From 9085ad586ac3c314946f29d730fe67f79b5ecb78 Mon Sep 17 00:00:00 2001
From: David Schoch <david@schochastics.net>
Date: Thu, 23 Oct 2025 10:29:11 +0200
Subject: [PATCH] fix NA check for lower upper tri

---
 R/adjacency.R                   |  2 +-
 R/utils-assert-args.R           |  7 ++++++-
 tests/testthat/test-adjacency.R | 24 ++++++++++++++++++++++++
 3 files changed, 31 insertions(+), 2 deletions(-)

diff --git a/R/adjacency.R b/R/adjacency.R
index c96f3f1a54d..3823ec1ad71 100644
--- a/R/adjacency.R
+++ b/R/adjacency.R
@@ -289,8 +289,8 @@ graph_from_adjacency_matrix <- function(
   add.colnames = NULL,
   add.rownames = NA
 ) {
-  ensure_no_na(adjmatrix, "adjacency matrix")
   mode <- igraph.match.arg(mode)
+  ensure_no_na(adjmatrix, "adjacency matrix", mode)
 
   if (!is.matrix(adjmatrix) && !inherits(adjmatrix, "Matrix")) {
     lifecycle::deprecate_soft(
diff --git a/R/utils-assert-args.R b/R/utils-assert-args.R
index 98f63ea5240..f39324cd419 100644
--- a/R/utils-assert-args.R
+++ b/R/utils-assert-args.R
@@ -40,7 +40,12 @@ igraph.match.arg <- function(
 }
 
 #' @importFrom rlang caller_env
-ensure_no_na <- function(x, what, call = caller_env()) {
+ensure_no_na <- function(x, what, mode = "", call = caller_env()) {
+  if (mode == "upper") {
+    x <- x[upper.tri(x)]
+  } else if (mode == "lower") {
+    x <- x[lower.tri(x)]
+  }
   if (anyNA(x)) {
     cli::cli_abort(
       "Cannot create a graph object because the {what} contains NAs.",
diff --git a/tests/testthat/test-adjacency.R b/tests/testthat/test-adjacency.R
index b488ca4302d..f4040b694b3 100644
--- a/tests/testthat/test-adjacency.R
+++ b/tests/testthat/test-adjacency.R
@@ -855,3 +855,27 @@ test_that("graph_from_adjacency_matrix handles add.colnames and add.rownames = F
   g_false_row <- graph_from_adjacency_matrix(M, add.rownames = FALSE)
   expect_equal(vertex_attr_names(g_na_row), vertex_attr_names(g_false_row))
 })
+
+test_that("graph_from_adjacency Na check for upper/lower", {
+  x <- matrix(runif(100), ncol=10, nrow=10)
+  x[lower.tri(x)] <- NA
+  expect_no_error(
+    graph_from_adjacency_matrix(
+      x,
+      mode = "upper",
+      weighted = TRUE,
+      diag = FALSE
+    )
+  )
+
+  x <- matrix(runif(100), ncol=10, nrow=10)
+  x[upper.tri(x)] <- NA
+  expect_no_error(
+    graph_from_adjacency_matrix(
+      x,
+      mode = "lower",
+      weighted = TRUE,
+      diag = FALSE
+    )
+  )
+})