From 7331b3acb339ea3845864f083dd25fe568628b68 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 6 May 2026 05:30:54 +0000
Subject: [PATCH 1/3] Initial plan


From d329174078a0d5440deedc7dd88a6f5f9e20df29 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 6 May 2026 05:40:55 +0000
Subject: [PATCH 2/3] fix: avoid memory overflow in ensure_no_na for large
 sparse matrices with mode=lower/upper

Agent-Logs-Url: https://github.com/igraph/rigraph/sessions/a080274e-c869-44c6-b491-4748a81bfc9c

Co-authored-by: schochastics <17147355+schochastics@users.noreply.github.com>
---
 R/adjacency.R                   |  5 +++--
 R/utils-assert-args.R           | 12 ++++++++++--
 tests/testthat/test-adjacency.R | 34 +++++++++++++++++++++++++++++++++
 3 files changed, 47 insertions(+), 4 deletions(-)

diff --git a/R/adjacency.R b/R/adjacency.R
index 65b4eb21411..10497e4f3ff 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -494,8 +494,9 @@ graph.adjacency.sparse <- function(
   }
 
   vc <- nrow(adjmatrix)
-  # Exit early for empty graphs
-  if (vc == 1 || Matrix::nnzero(adjmatrix) == 0) {
+  # Exit early for empty graphs. Use na.counted = TRUE so that NA entries
+  # (which are stored explicitly) do not cause nnzero() to return NA.
+  if (vc == 1 || Matrix::nnzero(adjmatrix, na.counted = TRUE) == 0) {
     return(make_empty_graph(n = vc, directed = (mode == "directed")))
   }
 
diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index cfb2ddf3025..c80e7cb9cfd 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -66,9 +66,17 @@ igraph_match_arg <- function(
 #' @importFrom rlang caller_env
 ensure_no_na <- function(x, what, mode = "", call = caller_env()) {
   if (mode == "upper") {
-    x <- x[upper.tri(x)]
+    if (inherits(x, "sparseMatrix")) {
+      x <- Matrix::triu(x)@x
+    } else {
+      x <- x[upper.tri(x)]
+    }
   } else if (mode == "lower") {
-    x <- x[lower.tri(x)]
+    if (inherits(x, "sparseMatrix")) {
+      x <- Matrix::tril(x)@x
+    } else {
+      x <- x[lower.tri(x)]
+    }
   }
   if (anyNA(x)) {
     cli::cli_abort(
diff --git a/tests/testthat/test-adjacency.R b/tests/testthat/test-adjacency.R
index c4f2669202b..67755897b20 100644
--- a/tests/testthat/test-adjacency.R
+++ b/tests/testthat/test-adjacency.R
@@ -879,3 +879,37 @@ test_that("graph_from_adjacency Na check for upper/lower", {
     )
   )
 })
+
+test_that("graph_from_adjacency Na check for upper/lower with sparse matrices", {
+  # Sparse matrix with NA only in upper triangle: mode="upper" should error,
+  # mode="lower" should succeed
+  sp <- Matrix::sparseMatrix(
+    i = c(1, 2, 1),
+    j = c(2, 1, 1),
+    x = c(NA_real_, 1, 1),
+    dims = c(3, 3)
+  )
+  expect_error(
+    graph_from_adjacency_matrix(sp, mode = "upper", weighted = TRUE),
+    "contains NAs"
+  )
+  expect_no_error(
+    graph_from_adjacency_matrix(sp, mode = "lower", weighted = TRUE)
+  )
+
+  # Sparse matrix with NA only in lower triangle: mode="lower" should error,
+  # mode="upper" should succeed
+  sp2 <- Matrix::sparseMatrix(
+    i = c(2, 1, 1),
+    j = c(1, 2, 1),
+    x = c(NA_real_, 1, 1),
+    dims = c(3, 3)
+  )
+  expect_error(
+    graph_from_adjacency_matrix(sp2, mode = "lower", weighted = TRUE),
+    "contains NAs"
+  )
+  expect_no_error(
+    graph_from_adjacency_matrix(sp2, mode = "upper", weighted = TRUE)
+  )
+})

From 0f89ecf352ab7fe0128814ae6e73154da25f7242 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 6 May 2026 05:41:22 +0000
Subject: [PATCH 3/3] style: fix test name capitalization (Na -> NA)

Agent-Logs-Url: https://github.com/igraph/rigraph/sessions/a080274e-c869-44c6-b491-4748a81bfc9c

Co-authored-by: schochastics <17147355+schochastics@users.noreply.github.com>
---
 tests/testthat/test-adjacency.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-adjacency.R b/tests/testthat/test-adjacency.R
index 67755897b20..b43e54c3450 100644
--- a/tests/testthat/test-adjacency.R
+++ b/tests/testthat/test-adjacency.R
@@ -880,7 +880,7 @@ test_that("graph_from_adjacency Na check for upper/lower", {
   )
 })
 
-test_that("graph_from_adjacency Na check for upper/lower with sparse matrices", {
+test_that("graph_from_adjacency NA check for upper/lower with sparse matrices", {
   # Sparse matrix with NA only in upper triangle: mode="upper" should error,
   # mode="lower" should succeed
   sp <- Matrix::sparseMatrix(