Unused objects in tests

tests/testthat/_snaps/community.md

@@ -1,7 +1,7 @@
 # modularity_matrix no longer accepts a membership argument for compatibility
 
     Code
-      x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
+      modularity_matrix(karate, membership = rep(1, vcount(karate)))
     Condition
       Error:
       ! The `membership` argument of `modularity_matrix()` is no longer used as of igraph 2.1.0.

tests/testthat/_snaps/foreign.md

@@ -45,20 +45,15 @@
 # graph_from_graphdb works
 
     Code
-      g <- graph_from_graphdb(nodes = 1000)
-
----
-
-    Code
-      g <- graph_from_graphdb()
+      graph_from_graphdb()
     Condition
       Error in `graph_from_graphdb()`:
       ! Either `nodes`' or ``url`' must be non-null.
 
 ---
 
     Code
-      g <- graph_from_graphdb(nodes = 10, prefix = "not_existing")
+      graph_from_graphdb(nodes = 10, prefix = "not_existing")
     Condition
       Error in `graph_from_graphdb()`:
       ! not_existing is not a valid prefix.
@@ -67,7 +62,7 @@
 ---
 
     Code
-      g <- graph_from_graphdb(nodes = 10, type = "not_existing")
+      graph_from_graphdb(nodes = 10, type = "not_existing")
     Condition
       Error in `graph_from_graphdb()`:
       ! not_existing is not a valid graph type.

tests/testthat/_snaps/incidence.md

@@ -61,7 +61,7 @@
 # graph_from_biadjacency_matrix() errors well
 
     Code
-      (g <- graph_from_biadjacency_matrix(inc, weight = FALSE))
+      (graph_from_biadjacency_matrix(inc, weight = FALSE))
     Condition
       Error in `graph_from_biadjacency_matrix()`:
       ! `weighted` can't be `FALSE`.
@@ -70,7 +70,7 @@
 ---
 
     Code
-      (g <- graph_from_biadjacency_matrix(inc, weight = 42))
+      (graph_from_biadjacency_matrix(inc, weight = 42))
     Condition
       Error in `graph_from_biadjacency_matrix()`:
       ! `weighted` can't be a number.
@@ -79,7 +79,7 @@
 ---
 
     Code
-      (g <- graph_from_biadjacency_matrix(inc, multiple = TRUE, weighted = TRUE))
+      (graph_from_biadjacency_matrix(inc, multiple = TRUE, weighted = TRUE))
     Condition
       Error in `graph_from_biadjacency_matrix()`:
       ! `multiple` and `weighted` cannot be both `TRUE`.

tests/testthat/test-attributes.R

@@ -11,14 +11,17 @@ 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")
 })
@@ -33,10 +36,12 @@ test_that("bracketing works with a function (not changing attribute of similar g
 
   copy_test <- function(g) {
     graph2 <- set_vertex_attr(g, name = "weight", value = rep(1, vcount(g)))
-    graph2 <- set_edge_attr(g, name = "weight", value = rep(1, ecount(g)))
-    graph2 <- set_graph_attr(g, name = "name", "foobar")
+    graph2 <- set_edge_attr(graph2, name = "weight", value = rep(1, ecount(g)))
+    graph2 <- set_graph_attr(graph2, name = "name", "foobar")
+    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)
@@ -56,6 +61,7 @@ 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)

tests/testthat/test-centrality.R

@@ -745,7 +745,7 @@ test_that("undirected alpha_centrality() works, #653", {
   expect_equal(ac1, ac2)
 
   g2 <- as_directed(g, mode = "mutual")
-  ac3 <- alpha_centrality(g, sparse = FALSE)
+  ac3 <- alpha_centrality(g2, sparse = FALSE)
   expect_equal(ac1, ac3)
 })
 
@@ -776,11 +776,12 @@ test_that("spectrum() works for symmetric matrices", {
 
   rlang::local_options(lifecycle_verbosity = "warning")
   expect_warning(
-    e3 <- spectrum(
+    spectrum(
       g,
       which = list(howmany = 4, pos = "SA"),
       options = arpack_defaults
-    )
+    ),
+    "must be a list"
   )
 })
 

tests/testthat/test-community.R

@@ -223,7 +223,7 @@ test_that("cluster_leading_eigen works", {
       multiplier(v)
     })
     ev <- eigen(M)
-    ret <- 0
+
     expect_equal(ev$values[1], value)
     if (sign(ev$vectors[1, 1]) != sign(vector[1])) {
       ev$vectors <- -ev$vectors
@@ -284,7 +284,7 @@ test_that("cluster_leading_eigen works", {
   A <- as_adjacency_matrix(karate, sparse = FALSE)
   ec <- ecount(karate)
   deg <- degree(karate)
-  karate_lc2 <- cluster_leading_eigen(karate, callback = mod_mat_caller)
+  cluster_leading_eigen(karate, callback = mod_mat_caller)
 })
 
 test_that("cluster_leading_eigen is deterministic", {
@@ -474,7 +474,7 @@ test_that("modularity_matrix works", {
 test_that("modularity_matrix no longer accepts a membership argument for compatibility", {
   karate <- make_graph("zachary")
   expect_snapshot(error = TRUE, {
-    x <- modularity_matrix(karate, membership = rep(1, vcount(karate)))
+    modularity_matrix(karate, membership = rep(1, vcount(karate)))
   })
 })
 

tests/testthat/test-conversion.R

@@ -701,7 +701,7 @@ test_that("graphNEL conversion works", {
 
   A <- as_adjacency_matrix(g, weights = "weight", sparse = FALSE)
   A2 <- as_adjacency_matrix(g2, weights = "weight", sparse = FALSE)
-  expect_equal(A, A)
+  expect_equal(A, A2)
   expect_equal(g$name, g2$name)
 })
 

tests/testthat/test-cycles.R

@@ -27,7 +27,10 @@ test_that("simple_cycle() works directed", {
 })
 
 test_that("simple_cycle() works undirected", {
-  g <- graph_from_literal(A -+ B -+ C -+ A -+ D -+ E +- F -+ A, E -+ E, A -+ F, simplify = FALSE)
+  g <- graph_from_literal(
+    A -+ B -+ C -+ A -+ D -+ E +- F -+ A, E -+ E, A -+ F, 
+    simplify = FALSE
+  )
   all_simple_cycles <- simple_cycles(g, mode = "all")
   expect_length(all_simple_cycles$vertices, 5)
   expect_length(all_simple_cycles$edges, 5)
@@ -40,8 +43,8 @@ test_that("simple_cycle() works undirected", {
   expect_equal(as.numeric(all_simple_cycles$vertices[[2]]), c(1, 4, 5, 6))
 
   all_simple_cycles_23 <- simple_cycles(g, mode = "all", min = 2, max = 3)
-  expect_length(all_simple_cycles$vertices, 5)
-  expect_length(all_simple_cycles$edges, 5)
+  expect_length(all_simple_cycles_23$vertices, 2)
+  expect_length(all_simple_cycles_23$edges, 2)
 })
 
 # Tests for callback function

tests/testthat/test-foreign.R

@@ -66,12 +66,12 @@ test_that("graph_from_graphdb works", {
   # docker run --rm -ti -v $PWD:/rigraph -e MAKEFLAGS=-j4 ghcr.io/cynkra/docker-images/rigraph-san:latest RDcsan -q -e 'filename <- "/rigraph/DESCRIPTION"; gz_file_con <- file(filename, open = "rb"); file_con <- gzcon(gz_file_con); close(file_con); gc()'
   skip_if(Sys.getenv("R_SANITIZER") == "true")
 
-  expect_snapshot(g <- graph_from_graphdb(nodes = 1000))
-  expect_snapshot_igraph_error(g <- graph_from_graphdb())
+  expect_silent(graph_from_graphdb(nodes = 1000))
+  expect_snapshot_igraph_error(graph_from_graphdb())
   expect_snapshot_igraph_error(
-    g <- graph_from_graphdb(nodes = 10, prefix = "not_existing")
+    graph_from_graphdb(nodes = 10, prefix = "not_existing")
   )
   expect_snapshot_igraph_error(
-    g <- graph_from_graphdb(nodes = 10, type = "not_existing")
+    graph_from_graphdb(nodes = 10, type = "not_existing")
   )
 })

tests/testthat/test-glet.R

@@ -50,7 +50,6 @@ test_that("Graphlets filtering works", {
 })
 
 threshold.net <- function(graph, level) {
-  N <- vcount(graph)
   graph.t <- delete_edges(graph, which(E(graph)$weight < level))
 
   clqt <- unvs(max_cliques(graph.t))

tests/testthat/test-incidence.R

@@ -209,13 +209,13 @@ test_that("graph_from_biadjacency_matrix() errors well", {
   rownames(inc) <- LETTERS[1:3]
 
   expect_snapshot_igraph_error({
-    (g <- graph_from_biadjacency_matrix(inc, weight = FALSE))
+    (graph_from_biadjacency_matrix(inc, weight = FALSE))
   })
   expect_snapshot_igraph_error({
-    (g <- graph_from_biadjacency_matrix(inc, weight = 42))
+    (graph_from_biadjacency_matrix(inc, weight = 42))
   })
   expect_snapshot_igraph_error({
-    (g <- graph_from_biadjacency_matrix(inc, multiple = TRUE, weighted = TRUE))
+    (graph_from_biadjacency_matrix(inc, multiple = TRUE, weighted = TRUE))
   })
 })
 

tests/testthat/test-indexing.R

@@ -310,8 +310,6 @@ test_that("[[ queries edges with vertex names", {
   )
 })
 test_that("[ handles from and to properly", {
-  g <- make_test_named_tree()
-
   g <- make_tree(20)
   expect_equal(g[from = c(1, 2, 2, 3), to = c(3, 4, 8, 7)], c(1, 1, 0, 1))
 

tests/testthat/test-iterators.R

@@ -243,6 +243,7 @@ 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)

tests/testthat/test-layout.R

@@ -307,7 +307,6 @@ test_that("parameters are evaluated early", {
 
   cc <- 5
   spec <- as_star(center = cc)
-  cc <- 10
   l2 <- layout_(g, spec)
   expect_identical(l1, l2)
 })

tests/testthat/test-make.R

@@ -367,7 +367,6 @@ test_that("make_de_bruijn_graph works", {
 
 test_that("make_bipartite_graph works", {
   inc_mat_rand <- matrix(sample(0:1, 35, replace = TRUE, prob = c(3, 1)), ncol = 5)
-  bip_from_inc <- graph_from_biadjacency_matrix(inc_mat_rand)
 
   edges <- unlist(sapply(seq_len(nrow(inc_mat_rand)), function(x) {
     w <- which(inc_mat_rand[x, ] != 0) + nrow(inc_mat_rand)

tests/testthat/test-palette.R

@@ -127,7 +127,7 @@ test_that("r_pal() works correctly", {
 test_that("r_pal() handles edge cases", {
   # Warning for too many colors (note: message says "divergent" - this might be a bug!)
   expect_warning(
-    result <- r_pal(15),
+    r_pal(15),
     "Cannot make 15 divergent colors" # This warning message seems wrong
   )
 

tests/testthat/test-random_walk.R

@@ -16,8 +16,8 @@ test_that("directed random_walk works", {
   expect_equal(w2, c(4:1, 10:9))
 
   w3 <- as_ids(random_walk(g, start = 1, steps = 5, mode = "all"))
-  expect_length(w, 6)
-  expect_true(all(abs(diff(as.numeric(w))) %in% c(1, 9)))
+  expect_length(w3, 6)
+  expect_true(all(abs(diff(as.numeric(w3))) %in% c(1, 9)))
 })
 
 test_that("directed random_walk can return wtih an error when stuck", {

tests/testthat/test-structural-properties.R

@@ -590,7 +590,7 @@ test_that("ego() works", {
   neig <- function(graph, order, vertices) {
     sp <- distances(graph)
     v <- unique(unlist(lapply(vertices, function(x) {
-      w <- which(sp[x, ] <= order)
+      which(sp[x, ] <= order)
     })))
     induced_subgraph(graph, c(v, vertices))
   }
@@ -607,7 +607,7 @@ test_that("ego() works", {
   nei <- function(graph, order, vertices) {
     sp <- distances(graph)
     v <- unique(unlist(lapply(vertices, function(x) {
-      w <- which(sp[x, ] <= order)
+      which(sp[x, ] <= order)
     })))
     v
   }

tests/testthat/test-weakref.R

@@ -27,6 +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)