From 4477299fb321fd10647371732aa61d902b264af2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Fri, 21 Aug 2026 12:17:56 +0200
Subject: [PATCH 1/5] chore: seq

---
 R/glet.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/glet.R b/R/glet.R
index be7843b6c28..28917e03e63 100644
--- a/R/glet.R
+++ b/R/glet.R
@@ -123,7 +123,7 @@ graphlets.candidate.basis <- function(graph, weights = NULL) {
 #' gl <- graphlets(g, niter = 1000)
 #'
 #' ## Plot graphlets
-#' for (i in 1:length(gl$cliques)) {
+#' for (i in seq_along(gl$cliques)) {
 #'   sel <- gl$cliques[[i]]
 #'   V(g)$color <- "white"
 #'   V(g)[sel]$color <- "#E495A5"

From d0a4a391e760235226209fa8e24073e86755ba2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Fri, 21 Aug 2026 12:18:09 +0200
Subject: [PATCH 2/5] chore: lengths

---
 R/operators.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/operators.R b/R/operators.R
index 7b558ebcd61..e16c9378372 100644
--- a/R/operators.R
+++ b/R/operators.R
@@ -229,7 +229,7 @@ apply_attr_combiner <- function(comb, vals, type) {
     x <- x[!is.na(x)]
     apply_one_combiner(comb, x)
   })
-  if (all(vapply(out, length, integer(1)) == 1L)) {
+  if (all(lengths(out) == 1L)) {
     unlist(out)
   } else {
     out

From 6930b199853952c52775dba7c7234b7d12218c54 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Wed, 26 Aug 2026 12:24:44 +0200
Subject: [PATCH 3/5] chore: rm useless comments via `outdated_suppression`

---
 R/print.R                                   | 1 -
 tests/testthat/test-attributes.R            | 5 -----
 tests/testthat/test-iterators.R             | 1 -
 tests/testthat/test-plot.shapes.R           | 1 -
 tests/testthat/test-structural-properties.R | 2 +-
 tests/testthat/test-weakref.R               | 2 --
 6 files changed, 1 insertion(+), 11 deletions(-)

diff --git a/R/print.R b/R/print.R
index 1c2afaf9942..9c383aa4cea 100644
--- a/R/print.R
+++ b/R/print.R
@@ -373,7 +373,6 @@ print_edge_detail <- function(graph, edges) {
   if (!is.null(x)) {
     arrow <- c("--", "->")[is_directed(x) + 1]
 
-    # jarl-ignore unused_object: then assigned to with <<-
     can_max <- NA
     el <- NA
 
diff --git a/tests/testthat/test-attributes.R b/tests/testthat/test-attributes.R
index f46f03db367..2568534cb9c 100644
--- a/tests/testthat/test-attributes.R
+++ b/tests/testthat/test-attributes.R
@@ -11,17 +11,14 @@ test_that("bracketing works (not changing attribute of similar graphs)", {
   g <- make_graph(c(1, 2, 1, 3, 3, 4))
 
   g <- set_vertex_attr(g, name = "weight", value = 1:vcount(g))
-  # jarl-ignore unused_object: test design
   graph2 <- set_vertex_attr(g, name = "weight", value = rep(1, vcount(g)))
   expect_equal(vertex_attr(g, name = "weight"), 1:4)
 
   g <- set_edge_attr(g, name = "weight", value = 1:ecount(g))
-  # jarl-ignore unused_object: test design
   graph2 <- set_edge_attr(g, name = "weight", value = rep(1, ecount(g)))
   expect_equal(edge_attr(g, name = "weight"), 1:3)
 
   g <- set_graph_attr(g, name = "name", "foo")
-  # jarl-ignore unused_object: test design
   graph2 <- set_graph_attr(g, name = "name", "foobar")
   expect_equal(graph_attr(g, name = "name"), "foo")
 })
@@ -41,7 +38,6 @@ test_that("bracketing works with a function (not changing attribute of similar g
     graph2
   }
 
-  # jarl-ignore unused_object: test design
   g2 <- copy_test(g)
   expect_equal(vertex_attr(g, name = "weight"), 1:4)
   expect_equal(edge_attr(g, name = "weight"), 1:3)
@@ -61,7 +57,6 @@ test_that("bracketing works with shortcuts (not changing attribute of similar gr
     graph$name <- "foobar"
   }
 
-  # jarl-ignore unused_object: test design
   g_copy <- copy_test(g)
   expect_equal(vertex_attr(g, name = "weight"), 1:4)
   expect_equal(edge_attr(g, name = "weight"), 1:3)
diff --git a/tests/testthat/test-iterators.R b/tests/testthat/test-iterators.R
index 59a6a274fee..b8940921c94 100644
--- a/tests/testthat/test-iterators.R
+++ b/tests/testthat/test-iterators.R
@@ -244,7 +244,6 @@ test_that("vs/es refers to the original graph", {
   vs <- V(ring1)
   es <- E(ring1)
 
-  # jarl-ignore unused_object: test design
   ring1 <- ring1 + 4
 
   expect_identical(get_vs_graph(vs), ring2)
diff --git a/tests/testthat/test-plot.shapes.R b/tests/testthat/test-plot.shapes.R
index a424f96b7cd..9cb83f0596a 100644
--- a/tests/testthat/test-plot.shapes.R
+++ b/tests/testthat/test-plot.shapes.R
@@ -1,4 +1,3 @@
-# jarl-ignore-file implicit_assignment: just the way it works
 test_that("shapes() lists all available shapes", {
   all_shapes <- shapes()
   expect_type(all_shapes, "character")
diff --git a/tests/testthat/test-structural-properties.R b/tests/testthat/test-structural-properties.R
index 6c4e5752024..594d7ec0bf3 100644
--- a/tests/testthat/test-structural-properties.R
+++ b/tests/testthat/test-structural-properties.R
@@ -198,7 +198,7 @@ test_that("BFS callback does not blow up when an invalid value is returned", {
 })
 
 test_that("BFS callback does not blow up when an error is raised within the callback", {
-  # jarl-ignore unreachable_code: <reason>
+  # jarl-ignore unreachable_code: test design
   callback <- function(graph, data, extra) {
     cli::cli_abort("test")
     FALSE
diff --git a/tests/testthat/test-weakref.R b/tests/testthat/test-weakref.R
index 8d4da9b23b2..de2a330f50c 100644
--- a/tests/testthat/test-weakref.R
+++ b/tests/testthat/test-weakref.R
@@ -27,9 +27,7 @@ test_that("weak reference finalizer is called", {
   value <- "foobar"
   hello <- ""
   fin <- function(env) hello <<- "world"
-  # jarl-ignore unused_object: test design
   vs <- make_weak_ref(key = g, value = value, finalizer = fin)
-
   rm(g)
   gc()
 

From de03e40b8f3ddd5fa606910329748d1f96fc9668 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Wed, 26 Aug 2026 12:27:59 +0200
Subject: [PATCH 4/5] chore: jarl ignore missing argument

---
 tests/testthat/test-migration-fixture.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-migration-fixture.R b/tests/testthat/test-migration-fixture.R
index 8746f9bd7be..7d9f4f82d45 100644
--- a/tests/testthat/test-migration-fixture.R
+++ b/tests/testthat/test-migration-fixture.R
@@ -1,3 +1,4 @@
+# jarl-ignore-file missing_argument: this is the test's point
 # Tests for the in-place argument-migration generator (tools/generate-migrations.R)
 # via the fixture `migration_fixture()` (R/migration-fixture.R). Old signature
 # f(graph, n, weight, kind, directed); new f(graph, n, ..., weights, type,

From 9c03eecb3c511789d19d098dfb0fa70ba1e830e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= <maelle.salmon@yahoo.se>
Date: Wed, 26 Aug 2026 12:37:57 +0200
Subject: [PATCH 5/5] chore: stringAsFactors

---
 R/conversion.R                   |  6 ++++--
 R/print.R                        |  6 +++++-
 man/graph_from_data_frame.Rd     |  6 ++++--
 man/graphlet_basis.Rd            |  2 +-
 tests/testthat/test-conversion.R | 18 ++++++++++++++----
 tests/testthat/test-glet.R       |  3 ++-
 tests/testthat/test-interface.R  |  2 +-
 tests/testthat/test-sparsedf.R   | 14 +++++++++-----
 8 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index 61791722a72..e6137baf3d0 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -1944,7 +1944,8 @@ graph.data.frame <- function(d, directed = TRUE, vertices = NULL) {
 #'     "Esmeralda"
 #'   ),
 #'   age = c(48, 33, 45, 34, 21),
-#'   gender = c("F", "M", "F", "M", "F")
+#'   gender = c("F", "M", "F", "M", "F"),
+#'   stringsAsFactors = FALSE
 #' )
 #' relations <- data.frame(
 #'   from = c(
@@ -1953,7 +1954,8 @@ graph.data.frame <- function(d, directed = TRUE, vertices = NULL) {
 #'   ),
 #'   to = c("Alice", "Bob", "Alice", "Alice", "Bob", "Alice"),
 #'   same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),
-#'   friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3)
+#'   friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3),
+#'   stringsAsFactors = FALSE
 #' )
 #' g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)
 #' print(g, e = TRUE, v = TRUE)
diff --git a/R/print.R b/R/print.R
index 9c383aa4cea..33f906cdb24 100644
--- a/R/print.R
+++ b/R/print.R
@@ -173,7 +173,11 @@
         }))
     ) {
       ## create a table
-      tab <- data.frame(v = paste(sep = "", "[", ind, "]"), row.names = "v")
+      tab <- data.frame(
+        v = paste(sep = "", "[", ind, "]"),
+        row.names = "v",
+        stringsAsFactors = FALSE
+      )
       for (i in list) {
         tab[i] <- vertex_attr(x, i, ind)
       }
diff --git a/man/graph_from_data_frame.Rd b/man/graph_from_data_frame.Rd
index f435b5f650d..9bd354f0d21 100644
--- a/man/graph_from_data_frame.Rd
+++ b/man/graph_from_data_frame.Rd
@@ -108,7 +108,8 @@ actors <- data.frame(
     "Esmeralda"
   ),
   age = c(48, 33, 45, 34, 21),
-  gender = c("F", "M", "F", "M", "F")
+  gender = c("F", "M", "F", "M", "F"),
+  stringsAsFactors = FALSE
 )
 relations <- data.frame(
   from = c(
@@ -117,7 +118,8 @@ relations <- data.frame(
   ),
   to = c("Alice", "Bob", "Alice", "Alice", "Bob", "Alice"),
   same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),
-  friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3)
+  friendship = c(4, 5, 5, 2, 1, 1), advice = c(4, 5, 5, 4, 2, 3),
+  stringsAsFactors = FALSE
 )
 g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)
 print(g, e = TRUE, v = TRUE)
diff --git a/man/graphlet_basis.Rd b/man/graphlet_basis.Rd
index a6e97086249..88ce6849e76 100644
--- a/man/graphlet_basis.Rd
+++ b/man/graphlet_basis.Rd
@@ -102,7 +102,7 @@ plot(g, layout = co)
 gl <- graphlets(g, niter = 1000)
 
 ## Plot graphlets
-for (i in 1:length(gl$cliques)) {
+for (i in seq_along(gl$cliques)) {
   sel <- gl$cliques[[i]]
   V(g)$color <- "white"
   V(g)[sel]$color <- "#E495A5"
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index b5014209aba..f366542d0fb 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -905,7 +905,8 @@ test_that("graph_from_data_frame works with factors", {
   actors <- data.frame(
     name = c("Alice", "Bob", "Cecil", "David", "Esmeralda"),
     age = c(48, 33, 45, 34, 21),
-    gender = factor(c("F", "M", "F", "M", "F"))
+    gender = factor(c("F", "M", "F", "M", "F")),
+    stringsAsFactors = FALSE
   )
   relations <- data.frame(
     from = c(
@@ -915,7 +916,8 @@ test_that("graph_from_data_frame works with factors", {
     to = c("Alice", "Bob", "Alice", "Alice", "Bob", "Alice"),
     same.dept = c(FALSE, FALSE, TRUE, FALSE, FALSE, TRUE),
     friendship = c(4, 5, 5, 2, 1, 1),
-    advice = c(4, 5, 5, 4, 2, 3)
+    advice = c(4, 5, 5, 4, 2, 3),
+    stringsAsFactors = FALSE
   )
   g <- graph_from_data_frame(relations, directed = TRUE, vertices = actors)
 
@@ -1188,8 +1190,16 @@ test_that("graph_from_adj_list() covers duplicate by name and recovers positiona
 })
 
 test_that("graph_from_data_frame() recovers positional vertices with a deprecation", {
-  edges <- data.frame(from = c("a", "b"), to = c("b", "c"))
-  verts <- data.frame(name = c("a", "b", "c"), size = 1:3)
+  edges <- data.frame(
+    from = c("a", "b"),
+    to = c("b", "c"),
+    stringsAsFactors = FALSE
+  )
+  verts <- data.frame(
+    name = c("a", "b", "c"),
+    size = 1:3,
+    stringsAsFactors = FALSE
+  )
 
   lifecycle::expect_deprecated(
     res <- graph_from_data_frame(edges, TRUE, verts)
diff --git a/tests/testthat/test-glet.R b/tests/testthat/test-glet.R
index af039389da0..72d98df6a38 100644
--- a/tests/testthat/test-glet.R
+++ b/tests/testthat/test-glet.R
@@ -31,7 +31,8 @@ test_that("Graphlets filtering works", {
   df <- data.frame(
     from = c("A", "A", "B", "B", "B", "C", "C", "D"),
     to = c("B", "C", "C", "D", "E", "D", "E", "E"),
-    weight = c(8, 8, 8, 5, 5, 5, 5, 5)
+    weight = c(8, 8, 8, 5, 5, 5, 5, 5),
+    stringsAsFactors = FALSE
   )
 
   g <- graph_from_data_frame(
diff --git a/tests/testthat/test-interface.R b/tests/testthat/test-interface.R
index a9c36f18c90..80c29e448f3 100644
--- a/tests/testthat/test-interface.R
+++ b/tests/testthat/test-interface.R
@@ -214,7 +214,7 @@ test_that("get_edge_id() errors correctly for wrong vp", {
   expect_error(get_edge_ids(g, NA))
 
   V(g)$name <- letters[1:3]
-  df <- data.frame(from = c("a", "b"), to = c(1, 2))
+  df <- data.frame(from = c("a", "b"), to = c(1, 2), stringsAsFactors = FALSE)
   expect_snapshot_igraph_error({
     get_edge_ids(g, df)
   })
diff --git a/tests/testthat/test-sparsedf.R b/tests/testthat/test-sparsedf.R
index f5298b186b2..ca7829f59e4 100644
--- a/tests/testthat/test-sparsedf.R
+++ b/tests/testthat/test-sparsedf.R
@@ -7,7 +7,7 @@ test_that("sdf works", {
   sdf <- sdf(id = 1:10, color = "black")
   expect_equal(
     as.data.frame(sdf),
-    data.frame(id = 1:10, color = "black")
+    data.frame(id = 1:10, color = "black", stringsAsFactors = FALSE)
   )
 
   ## access
@@ -26,28 +26,32 @@ test_that("sdf works", {
   sdf2[5, "id"] <- 100
   expect_equal(
     as.data.frame(sdf2),
-    data.frame(id = c(1:4, 100, 6:10), color = "black")
+    data.frame(
+      id = c(1:4, 100, 6:10),
+      color = "black",
+      stringsAsFactors = FALSE
+    )
   )
 
   sdf2 <- sdf
   sdf2[, "id"] <- 0
   expect_equal(
     as.data.frame(sdf2),
-    data.frame(id = rep(0, 10), color = "black")
+    data.frame(id = rep(0, 10), color = "black", stringsAsFactors = FALSE)
   )
 
   sdf2 <- sdf
   sdf2[2:10, "id"] <- 1
   expect_equal(
     as.data.frame(sdf2),
-    data.frame(id = rep(1, 10), color = "black")
+    data.frame(id = rep(1, 10), color = "black", stringsAsFactors = FALSE)
   )
 
   sdf2 <- sdf
   sdf2[, "color"] <- "white"
   expect_equal(
     as.data.frame(sdf2),
-    data.frame(id = 1:10, color = "white")
+    data.frame(id = 1:10, color = "white", stringsAsFactors = FALSE)
   )
 
   sdf2 <- sdf