @@ hrg.predict <- function(
 #' @export
 hrg.fit <- function(graph, hrg = NULL, start = FALSE, steps = 0) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.fit()", "fit_hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.fit()", "fit_hrg()")
   fit_hrg(graph = graph, hrg = hrg, start = start, steps = steps)
 } # nocov end
 
@@ -54,7 +54,7 @@ hrg.fit <- function(graph, hrg = NULL, start = FALSE, steps = 0) {
 #' @export
 hrg.game <- function(hrg) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.game()", "sample_hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.game()", "sample_hrg()")
   sample_hrg(hrg = hrg)
 } # nocov end
 
@@ -70,7 +70,7 @@ hrg.game <- function(hrg) {
 #' @export
 hrg.dendrogram <- function(hrg) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.dendrogram()", "hrg_tree()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.dendrogram()", "hrg_tree()")
   hrg_tree(hrg = hrg)
 } # nocov end
 
@@ -86,7 +86,7 @@ hrg.dendrogram <- function(hrg) {
 #' @export
 hrg.create <- function(graph, prob) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.create()", "hrg()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.create()", "hrg()")
   hrg(graph = graph, prob = prob)
 } # nocov end
 
@@ -107,7 +107,7 @@ hrg.consensus <- function(
   num.samples = 10000
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hrg.consensus()", "consensus_tree()")
+  lifecycle::deprecate_warn("2.0.0", "hrg.consensus()", "consensus_tree()")
   consensus_tree(
     graph = graph,
     hrg = hrg,
diff --git a/R/incidence.R b/R/incidence.R
index 3937ad025af..886aa1a9f8c 100644
--- a/R/incidence.R
+++ b/R/incidence.R
@@ -17,7 +17,7 @@ graph.incidence <- function(
   add.names = NULL
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "graph.incidence()",
     "graph_from_biadjacency_matrix()"
@@ -271,7 +271,7 @@ graph_from_biadjacency_matrix <- function(
 #' @export
 from_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "graph_from_incidence_matrix()",
     "graph_from_biadjacency_matrix()"
@@ -294,7 +294,7 @@ from_incidence_matrix <- function(...) {
 #' @export
 graph_from_incidence_matrix <- function(...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "1.6.0",
     "graph_from_incidence_matrix()",
     "graph_from_biadjacency_matrix()"
diff --git a/R/interface.R b/R/interface.R
index 7533cfb8285..9cd977cb47c 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -10,7 +10,7 @@
 #' @export
 is.directed <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "is.directed()", "is_directed()")
+  lifecycle::deprecate_warn("2.0.0", "is.directed()", "is_directed()")
   is_directed(graph = graph)
 } # nocov end
 
@@ -26,7 +26,7 @@ is.directed <- function(graph) {
 #' @export
 delete.vertices <- function(graph, v) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "delete.vertices()", "delete_vertices()")
+  lifecycle::deprecate_warn("2.0.0", "delete.vertices()", "delete_vertices()")
   delete_vertices(graph = graph, v = v)
 } # nocov end
 
@@ -42,7 +42,7 @@ delete.vertices <- function(graph, v) {
 #' @export
 delete.edges <- function(graph, edges) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "delete.edges()", "delete_edges()")
+  lifecycle::deprecate_warn("2.0.0", "delete.edges()", "delete_edges()")
   delete_edges(graph = graph, edges = edges)
 } # nocov end
 
@@ -58,7 +58,7 @@ delete.edges <- function(graph, edges) {
 #' @export
 add.vertices <- function(graph, nv, ..., attr = list()) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "add.vertices()", "add_vertices()")
+  lifecycle::deprecate_warn("2.0.0", "add.vertices()", "add_vertices()")
   add_vertices(graph = graph, nv = nv, attr = attr, ...)
 } # nocov end
 
@@ -74,7 +74,7 @@ add.vertices <- function(graph, nv, ..., attr = list()) {
 #' @export
 add.edges <- function(graph, edges, ..., attr = list()) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "add.edges()", "add_edges()")
+  lifecycle::deprecate_warn("2.0.0", "add.edges()", "add_edges()")
   add_edges(graph = graph, edges = edges, attr = attr, ...)
 } # nocov end
 #   IGraph R package
@@ -474,7 +474,7 @@ el_to_vec <- function(x, call = rlang::caller_env()) {
         "get_edge_ids(vp = 'is not allowed to be a 2 times 2 matrix')"
       )
     } else if (nrow == 2) {
-      lifecycle::deprecate_warn(
+      lifecycle::deprecate_stop(
         "2.1.5",
         "get_edge_ids(vp = 'supplied as a matrix should be a n times 2 matrix, not 2 times n')",
         details = "either transpose the matrix with t() or convert it to a data.frame with two columns."
@@ -584,9 +584,9 @@ get.edge.ids <- function(
       lifecycle::deprecate_stop("2.0.0", "get.edge.ids(multi = )")
     }
 
-    lifecycle::deprecate_soft("2.0.0", "get.edge.ids(multi = )")
+    lifecycle::deprecate_warn("2.0.0", "get.edge.ids(multi = )")
   }
-  lifecycle::deprecate_soft("2.1.0", "get.edge.ids()", "get_edge_ids()")
+  lifecycle::deprecate_warn("2.1.0", "get.edge.ids()", "get_edge_ids()")
   get_edge_ids(graph = graph, vp = vp, directed = directed, error = error)
 }
 
diff --git a/R/iterators.R b/R/iterators.R
index 2cfd3101348..0094a7b2c27 100644
--- a/R/iterators.R
+++ b/R/iterators.R
@@ -599,21 +599,12 @@ simple_vs_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  nei <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "nei()", ".nei()")
-  }
   .innei <- function(v, mode = c("in", "all", "out", "total")) {
     .nei(v, mode = mode[1])
   }
-  innei <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "innei()", ".innei()")
-  }
   .outnei <- function(v, mode = c("out", "all", "in", "total")) {
     .nei(v, mode = mode[1])
   }
-  outnei <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "outnei()", ".outnei()")
-  }
   .inc <- function(e) {
     ## TRUE iff the vertex (in the vs) is incident
     ## to at least one edge in e
@@ -630,12 +621,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  inc <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "inc()", ".inc()")
-  }
-  adj <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "adj()", ".inc()")
-  }
   .from <- function(e) {
     ## TRUE iff the vertex is the source of at least one edge in e
     if (is.logical(e)) {
@@ -651,9 +636,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  from <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "from()", ".from()")
-  }
   .to <- function(e) {
     ## TRUE iff the vertex is the target of at least one edge in e
     if (is.logical(e)) {
@@ -669,10 +651,6 @@ simple_vs_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  to <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "to()", ".to()")
-  }
-
   graph <- get_vs_graph(x)
 
   if (is.null(graph)) {
@@ -694,18 +672,18 @@ simple_vs_index <- function(x, i, na_ok = FALSE) {
     # Functions (only visible if called or if no duplicate)
     top <- rlang::new_environment(list(
       .nei = .nei,
-      nei = nei,
+      nei = .nei,
       .innei = .innei,
-      innei = innei,
+      innei = .innei,
       .outnei = .outnei,
-      outnei = outnei,
+      outnei = .outnei,
       .inc = .inc,
-      inc = inc,
-      adj = adj,
+      inc = .inc,
+      adj = .inc,
       .from = .from,
-      from = from,
+      from = .from,
       .to = .to,
-      to = to,
+      to = .to,
       .data = list(attrs)
     ))
 
@@ -992,12 +970,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  adj <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "adj()", ".inc()")
-  }
-  inc <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "inc()", ".inc()")
-  }
   .from <- function(v) {
     ## TRUE iff the edge originates from at least one vertex in v
     on.exit(.Call(Rx_igraph_finalizer))
@@ -1010,9 +982,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  from <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "from()", ".from()")
-  }
   .to <- function(v) {
     ## TRUE iff the edge points to at least one vertex in v
     on.exit(.Call(Rx_igraph_finalizer))
@@ -1025,10 +994,6 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
     )
     tmp[as.numeric(x)]
   }
-  to <- function(...) {
-    lifecycle::deprecate_stop("2.1.0", "to()", ".to()")
-  }
-
   graph <- get_es_graph(x)
 
   if (is.null(graph)) {
@@ -1045,12 +1010,12 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
     # Functions (only visible if called or if no duplicate)
     top <- rlang::new_environment(list(
       .inc = .inc,
-      inc = inc,
-      adj = adj,
+      inc = .inc,
+      adj = .inc,
       .from = .from,
-      from = from,
+      from = .from,
       .to = .to,
-      to = to,
+      to = .to,
       `%--%` = `%--%`,
       `%->%` = `%->%`,
       `%<-%` = `%<-%`
diff --git a/R/layout.R b/R/layout.R
index 1f14bbe0fb6..cd1166e1b5b 100644
--- a/R/layout.R
+++ b/R/layout.R
@@ -10,7 +10,7 @@
 #' @export
 piecewise.layout <- function(graph, layout = layout_with_kk, ...) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "piecewise.layout()",
     "layout_components()"
@@ -38,7 +38,7 @@ layout.sugiyama <- function(
   attributes = c("default", "all", "none")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.sugiyama()",
     "layout_with_sugiyama()"
@@ -66,7 +66,7 @@ layout.sugiyama <- function(
 #' @export
 layout.star <- function(graph, center = V(graph)[1], order = NULL) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.star()", "layout_as_star()")
+  lifecycle::deprecate_warn("2.0.0", "layout.star()", "layout_as_star()")
   layout_as_star(graph = graph, center = center, order = order)
 } # nocov end
 
@@ -90,7 +90,7 @@ layout.norm <- function(
   zmax = 1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.norm()", "norm_coords()")
+  lifecycle::deprecate_warn("2.0.0", "layout.norm()", "norm_coords()")
   norm_coords(
     layout = layout,
     xmin = xmin,
@@ -114,7 +114,7 @@ layout.norm <- function(
 #' @export
 layout.merge <- function(graphs, layouts, method = "dla") {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.merge()", "merge_coords()")
+  lifecycle::deprecate_warn("2.0.0", "layout.merge()", "merge_coords()")
   merge_coords(graphs = graphs, layouts = layouts, method = method)
 } # nocov end
 
@@ -135,7 +135,7 @@ layout.mds <- function(
   options = arpack_defaults()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.mds()", "layout_with_mds()")
+  lifecycle::deprecate_warn("2.0.0", "layout.mds()", "layout_with_mds()")
   layout_with_mds(graph = graph, dist = dist, dim = dim, options = options)
 } # nocov end
 
@@ -151,7 +151,7 @@ layout.mds <- function(
 #' @export
 layout.grid <- function(graph, width = 0, height = 0, dim = 2) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.grid()", "layout_on_grid()")
+  lifecycle::deprecate_warn("2.0.0", "layout.grid()", "layout_on_grid()")
   layout_on_grid(graph = graph, width = width, height = height, dim = dim)
 } # nocov end
 
@@ -176,7 +176,7 @@ layout.graphopt <- function(
   max.sa.movement = 5
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.graphopt()",
     "layout_with_graphopt()"
@@ -212,7 +212,7 @@ layout.gem <- function(
   temp.init = sqrt(max(vcount(graph), 1))
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.gem()", "layout_with_gem()")
+  lifecycle::deprecate_warn("2.0.0", "layout.gem()", "layout_with_gem()")
   layout_with_gem(
     graph = graph,
     coords = coords,
@@ -246,7 +246,7 @@ layout.davidson.harel <- function(
   weight.node.edge.dist = 0.2 * (1 - edge_density(graph))
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.davidson.harel()",
     "layout_with_dh()"
@@ -283,7 +283,7 @@ layout.bipartite <- function(
   maxiter = 100
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.0.0",
     "layout.bipartite()",
     "layout_as_bipartite()"
@@ -309,7 +309,7 @@ layout.bipartite <- function(
 #' @export
 layout.auto <- function(graph, dim = 2, ...) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.auto()", "layout_nicely()")
+  lifecycle::deprecate_warn("2.0.0", "layout.auto()", "layout_nicely()")
   layout_nicely(graph = graph, dim = dim, ...)
 } # nocov end
 
@@ -890,7 +890,7 @@ as_tree <- function(...) layout_spec(layout_as_tree, ...)
 #' @keywords internal
 #' @export
 layout.reingold.tilford <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.reingold.tilford()",
     "layout_as_tree()"
@@ -955,7 +955,7 @@ in_circle <- function(...) layout_spec(layout_in_circle, ...)
 #' @keywords internal
 #' @export
 layout.circle <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.circle()", "layout_in_circle()")
+  lifecycle::deprecate_warn("2.1.0", "layout.circle()", "layout_in_circle()")
   do_call(layout_in_circle, .args = c(list(...), params))
 }
 
@@ -1144,21 +1144,6 @@ layout_on_grid <- function(graph, width = 0, height = 0, dim = 2) {
 #' @param ... Passed to `layout_on_grid()`.
 #' @export
 on_grid <- function(...) layout_spec(layout_on_grid, ...)
-
-
-#' Simple grid layout
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' Use [layout_on_grid()].
-#' @inheritParams layout_on_grid
-#' @export
-#' @export
-#' @keywords internal
-layout.grid.3d <- function(graph, width = 0, height = 0) {
-  lifecycle::deprecate_stop("2.1.0", "layout.grid.3d()", "layout_on_grid()")
-}
-
 ## ----------------------------------------------------------------
 
 #' Graph layout with vertices on the surface of a sphere
@@ -1203,7 +1188,7 @@ on_sphere <- function(...) layout_spec(layout_on_sphere, ...)
 #' @keywords internal
 #' @export
 layout.sphere <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.sphere()", "layout_on_sphere()")
+  lifecycle::deprecate_warn("2.1.0", "layout.sphere()", "layout_on_sphere()")
   do_call(layout_on_sphere, .args = c(list(...), params))
 }
 
@@ -1258,7 +1243,7 @@ randomly <- function(...) layout_spec(layout_randomly, ...)
 #' @keywords internal
 #' @export
 layout.random <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.random()", "layout_randomly()")
+  lifecycle::deprecate_warn("2.1.0", "layout.random()", "layout_randomly()")
   do_call(layout_randomly, .args = c(list(...), params))
 }
 
@@ -1624,7 +1609,7 @@ with_fr <- function(...) layout_spec(layout_with_fr, ...)
 #' @keywords internal
 #' @export
 layout.fruchterman.reingold <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.fruchterman.reingold()",
     "layout_with_fr()"
@@ -1982,7 +1967,7 @@ with_kk <- function(...) layout_spec(layout_with_kk, ...)
 #' @keywords internal
 #' @export
 layout.kamada.kawai <- function(..., params = list()) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "layout.kamada.kawai()",
     "layout_with_kk()"
@@ -2068,7 +2053,7 @@ with_lgl <- function(...) layout_spec(layout_with_lgl, ...)
 #' @keywords internal
 #' @export
 layout.lgl <- function(..., params = list()) {
-  lifecycle::deprecate_soft("2.1.0", "layout.lgl()", "layout_with_lgl()")
+  lifecycle::deprecate_warn("2.1.0", "layout.lgl()", "layout_with_lgl()")
   do_call(layout_with_lgl, .args = c(list(...), params))
 }
 
@@ -2124,7 +2109,7 @@ layout_with_mds <- function(
   options = arpack_defaults()
 ) {
   if (is.function(options)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "1.6.0",
       "layout_with_mds(options = 'must be a list')",
       details = c(
@@ -2659,7 +2644,7 @@ layout_components <- function(graph, layout = layout_with_kk, ...) {
 #' @export
 #' @keywords internal
 layout.spring <- function(graph, ...) {
-  lifecycle::deprecate_warn("2.1.0", "layout.spring()", "layout_with_fr()")
+  lifecycle::deprecate_stop("2.1.0", "layout.spring()", "layout_with_fr()")
   layout_with_fr(graph)
 }
 
@@ -2677,7 +2662,7 @@ layout.spring <- function(graph, ...) {
 #' @keywords internal
 #' @export
 layout.svd <- function(graph, ...) {
-  lifecycle::deprecate_warn("2.1.0", "layout.svd()", "layout_with_fr()")
+  lifecycle::deprecate_stop("2.1.0", "layout.svd()", "layout_with_fr()")
   layout_with_fr(graph)
 }
 
@@ -2696,7 +2681,7 @@ layout.svd <- function(graph, ...) {
 #' @keywords internal
 #' @export
 layout.fruchterman.reingold.grid <- function(graph, ...) {
-  lifecycle::deprecate_warn(
+  lifecycle::deprecate_stop(
     "2.1.0",
     "layout.fruchterman.reingold.grid()",
     "layout_with_fr()"
@@ -2723,7 +2708,7 @@ layout.drl <- function(
   dim = 2
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.0.0", "layout.drl()", "layout_with_drl()")
+  lifecycle::deprecate_warn("2.0.0", "layout.drl()", "layout_with_drl()")
   layout_with_drl(
     graph = graph,
     use.seed = use.seed,
diff --git a/R/make.R b/R/make.R
index ebb264bed6f..9301e1552f1 100644
--- a/R/make.R
+++ b/R/make.R
@@ -18,7 +18,7 @@ graph <- function(
   simplify = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph()", "make_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph()", "make_graph()")
   if (inherits(edges, "formula")) {
     if (!missing(n)) {
       cli::cli_abort("{.arg n} should not be given for graph literals")
@@ -143,7 +143,7 @@ graph.famous <- function(
   simplify = TRUE
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.famous()", "make_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.famous()", "make_graph()")
   if (inherits(edges, "formula")) {
     if (!missing(n)) {
       cli::cli_abort("{.arg n} should not be given for graph literals")
@@ -260,7 +260,7 @@ graph.famous <- function(
 #' @export
 line.graph <- function(graph) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "line.graph()", "make_line_graph()")
+  lifecycle::deprecate_warn("2.1.0", "line.graph()", "make_line_graph()")
   ensure_igraph(graph)
 
   res <- linegraph_impl(
@@ -284,7 +284,7 @@ line.graph <- function(graph) {
 #' @export
 graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.ring()", "make_ring()")
+  lifecycle::deprecate_warn("2.1.0", "graph.ring()", "make_ring()")
   res <- ring_impl(
     n,
     directed,
@@ -311,7 +311,7 @@ graph.ring <- function(n, directed = FALSE, mutual = FALSE, circular = TRUE) {
 #' @export
 graph.tree <- function(n, children = 2, mode = c("out", "in", "undirected")) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.tree()", "make_tree()")
+  lifecycle::deprecate_warn("2.1.0", "graph.tree()", "make_tree()")
   mode <- igraph_match_arg(mode)
 
   res <- kary_tree_impl(
@@ -343,7 +343,7 @@ graph.star <- function(
   center = 1
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.star()", "make_star()")
+  lifecycle::deprecate_warn("2.1.0", "graph.star()", "make_star()")
   mode <- igraph_match_arg(mode)
 
   res <- star_impl(
@@ -371,7 +371,7 @@ graph.star <- function(
 #' @export
 graph.lcf <- function(n, shifts, repeats = 1) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.lcf()", "graph_from_lcf()")
+  lifecycle::deprecate_warn("2.1.0", "graph.lcf()", "graph_from_lcf()")
   # Use the _impl function
   lcf_vector_impl(
     n = n,
@@ -401,14 +401,14 @@ graph.lattice <- function(
   circular = deprecated()
 ) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.lattice()", "make_lattice()")
+  lifecycle::deprecate_warn("2.1.0", "graph.lattice()", "make_lattice()")
   if (is.numeric(length) && length != floor(length)) {
     cli::cli_warn("{.arg length} was rounded to the nearest integer.")
     length <- round(length)
   }
 
   if (lifecycle::is_present(circular)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.0.3",
       "graph.lattice(circular = 'use periodic argument instead')",
       details = c("`circular` is now deprecated, use `periodic` instead.")
@@ -459,7 +459,7 @@ graph.lattice <- function(
 #' @export
 graph.kautz <- function(m, n) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.kautz()", "make_kautz_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.kautz()", "make_kautz_graph()")
   res <- kautz_impl(
     m = m,
     n = n
@@ -484,7 +484,7 @@ graph.kautz <- function(m, n) {
 #' @export
 graph.full.citation <- function(n, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.full.citation()",
     "make_full_citation_graph()"
@@ -516,7 +516,7 @@ graph.full.bipartite <- function(
   mode = c("all", "out", "in")
 ) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.full.bipartite()",
     "make_full_bipartite_graph()"
@@ -559,7 +559,7 @@ graph.full.bipartite <- function(
 #' @export
 graph.full <- function(n, directed = FALSE, loops = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.full()", "make_full_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.full()", "make_full_graph()")
   res <- full_impl(
     n,
     directed,
@@ -584,7 +584,7 @@ graph.full <- function(n, directed = FALSE, loops = FALSE) {
 #' @export
 graph.formula <- function(..., simplify = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.formula()", "graph_from_literal()")
+  lifecycle::deprecate_warn("2.1.0", "graph.formula()", "graph_from_literal()")
   mf <- as.list(match.call())[-1]
   graph_from_literal_i(mf)
 } # nocov end
@@ -601,7 +601,7 @@ graph.formula <- function(..., simplify = TRUE) {
 #' @export
 graph.extended.chordal.ring <- function(n, w, directed = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.extended.chordal.ring()",
     "make_chordal_ring()"
@@ -630,7 +630,7 @@ graph.extended.chordal.ring <- function(n, w, directed = FALSE) {
 #' @export
 graph.empty <- function(n = 0, directed = TRUE) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.empty()", "make_empty_graph()")
+  lifecycle::deprecate_warn("2.1.0", "graph.empty()", "make_empty_graph()")
   # Function call
   res <- empty_impl(
     n = n,
@@ -652,7 +652,7 @@ graph.empty <- function(n = 0, directed = TRUE) {
 #' @export
 graph.de.bruijn <- function(m, n) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.de.bruijn()",
     "make_de_bruijn_graph()"
@@ -681,7 +681,7 @@ graph.de.bruijn <- function(m, n) {
 #' @export
 graph.bipartite <- function(types, edges, directed = FALSE) {
   # nocov start
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph.bipartite()",
     "make_bipartite_graph()"
@@ -732,7 +732,7 @@ graph.bipartite <- function(types, edges, directed = FALSE) {
 #' @export
 graph.atlas <- function(n) {
   # nocov start
-  lifecycle::deprecate_soft("2.1.0", "graph.atlas()", "graph_from_atlas()")
+  lifecycle::deprecate_warn("2.1.0", "graph.atlas()", "graph_from_atlas()")
   res <- atlas_impl(
     number = n
   )
@@ -1023,7 +1023,7 @@ sample_ <- function(...) {
 #' graph_(cbind(1:5, 2:6), from_edgelist(directed = FALSE))
 #' graph_(cbind(1:5, 2:6), from_edgelist(), directed = FALSE)
 graph_ <- function(...) {
-  lifecycle::deprecate_soft(
+  lifecycle::deprecate_warn(
     "2.1.0",
     "graph_()",
     details = c(
@@ -1957,7 +1957,7 @@ make_lattice <- function(
   circular = deprecated()
 ) {
   if (lifecycle::is_present(circular)) {
-    lifecycle::deprecate_soft(
+    lifecycle::deprecate_warn(
       "2.0.3",
       "make_lattice(circular = 'use periodic argument instead')",
       details = c("`circular` is now deprecated, use `periodic` instead.")
diff --git a/lifecycle-TODO.md b/lifecycle-TODO.md
new file mode 100644
index 00000000000..e84f9e5ec37
--- /dev/null
+++ b/lifecycle-TODO.md
@@ -0,0 +1,216 @@
+# lifecycle bump — unresolved test failures
+
+These commits were made but left tests failing that need manual fixes (tests call deprecated functions expecting a result, not an error):
+
+
+
+## `feat!: bump make_lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph_() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.atlas() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.bipartite() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.de.bruijn() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.empty() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.extended.chordal.ring() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.formula() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.full() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.full.bipartite() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.full.citation() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.kautz() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.lattice(circular = 'use periodic argument instead') from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.lattice() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.lcf() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.star() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.tree() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.ring() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump line.graph() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph.famous() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
+## `feat!: bump graph() from deprecate_soft to deprecate_warn`
+
+- graph_from_literal() and simple undirected graphs
+- graph_from_literal() and undirected explosion
+- graph_from_literal() and simple directed graphs
+- graph_from_literal() and directed explosion
+- graph_from_literal(simplify = FALSE)
+- graph is not updated if not in LHS
+- graph is updated if in LHS
+
diff --git a/tests/testthat/_snaps/centrality.md b/tests/testthat/_snaps/centrality.md
index f6ffca6419b..bcb12bae957 100644
--- a/tests/testthat/_snaps/centrality.md
+++ b/tests/testthat/_snaps/centrality.md
@@ -38,8 +38,8 @@
     Code
       invisible(eigen_centrality(g, scale = FALSE))
     Condition
-      Warning:
-      The `scale` argument of `eigen_centrality()` always as if TRUE as of igraph 2.1.1.
+      Error:
+      ! The `scale` argument of `eigen_centrality()` always as if TRUE as of igraph 2.1.1.
       i Normalization is always performed
 
 # arpack() errors well
diff --git a/tests/testthat/_snaps/community.md b/tests/testthat/_snaps/community.md
index e01280a95f5..757b8b0be73 100644
--- a/tests/testthat/_snaps/community.md
+++ b/tests/testthat/_snaps/community.md
@@ -1,8 +1,8 @@
-# modularity_matrix still accepts a membership argument for compatibility
+# modularity_matrix no longer accepts a membership argument for compatibility
 
     Code
       x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
     Condition
-      Warning:
-      The `membership` argument of `modularity_matrix()` is no longer used as of igraph 2.1.0.
+      Error:
+      ! The `membership` argument of `modularity_matrix()` is no longer used as of igraph 2.1.0.
 
diff --git a/tests/testthat/test-centrality.R b/tests/testthat/test-centrality.R
index 71bd753a7e6..4c806459f42 100644
--- a/tests/testthat/test-centrality.R
+++ b/tests/testthat/test-centrality.R
@@ -838,7 +838,7 @@ test_that("eigen_centrality() deprecated scale argument", {
     invisible(eigen_centrality(g, scale = TRUE))
   })
   # For some reason, this produces different outputs on Windows and macOS
-  expect_snapshot({
+  expect_snapshot(error = TRUE, {
     invisible(eigen_centrality(g, scale = FALSE))
   })
 })
diff --git a/tests/testthat/test-community.R b/tests/testthat/test-community.R
index a5ba5644e72..6891cc9e76d 100644
--- a/tests/testthat/test-community.R
+++ b/tests/testthat/test-community.R
@@ -376,11 +376,11 @@ test_that("modularity_matrix works", {
   expect_equal(karate_modmat1, karate_modmat2)
 })
 
-test_that("modularity_matrix still accepts a membership argument for compatibility", {
+test_that("modularity_matrix no longer accepts a membership argument for compatibility", {
   karate <- make_graph("zachary")
-  expect_snapshot(
+  expect_snapshot(error = TRUE, {
     x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
-  )
+  })
 })
 
 test_that("cluster_louvain works", {
diff --git a/tests/testthat/test-games.R b/tests/testthat/test-games.R
index 46b4c1e7bb5..8f68f2842b0 100644
--- a/tests/testthat/test-games.R
+++ b/tests/testthat/test-games.R
@@ -155,17 +155,17 @@ test_that("sample_degseq supports the sample_(...) syntax", {
 test_that("sample_degseq works() -- old method names", {
   withr::local_options("lifecycle_verbosity" = "warning")
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple"),
     "must be"
   )
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple.no.multiple"),
     "must be"
   )
 
-  expect_warning(
+  expect_error(
     sample_degseq(c(1, 1, 2, 2, 2), method = "simple.no.multiple.uniform"),
     "must be"
   )
diff --git a/tests/testthat/test-interface.R b/tests/testthat/test-interface.R
index 0e73189645e..9be76e65bc9 100644
--- a/tests/testthat/test-interface.R
+++ b/tests/testthat/test-interface.R
@@ -220,7 +220,7 @@ test_that("get_edge_id() errors correctly for wrong matrices", {
   mat <- matrix(c(1, 2, 3, 4), nrow = 2, ncol = 2)
   lifecycle::expect_defunct(get_edge_ids(g, mat))
   mat <- matrix(c(1, 2, 1, 3, 1, 4), nrow = 2, ncol = 3)
-  lifecycle::expect_deprecated(get_edge_ids(g, mat))
+  lifecycle::expect_defunct(get_edge_ids(g, mat))
 })
 
 test_that("invalidate_cache works", {
diff --git a/tools/bump-lifecycle.R b/tools/bump-lifecycle.R
new file mode 100644
index 00000000000..24bccd6e139
--- /dev/null
+++ b/tools/bump-lifecycle.R
@@ -0,0 +1,440 @@
+library(treesitter)
+library(treesitter.r)
+
+# --- Reset to baseline (undo any previous partial run) ---
+# .claude/settings.local.json is untracked, so git reset --hard leaves it alone.
+# This script is tracked, so we save and restore it across the reset.
+local({
+  baseline <- "fb68fc60b2e673a2994885ed454dbbaca709096c"
+  script_path <- here::here("tools", "bump-lifecycle.R")
+  saved <- readLines(script_path, warn = FALSE)
+  cli::cli_alert_info("Resetting to {substr(baseline, 1L, 7L)} ...")
+  system2("git", c("-C", here::here(), "reset", "--hard", baseline))
+  writeLines(saved, script_path)
+  cli::cli_alert_success("Restored tools/bump-lifecycle.R")
+})
+
+lang <- treesitter.r::language()
+
+# deprecate_soft / deprecate_warn / deprecate_stop are all 14 chars — same length,
+# so substr<-() replacement never shifts line/column positions.
+next_level <- c(
+  deprecate_soft = "deprecate_warn",
+  deprecate_warn = "deprecate_stop"
+)
+
+# Uncomment to inspect node types for a sample expression:
+# text <- 'lifecycle::deprecate_soft("1.0.0", "foo()")'
+# node_show_s_expression(tree_root_node(parser_parse(parser(lang), text)))
+
+# --- tree navigation helpers ---
+
+fn_to_call <- function(fn_node) {
+  # "deprecate_X" identifier -> namespace_operator -> call
+  node_parent(node_parent(fn_node))
+}
+
+# A pure shim is a function whose body contains exactly one statement: the deprecate_stop() call.
+is_pure_shim <- function(fn_node) {
+  call_node <- fn_to_call(fn_node)
+  body_node <- node_parent(call_node) # braced_expression (the { } body)
+  fn_def_node <- node_parent(body_node) # function_definition
+  asgn_node <- node_parent(fn_def_node) # binary_operator (<-)
+
+  if (node_type(fn_def_node) != "function_definition") {
+    return(FALSE)
+  }
+  if (node_type(asgn_node) != "binary_operator") {
+    return(FALSE)
+  }
+  length(node_named_children(body_node)) == 1L
+}
+
+get_asgn_node <- function(fn_node) {
+  node_parent(node_parent(node_parent(fn_to_call(fn_node))))
+}
+
+get_fn_name <- function(fn_node) {
+  node_text(node_named_children(get_asgn_node(fn_node))[[1L]])
+}
+
+# Returns TRUE if fn_name appears as an identifier in any R file other than current_path.
+# Used to protect shims that are still referenced internally.
+is_referenced_elsewhere <- function(fn_name, current_path) {
+  escaped <- gsub("([.^$|*+?(){}\\[\\]])", "\\\\\\1", fn_name)
+  pattern <- paste0("(?<![A-Za-z0-9._])", escaped, "(?![A-Za-z0-9._])")
+  other_files <- setdiff(r_files, current_path)
+  any(vapply(other_files, function(f) {
+    any(grepl(pattern, readLines(f, warn = FALSE), perl = TRUE))
+  }, logical(1)))
+}
+
+# Scan backwards from first_fn_line (1-indexed) past blank lines and roxygen #' lines.
+preceding_doc_range <- function(lines, first_fn_line) {
+  i <- first_fn_line - 1L
+  while (i >= 1L && grepl("^\\s*(#'.*)?$", lines[i])) {
+    i <- i - 1L
+  }
+  if (i + 1L > first_fn_line - 1L) {
+    integer(0L)
+  } else {
+    seq(i + 1L, first_fn_line - 1L)
+  }
+}
+
+# --- test helpers ---
+
+# Add `error = TRUE` to the expect_snapshot() call at row_1indexed in test_file.
+add_error_true <- function(test_file, row_1indexed) {
+  if (!file.exists(test_file)) {
+    return(invisible(FALSE))
+  }
+  lines <- readLines(test_file, warn = FALSE)
+  text <- paste(lines, collapse = "\n")
+  root <- tree_root_node(parser_parse(parser(lang), text))
+
+  q <- query(
+    lang,
+    '(call function: (identifier) @fn (#eq? @fn "expect_snapshot"))'
+  )
+  caps <- query_captures(q, root)
+  fn_nodes <- caps$node[caps$name == "fn"]
+
+  for (fn in fn_nodes) {
+    if (point_row(node_start_point(fn)) + 1L != row_1indexed) {
+      next
+    }
+
+    call_node <- node_parent(fn)
+    args_node <- Filter(
+      \(n) node_type(n) == "arguments",
+      node_children(call_node)
+    )
+    if (length(args_node) == 0L) {
+      next
+    }
+    args_node <- args_node[[1L]]
+
+    if (grepl("error\\s*=\\s*TRUE", node_text(args_node))) {
+      return(invisible(FALSE))
+    }
+
+    # Insert `error = TRUE, ` right after the opening `(`
+    open_row <- point_row(node_start_point(args_node)) + 1L
+    open_col <- point_column(node_start_point(args_node)) + 1L
+    line <- lines[open_row]
+    lines[open_row] <- paste0(
+      substr(line, 1L, open_col),
+      "error = TRUE, ",
+      substr(line, open_col + 1L, nchar(line))
+    )
+    writeLines(lines, test_file)
+    return(invisible(TRUE))
+  }
+  invisible(FALSE)
+}
+
+# Patch expect_snapshot() calls for lifecycle errors found by run_one().
+# failures: list of {msg, src_file, line} returned from the callr subprocess.
+fix_lifecycle_snapshot_failures <- function(failures, root) {
+  fixed <- FALSE
+  for (f in failures) {
+    if (!grepl("lifecycle_error_deprecated|defunctError|defunct", f$msg)) next
+    src_file <- f$src_file
+    line     <- f$line
+    if (is.null(src_file) || is.null(line) || is.na(line)) next
+    file_path <- if (file.exists(src_file)) src_file else {
+      file.path(root, "tests", "testthat", basename(src_file))
+    }
+    if (!file.exists(file_path)) next
+    if (add_error_true(file_path, line)) fixed <- TRUE
+  }
+  fixed
+}
+
+# --- test runner ---
+
+# Accumulates {commit, tests} pairs for changes that left tests failing.
+unresolved_failures <- list()
+n_commits <- 0L
+
+# Returns character vector of still-failing test names (empty if all pass).
+run_tests <- function(path) {
+  src_name  <- fs::path_ext_remove(fs::path_file(path))
+  test_file <- here::here("tests", "testthat", paste0("test-", src_name, ".R"))
+  if (!file.exists(test_file)) return(character(0))
+
+  root <- here::here()
+
+  # Each call runs in a fresh subprocess — no memory accumulation in the main session.
+  run_one <- function(update_snapshots = FALSE) {
+    callr::r(
+      function(root, src_name, update_snapshots) {
+        if (update_snapshots) options(testthat.snapshot.update = TRUE)
+        result <- testthat::test_local(
+          root, filter = src_name, stop_on_failure = FALSE, reporter = "minimal"
+        )
+        df <- as.data.frame(result)
+        failures <- list()
+        for (fr in result) {
+          for (exp in fr) {
+            if (!inherits(exp, c("expectation_failure", "expectation_error"))) next
+            msg      <- tryCatch(conditionMessage(exp), error = function(e) "")
+            srcref   <- tryCatch(exp$srcref, error = function(e) NULL)
+            src_file <- tryCatch(attr(srcref, "srcfile")$filename, error = function(e) NULL)
+            line     <- tryCatch(as.integer(srcref)[1L], error = function(e) NA_integer_)
+            failures[[length(failures) + 1L]] <- list(msg = msg, src_file = src_file, line = line)
+          }
+        }
+        list(
+          n_fail    = sum(df$failed, na.rm = TRUE) + sum(df$error, na.rm = TRUE),
+          bad_tests = df$test[df$failed + df$error > 0L],
+          failures  = failures
+        )
+      },
+      args = list(root = root, src_name = src_name, update_snapshots = update_snapshots)
+    )
+  }
+
+  out <- run_one()
+
+  if (out$n_fail > 0L && fix_lifecycle_snapshot_failures(out$failures, root)) {
+    out <- run_one()
+  }
+
+  if (out$n_fail > 0L) {
+    out <- run_one(update_snapshots = TRUE)
+    if (out$n_fail > 0L) {
+      bad <- out$bad_tests
+      cli::cli_alert_warning(
+        "{out$n_fail} test(s) still failing after snapshot update (need manual fixes): {paste(bad, collapse = ', ')}"
+      )
+      return(bad)
+    }
+  }
+
+  character(0)
+}
+
+commit_change <- function(path, msg) {
+  bad <- run_tests(path)
+  if (length(bad) > 0L) {
+    unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
+      commit = msg,
+      tests  = bad
+    )
+  }
+  gert::git_add(fs::path_rel(path, here::here()))
+  # Stage any modified test or snapshot files produced during the test run
+  status <- gert::git_status()
+  extra <- status$file[startsWith(status$file, "tests/") & !status$staged]
+  if (length(extra) > 0L) {
+    gert::git_add(extra)
+  }
+  gert::git_commit(msg)
+  n_commits <<- n_commits + 1L
+}
+
+write_unresolved_report <- function() {
+  if (length(unresolved_failures) == 0L) return(invisible(NULL))
+  out <- here::here("lifecycle-TODO.md")
+  lines <- c(
+    "# lifecycle bump — unresolved test failures",
+    "",
+    paste0(
+      "These commits were made but left tests failing that need manual fixes ",
+      "(tests call deprecated functions expecting a result, not an error):"
+    ),
+    ""
+  )
+  for (item in unresolved_failures) {
+    lines <- c(
+      lines,
+      paste0("## `", item$commit, "`"),
+      "",
+      paste0("- ", item$tests),
+      ""
+    )
+  }
+  writeLines(lines, out)
+  cli::cli_alert_warning("Wrote {length(unresolved_failures)} unresolved item(s) to lifecycle-TODO.md")
+}
+
+# --- queries ---
+
+bump_query <- query(
+  lang,
+  '
+  (call
+    function: (namespace_operator
+      lhs: (identifier) @ns
+      rhs: (identifier) @fn)
+    arguments: (arguments
+      (argument)
+      (argument value: (string content: (string_content) @what)))
+    (#eq? @ns "lifecycle")
+    (#match? @fn "^deprecate_(soft|warn)$"))
+'
+)
+
+stop_query <- query(
+  lang,
+  '
+  (call
+    function: (namespace_operator
+      lhs: (identifier) @ns
+      rhs: (identifier) @fn)
+    arguments: (arguments
+      (argument)
+      (argument value: (string content: (string_content) @what)))
+    (#eq? @ns "lifecycle")
+    (#eq? @fn "deprecate_stop"))
+'
+)
+
+# --- per-file processing ---
+
+process_file <- function(path) {
+
+  # ---- 1. BUMP: deprecate_soft -> deprecate_warn, deprecate_warn -> deprecate_stop ----
+
+  lines <- readLines(path, warn = FALSE)
+  root <- tree_root_node(parser_parse(
+    parser(lang),
+    paste(lines, collapse = "\n")
+  ))
+  matches <- query_matches(bump_query, root)[[1]]
+
+  if (length(matches) > 0L) {
+    fn_nodes <- lapply(matches, \(m) m$node[m$name == "fn"][[1]])
+    what_nodes <- lapply(matches, \(m) m$node[m$name == "what"][[1]])
+    rows <- vapply(fn_nodes, \(n) point_row(node_start_point(n)), numeric(1))
+    cols <- vapply(fn_nodes, \(n) point_column(node_start_point(n)), numeric(1))
+    old_names <- vapply(fn_nodes, node_text, character(1))
+    whats <- vapply(what_nodes, node_text, character(1))
+
+    # Calls with >2 args produce a duplicate match for the same @fn node.
+    # Keep only the first occurrence (args 1+2 = version+what).
+    dups <- duplicated(paste(rows, cols, sep = ":"))
+    fn_nodes <- fn_nodes[!dups]
+    what_nodes <- what_nodes[!dups]
+    rows <- rows[!dups]
+    cols <- cols[!dups]
+    old_names <- old_names[!dups]
+    whats <- whats[!dups]
+
+    for (i in order(rows, decreasing = TRUE)) {
+      r <- rows[i] + 1L
+      c <- cols[i] + 1L
+      new_name <- next_level[[old_names[i]]]
+      substr(lines[r], c, c + 13L) <- new_name
+      writeLines(lines, path)
+      msg <- sprintf(
+        "feat!: bump %s from %s to %s",
+        whats[i],
+        old_names[i],
+        new_name
+      )
+      commit_change(path, msg)
+    }
+  }
+
+  # ---- 2. REMOVE: pure deprecate_stop shim functions ----
+
+  # Re-parse after bumps (newly-bumped deprecate_stop shims are included here).
+  lines <- readLines(path, warn = FALSE)
+  root <- tree_root_node(parser_parse(
+    parser(lang),
+    paste(lines, collapse = "\n")
+  ))
+  stop_matches <- query_matches(stop_query, root)[[1]]
+  fn_nodes <- lapply(stop_matches, \(m) m$node[m$name == "fn"][[1]])
+  what_nodes <- lapply(stop_matches, \(m) m$node[m$name == "what"][[1]])
+
+  # Same deduplication: calls with a third argument (e.g. `with`) match twice.
+  if (length(fn_nodes) > 0L) {
+    stop_rows <- vapply(
+      fn_nodes,
+      \(n) point_row(node_start_point(n)),
+      numeric(1)
+    )
+    stop_cols <- vapply(
+      fn_nodes,
+      \(n) point_column(node_start_point(n)),
+      numeric(1)
+    )
+    stop_dups <- duplicated(paste(stop_rows, stop_cols, sep = ":"))
+    fn_nodes <- fn_nodes[!stop_dups]
+    what_nodes <- what_nodes[!stop_dups]
+  }
+
+  if (length(fn_nodes) == 0L) {
+    return(invisible(NULL))
+  }
+
+  shim_mask <- vapply(fn_nodes, is_pure_shim, logical(1))
+  fn_shims <- fn_nodes[shim_mask]
+  what_shims <- what_nodes[shim_mask]
+  if (length(fn_shims) == 0L) {
+    return(invisible(NULL))
+  }
+
+  asgn_nodes <- lapply(fn_shims, get_asgn_node)
+  starts <- vapply(
+    asgn_nodes,
+    \(n) point_row(node_start_point(n)) + 1L,
+    numeric(1)
+  )
+  ends <- vapply(asgn_nodes, \(n) point_row(node_end_point(n)) + 1L, numeric(1))
+  whats <- vapply(what_shims, node_text, character(1))
+
+  for (j in order(starts, decreasing = TRUE)) {
+    fn_name <- get_fn_name(fn_shims[[j]])
+    if (is_referenced_elsewhere(fn_name, path)) {
+      cli::cli_alert_warning(
+        "Skipping removal of {fn_name}(): still referenced in other R files (fix iterators manually)"
+      )
+      unresolved_failures[[length(unresolved_failures) + 1L]] <<- list(
+        commit = sprintf("feat!: remove deprecated %s (lifecycle::deprecate_stop)", whats[j]),
+        tests  = paste0(fn_name, "() skipped: still referenced in other R files")
+      )
+      next
+    }
+    lines <- readLines(path, warn = FALSE)
+    doc_range <- preceding_doc_range(lines, starts[j])
+    fn_range <- seq(starts[j], ends[j])
+    after_line <- ends[j] + 1L
+    trail <- if (
+      after_line <= length(lines) && grepl("^\\s*$", lines[after_line])
+    ) {
+      after_line
+    } else {
+      integer(0L)
+    }
+    writeLines(lines[-c(doc_range, fn_range, trail)], path)
+    msg <- sprintf(
+      "feat!: remove deprecated %s (lifecycle::deprecate_stop)",
+      whats[j]
+    )
+    commit_change(path, msg)
+  }
+}
+
+# --- run over all R source files ---
+
+r_files <- fs::dir_ls(here::here("R"), glob = "*.R")
+
+cli::cli_progress_bar(
+  total = length(r_files),
+  format      = "{cli::pb_bar} {cli::pb_current}/{cli::pb_total} | {n_commits} commits | ETA {cli::pb_eta} | {cli::pb_status}",
+  format_done = "{cli::pb_total} files done | {n_commits} commits in {cli::pb_elapsed}",
+  clear = FALSE
+)
+for (path in r_files) {
+  cli::cli_progress_update(status = basename(path))
+  process_file(path)
+  cli::cli_progress_update(inc = 1L)
+}
+cli::cli_progress_done()
+
+write_unresolved_report()