From c1373e5f26dc13738174dfed92145e78badcedd0 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Wed, 16 Apr 2025 20:50:30 +0200
Subject: [PATCH 1/6] added NA handling for matrix inputs

---
 R/adjacency.R                       | 1 +
 R/conversion.R                      | 9 ++++-----
 R/incidence.R                       | 1 +
 R/utils-assert-args.R               | 6 ++++++
 tests/testthat/_snaps/adjacency.md  | 8 ++++++++
 tests/testthat/_snaps/conversion.md | 8 ++++++++
 tests/testthat/_snaps/incidence.md  | 8 ++++++++
 tests/testthat/test-adjacency.R     | 9 ++++++---
 tests/testthat/test-conversion.R    | 7 ++++++-
 tests/testthat/test-incidence.R     | 5 +++++
 10 files changed, 53 insertions(+), 9 deletions(-)

diff --git a/R/adjacency.R b/R/adjacency.R
index 9ebf52700c..c32240ae6e 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -228,6 +228,7 @@ graph_from_adjacency_matrix <- function(adjmatrix,
                                         ),
                                         weighted = NULL, diag = TRUE,
                                         add.colnames = NULL, add.rownames = NA) {
+  ensure_no_na(adjmatrix, "adjacency matrix", call = rlang::caller_env())
   mode <- igraph.match.arg(mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
diff --git a/R/conversion.R b/R/conversion.R
index d378893e1f..f466cb5bb2 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -1397,10 +1397,8 @@ graph_from_data_frame <- function(d, directed = TRUE, vertices = NULL) {
   }
 
   ## Handle if some elements are 'NA'
-  if (any(is.na(d[, 1:2]))) {
-    cli::cli_warn("In {.code d}, {.code NA} elements were replaced with string {.str NA}.")
-    d[, 1:2][is.na(d[, 1:2])] <- "NA"
-  }
+  ensure_no_na(d, "edge data frame", call = rlang::caller_env())
+
   if (!is.null(vertices) && any(is.na(vertices[, 1]))) {
     cli::cli_warn("In {.code vertices[,1]}, {.code NA} elements were replaced with string {.str NA}.")
     vertices[, 1][is.na(vertices[, 1])] <- "NA"
@@ -1495,8 +1493,9 @@ from_data_frame <- function(...) constructor_spec(graph_from_data_frame, ...)
 #' graph_from_edgelist(cbind(1:10, c(2:10, 1)))
 graph_from_edgelist <- function(el, directed = TRUE) {
   if (!is.matrix(el) || ncol(el) != 2) {
-    cli::cli_abort("graph_from_edgelist expects a matrix with two columns")
+    cli::cli_abort("graph_from_edgelist expects a matrix with two columns.")
   }
+  ensure_no_na(el, "edgelist", call = rlang::caller_env())
 
   if (nrow(el) == 0) {
     res <- make_empty_graph(directed = directed)
diff --git a/R/incidence.R b/R/incidence.R
index dd1118b735..cefec10a60 100644
--- a/R/incidence.R
+++ b/R/incidence.R
@@ -168,6 +168,7 @@ graph_from_biadjacency_matrix <- function(incidence, directed = FALSE,
                                           multiple = FALSE, weighted = NULL,
                                           add.names = NULL) {
   # Argument checks
+  ensure_no_na(incidence, "biadjacency matrix", call = rlang::caller_env())
   directed <- as.logical(directed)
   mode <- igraph.match.arg(mode)
 
diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index 3bb7d16736..53f3c6e24c 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -32,3 +32,9 @@ igraph.match.arg <- function(arg, values, error_call = rlang::caller_env()) {
     error_call = error_call
   )
 }
+
+ensure_no_na <- function(x, what, call) {
+  if (any(is.na(x))) {
+    cli::cli_abort("Cannot create a graph object because the {what} contains NAs.", call = call)
+  }
+}
diff --git a/tests/testthat/_snaps/adjacency.md b/tests/testthat/_snaps/adjacency.md
index c46c414628..6a5b41d0df 100644
--- a/tests/testthat/_snaps/adjacency.md
+++ b/tests/testthat/_snaps/adjacency.md
@@ -139,3 +139,11 @@
       IGRAPH U--- 2 0 -- 
       + edges:
 
+# graph_from_adjacency_matrix errors for NAs
+
+    Code
+      graph_from_adjacency_matrix(A)
+    Condition
+      Error:
+      ! Cannot create a graph object because the adjacency matrix contains NAs.
+
diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 8da10b7890..33624b7d48 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -87,3 +87,11 @@
       2    2  3    2         b          B       c        C
       3    1  3    1         a          A       c        C
 
+# graph_from_edgelist errors for NAs
+
+    Code
+      graph_from_edgelist(A)
+    Condition
+      Error:
+      ! Cannot create a graph object because the edgelist contains NAs.
+
diff --git a/tests/testthat/_snaps/incidence.md b/tests/testthat/_snaps/incidence.md
index 2b9e6ff16a..81283445e3 100644
--- a/tests/testthat/_snaps/incidence.md
+++ b/tests/testthat/_snaps/incidence.md
@@ -85,3 +85,11 @@
       ! `multiple` and `weighted` cannot be both `TRUE`.
       igraph either interprets numbers larger than 1 as weights or as multiplicities, but it cannot be both.
 
+# graph_from_biadjacency_matrix errors for NAs
+
+    Code
+      graph_from_biadjacency_matrix(A)
+    Condition
+      Error:
+      ! Cannot create a graph object because the biadjacency matrix contains NAs.
+
diff --git a/tests/testthat/test-adjacency.R b/tests/testthat/test-adjacency.R
index 2e9983b99f..0812b24973 100644
--- a/tests/testthat/test-adjacency.R
+++ b/tests/testthat/test-adjacency.R
@@ -670,7 +670,6 @@ test_that("sparse/dense matrices no loops works", {
   g <- graph_from_adjacency_matrix(A, diag = FALSE)
   expect_ecount(g, 1)
   expect_equal(get_edge_ids(g, c(1, 2)), 1)
-
 })
 
 test_that("sparse/dense matrices multiple works", {
@@ -681,11 +680,10 @@ test_that("sparse/dense matrices multiple works", {
   expect_ecount(g, 3)
   expect_equal(as_edgelist(g), matrix(c(1, 2), 3, 2, byrow = TRUE))
 
-  A <- as(A,"dgCMatrix")
+  A <- as(A, "dgCMatrix")
   g <- graph_from_adjacency_matrix(A, diag = FALSE)
   expect_ecount(g, 3)
   expect_equal(as_edgelist(g), matrix(c(1, 2), 3, 2, byrow = TRUE))
-
 })
 
 test_that("sparse/dense matrices min/max/plus", {
@@ -712,3 +710,8 @@ test_that("sparse/dense matrices min/max/plus", {
   g <- graph_from_adjacency_matrix(A, diag = FALSE, mode = "plus", weighted = TRUE)
   expect_equal(E(g)$weight[1], 5)
 })
+
+test_that("graph_from_adjacency_matrix errors for NAs", {
+  A <- matrix(c(1, 1, NA, 1), 2, 2)
+  expect_snapshot(graph_from_adjacency_matrix(A), error = TRUE)
+})
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index 4b6a881f21..c794115d8a 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -53,7 +53,7 @@ test_that("as.undirected() deprecation", {
 })
 
 test_that("as_undirected() keeps attributes", {
-  g <- graph_from_literal(A +-+ B, A --+ C, C +-+ D)
+  g <- graph_from_literal(A + -+B, A - -+C, C + -+D)
   g$name <- "Tiny graph"
   E(g)$weight <- seq_len(ecount(g))
 
@@ -596,3 +596,8 @@ test_that("edge names work", {
     structure(c("b", "c", "d", "e", "g", "h", "a", "c", "d", "e", "f", "h", "i", "j"), .Dim = c(7L, 2L))
   )
 })
+
+test_that("graph_from_edgelist errors for NAs", {
+  A <- matrix(c(1, 2, NA, 1), 2, 2)
+  expect_snapshot(graph_from_edgelist(A), error = TRUE)
+})
diff --git a/tests/testthat/test-incidence.R b/tests/testthat/test-incidence.R
index 47034a9deb..9966a8986c 100644
--- a/tests/testthat/test-incidence.R
+++ b/tests/testthat/test-incidence.R
@@ -175,3 +175,8 @@ test_that("graph_from_biadjacency_matrix() errors well", {
     (g <- graph_from_biadjacency_matrix(inc, multiple = TRUE, weighted = TRUE))
   })
 })
+
+test_that("graph_from_biadjacency_matrix errors for NAs", {
+  A <- matrix(c(1, 1, NA, 1), 2, 2)
+  expect_snapshot(graph_from_biadjacency_matrix(A), error = TRUE)
+})

From 22a4c6e8b0fb73abba9c96728b8a9c467e5667b1 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Wed, 16 Apr 2025 20:53:44 +0200
Subject: [PATCH 2/6] fixed a literal

---
 tests/testthat/test-conversion.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index c794115d8a..6cc08d982d 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -53,7 +53,7 @@ test_that("as.undirected() deprecation", {
 })
 
 test_that("as_undirected() keeps attributes", {
-  g <- graph_from_literal(A + -+B, A - -+C, C + -+D)
+  g <- graph_from_literal(A +-+ B, A --+ C, C +-+ D)
   g$name <- "Tiny graph"
   E(g)$weight <- seq_len(ecount(g))
 

From 82d089ec2f4c1ca8cd5762a3bbd4e92649d9fd00 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Tue, 29 Apr 2025 21:19:55 +0200
Subject: [PATCH 3/6] added caller_env as default

---
 NAMESPACE             | 1 +
 R/adjacency.R         | 2 +-
 R/conversion.R        | 4 ++--
 R/incidence.R         | 2 +-
 R/utils-assert-args.R | 3 ++-
 5 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 19c88795d6..f0cc95bf2c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -937,6 +937,7 @@ importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,as_function)
+importFrom(rlang,caller_env)
 importFrom(rlang,check_dots_empty)
 importFrom(rlang,check_installed)
 importFrom(rlang,global_env)
diff --git a/R/adjacency.R b/R/adjacency.R
index c32240ae6e..84ded07597 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -228,7 +228,7 @@ graph_from_adjacency_matrix <- function(adjmatrix,
                                         ),
                                         weighted = NULL, diag = TRUE,
                                         add.colnames = NULL, add.rownames = NA) {
-  ensure_no_na(adjmatrix, "adjacency matrix", call = rlang::caller_env())
+  ensure_no_na(adjmatrix, "adjacency matrix")
   mode <- igraph.match.arg(mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
diff --git a/R/conversion.R b/R/conversion.R
index f466cb5bb2..3c5bc593be 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -1397,7 +1397,7 @@ graph_from_data_frame <- function(d, directed = TRUE, vertices = NULL) {
   }
 
   ## Handle if some elements are 'NA'
-  ensure_no_na(d, "edge data frame", call = rlang::caller_env())
+  ensure_no_na(d, "edge data frame")
 
   if (!is.null(vertices) && any(is.na(vertices[, 1]))) {
     cli::cli_warn("In {.code vertices[,1]}, {.code NA} elements were replaced with string {.str NA}.")
@@ -1495,7 +1495,7 @@ graph_from_edgelist <- function(el, directed = TRUE) {
   if (!is.matrix(el) || ncol(el) != 2) {
     cli::cli_abort("graph_from_edgelist expects a matrix with two columns.")
   }
-  ensure_no_na(el, "edgelist", call = rlang::caller_env())
+  ensure_no_na(el, "edgelist")
 
   if (nrow(el) == 0) {
     res <- make_empty_graph(directed = directed)
diff --git a/R/incidence.R b/R/incidence.R
index cefec10a60..9a3c90010a 100644
--- a/R/incidence.R
+++ b/R/incidence.R
@@ -168,7 +168,7 @@ graph_from_biadjacency_matrix <- function(incidence, directed = FALSE,
                                           multiple = FALSE, weighted = NULL,
                                           add.names = NULL) {
   # Argument checks
-  ensure_no_na(incidence, "biadjacency matrix", call = rlang::caller_env())
+  ensure_no_na(incidence, "biadjacency matrix")
   directed <- as.logical(directed)
   mode <- igraph.match.arg(mode)
 
diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index 53f3c6e24c..e66cd3b31d 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -33,7 +33,8 @@ igraph.match.arg <- function(arg, values, error_call = rlang::caller_env()) {
   )
 }
 
-ensure_no_na <- function(x, what, call) {
+#' @importFrom rlang caller_env
+ensure_no_na <- function(x, what, call = caller_env()) {
   if (any(is.na(x))) {
     cli::cli_abort("Cannot create a graph object because the {what} contains NAs.", call = call)
   }

From 4857e1c216556a7bd1e28ef81e07b2bbaaaca37d Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Tue, 29 Apr 2025 21:35:42 +0200
Subject: [PATCH 4/6] updated snapshots

---
 tests/testthat/_snaps/adjacency.md | 2 +-
 tests/testthat/_snaps/incidence.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/_snaps/adjacency.md b/tests/testthat/_snaps/adjacency.md
index 6a5b41d0df..1af5c9cbce 100644
--- a/tests/testthat/_snaps/adjacency.md
+++ b/tests/testthat/_snaps/adjacency.md
@@ -144,6 +144,6 @@
     Code
       graph_from_adjacency_matrix(A)
     Condition
-      Error:
+      Error in `graph_from_adjacency_matrix()`:
       ! Cannot create a graph object because the adjacency matrix contains NAs.
 
diff --git a/tests/testthat/_snaps/incidence.md b/tests/testthat/_snaps/incidence.md
index 81283445e3..dbb1ba9a91 100644
--- a/tests/testthat/_snaps/incidence.md
+++ b/tests/testthat/_snaps/incidence.md
@@ -90,6 +90,6 @@
     Code
       graph_from_biadjacency_matrix(A)
     Condition
-      Error:
+      Error in `graph_from_biadjacency_matrix()`:
       ! Cannot create a graph object because the biadjacency matrix contains NAs.
 

From 1d8385aae285fa81caa1641f2e60fa2417df7f82 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Tue, 3 Jun 2025 09:24:14 +0200
Subject: [PATCH 5/6] fixed failing test

---
 tests/testthat/_snaps/conversion.md | 2 +-
 tests/testthat/test-conversion.R    | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 33624b7d48..2f981abe68 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -92,6 +92,6 @@
     Code
       graph_from_edgelist(A)
     Condition
-      Error:
+      Error in `graph_from_edgelist()`:
       ! Cannot create a graph object because the edgelist contains NAs.
 
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index b097db125f..21ba3d302f 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -600,6 +600,8 @@ test_that("edge names work", {
 test_that("graph_from_edgelist errors for NAs", {
   A <- matrix(c(1, 2, NA, 1), 2, 2)
   expect_snapshot(graph_from_edgelist(A), error = TRUE)
+})
+
 test_that("graph_from_data_frame works with factors", {
   actors <- data.frame(
     name = c("Alice", "Bob", "Cecil", "David", "Esmeralda"),

From 6380c2f222dd069b083338c055fba11334297bbc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr@users.noreply.github.com>
Date: Thu, 5 Jun 2025 11:12:29 +0200
Subject: [PATCH 6/6] Update R/utils-assert-args.R

---
 R/utils-assert-args.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index e66cd3b31d..75952217db 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -35,7 +35,7 @@ igraph.match.arg <- function(arg, values, error_call = rlang::caller_env()) {
 
 #' @importFrom rlang caller_env
 ensure_no_na <- function(x, what, call = caller_env()) {
-  if (any(is.na(x))) {
+  if (anyNA(x)) {
     cli::cli_abort("Cannot create a graph object because the {what} contains NAs.", call = call)
   }
 }