From 80ca590e53f41985dcc0fb4ad2a710c2f80b509e Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Fri, 20 Sep 2024 21:06:59 +0200
Subject: [PATCH 01/11] removed for loops in get.adjacency.dense

---
 R/conversion.R | 63 ++++++++------------------------------------------
 1 file changed, 9 insertions(+), 54 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index ec548d0129..f31e47c5b4 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -1,4 +1,3 @@
-
 #' Convert igraph graphs to graphNEL objects from the graph package
 #'
 #' @description
@@ -159,11 +158,6 @@ get.adjacency.dense <- function(graph, type = c("both", "upper", "lower"),
   ensure_igraph(graph)
 
   type <- igraph.match.arg(type)
-  type <- switch(type,
-    "upper" = 0,
-    "lower" = 1,
-    "both" = 2
-  )
 
   if (is.logical(loops)) {
     loops <- ifelse(loops, "once", "ignore")
@@ -183,61 +177,22 @@ get.adjacency.dense <- function(graph, type = c("both", "upper", "lower"),
 
   if (is.null(attr)) {
     on.exit(.Call(R_igraph_finalizer))
+    type <- switch(type,
+      "upper" = 0,
+      "lower" = 1,
+      "both" = 2
+    )
     res <- .Call(
       R_igraph_get_adjacency, graph, as.numeric(type), weights,
       loops
     )
   } else {
-    attr <- as.character(attr)
-    if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute")
-    }
-    exattr <- edge_attr(graph, attr)
-    if (is.logical(exattr)) {
-      res <- matrix(FALSE, nrow = vcount(graph), ncol = vcount(graph))
-    } else if (is.numeric(exattr)) {
-      res <- matrix(0, nrow = vcount(graph), ncol = vcount(graph))
-    } else {
-      stop(
-        "Matrices must be either numeric or logical, ",
-        "and the edge attribute is not"
-      )
-    }
-    if (is_directed(graph)) {
-      for (i in seq(length.out = ecount(graph))) {
-        e <- ends(graph, i, names = FALSE)
-        res[e[1], e[2]] <- exattr[i]
-      }
-    } else {
-      if (type == 0) {
-        ## upper
-        for (i in seq(length.out = ecount(graph))) {
-          e <- ends(graph, i, names = FALSE)
-          res[min(e), max(e)] <- exattr[i]
-        }
-      } else if (type == 1) {
-        ## lower
-        for (i in seq(length.out = ecount(graph))) {
-          e <- ends(graph, i, names = FALSE)
-          res[max(e), min(e)] <- exattr[i]
-        }
-      } else if (type == 2) {
-        ## both
-        for (i in seq(length.out = ecount(graph))) {
-          e <- ends(graph, i, names = FALSE)
-          res[e[1], e[2]] <- exattr[i]
-          if (e[1] != e[2]) {
-            res[e[2], e[1]] <- exattr[i]
-          }
-        }
-      }
-    }
+    res <- as.matrix(get.adjacency.sparse(graph, type = type, attr = attr, names = names))
   }
 
   if (names && "name" %in% vertex_attr_names(graph)) {
     colnames(res) <- rownames(res) <- V(graph)$name
   }
-
   res
 }
 
@@ -1004,7 +959,7 @@ get.incidence.sparse <- function(graph, types, names, attr) {
 #' as_biadjacency_matrix(g)
 #'
 as_biadjacency_matrix <- function(graph, types = NULL, attr = NULL,
-                                names = TRUE, sparse = FALSE) {
+                                  names = TRUE, sparse = FALSE) {
   # Argument checks
   ensure_igraph(graph)
   types <- handle_vertex_type_arg(types, graph)
@@ -1033,8 +988,8 @@ as_biadjacency_matrix <- function(graph, types = NULL, attr = NULL,
 #' this naming to avoid confusion with the edge-vertex incidence matrix.
 #' @export
 as_incidence_matrix <- function(...) { # nocov start
-   lifecycle::deprecate_soft("1.6.0", "as_incidence_matrix()", "as_biadjacency_matrix()")
-   as_biadjacency_matrix(...)
+  lifecycle::deprecate_soft("1.6.0", "as_incidence_matrix()", "as_biadjacency_matrix()")
+  as_biadjacency_matrix(...)
 } # nocov end
 #' @rdname graph_from_data_frame
 #' @param x An igraph object.

From 78403ce6c06621c2b289472b703a788e8066fb0b Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Wed, 9 Oct 2024 21:01:38 +0200
Subject: [PATCH 02/11] added comment that as.matrix on sparse adj is fastest
 solution

---
 R/conversion.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/conversion.R b/R/conversion.R
index f31e47c5b4..e155697595 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -187,6 +187,7 @@ get.adjacency.dense <- function(graph, type = c("both", "upper", "lower"),
       loops
     )
   } else {
+    # faster than a specialized implementation
     res <- as.matrix(get.adjacency.sparse(graph, type = type, attr = attr, names = names))
   }
 

From 16a7fe138e161764c954adb234283db5a7e1c587 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Mon, 13 Jan 2025 21:11:11 +0100
Subject: [PATCH 03/11] fix failing tests due to #1551

---
 tests/testthat/_snaps/conversion.md |  4 +--
 tests/testthat/test-conversion.R    | 50 +++++++++++++++++++----------
 2 files changed, 35 insertions(+), 19 deletions(-)

diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 12b0bc0c7f..98423b4262 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -41,7 +41,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error in `get.adjacency.dense()`:
+      Error in `get.adjacency.sparse()`:
       ! no such edge attribute
 
 ---
@@ -49,6 +49,6 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error in `get.adjacency.dense()`:
+      Error in `get.adjacency.sparse()`:
       ! Matrices must be either numeric or logical, and the edge attribute is not
 
diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index aa8ca51fe7..e8278b06c5 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -71,7 +71,7 @@ test_that("as_undirected() keeps attributes", {
 })
 
 test_that("as_adjacency_matrix() works -- sparse", {
-  g <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  g <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   basic_adj_matrix <- as_adjacency_matrix(g)
   expect_s4_class(basic_adj_matrix, "dgCMatrix")
   expected_matrix <- matrix(
@@ -93,17 +93,19 @@ test_that("as_adjacency_matrix() works -- sparse", {
   E(g)$weight <- c(1.2, 3.4, 2.7, 5.6, 6.0, 0.1, 6.1, 3.3, 4.3)
   weight_adj_matrix <- as_adjacency_matrix(g, attr = "weight")
   expect_s4_class(weight_adj_matrix, "dgCMatrix")
-  expect_equal(as.matrix(weight_adj_matrix),
+  expect_equal(
+    as.matrix(weight_adj_matrix),
     matrix(
       c(0, 3.4, 0, 0, 1.2, 2.7, 0, 13.7, 0, 0, 11.6, 0, 0, 0, 0.1, 0),
       nrow = 4L,
       ncol = 4L,
       dimnames = list(c("a", "b", "c", "d"), c("a", "b", "c", "d"))
-    ))
+    )
+  )
 })
 
 test_that("as_adjacency_matrix() works -- sparse + not both", {
-  dg <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  dg <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   g <- as_undirected(dg, mode = "each")
 
   lower_adj_matrix <- as_adjacency_matrix(g, type = "lower")
@@ -128,16 +130,15 @@ test_that("as_adjacency_matrix() works -- sparse + not both", {
 })
 
 test_that("as_adjacency_matrix() errors well -- sparse", {
-  g <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  g <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   expect_snapshot(as_adjacency_matrix(g, attr = "bla"), error = TRUE)
 
   E(g)$bla <- letters[1:ecount(g)]
   expect_snapshot(as_adjacency_matrix(g, attr = "bla"), error = TRUE)
-
 })
 
 test_that("as_adjacency_matrix() works -- sparse undirected", {
-  dg <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  dg <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   ug <- as_undirected(dg, mode = "each")
   adj_matrix <- as_adjacency_matrix(ug)
   expect_s4_class(adj_matrix, "dgCMatrix")
@@ -155,7 +156,7 @@ test_that("as_adjacency_matrix() works -- sparse undirected", {
 })
 
 test_that("as_adjacency_matrix() works -- dense", {
-  g <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  g <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
 
   basic_adj_matrix <- as_adjacency_matrix(g, sparse = FALSE)
   expected_matrix <- matrix(
@@ -175,7 +176,11 @@ test_that("as_adjacency_matrix() works -- dense", {
   expect_equal(
     weight_adj_matrix,
     matrix(
-      c(0, 3.4, 0, 0, 1.2, 2.7, 0, 4.3, 0, 0, 6, 0, 0, 0, 0.1, 0),
+      c(0, 3.4, 0, 0, 1.2, 2.7, 0, 13.7, 0, 0, 11.6, 0, 0, 0, 0.1, 0),
+      # below is wrong test result due to a bug (#1551). Weights of ties
+      # between the same node pair should be aggregated and not only the last
+      # weight should be considered. The above is consistent with the sparse case
+      # c(0, 3.4, 0, 0, 1.2, 2.7, 0, 4.3, 0, 0, 6, 0, 0, 0, 0.1, 0),
       nrow = 4L,
       ncol = 4L,
       dimnames = list(c("a", "b", "c", "d"), c("a", "b", "c", "d"))
@@ -184,17 +189,16 @@ test_that("as_adjacency_matrix() works -- dense", {
 })
 
 test_that("as_adjacency_matrix() errors well -- dense", {
-  g <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  g <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   expect_snapshot(as_adjacency_matrix(g, attr = "bla", sparse = FALSE), error = TRUE)
 
   E(g)$bla <- letters[1:ecount(g)]
   expect_snapshot(as_adjacency_matrix(g, attr = "bla", sparse = FALSE), error = TRUE)
-
 })
 
 
 test_that("as_adjacency_matrix() works -- dense undirected", {
-  dg <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  dg <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   ug <- as_undirected(dg, mode = "each")
   # no different treatment than undirected if no attribute?!
   adj_matrix <- as_adjacency_matrix(ug, sparse = FALSE)
@@ -211,7 +215,11 @@ test_that("as_adjacency_matrix() works -- dense undirected", {
   expect_equal(
     weight_adj_matrix,
     matrix(
-      c(0, 3.4, 0, 0, 3.4, 2.7, 0, 4.3, 0, 0, 6, 0.1, 0, 4.3, 0.1, 0),
+      c(0, 4.6, 0, 0, 4.6, 2.7, 0, 13.7, 0, 0, 11.6, 0.1, 0, 13.7, 0.1, 0),
+      # below is wrong test result due to a bug (#1551). Weights of ties
+      # between the same node pair should be aggregated and not only the last
+      # weight should be considered. The above is consistent with the sparse case
+      # c(0, 3.4, 0, 0, 3.4, 2.7, 0, 4.3, 0, 0, 6, 0.1, 0, 4.3, 0.1, 0),
       nrow = 4L,
       ncol = 4L
     )
@@ -219,7 +227,7 @@ test_that("as_adjacency_matrix() works -- dense undirected", {
 })
 
 test_that("as_adjacency_matrix() works -- dense + not both", {
-  dg <- make_graph(c(1,2, 2,1, 2,2, 3,3, 3,3, 3,4, 4,2, 4,2, 4,2), directed = TRUE)
+  dg <- make_graph(c(1, 2, 2, 1, 2, 2, 3, 3, 3, 3, 3, 4, 4, 2, 4, 2, 4, 2), directed = TRUE)
   g <- as_undirected(dg, mode = "each")
   E(g)$attribute <- c(1.2, 3.4, 2.7, 5.6, 6.0, 0.1, 6.1, 3.3, 4.3)
 
@@ -233,13 +241,17 @@ test_that("as_adjacency_matrix() works -- dense + not both", {
   expect_equal(
     lower_adj_matrix,
     matrix(
-      c(0, 3.4, 0, 0, 0, 2.7, 0, 4.3, 0, 0, 6, 0.1, 0, 0, 0, 0),
+      c(0, 4.6, 0, 0, 0, 2.7, 0, 13.7, 0, 0, 11.6, 0.1, 0, 0, 0, 0),
+      # below is wrong test result due to a bug (#1551). Weights of ties
+      # between the same node pair should be aggregated and not only the last
+      # weight should be considered. The above is consistent with the sparse case
+      # c(0, 3.4, 0, 0, 0, 2.7, 0, 4.3, 0, 0, 6, 0.1, 0, 0, 0, 0),
       nrow = 4L,
       ncol = 4L
     )
   )
 
-  upper_adj_matrix  <- as_adjacency_matrix(
+  upper_adj_matrix <- as_adjacency_matrix(
     g,
     type = "upper",
     sparse = FALSE,
@@ -249,7 +261,11 @@ test_that("as_adjacency_matrix() works -- dense + not both", {
   expect_equal(
     upper_adj_matrix,
     matrix(
-      c(0, 0, 0, 0, 3.4, 2.7, 0, 0, 0, 0, 6, 0, 0, 4.3, 0.1, 0),
+      c(0, 0, 0, 0, 4.6, 2.7, 0, 0, 0, 0, 11.6, 0, 0, 13.7, 0.1, 0),
+      # below is wrong test result due to a bug (#1551). Weights of ties
+      # between the same node pair should be aggregated and not only the last
+      # weight should be considered. The above is consistent with the sparse case
+      # c(0, 0, 0, 0, 3.4, 2.7, 0, 0, 0, 0, 6, 0, 0, 4.3, 0.1, 0),
       nrow = 4L,
       ncol = 4L
     )

From 563ed24e838c1faf57b38b921070233ce0a4cbf3 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Thu, 16 Jan 2025 13:18:34 +0100
Subject: [PATCH 04/11] added call. = FALSE to stop calls for clearer error
 reporting

---
 R/conversion.R                      | 14 +++++++-------
 tests/testthat/_snaps/conversion.md |  8 ++++----
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index e155697595..9a38a3dd11 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -211,13 +211,14 @@ get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"),
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute")
+      stop("no such edge attribute", call. = FALSE)
     }
     value <- edge_attr(graph, name = attr)
     if (!is.numeric(value) && !is.logical(value)) {
       stop(
         "Matrices must be either numeric or logical, ",
-        "and the edge attribute is not"
+        "and the edge attribute is not",
+        call. = FALSE
       )
     }
   } else {
@@ -334,7 +335,6 @@ as_adjacency_matrix <- function(graph, type = c("both", "upper", "lower"),
 as_adj <- function(graph, type = c("both", "upper", "lower"),
                    attr = NULL, edges = deprecated(), names = TRUE,
                    sparse = igraph_opt("sparsematrices")) {
-
   lifecycle::deprecate_soft("2.1.0", "as_adj()", "as_adjacency_matrix()")
 
   as_adjacency_matrix(
@@ -834,7 +834,7 @@ get.incidence.dense <- function(graph, types, names, attr) {
   } else {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute")
+      stop("no such edge attribute", call. = FALSE)
     }
 
     vc <- vcount(graph)
@@ -871,12 +871,12 @@ get.incidence.dense <- function(graph, types, names, attr) {
 get.incidence.sparse <- function(graph, types, names, attr) {
   vc <- vcount(graph)
   if (length(types) != vc) {
-    stop("Invalid types vector")
+    stop("Invalid types vector", call. = FALSE)
   }
 
   el <- as_edgelist(graph, names = FALSE)
   if (any(types[el[, 1]] == types[el[, 2]])) {
-    stop("Invalid types vector, not a bipartite graph")
+    stop("Invalid types vector, not a bipartite graph", call. = FALSE)
   }
 
   n1 <- sum(!types)
@@ -896,7 +896,7 @@ get.incidence.sparse <- function(graph, types, names, attr) {
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute")
+      stop("no such edge attribute", call. = FALSE)
     }
     value <- edge_attr(graph, name = attr)
   } else {
diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 98423b4262..66ee0de5fc 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -25,7 +25,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla")
     Condition
-      Error in `get.adjacency.sparse()`:
+      Error:
       ! no such edge attribute
 
 ---
@@ -33,7 +33,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla")
     Condition
-      Error in `get.adjacency.sparse()`:
+      Error:
       ! Matrices must be either numeric or logical, and the edge attribute is not
 
 # as_adjacency_matrix() errors well -- dense
@@ -41,7 +41,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error in `get.adjacency.sparse()`:
+      Error:
       ! no such edge attribute
 
 ---
@@ -49,6 +49,6 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error in `get.adjacency.sparse()`:
+      Error:
       ! Matrices must be either numeric or logical, and the edge attribute is not
 

From 1ecedd89242950ae1c15115ba8be3cae517e801d Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Thu, 16 Jan 2025 13:34:44 +0100
Subject: [PATCH 05/11] fixed failing tests on R 4.0

---
 tests/testthat/test-conversion.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index e8278b06c5..3ff70fd7f1 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -202,6 +202,7 @@ test_that("as_adjacency_matrix() works -- dense undirected", {
   ug <- as_undirected(dg, mode = "each")
   # no different treatment than undirected if no attribute?!
   adj_matrix <- as_adjacency_matrix(ug, sparse = FALSE)
+  dimnames(adj_matrix) <- NULL
   expect_equal(
     adj_matrix,
     matrix(
@@ -212,6 +213,7 @@ test_that("as_adjacency_matrix() works -- dense undirected", {
 
   E(ug)$weight <- c(1.2, 3.4, 2.7, 5.6, 6.0, 0.1, 6.1, 3.3, 4.3)
   weight_adj_matrix <- as_adjacency_matrix(ug, sparse = FALSE, attr = "weight")
+  dimnames(weight_adj_matrix) <- NULL
   expect_equal(
     weight_adj_matrix,
     matrix(
@@ -237,6 +239,7 @@ test_that("as_adjacency_matrix() works -- dense + not both", {
     sparse = FALSE,
     attr = "attribute"
   )
+  dimnames(lower_adj_matrix) <- NULL
 
   expect_equal(
     lower_adj_matrix,
@@ -257,7 +260,7 @@ test_that("as_adjacency_matrix() works -- dense + not both", {
     sparse = FALSE,
     attr = "attribute"
   )
-
+  dimnames(upper_adj_matrix) <- NULL
   expect_equal(
     upper_adj_matrix,
     matrix(

From d303690ac4bc51ede59fd4b7ee1846f4611ccb03 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Tue, 21 Jan 2025 12:36:53 +0100
Subject: [PATCH 06/11] switched to cli::abort error handling

---
 R/conversion.R                      | 13 ++++++-------
 tests/testthat/_snaps/conversion.md |  8 ++++----
 2 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index 9a38a3dd11..42076c576b 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -188,7 +188,7 @@ get.adjacency.dense <- function(graph, type = c("both", "upper", "lower"),
     )
   } else {
     # faster than a specialized implementation
-    res <- as.matrix(get.adjacency.sparse(graph, type = type, attr = attr, names = names))
+    res <- as.matrix(get.adjacency.sparse(graph, type = type, attr = attr, names = names, call = rlang::caller_env()))
   }
 
   if (names && "name" %in% vertex_attr_names(graph)) {
@@ -198,7 +198,7 @@ get.adjacency.dense <- function(graph, type = c("both", "upper", "lower"),
 }
 
 get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"),
-                                 attr = NULL, names = TRUE) {
+                                 attr = NULL, names = TRUE, call = rlang::caller_env()) {
   ensure_igraph(graph)
 
   type <- igraph.match.arg(type)
@@ -211,14 +211,13 @@ get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"),
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute", call. = FALSE)
+      cli::cli_abort("no such edge attribute", call = call)
     }
     value <- edge_attr(graph, name = attr)
     if (!is.numeric(value) && !is.logical(value)) {
-      stop(
-        "Matrices must be either numeric or logical, ",
-        "and the edge attribute is not",
-        call. = FALSE
+      cli::cli_abort(
+        "Matrices must be either numeric or logical, and the edge attribute is not",
+        call = call
       )
     }
   } else {
diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 66ee0de5fc..6c33bfbd57 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -25,7 +25,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla")
     Condition
-      Error:
+      Error in `as_adjacency_matrix()`:
       ! no such edge attribute
 
 ---
@@ -33,7 +33,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla")
     Condition
-      Error:
+      Error in `as_adjacency_matrix()`:
       ! Matrices must be either numeric or logical, and the edge attribute is not
 
 # as_adjacency_matrix() errors well -- dense
@@ -41,7 +41,7 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error:
+      Error in `as_adjacency_matrix()`:
       ! no such edge attribute
 
 ---
@@ -49,6 +49,6 @@
     Code
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
-      Error:
+      Error in `as_adjacency_matrix()`:
       ! Matrices must be either numeric or logical, and the edge attribute is not
 

From ce7158d27244c348a4616de49c1392cd59093665 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Fri, 24 Jan 2025 19:28:17 +0100
Subject: [PATCH 07/11] changed all stop calls to cli_abort

---
 R/conversion.R                      | 16 ++++++++--------
 tests/testthat/_snaps/conversion.md |  4 ++--
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index 42076c576b..7f79bba798 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -211,7 +211,7 @@ get.adjacency.sparse <- function(graph, type = c("both", "upper", "lower"),
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      cli::cli_abort("no such edge attribute", call = call)
+      cli::cli_abort("No such edge attribute", call = call)
     }
     value <- edge_attr(graph, name = attr)
     if (!is.numeric(value) && !is.logical(value)) {
@@ -816,7 +816,7 @@ as_graphnel <- function(graph) {
   res
 }
 
-get.incidence.dense <- function(graph, types, names, attr) {
+get.incidence.dense <- function(graph, types, names, attr, call = rlang::caller_env()) {
   if (is.null(attr)) {
     on.exit(.Call(R_igraph_finalizer))
     ## Function call
@@ -833,7 +833,7 @@ get.incidence.dense <- function(graph, types, names, attr) {
   } else {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute", call. = FALSE)
+      cli::cli_abort("No such edge attribute", call = call)
     }
 
     vc <- vcount(graph)
@@ -867,15 +867,15 @@ get.incidence.dense <- function(graph, types, names, attr) {
   }
 }
 
-get.incidence.sparse <- function(graph, types, names, attr) {
+get.incidence.sparse <- function(graph, types, names, attr, call = rlang::caller_env()) {
   vc <- vcount(graph)
   if (length(types) != vc) {
-    stop("Invalid types vector", call. = FALSE)
+    cli::cli_abort("Invalid types vector", call = call)
   }
 
   el <- as_edgelist(graph, names = FALSE)
   if (any(types[el[, 1]] == types[el[, 2]])) {
-    stop("Invalid types vector, not a bipartite graph", call. = FALSE)
+    cli::cli_abort("Invalid types vector, not a bipartite graph", call = call)
   }
 
   n1 <- sum(!types)
@@ -895,7 +895,7 @@ get.incidence.sparse <- function(graph, types, names, attr) {
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      stop("no such edge attribute", call. = FALSE)
+      cli::cli_abort("No such edge attribute", call = calls)
     }
     value <- edge_attr(graph, name = attr)
   } else {
@@ -968,7 +968,7 @@ as_biadjacency_matrix <- function(graph, types = NULL, attr = NULL,
   sparse <- as.logical(sparse)
 
   if (sparse) {
-    get.incidence.sparse(graph, types = types, names = names, attr = attr)
+    get.incidence.sparse(graph, types = types, names = names, attr = attr, call = rlang::caller_env())
   } else {
     get.incidence.dense(graph, types = types, names = names, attr = attr)
   }
diff --git a/tests/testthat/_snaps/conversion.md b/tests/testthat/_snaps/conversion.md
index 6c33bfbd57..901eeddd70 100644
--- a/tests/testthat/_snaps/conversion.md
+++ b/tests/testthat/_snaps/conversion.md
@@ -26,7 +26,7 @@
       as_adjacency_matrix(g, attr = "bla")
     Condition
       Error in `as_adjacency_matrix()`:
-      ! no such edge attribute
+      ! No such edge attribute
 
 ---
 
@@ -42,7 +42,7 @@
       as_adjacency_matrix(g, attr = "bla", sparse = FALSE)
     Condition
       Error in `as_adjacency_matrix()`:
-      ! no such edge attribute
+      ! No such edge attribute
 
 ---
 

From 0e5da2cf0cc1967bdb5ed0b089d11133af167343 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Fri, 24 Jan 2025 19:40:16 +0100
Subject: [PATCH 08/11] added some more tests

---
 tests/testthat/test-conversion.R | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index 3ff70fd7f1..1f1ccf0a09 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -274,3 +274,26 @@ test_that("as_adjacency_matrix() works -- dense + not both", {
     )
   )
 })
+
+test_that("as_adjacency_matrix() works -- dense + weights", {
+  g <- make_full_graph(5, directed = FALSE)
+  E(g)$weight <- 1:10
+  mat <- matrix(0, 5, 5)
+  mat[lower.tri(mat)] <- 1:10
+  mat <- mat + t(mat)
+  A <- as_adjacency_matrix(g, attr = "weight", sparse = FALSE)
+  expect_equal(A, mat)
+})
+
+test_that("as_biadjacency_matrix() works -- dense + weights", {
+  g <- make_bipartite_graph(c(0, 1, 0, 1, 0, 0), c(1, 2, 2, 3, 3, 4))
+  E(g)$weight <- c(2, 4, 6)
+  A <- as_biadjacency_matrix(g, attr = "weight", sparse = FALSE)
+  mat <- matrix(
+    c(2, 4, 0, 0, 0, 6, 0, 0),
+    nrow = 4L,
+    ncol = 2L,
+    dimnames = list(c("1", "3", "5", "6"), c("2", "4"))
+  )
+  expect_equal(A, mat)
+})

From 64884cef1f2ac0eb801fd3fc317528a9463ba3c4 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Sat, 25 Jan 2025 07:12:43 +0100
Subject: [PATCH 09/11] fixed a typo

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

diff --git a/R/conversion.R b/R/conversion.R
index 7c96306d10..808d19ab96 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -899,7 +899,7 @@ get.incidence.sparse <- function(graph, types, names, attr, call = rlang::caller
   if (!is.null(attr)) {
     attr <- as.character(attr)
     if (!attr %in% edge_attr_names(graph)) {
-      cli::cli_abort("No such edge attribute", call = calls)
+      cli::cli_abort("No such edge attribute", call = call)
     }
     value <- edge_attr(graph, name = attr)
   } else {

From ada8e5f979ebe697a73a6786396ce480cc851095 Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Sat, 25 Jan 2025 15:28:19 +0100
Subject: [PATCH 10/11] canonicalize matrices

---
 tests/testthat/test-conversion.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-conversion.R b/tests/testthat/test-conversion.R
index 1f1ccf0a09..d9212902b0 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -282,7 +282,7 @@ test_that("as_adjacency_matrix() works -- dense + weights", {
   mat[lower.tri(mat)] <- 1:10
   mat <- mat + t(mat)
   A <- as_adjacency_matrix(g, attr = "weight", sparse = FALSE)
-  expect_equal(A, mat)
+  expect_equal(canonicalize_matrix(A), mat)
 })
 
 test_that("as_biadjacency_matrix() works -- dense + weights", {
@@ -295,5 +295,5 @@ test_that("as_biadjacency_matrix() works -- dense + weights", {
     ncol = 2L,
     dimnames = list(c("1", "3", "5", "6"), c("2", "4"))
   )
-  expect_equal(A, mat)
+  expect_equal(canonicalize_matrix(A), mat)
 })

From 630508d451a61e9826aca60e69dc25282f0c1aff Mon Sep 17 00:00:00 2001
From: schochastics <david@schochastics.net>
Date: Sat, 25 Jan 2025 19:38:44 +0100
Subject: [PATCH 11/11] canonicalize expected result

---
 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 d9212902b0..176b8ff9f0 100644
--- a/tests/testthat/test-conversion.R
+++ b/tests/testthat/test-conversion.R
@@ -295,5 +295,5 @@ test_that("as_biadjacency_matrix() works -- dense + weights", {
     ncol = 2L,
     dimnames = list(c("1", "3", "5", "6"), c("2", "4"))
   )
-  expect_equal(canonicalize_matrix(A), mat)
+  expect_equal(canonicalize_matrix(A), canonicalize_matrix(mat))
 })