From 279a152acae5c9917842069898cf015fab8d9088 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sat, 21 Jan 2023 10:54:56 +0100
Subject: [PATCH 01/26] Use high-level attribute setters when adding vertices
 and edges

---
 R/interface.R | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/R/interface.R b/R/interface.R
index 387f8f114e1..e027e27e947 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -84,12 +84,11 @@ add_edges <- function(graph, edges, ..., attr = list()) {
     idx <- numeric()
   }
 
-  eattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
   for (i in seq(attrs)) {
-    eattrs[[nam[i]]][idx] <- attrs[[nam[i]]]
+    edge_attr(graph, nam[[i]], idx) <- attrs[[nam[i]]]
   }
 
-  .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_edge, eattrs)
+  graph
 }
 
 #' Add vertices to a graph
@@ -148,12 +147,11 @@ add_vertices <- function(graph, nv, ..., attr = list()) {
     idx <- numeric()
   }
 
-  vattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
   for (i in seq(attrs)) {
-    vattrs[[nam[i]]][idx] <- attrs[[nam[i]]]
+    vertex_attr(graph, nam[[i]], idx) <- attrs[[nam[i]]]
   }
 
-  .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_vertex, vattrs)
+  graph
 }
 
 #' Delete edges from a graph

From d382a8c8598541e089b5915c8d8ce3ab1ddd46fb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sat, 21 Jan 2023 10:57:08 +0100
Subject: [PATCH 02/26] Use set_*() instead of assignment functions

---
 R/interface.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/interface.R b/R/interface.R
index e027e27e947..5c9d5277fa1 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -85,7 +85,7 @@ add_edges <- function(graph, edges, ..., attr = list()) {
   }
 
   for (i in seq(attrs)) {
-    edge_attr(graph, nam[[i]], idx) <- attrs[[nam[i]]]
+    graph <- set_edge_attr(graph, nam[[i]], idx, attrs[[nam[i]]])
   }
 
   graph
@@ -148,7 +148,7 @@ add_vertices <- function(graph, nv, ..., attr = list()) {
   }
 
   for (i in seq(attrs)) {
-    vertex_attr(graph, nam[[i]], idx) <- attrs[[nam[i]]]
+    graph <- set_vertex_attr(graph, nam[[i]], idx, attrs[[nam[i]]])
   }
 
   graph

From dbea45ee9eb289a91c89367e0fe8e1d32cc24e33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sat, 21 Jan 2023 10:58:23 +0100
Subject: [PATCH 03/26] Avoid NULL attributes

---
 R/interface.R | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/R/interface.R b/R/interface.R
index 5c9d5277fa1..6b9d5c3cd31 100644
--- a/R/interface.R
+++ b/R/interface.R
@@ -85,7 +85,10 @@ add_edges <- function(graph, edges, ..., attr = list()) {
   }
 
   for (i in seq(attrs)) {
-    graph <- set_edge_attr(graph, nam[[i]], idx, attrs[[nam[i]]])
+    attr <- attrs[[nam[i]]]
+    if (!is.null(attr)) {
+      graph <- set_edge_attr(graph, nam[[i]], idx, attr)
+    }
   }
 
   graph
@@ -148,7 +151,10 @@ add_vertices <- function(graph, nv, ..., attr = list()) {
   }
 
   for (i in seq(attrs)) {
-    graph <- set_vertex_attr(graph, nam[[i]], idx, attrs[[nam[i]]])
+    attr <- attrs[[nam[i]]]
+    if (!is.null(attr)) {
+      graph <- set_vertex_attr(graph, nam[[i]], idx, attr)
+    }
   }
 
   graph

From 8eaaab860c20d42ae879ebce49b29e0f5715913c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 09:15:44 +0100
Subject: [PATCH 04/26] Fix artifact from #607

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

diff --git a/R/attributes.R b/R/attributes.R
index 961f8350bb1..ff36d7a687e 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -355,7 +355,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
   } else {
     name <- as.character(name)
     myattr <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)[[name]]
-    if (is.null(index)) {
+    if (is_complete_iterator(index)) {
       myattr
     } else {
       index <- as.igraph.es(graph, index)

From 714b447cb778981656009041236b846231f79a4a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 09:17:06 +0100
Subject: [PATCH 05/26] Use is_complete_iterator()

---
 R/attributes.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index ff36d7a687e..e15fee42697 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -174,11 +174,12 @@ vertex_attr <- function(graph, name, index = V(graph)) {
   } else {
     myattr <-
       .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)[[as.character(name)]]
-    if (!missing(index)) {
+    if (is_complete_iterator(index)) {
+      myattr
+    } else {
       index <- as.igraph.vs(graph, index)
-      myattr <- myattr[index]
+      myattr[index]
     }
-    myattr
   }
 }
 

From 4d36ca68b8a0d2bc6627e8a09ea3c8fa0aeebe38 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 09:26:24 +0100
Subject: [PATCH 06/26] Type-stable vertex attributes

---
 R/attributes.R | 43 ++++++++++++++++++++++++++++++++++---------
 1 file changed, 34 insertions(+), 9 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index e15fee42697..0ddf110c1bb 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -34,6 +34,9 @@
 ##
 
 
+
+ATTRIBUTE_STRICT_RECYCLING <- FALSE
+
 #' Graph attributes of a graph
 #'
 #' @param graph Input graph.
@@ -236,31 +239,53 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #' g
 #' plot(g)
 set_vertex_attr <- function(graph, name, index = V(graph), value) {
-  i_set_vertex_attr(
-    graph = graph, name = name, index = index,
-    value = value
-  )
+  if (is_complete_iterator(index)) {
+    i_set_vertex_attr(graph = graph, name = name, value = value, check = FALSE)
+  } else {
+    i_set_vertex_attr(graph = graph, name = name, index = index, value = value)
+  }
 }
 
-i_set_vertex_attr <- function(graph, name, index = V(graph), value,
-                              check = TRUE) {
+i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE) {
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
   single <- is_single_index(index)
+  complete <- is_complete_iterator(index)
   if (!missing(index) && check) {
     index <- as.igraph.vs(graph, index)
   }
   name <- as.character(name)
-  vc <- vcount(graph)
 
   vattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
+
+  if (!(name %in% names(vattrs))) {
+    vattrs[[name]] <- value[rep.int(NA_integer_, vcount(graph))]
+  }
+
   if (single) {
     vattrs[[name]][[index]] <- value
   } else {
-    vattrs[[name]][index] <- value
+    if (ATTRIBUTE_STRICT_RECYCLING) {
+      if (length(value) == 1) {
+        value_in <- rep(value, length(index))
+      } else if (length(value) == length(index)) {
+        value_in <- value
+      } else {
+        stop("strict recycling (1)")
+      }
+    } else {
+      value_in <- rep(value, length.out = length(index))
+      # Trigger recycling warning
+      value_in[seq_along(value_in)] <- value
+    }
+
+    if (complete) {
+      vattrs[[name]] <- value_in
+    } else {
+      vattrs[[name]][index] <- value_in
+    }
   }
-  length(vattrs[[name]]) <- vc
 
   .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_vertex, vattrs)
 }

From e0536d1d17e7818124f76d24d275ca5e8e5aa3c7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 09:29:51 +0100
Subject: [PATCH 07/26] Type-stable edge attributes

---
 R/attributes.R | 41 ++++++++++++++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index 0ddf110c1bb..a8cfde16abc 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -443,26 +443,53 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #' g
 #' plot(g)
 set_edge_attr <- function(graph, name, index = E(graph), value) {
-  i_set_edge_attr(graph = graph, name = name, index = index, value = value)
+  if (is_complete_iterator(index)) {
+    i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE)
+  } else {
+    i_set_edge_attr(graph = graph, name = name, index = index, value = value)
+  }
 }
 
-i_set_edge_attr <- function(graph, name, index = E(graph), value,
-                            check = TRUE) {
+i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE) {
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
+  complete <- is_complete_iterator(index)
   single <- is_single_index(index)
   name <- as.character(name)
-  if (!missing(index) && check) index <- as.igraph.es(graph, index)
-  ec <- ecount(graph)
+  if (!missing(index) && check) {
+    index <- as.igraph.es(graph, index)
+  }
 
   eattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
+
+  if (!(name %in% names(eattrs))) {
+    eattrs[[name]] <- value[rep.int(NA_integer_, ecount(graph))]
+  }
+
   if (single) {
     eattrs[[name]][[index]] <- value
   } else {
-    eattrs[[name]][index] <- value
+    if (ATTRIBUTE_STRICT_RECYCLING) {
+      if (length(value) == 1) {
+        value_in <- rep(value, length(index))
+      } else if (length(value) == length(index)) {
+        value_in <- value
+      } else {
+        stop("strict recycling (2)")
+      }
+    } else {
+      value_in <- rep(value, length.out = length(index))
+      # Trigger recycling warning
+      value_in[seq_along(value_in)] <- value
+    }
+
+    if (complete) {
+      eattrs[[name]] <- value_in
+    } else {
+      eattrs[[name]][index] <- value_in
+    }
   }
-  length(eattrs[[name]]) <- ec
 
   .Call(C_R_igraph_mybracket2_set, graph, igraph_t_idx_attr, igraph_attr_idx_edge, eattrs)
 }

From 66ff1e8475c6023b62772438b6a905f1ba079bde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 10:38:32 +0100
Subject: [PATCH 08/26] Add test

---
 tests/testthat/test-attributes.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tests/testthat/test-attributes.R b/tests/testthat/test-attributes.R
index e8120864373..5577dab3a0a 100644
--- a/tests/testthat/test-attributes.R
+++ b/tests/testthat/test-attributes.R
@@ -211,3 +211,21 @@ test_that("attribute combinations handle errors correctly", {
   expect_error(as.undirected(g, edge.attr.comb = list(weight = "sum")), "invalid 'type'")
   expect_error(as.undirected(g, edge.attr.comb = list(weight = sum)), "invalid 'type'")
 })
+
+test_that("can change type of attributes (#466)", {
+  g <- make_ring(10)
+
+  V(g)$foo <- 1
+  expect_equal(V(g)$foo, rep(1, 10))
+  V(g)$foo <- "a"
+  expect_equal(V(g)$foo, rep("a", 10))
+  V(g)$foo <- 2
+  expect_equal(V(g)$foo, rep(2, 10))
+
+  E(g)$foo <- 1
+  expect_equal(E(g)$foo, rep(1, 10))
+  E(g)$foo <- "a"
+  expect_equal(E(g)$foo, rep("a", 10))
+  E(g)$foo <- 2
+  expect_equal(E(g)$foo, rep(2, 10))
+})

From 4cde819c590a26aa5cf68647561163aba22841a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 10:44:11 +0100
Subject: [PATCH 09/26] Strict rules

---
 R/attributes.R              | 10 +++++-----
 tests/testthat/test-pajek.R |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index a8cfde16abc..cdb87d76def 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -35,7 +35,7 @@
 
 
 
-ATTRIBUTE_STRICT_RECYCLING <- FALSE
+ATTRIBUTE_STRICT_RECYCLING <- TRUE
 
 #' Graph attributes of a graph
 #'
@@ -268,9 +268,9 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
   } else {
     if (ATTRIBUTE_STRICT_RECYCLING) {
       if (length(value) == 1) {
-        value_in <- rep(value, length(index))
+        value_in <- rep(unname(value), length(index))
       } else if (length(value) == length(index)) {
-        value_in <- value
+        value_in <- unname(value)
       } else {
         stop("strict recycling (1)")
       }
@@ -472,9 +472,9 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
   } else {
     if (ATTRIBUTE_STRICT_RECYCLING) {
       if (length(value) == 1) {
-        value_in <- rep(value, length(index))
+        value_in <- rep(unname(value), length(index))
       } else if (length(value) == length(index)) {
-        value_in <- value
+        value_in <- unname(value)
       } else {
         stop("strict recycling (2)")
       }
diff --git a/tests/testthat/test-pajek.R b/tests/testthat/test-pajek.R
index 6a912e8e7a4..ad38f117915 100644
--- a/tests/testthat/test-pajek.R
+++ b/tests/testthat/test-pajek.R
@@ -1,6 +1,6 @@
 test_that("writing Pajek files works", {
   g <- make_ring(9)
-  V(g)$color <- c("red", "green", "yellow")
+  V(g)$color <- rep(c("red", "green", "yellow"), 3)
 
   tc <- rawConnection(raw(0), "w")
   write_graph(g, format = "pajek", file = tc)

From 8ee458720073f542e3e669ba50dec07992d2e52b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 13:33:57 +0100
Subject: [PATCH 10/26] revdep results

---
 revdep/README.md   |  26 +-
 revdep/cran.md     |  61 ++-
 revdep/failures.md |  10 +-
 revdep/problems.md | 924 ++++++++++++++++++++++++++++++++++++++++++---
 4 files changed, 956 insertions(+), 65 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 0d231dbdf25..5c92312a230 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -14,11 +14,27 @@
 |vivid     |?       |      |        |     |
 |NA        |?       |      |        |     |
 
-## New problems (3)
+## New problems (19)
 
-|package      |version |error  |warning |note |
-|:------------|:-------|:------|:-------|:----|
-|[causaleffect](problems.md#causaleffect)|1.3.15  |__+1__ |1       |     |
-|[R6causal](problems.md#r6causal)|0.7.0   |       |__+1__  |     |
+|package        |version |error  |warning |note |
+|:--------------|:-------|:------|:-------|:----|
+|[backbone](problems.md#backbone)|2.1.1   |__+1__ |        |     |
+|[clustAnalytics](problems.md#clustanalytics)|0.5.2   |       |__+1__  |1    |
+|[deepdep](problems.md#deepdep)|0.4.1   |__+1__ |        |     |
+|[Diderot](problems.md#diderot)|0.13    |__+1__ |        |     |
+|[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
+|[gemtc](problems.md#gemtc)|1.0-1   |__+2__ |        |     |
+|[gRbase](problems.md#grbase)|1.8.9   |__+1__ |1       |1    |
+|[GREMLINS](problems.md#gremlins)|0.2.0   |__+1__ |__+1__  |1    |
+|[incidentally](problems.md#incidentally)|1.0.1   |       |__+1__  |     |
+|[metanetwork](problems.md#metanetwork)|0.7.0   |__+1__ |        |     |
+|[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
+|[nat](problems.md#nat)|1.8.19  |__+2__ |        |     |
+|[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
+|[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
+|[netseg](problems.md#netseg)|1.0-1   |__+2__ |__+1__  |     |
+|[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
+|[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
+|[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index 663321bf57c..8208607ee10 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,8 +1,8 @@
 ## revdepcheck results
 
-We checked 752 reverse dependencies (750 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 755 reverse dependencies (753 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 3 new problems
+ * We saw 19 new problems
  * We failed to check 7 packages
 
 Issues with CRAN packages are summarised below.
@@ -10,15 +10,68 @@ Issues with CRAN packages are summarised below.
 ### New problems
 (This reports the first line of each new failure)
 
-* causaleffect
+* backbone
+  checking tests ... ERROR
+
+* clustAnalytics
+  checking re-building of vignette outputs ... WARNING
+
+* deepdep
+  checking tests ... ERROR
+
+* Diderot
   checking examples ... ERROR
 
-* R6causal
+* egor
+  checking tests ... ERROR
+
+* gemtc
+  checking examples ... ERROR
+  checking tests ... ERROR
+
+* gRbase
+  checking examples ... ERROR
+
+* GREMLINS
+  checking examples ... ERROR
   checking re-building of vignette outputs ... WARNING
 
+* incidentally
+  checking re-building of vignette outputs ... WARNING
+
+* metanetwork
+  checking tests ... ERROR
+
+* mstknnclust
+  checking re-building of vignette outputs ... WARNING
+
+* nat
+  checking examples ... ERROR
+  checking tests ... ERROR
+
+* netmeta
+  checking examples ... ERROR
+
+* NetOrigin
+  checking examples ... ERROR
+
+* netseg
+  checking examples ... ERROR
+  checking tests ... ERROR
+  checking re-building of vignette outputs ... WARNING
+
+* poppr
+  checking tests ... ERROR
+
+* riverconn
+  checking examples ... ERROR
+
 * sfnetworks
   checking tests ... ERROR
 
+* signnet
+  checking examples ... ERROR
+
 ### Failed to check
 
 * DRviaSPCN (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index a4da12d38e4..9daa4c5b6ba 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -204,11 +204,11 @@ Status: 1 ERROR
 
 <details>
 
-* Version: 1.1.0
+* Version: 1.2.1
 * GitHub: https://github.com/kharchenkolab/numbat
 * Source code: https://github.com/cran/numbat
-* Date/Publication: 2022-11-29 18:30:02 UTC
-* Number of recursive dependencies: 183
+* Date/Publication: 2023-01-11 00:20:02 UTC
+* Number of recursive dependencies: 132
 
 Run `revdepcheck::cloud_details(, "numbat")` for more info
 
@@ -225,7 +225,7 @@ Run `revdepcheck::cloud_details(, "numbat")` for more info
 * using session charset: UTF-8
 * using option ‘--no-manual’
 * checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.1.0’
+* this is package ‘numbat’ version ‘1.2.1’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... ERROR
@@ -250,7 +250,7 @@ Status: 1 ERROR
 * using session charset: UTF-8
 * using option ‘--no-manual’
 * checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.1.0’
+* this is package ‘numbat’ version ‘1.2.1’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... ERROR
diff --git a/revdep/problems.md b/revdep/problems.md
index 0ccd26295d0..3aac8121052 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,14 +1,141 @@
-# causaleffect
+# backbone
 
 <details>
 
-* Version: 1.3.15
-* GitHub: https://github.com/santikka/causaleffect
-* Source code: https://github.com/cran/causaleffect
-* Date/Publication: 2022-07-14 09:10:05 UTC
-* Number of recursive dependencies: 13
+* Version: 2.1.1
+* GitHub: https://github.com/zpneal/backbone
+* Source code: https://github.com/cran/backbone
+* Date/Publication: 2022-10-18 17:35:06 UTC
+* Number of recursive dependencies: 36
 
-Run `revdepcheck::cloud_details(, "causaleffect")` for more info
+Run `revdepcheck::cloud_details(, "backbone")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘tinytest.R’
+    Running the tests in ‘tests/tinytest.R’ failed.
+    Last 13 lines of output:
+      test_backbone.R...............   29 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   31 tests OK 
+      test_backbone.R...............   32 tests OK 
+      test_backbone.R...............   33 tests OK 
+      test_backbone.R...............   34 tests OK 
+      test_backbone.R...............   35 tests OK 
+      test_backbone.R...............   36 tests OK 
+      test_backbone.R...............   36 tests OK Error in i_set_vertex_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+        strict recycling (1)
+      Calls: <Anonymous> ... FUN -> eval -> eval -> <Anonymous> -> i_set_vertex_attr
+      Execution halted
+    ```
+
+# clustAnalytics
+
+<details>
+
+* Version: 0.5.2
+* GitHub: NA
+* Source code: https://github.com/cran/clustAnalytics
+* Date/Publication: 2022-11-09 11:50:09 UTC
+* Number of recursive dependencies: 69
+
+Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘cluster_stability.Rmd’ using rmarkdown
+    --- finished re-building ‘cluster_stability.Rmd’
+    
+    --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown
+    --- finished re-building ‘graph_rewiring_functions.Rmd’
+    
+    --- re-building ‘other_functions.Rmd’ using rmarkdown
+    --- finished re-building ‘other_functions.Rmd’
+    ...
+    Quitting from lines 109-111 (stability_significance_examples.Rmd) 
+    Error: processing vignette 'stability_significance_examples.Rmd' failed with diagnostics:
+    strict recycling (1)
+    --- failed re-building ‘stability_significance_examples.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘stability_significance_examples.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.6Mb
+      sub-directories of 1Mb or more:
+        libs   6.1Mb
+    ```
+
+# deepdep
+
+<details>
+
+* Version: 0.4.1
+* GitHub: https://github.com/DominikRafacz/deepdep
+* Source code: https://github.com/cran/deepdep
+* Date/Publication: 2021-12-20 16:20:02 UTC
+* Number of recursive dependencies: 144
+
+Run `revdepcheck::cloud_details(, "deepdep")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘spelling.R’
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+        6.     └─ggraph:::create_layout.default(graph, layout, ...)
+        7.       ├─ggraph::create_layout(graph, layout, ...)
+        8.       └─ggraph:::create_layout.tbl_graph(graph, layout, ...)
+        9.         ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order()))
+       10.         └─tidygraph:::mutate.tbl_graph(...)
+       11.           └─tidygraph::mutate_as_tbl(.data, !!!dot)
+       12.             ├─tidygraph:::set_graph_data(.data, d_tmp)
+       13.             └─tidygraph:::set_graph_data.tbl_graph(.data, d_tmp)
+       14.               └─tidygraph:::set_node_attributes(x, value)
+       15.                 └─igraph::`vertex_attr<-`(`*tmp*`, value = as.list(value))
+       16.                   └─igraph::`vertex.attributes<-`(graph, index = index, value = value)
+      
+      [ FAIL 9 | WARN 0 | SKIP 2 | PASS 25 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# Diderot
+
+<details>
+
+* Version: 0.13
+* GitHub: NA
+* Source code: https://github.com/cran/Diderot
+* Date/Publication: 2020-04-19 11:20:02 UTC
+* Number of recursive dependencies: 15
+
+Run `revdepcheck::cloud_details(, "Diderot")` for more info
 
 </details>
 
@@ -16,26 +143,168 @@ Run `revdepcheck::cloud_details(, "causaleffect")` for more info
 
 *   checking examples ... ERROR
     ```
-    Running examples in ‘causaleffect-Ex.R’ failed
+    Running examples in ‘Diderot-Ex.R’ failed
     The error most likely occurred in:
     
-    > ### Name: causal.effect
-    > ### Title: Identify a causal effect
-    > ### Aliases: causal.effect
+    > ### Name: build_graph
+    > ### Title: Builds a citation graph.
+    > ### Aliases: build_graph 'Citation Graph Building'
     > 
     > ### ** Examples
     > 
-    > library(igraph)
+    > ## Don't show: 
     ...
-    > g <- graph.formula(x -+ y, z -+ x, z -+ y , x -+ z, z -+ x, simplify = FALSE)
+    > unlink(c(tempfi1, tempfi2))
+    > ## End(Don't show)
     > 
-    > # Here the bidirected edge between X and Z is set to be unobserved in graph g
-    > # This is denoted by giving them a description attribute with the value "U"
-    > # The edges in question are the fourth and the fifth edge
-    > g <- set.edge.attribute(graph = g, name = "description", index = c(4,5), value = "U")
-    > causal.effect("y", "x", G = g)
-    Error in 0:(ind[i] - 1) : argument of length 0
-    Calls: causal.effect -> id
+    > # Build graph
+    > gr<-build_graph(db=db,small.year.mismatch=TRUE, attrs=c("Corpus","Year","Authors"), nb.cores=1)
+    starting worker pid=11555 on localhost:11308 at 10:12:11.957
+    Error in i_set_vertex_attr(graph = graph, name = name, value = value,  : 
+      strict recycling (1)
+    Calls: build_graph -> set.vertex.attribute -> i_set_vertex_attr
+    Execution halted
+    ```
+
+# egor
+
+<details>
+
+* Version: 1.22.12
+* GitHub: https://github.com/tilltnet/egor
+* Source code: https://github.com/cran/egor
+* Date/Publication: 2022-12-20 06:20:02 UTC
+* Number of recursive dependencies: 89
+
+Run `revdepcheck::cloud_details(, "egor")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+      Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Filtering out empty alter entries using provided network size values: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: [ FAIL 1 | WARN 4 | SKIP 15 | PASS 205 ]
+      
+      ══ Skipped tests ═══════════════════════════════════════════════════════════════
+      • On CRAN (15)
+      
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Failure ('test-clustered_graphs.R:55'): Methods work (properly) with grouping variable being completly NA. ──
+      igraph::V(clustered_graphs(mpf, "country")[[1]])$grp.size is not NULL
+      
+      `actual` is a double vector ()
+      `expected` is NULL
+      
+      [ FAIL 1 | WARN 4 | SKIP 15 | PASS 205 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# gemtc
+
+<details>
+
+* Version: 1.0-1
+* GitHub: https://github.com/gertvv/gemtc
+* Source code: https://github.com/cran/gemtc
+* Date/Publication: 2021-05-14 23:20:02 UTC
+* Number of recursive dependencies: 56
+
+Run `revdepcheck::cloud_details(, "gemtc")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘gemtc-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: atrialFibrillation
+    > ### Title: Prevention of stroke in atrial fibrillation patients
+    > ### Aliases: atrialFibrillation
+    > 
+    > ### ** Examples
+    > 
+    > # Build a model similar to Model 4(b) from Cooper et al. (2009):
+    ...
+    +                   classes=classes)
+    > 
+    > model <- mtc.model(atrialFibrillation,
+    +                    type="regression",
+    +                    regressor=regressor,
+    +                    om.scale=10)
+    Error in i_set_edge_attr(graph = graph, name = name, index = index, value = value) : 
+      strict recycling (2)
+    Calls: mtc.model ... add_edges -> edge_attr<- -> set_edge_attr -> i_set_edge_attr
+    Execution halted
+    ```
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test.R’
+    Running the tests in ‘tests/test.R’ failed.
+    Last 13 lines of output:
+           ▆
+        1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2
+        2.   ├─base::as.matrix(...)
+        3.   └─gemtc::relative.effect(...)
+        4.     └─gemtc:::spanning.tree.mtc.result(result)
+        5.       └─gemtc:::graph.create(...)
+        6.         └─igraph:::`+.igraph`(g, edges.create(e, ...))
+        7.           └─igraph::add_edges(e1, as.igraph.vs(e1, toadd), attr = attr)
+        8.             └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
+        9.               └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
+       10.                 └─igraph:::i_set_edge_attr(...)
+      
+      [ FAIL 35 | WARN 0 | SKIP 0 | PASS 269 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# gRbase
+
+<details>
+
+* Version: 1.8.9
+* GitHub: NA
+* Source code: https://github.com/cran/gRbase
+* Date/Publication: 2022-11-10 10:40:02 UTC
+* Number of recursive dependencies: 50
+
+Run `revdepcheck::cloud_details(, "gRbase")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘gRbase-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: graph-moralize
+    > ### Title: Moralize a directed acyclic graph
+    > ### Aliases: graph-moralize moralize moralize.default moralizeMAT
+    > ### Keywords: utilities
+    > 
+    > ### ** Examples
+    > 
+    ...
+    
+        decompose, spectrum
+    
+    The following object is masked from ‘package:base’:
+    
+        union
+    
+    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
+    Calls: moralize ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
     Execution halted
     ```
 
@@ -44,39 +313,197 @@ Run `revdepcheck::cloud_details(, "causaleffect")` for more info
 *   checking re-building of vignette outputs ... WARNING
     ```
     Error(s) in re-building vignettes:
-    --- re-building ‘causaleffect.ltx’ using tex
-    Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
-    Running 'texi2dvi' on 'causaleffect.ltx' failed.
+    --- re-building ‘arrays.Rnw’ using knitr
+    Error: processing vignette 'arrays.Rnw' failed with diagnostics:
+    Running 'texi2dvi' on 'arrays.tex' failed.
     LaTeX errors:
-    ! LaTeX Error: File `ae.sty' not found.
+    ! LaTeX Error: File `boxedminipage.sty' not found.
     
     Type X to quit or <RETURN> to proceed,
     or enter new name. (Default extension: sty)
     
     ...
-    l.16 \usepackage
-                    {csquotes}^^M
+    l.63 ^^M
+            
     !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘simplification.ltx’
+    --- failed re-building ‘graphs.Rnw’
     
     SUMMARY: processing the following files failed:
-      ‘causaleffect.ltx’ ‘simplification.ltx’
+      ‘arrays.Rnw’ ‘graphs.Rnw’
     
     Error: Vignette re-building failed.
     Execution halted
     ```
 
-# R6causal
+*   checking installed package size ... NOTE
+    ```
+      installed size is 26.4Mb
+      sub-directories of 1Mb or more:
+        libs  24.3Mb
+    ```
+
+# GREMLINS
+
+<details>
+
+* Version: 0.2.0
+* GitHub: https://github.com/demiperimetre/GREMLINS
+* Source code: https://github.com/cran/GREMLINS
+* Date/Publication: 2020-11-25 13:50:04 UTC
+* Number of recursive dependencies: 62
+
+Run `revdepcheck::cloud_details(, "GREMLINS")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘GREMLINS-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: plotMBM
+    > ### Title: Plot the mesoscopic view of the estimated MBM
+    > ### Aliases: plotMBM
+    > 
+    > ### ** Examples
+    > 
+    > namesFG <- c('A','B')
+    ...
+    [1] "gaussian"  "bernoulli"
+    [1] "-------------------------------------------------------------------"
+    [1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks"
+    [1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]"
+    [1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
+    > plotMBM(res_MBMsimu)
+    Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
+      strict recycling (2)
+    Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
+    Execution halted
+    ```
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
+    Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
+    Error: processing vignette 'EcologicalNetwork.Rmd' failed with diagnostics:
+    strict recycling (2)
+    --- failed re-building ‘EcologicalNetwork.Rmd’
+    
+    --- re-building ‘Introduction.Rmd’ using rmarkdown
+    --- finished re-building ‘Introduction.Rmd’
+    
+    --- re-building ‘SimulatedNetwork.Rmd’ using rmarkdown
+    --- finished re-building ‘SimulatedNetwork.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘EcologicalNetwork.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘mclust’
+      All declared Imports should be used.
+    ```
+
+# incidentally
+
+<details>
+
+* Version: 1.0.1
+* GitHub: https://github.com/zpneal/incidentally
+* Source code: https://github.com/cran/incidentally
+* Date/Publication: 2022-08-05 22:40:09 UTC
+* Number of recursive dependencies: 37
+
+Run `revdepcheck::cloud_details(, "incidentally")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘congress.Rmd’ using rmarkdown
+    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
+    Content type 'application/zip' length 2070239 bytes (2.0 MB)
+    ==================================================
+    downloaded 2.0 MB
+    
+    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
+    Content type 'application/zip' length 2070239 bytes (2.0 MB)
+    ...
+    --- failed re-building ‘congress.Rmd’
+    
+    --- re-building ‘incidentally.Rmd’ using rmarkdown
+    --- finished re-building ‘incidentally.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘congress.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+# metanetwork
 
 <details>
 
 * Version: 0.7.0
+* GitHub: https://github.com/MarcOhlmann/metanetwork
+* Source code: https://github.com/cran/metanetwork
+* Date/Publication: 2022-12-05 14:10:02 UTC
+* Number of recursive dependencies: 105
+
+Run `revdepcheck::cloud_details(, "metanetwork")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+      Epoch: Iteration #300 error is: 199.576452337935
+      x_max = 1356.85756899361
+      y_max = 351.62429330114
+      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
+      
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Failure ('test-compute_TL.R:25'): Computation of trophic levels of norway dataset ──
+      V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`).
+      
+      `names(actual)` is a character vector ('Trachurus', 'Sardinella', 'Sciaenidae', 'Ariidae', 'Merluccius', ...)
+      `names(expected)` is absent
+      
+      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# mstknnclust
+
+<details>
+
+* Version: 0.3.1
 * GitHub: NA
-* Source code: https://github.com/cran/R6causal
-* Date/Publication: 2022-11-04 08:00:02 UTC
-* Number of recursive dependencies: 100
+* Source code: https://github.com/cran/mstknnclust
+* Date/Publication: 2020-09-17 12:20:03 UTC
+* Number of recursive dependencies: 34
 
-Run `revdepcheck::cloud_details(, "R6causal")` for more info
+Run `revdepcheck::cloud_details(, "mstknnclust")` for more info
 
 </details>
 
@@ -86,19 +513,364 @@ Run `revdepcheck::cloud_details(, "R6causal")` for more info
     ```
     Error(s) in re-building vignettes:
       ...
-    --- re-building ‘using_R6causal.Rmd’ using rmarkdown
-    Quitting from lines 196-198 (using_R6causal.Rmd) 
-    Error: processing vignette 'using_R6causal.Rmd' failed with diagnostics:
-    Not identifiable.
-    --- failed re-building ‘using_R6causal.Rmd’
+    --- re-building ‘guide.Rmd’ using rmarkdown
+    Quitting from lines 103-110 (guide.Rmd) 
+    Error: processing vignette 'guide.Rmd' failed with diagnostics:
+    strict recycling (1)
+    --- failed re-building ‘guide.Rmd’
     
     SUMMARY: processing the following file failed:
-      ‘using_R6causal.Rmd’
+      ‘guide.Rmd’
     
     Error: Vignette re-building failed.
     Execution halted
     ```
 
+# nat
+
+<details>
+
+* Version: 1.8.19
+* GitHub: https://github.com/natverse/nat
+* Source code: https://github.com/cran/nat
+* Date/Publication: 2022-04-06 11:50:02 UTC
+* Number of recursive dependencies: 86
+
+Run `revdepcheck::cloud_details(, "nat")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘nat-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: prune_strahler
+    > ### Title: Prune a neuron by removing segments with a given Strahler order
+    > ### Aliases: prune_strahler
+    > 
+    > ### ** Examples
+    > 
+    > x=Cell07PNs[[1]]
+    > pruned12=prune_strahler(x)
+    Error in value[[3L]](cond) : 
+      No points left after pruning. Consider lowering orders to prune!
+    Calls: prune_strahler ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
+    Execution halted
+    ```
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test-all.R’
+    Running the tests in ‘tests/test-all.R’ failed.
+    Last 13 lines of output:
+      Backtrace:
+          ▆
+       1. ├─testthat::expect_equal(...) at test-ngraph.R:193:2
+       2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
+       3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
+       4. └─nat::strahler_order(n)
+       5.   └─nat::segmentgraph(x, weights = F)
+       6.     └─igraph::add.edges(g, elred, segid = segids)
+       7.       └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
+       8.         └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
+       9.           └─igraph:::i_set_edge_attr(...)
+      
+      [ FAIL 5 | WARN 414 | SKIP 5 | PASS 774 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# netmeta
+
+<details>
+
+* Version: 2.7-0
+* GitHub: https://github.com/guido-s/netmeta
+* Source code: https://github.com/cran/netmeta
+* Date/Publication: 2022-12-22 09:30:02 UTC
+* Number of recursive dependencies: 90
+
+Run `revdepcheck::cloud_details(, "netmeta")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘netmeta-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: netcontrib
+    > ### Title: Contribution matrix in network meta-analysis
+    > ### Aliases: netcontrib print.netcontrib
+    > ### Keywords: contribution
+    > 
+    > ### ** Examples
+    > 
+    ...
+    > #
+    > data("Woods2010")
+    > p1 <- pairwise(treatment, event = r, n = N,
+    +   studlab = author, data = Woods2010, sm = "OR")
+    > 
+    > net1 <- netmeta(p1)
+    > cm <- netcontrib(net1)
+    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
+    Calls: netcontrib ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
+    Execution halted
+    ```
+
+## In both
+
+*   checking data for non-ASCII characters ... NOTE
+    ```
+      Note: found 2 marked UTF-8 strings
+    ```
+
+# NetOrigin
+
+<details>
+
+* Version: 1.1-4
+* GitHub: https://github.com/jmanitz/NetOrigin
+* Source code: https://github.com/cran/NetOrigin
+* Date/Publication: 2022-01-20 08:32:42 UTC
+* Number of recursive dependencies: 77
+
+Run `revdepcheck::cloud_details(, "NetOrigin")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘NetOrigin-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: origin
+    > ### Title: Origin Estimation for Propagation Processes on Complex Networks
+    > ### Aliases: origin origin_edm origin_backtracking origin_centrality
+    > ###   origin_bayesian
+    > 
+    > ### ** Examples
+    > 
+    ...
+    > performance(om, start=1, graph=ptnGoe)
+                      start                         est  hitt rank spj dist
+    1 X.Adolf.Hoyer.Strasse X.Gotthelf.Leimbach.Strasse FALSE    2   2 1332
+    > 
+    > # backtracking origin estimation (Manitz et al., 2016)
+    > ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe)
+    Error in `[.data.frame`(value, rep.int(NA_integer_, vcount(graph))) : 
+      undefined columns selected
+    Calls: origin ... origin_backtracking -> V<- -> i_set_vertex_attr -> [ -> [.data.frame
+    Execution halted
+    ```
+
+# netseg
+
+<details>
+
+* Version: 1.0-1
+* GitHub: https://github.com/mbojan/netseg
+* Source code: https://github.com/cran/netseg
+* Date/Publication: 2022-08-25 12:10:06 UTC
+* Number of recursive dependencies: 59
+
+Run `revdepcheck::cloud_details(, "netseg")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘netseg-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: ssi
+    > ### Title: Spectral Segregation Index for Social Networks
+    > ### Aliases: ssi
+    > 
+    > ### ** Examples
+    > 
+    > if(requireNamespace("igraph", quietly = TRUE)) {
+    ...
+    + vertex.label.family="",
+    + vertex.label=igraph::V(WhiteKinship)$name,
+    + vertex.color= gray(k),
+    + vertex.shape=c("circle", "csquare")[a],
+    + vertex.label.color="black")
+    + legend( "topleft", legend=c("Men", "Women"), pch=c(0,1), col=1)
+    + }
+    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
+    Calls: ssi ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
+    Execution halted
+    ```
+
+*   checking tests ... ERROR
+    ```
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+      Error in `simple_vs_index(x, ii, na_ok)`: Unknown vertex selected
+      Backtrace:
+          ▆
+       1. └─netseg::ssi(EF3, "race") at test-ssi.R:4:2
+       2.   └─igraph::`V<-`(`*tmp*`, value = `*vtmp*`)
+       3.     └─igraph:::i_set_vertex_attr(...)
+       4.       ├─value[rep.int(NA_integer_, vcount(graph))]
+       5.       └─igraph:::`[.igraph.vs`(value, rep.int(NA_integer_, vcount(graph)))
+       6.         └─base::lapply(...)
+       7.           └─igraph (local) FUN(X[[i]], ...)
+       8.             └─igraph:::simple_vs_index(x, ii, na_ok)
+      
+      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘netseg.Rmd’ using rmarkdown
+    Quitting from lines 252-253 (netseg.Rmd) 
+    Error: processing vignette 'netseg.Rmd' failed with diagnostics:
+    Unknown vertex selected
+    --- failed re-building ‘netseg.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘netseg.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+# poppr
+
+<details>
+
+* Version: 2.9.3
+* GitHub: https://github.com/grunwaldlab/poppr
+* Source code: https://github.com/cran/poppr
+* Date/Publication: 2021-09-07 07:00:02 UTC
+* Number of recursive dependencies: 97
+
+Run `revdepcheck::cloud_details(, "poppr")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test-all.R’
+    Running the tests in ‘tests/test-all.R’ failed.
+    Last 13 lines of output:
+      Attributes: < Modes: list, NULL >
+      Attributes: < Lengths: 3, 0 >
+      Attributes: < names for target but not for current >
+      Attributes: < current is not list-like >
+      target is table, current is numeric
+      Backtrace:
+          ▆
+       1. └─poppr (local) expect_vertex_size_scale(pmsn, as.integer(table(mll(pc)))) at test-msn.R:439:2
+       2.   ├─base::eval(...) at test-msn.R:105:2
+       3.   │ └─base::eval(...)
+       4.   └─testthat::expect_equal(...)
+      
+      [ FAIL 2 | WARN 0 | SKIP 181 | PASS 378 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+## In both
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘algo.Rnw’ using knitr
+    Error: processing vignette 'algo.Rnw' failed with diagnostics:
+    Running 'texi2dvi' on 'algo.tex' failed.
+    LaTeX errors:
+    ! LaTeX Error: File `colortbl.sty' not found.
+    
+    Type X to quit or <RETURN> to proceed,
+    or enter new name. (Default extension: sty)
+    ...
+    l.270 \long
+               \def\@secondoffive#1#2#3#4#5{#2}^^M
+    !  ==> Fatal error occurred, no output PDF file produced!
+    --- failed re-building ‘algo.Rnw’
+    
+    SUMMARY: processing the following file failed:
+      ‘algo.Rnw’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘RClone’
+    ```
+
+# riverconn
+
+<details>
+
+* Version: 0.3.22
+* GitHub: NA
+* Source code: https://github.com/cran/riverconn
+* Date/Publication: 2022-08-06 14:00:07 UTC
+* Number of recursive dependencies: 98
+
+Run `revdepcheck::cloud_details(, "riverconn")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘riverconn-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: d_index_calculation
+    > ### Title: Calculate Reach- and Catchment-scale index improvement for
+    > ###   scenarios of barriers removal
+    > ### Aliases: d_index_calculation
+    > 
+    > ### ** Examples
+    > 
+    ...
+        union
+    
+    > library(igraph)
+    > g <- igraph::graph_from_literal(1-+2, 2-+4, 3-+2, 4-+6, 6-+7, 5-+6, 7-+8, 9-+5, 10-+5 )
+    > E(g)$id_dam <- c(NA, NA, "1", NA, NA, "2", NA, NA, NA)
+    > E(g)$type <- ifelse(is.na(E(g)$id_barrier), "joint", "dam")
+    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+      strict recycling (2)
+    Calls: E<- -> i_set_edge_attr
+    Execution halted
+    ```
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘markdown’
+      All declared Imports should be used.
+    ```
+
 # sfnetworks
 
 <details>
@@ -120,20 +892,70 @@ Run `revdepcheck::cloud_details(, "sfnetworks")` for more info
       Running ‘testthat.R’
     Running the tests in ‘tests/testthat.R’ failed.
     Last 13 lines of output:
-        2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
-        3. │   ├─testthat (local) .capture(...)
-        4. │   │ ├─withr::with_output_sink(...)
-        5. │   │ │ └─base::force(code)
-        6. │   │ ├─base::withCallingHandlers(...)
-        7. │   │ └─base::withVisible(code)
-        8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
-        9. ├─sfnetworks::st_network_cost(...)
-       10. └─sfnetworks:::st_network_cost.sfnetwork(...)
-       11.   ├─base::do.call(igraph::distances, c(args, dots))
-       12.   └─igraph (local) `<fn>`(`<sfnetwrk>`, 1, 10, weights = `<[m]>`, mode = "in", algorithm = "johnson")
+      > library(sfnetworks)
+      > 
+      > test_check("sfnetworks")
+      [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
       
-      [ FAIL 1 | WARN 1 | SKIP 0 | PASS 276 ]
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Failure ('test_paths.R:242'): ... is passed correcly onto igraph::distances ──
+      isTRUE(all.equal(cost_dijkstra, cost_johnson)) is not FALSE
+      
+      `actual`:   TRUE 
+      `expected`: FALSE
+      
+      [ FAIL 1 | WARN 1 | SKIP 0 | PASS 277 ]
       Error: Test failures
       Execution halted
     ```
 
+# signnet
+
+<details>
+
+* Version: 1.0.0
+* GitHub: https://github.com/schochastics/signnet
+* Source code: https://github.com/cran/signnet
+* Date/Publication: 2022-12-22 15:10:02 UTC
+* Number of recursive dependencies: 101
+
+Run `revdepcheck::cloud_details(, "signnet")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘signnet-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: triad_census_signed
+    > ### Title: signed triad census
+    > ### Aliases: triad_census_signed
+    > 
+    > ### ** Examples
+    > 
+    > library(igraph)
+    ...
+    The following object is masked from ‘package:base’:
+    
+        union
+    
+    > g <- graph.full(4, directed = TRUE)
+    > E(g)$sign <- c(-1, 1, 1, -1, -1, 1)
+    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+      strict recycling (2)
+    Calls: E<- -> i_set_edge_attr
+    Execution halted
+    ```
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  7.8Mb
+      sub-directories of 1Mb or more:
+        libs   6.2Mb
+    ```
+

From 3cbebfe09b914ee8e2e70811ab98ed999b98763d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 13:34:43 +0100
Subject: [PATCH 11/26] Revert "Strict rules"

This reverts commit 1d89314f22dea69af3710e452487f9656f986d20.
---
 R/attributes.R              | 2 +-
 tests/testthat/test-pajek.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index cdb87d76def..d195ecdd0a3 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -35,7 +35,7 @@
 
 
 
-ATTRIBUTE_STRICT_RECYCLING <- TRUE
+ATTRIBUTE_STRICT_RECYCLING <- FALSE
 
 #' Graph attributes of a graph
 #'
diff --git a/tests/testthat/test-pajek.R b/tests/testthat/test-pajek.R
index ad38f117915..6a912e8e7a4 100644
--- a/tests/testthat/test-pajek.R
+++ b/tests/testthat/test-pajek.R
@@ -1,6 +1,6 @@
 test_that("writing Pajek files works", {
   g <- make_ring(9)
-  V(g)$color <- rep(c("red", "green", "yellow"), 3)
+  V(g)$color <- c("red", "green", "yellow")
 
   tc <- rawConnection(raw(0), "w")
   write_graph(g, format = "pajek", file = tc)

From ecb037ffb23106ed1a37d99abc03e7d39843fd7c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 18:16:43 +0100
Subject: [PATCH 12/26] Updated revdepcheck results

---
 revdep/README.md   |  17 +-
 revdep/cran.md     |  32 +--
 revdep/problems.md | 484 ++-------------------------------------------
 3 files changed, 24 insertions(+), 509 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 5c92312a230..aa61e5319db 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -14,27 +14,18 @@
 |vivid     |?       |      |        |     |
 |NA        |?       |      |        |     |
 
-## New problems (19)
+## New problems (10)
 
-|package        |version |error  |warning |note |
-|:--------------|:-------|:------|:-------|:----|
-|[backbone](problems.md#backbone)|2.1.1   |__+1__ |        |     |
-|[clustAnalytics](problems.md#clustanalytics)|0.5.2   |       |__+1__  |1    |
-|[deepdep](problems.md#deepdep)|0.4.1   |__+1__ |        |     |
-|[Diderot](problems.md#diderot)|0.13    |__+1__ |        |     |
+|package     |version |error  |warning |note |
+|:-----------|:-------|:------|:-------|:----|
 |[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
-|[gemtc](problems.md#gemtc)|1.0-1   |__+2__ |        |     |
 |[gRbase](problems.md#grbase)|1.8.9   |__+1__ |1       |1    |
-|[GREMLINS](problems.md#gremlins)|0.2.0   |__+1__ |__+1__  |1    |
-|[incidentally](problems.md#incidentally)|1.0.1   |       |__+1__  |     |
 |[metanetwork](problems.md#metanetwork)|0.7.0   |__+1__ |        |     |
-|[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
-|[nat](problems.md#nat)|1.8.19  |__+2__ |        |     |
+|[nat](problems.md#nat)|1.8.19  |__+1__ |        |     |
 |[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
 |[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
 |[netseg](problems.md#netseg)|1.0-1   |__+2__ |__+1__  |     |
 |[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
 |[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
-|[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index 8208607ee10..05340724044 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -2,7 +2,7 @@
 
 We checked 755 reverse dependencies (753 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 19 new problems
+ * We saw 10 new problems
  * We failed to check 7 packages
 
 Issues with CRAN packages are summarised below.
@@ -10,43 +10,16 @@ Issues with CRAN packages are summarised below.
 ### New problems
 (This reports the first line of each new failure)
 
-* backbone
-  checking tests ... ERROR
-
-* clustAnalytics
-  checking re-building of vignette outputs ... WARNING
-
-* deepdep
-  checking tests ... ERROR
-
-* Diderot
-  checking examples ... ERROR
-
 * egor
   checking tests ... ERROR
 
-* gemtc
-  checking examples ... ERROR
-  checking tests ... ERROR
-
 * gRbase
   checking examples ... ERROR
 
-* GREMLINS
-  checking examples ... ERROR
-  checking re-building of vignette outputs ... WARNING
-
-* incidentally
-  checking re-building of vignette outputs ... WARNING
-
 * metanetwork
   checking tests ... ERROR
 
-* mstknnclust
-  checking re-building of vignette outputs ... WARNING
-
 * nat
-  checking examples ... ERROR
   checking tests ... ERROR
 
 * netmeta
@@ -69,9 +42,6 @@ Issues with CRAN packages are summarised below.
 * sfnetworks
   checking tests ... ERROR
 
-* signnet
-  checking examples ... ERROR
-
 ### Failed to check
 
 * DRviaSPCN (NA)
diff --git a/revdep/problems.md b/revdep/problems.md
index 3aac8121052..a3c5a696739 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,171 +1,3 @@
-# backbone
-
-<details>
-
-* Version: 2.1.1
-* GitHub: https://github.com/zpneal/backbone
-* Source code: https://github.com/cran/backbone
-* Date/Publication: 2022-10-18 17:35:06 UTC
-* Number of recursive dependencies: 36
-
-Run `revdepcheck::cloud_details(, "backbone")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘tinytest.R’
-    Running the tests in ‘tests/tinytest.R’ failed.
-    Last 13 lines of output:
-      test_backbone.R...............   29 tests OK 
-      test_backbone.R...............   30 tests OK 
-      test_backbone.R...............   30 tests OK 
-      test_backbone.R...............   30 tests OK 
-      test_backbone.R...............   30 tests OK 
-      test_backbone.R...............   31 tests OK 
-      test_backbone.R...............   32 tests OK 
-      test_backbone.R...............   33 tests OK 
-      test_backbone.R...............   34 tests OK 
-      test_backbone.R...............   35 tests OK 
-      test_backbone.R...............   36 tests OK 
-      test_backbone.R...............   36 tests OK Error in i_set_vertex_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-        strict recycling (1)
-      Calls: <Anonymous> ... FUN -> eval -> eval -> <Anonymous> -> i_set_vertex_attr
-      Execution halted
-    ```
-
-# clustAnalytics
-
-<details>
-
-* Version: 0.5.2
-* GitHub: NA
-* Source code: https://github.com/cran/clustAnalytics
-* Date/Publication: 2022-11-09 11:50:09 UTC
-* Number of recursive dependencies: 69
-
-Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘cluster_stability.Rmd’ using rmarkdown
-    --- finished re-building ‘cluster_stability.Rmd’
-    
-    --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown
-    --- finished re-building ‘graph_rewiring_functions.Rmd’
-    
-    --- re-building ‘other_functions.Rmd’ using rmarkdown
-    --- finished re-building ‘other_functions.Rmd’
-    ...
-    Quitting from lines 109-111 (stability_significance_examples.Rmd) 
-    Error: processing vignette 'stability_significance_examples.Rmd' failed with diagnostics:
-    strict recycling (1)
-    --- failed re-building ‘stability_significance_examples.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘stability_significance_examples.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.6Mb
-      sub-directories of 1Mb or more:
-        libs   6.1Mb
-    ```
-
-# deepdep
-
-<details>
-
-* Version: 0.4.1
-* GitHub: https://github.com/DominikRafacz/deepdep
-* Source code: https://github.com/cran/deepdep
-* Date/Publication: 2021-12-20 16:20:02 UTC
-* Number of recursive dependencies: 144
-
-Run `revdepcheck::cloud_details(, "deepdep")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘spelling.R’
-      Running ‘testthat.R’
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-        6.     └─ggraph:::create_layout.default(graph, layout, ...)
-        7.       ├─ggraph::create_layout(graph, layout, ...)
-        8.       └─ggraph:::create_layout.tbl_graph(graph, layout, ...)
-        9.         ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order()))
-       10.         └─tidygraph:::mutate.tbl_graph(...)
-       11.           └─tidygraph::mutate_as_tbl(.data, !!!dot)
-       12.             ├─tidygraph:::set_graph_data(.data, d_tmp)
-       13.             └─tidygraph:::set_graph_data.tbl_graph(.data, d_tmp)
-       14.               └─tidygraph:::set_node_attributes(x, value)
-       15.                 └─igraph::`vertex_attr<-`(`*tmp*`, value = as.list(value))
-       16.                   └─igraph::`vertex.attributes<-`(graph, index = index, value = value)
-      
-      [ FAIL 9 | WARN 0 | SKIP 2 | PASS 25 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-# Diderot
-
-<details>
-
-* Version: 0.13
-* GitHub: NA
-* Source code: https://github.com/cran/Diderot
-* Date/Publication: 2020-04-19 11:20:02 UTC
-* Number of recursive dependencies: 15
-
-Run `revdepcheck::cloud_details(, "Diderot")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘Diderot-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: build_graph
-    > ### Title: Builds a citation graph.
-    > ### Aliases: build_graph 'Citation Graph Building'
-    > 
-    > ### ** Examples
-    > 
-    > ## Don't show: 
-    ...
-    > unlink(c(tempfi1, tempfi2))
-    > ## End(Don't show)
-    > 
-    > # Build graph
-    > gr<-build_graph(db=db,small.year.mismatch=TRUE, attrs=c("Corpus","Year","Authors"), nb.cores=1)
-    starting worker pid=11555 on localhost:11308 at 10:12:11.957
-    Error in i_set_vertex_attr(graph = graph, name = name, value = value,  : 
-      strict recycling (1)
-    Calls: build_graph -> set.vertex.attribute -> i_set_vertex_attr
-    Execution halted
-    ```
-
 # egor
 
 <details>
@@ -204,69 +36,6 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       Execution halted
     ```
 
-# gemtc
-
-<details>
-
-* Version: 1.0-1
-* GitHub: https://github.com/gertvv/gemtc
-* Source code: https://github.com/cran/gemtc
-* Date/Publication: 2021-05-14 23:20:02 UTC
-* Number of recursive dependencies: 56
-
-Run `revdepcheck::cloud_details(, "gemtc")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘gemtc-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: atrialFibrillation
-    > ### Title: Prevention of stroke in atrial fibrillation patients
-    > ### Aliases: atrialFibrillation
-    > 
-    > ### ** Examples
-    > 
-    > # Build a model similar to Model 4(b) from Cooper et al. (2009):
-    ...
-    +                   classes=classes)
-    > 
-    > model <- mtc.model(atrialFibrillation,
-    +                    type="regression",
-    +                    regressor=regressor,
-    +                    om.scale=10)
-    Error in i_set_edge_attr(graph = graph, name = name, index = index, value = value) : 
-      strict recycling (2)
-    Calls: mtc.model ... add_edges -> edge_attr<- -> set_edge_attr -> i_set_edge_attr
-    Execution halted
-    ```
-
-*   checking tests ... ERROR
-    ```
-      Running ‘test.R’
-    Running the tests in ‘tests/test.R’ failed.
-    Last 13 lines of output:
-           ▆
-        1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2
-        2.   ├─base::as.matrix(...)
-        3.   └─gemtc::relative.effect(...)
-        4.     └─gemtc:::spanning.tree.mtc.result(result)
-        5.       └─gemtc:::graph.create(...)
-        6.         └─igraph:::`+.igraph`(g, edges.create(e, ...))
-        7.           └─igraph::add_edges(e1, as.igraph.vs(e1, toadd), attr = attr)
-        8.             └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
-        9.               └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
-       10.                 └─igraph:::i_set_edge_attr(...)
-      
-      [ FAIL 35 | WARN 0 | SKIP 0 | PASS 269 ]
-      Error: Test failures
-      Execution halted
-    ```
-
 # gRbase
 
 <details>
@@ -342,119 +111,6 @@ Run `revdepcheck::cloud_details(, "gRbase")` for more info
         libs  24.3Mb
     ```
 
-# GREMLINS
-
-<details>
-
-* Version: 0.2.0
-* GitHub: https://github.com/demiperimetre/GREMLINS
-* Source code: https://github.com/cran/GREMLINS
-* Date/Publication: 2020-11-25 13:50:04 UTC
-* Number of recursive dependencies: 62
-
-Run `revdepcheck::cloud_details(, "GREMLINS")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘GREMLINS-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: plotMBM
-    > ### Title: Plot the mesoscopic view of the estimated MBM
-    > ### Aliases: plotMBM
-    > 
-    > ### ** Examples
-    > 
-    > namesFG <- c('A','B')
-    ...
-    [1] "gaussian"  "bernoulli"
-    [1] "-------------------------------------------------------------------"
-    [1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks"
-    [1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]"
-    [1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
-    > plotMBM(res_MBMsimu)
-    Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
-      strict recycling (2)
-    Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
-    Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
-    Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
-    Error: processing vignette 'EcologicalNetwork.Rmd' failed with diagnostics:
-    strict recycling (2)
-    --- failed re-building ‘EcologicalNetwork.Rmd’
-    
-    --- re-building ‘Introduction.Rmd’ using rmarkdown
-    --- finished re-building ‘Introduction.Rmd’
-    
-    --- re-building ‘SimulatedNetwork.Rmd’ using rmarkdown
-    --- finished re-building ‘SimulatedNetwork.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘EcologicalNetwork.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘mclust’
-      All declared Imports should be used.
-    ```
-
-# incidentally
-
-<details>
-
-* Version: 1.0.1
-* GitHub: https://github.com/zpneal/incidentally
-* Source code: https://github.com/cran/incidentally
-* Date/Publication: 2022-08-05 22:40:09 UTC
-* Number of recursive dependencies: 37
-
-Run `revdepcheck::cloud_details(, "incidentally")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘congress.Rmd’ using rmarkdown
-    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
-    Content type 'application/zip' length 2070239 bytes (2.0 MB)
-    ==================================================
-    downloaded 2.0 MB
-    
-    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
-    Content type 'application/zip' length 2070239 bytes (2.0 MB)
-    ...
-    --- failed re-building ‘congress.Rmd’
-    
-    --- re-building ‘incidentally.Rmd’ using rmarkdown
-    --- finished re-building ‘incidentally.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘congress.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
 # metanetwork
 
 <details>
@@ -476,9 +132,9 @@ Run `revdepcheck::cloud_details(, "metanetwork")` for more info
       Running ‘testthat.R’
     Running the tests in ‘tests/testthat.R’ failed.
     Last 13 lines of output:
-      Epoch: Iteration #300 error is: 199.576452337935
+      Epoch: Iteration #300 error is: 199.570455828093
       x_max = 1356.85756899361
-      y_max = 351.62429330114
+      y_max = 349.758686734959
       [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
       
       ══ Failed tests ════════════════════════════════════════════════════════════════
@@ -493,39 +149,6 @@ Run `revdepcheck::cloud_details(, "metanetwork")` for more info
       Execution halted
     ```
 
-# mstknnclust
-
-<details>
-
-* Version: 0.3.1
-* GitHub: NA
-* Source code: https://github.com/cran/mstknnclust
-* Date/Publication: 2020-09-17 12:20:03 UTC
-* Number of recursive dependencies: 34
-
-Run `revdepcheck::cloud_details(, "mstknnclust")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘guide.Rmd’ using rmarkdown
-    Quitting from lines 103-110 (guide.Rmd) 
-    Error: processing vignette 'guide.Rmd' failed with diagnostics:
-    strict recycling (1)
-    --- failed re-building ‘guide.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘guide.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
 # nat
 
 <details>
@@ -542,43 +165,24 @@ Run `revdepcheck::cloud_details(, "nat")` for more info
 
 ## Newly broken
 
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘nat-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: prune_strahler
-    > ### Title: Prune a neuron by removing segments with a given Strahler order
-    > ### Aliases: prune_strahler
-    > 
-    > ### ** Examples
-    > 
-    > x=Cell07PNs[[1]]
-    > pruned12=prune_strahler(x)
-    Error in value[[3L]](cond) : 
-      No points left after pruning. Consider lowering orders to prune!
-    Calls: prune_strahler ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
-    Execution halted
-    ```
-
 *   checking tests ... ERROR
     ```
       Running ‘test-all.R’
     Running the tests in ‘tests/test-all.R’ failed.
     Last 13 lines of output:
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Failure ('test-neuroml-io.R:41'): parse neuroml files ───────────────────────
+      myidentical_graph(as.ngraph(read.morphml(nml)[[1]]), as.ngraph(read.neuron(swc))) is not TRUE
+      
+      `actual`:   FALSE
+      `expected`: TRUE 
       Backtrace:
           ▆
-       1. ├─testthat::expect_equal(...) at test-ngraph.R:193:2
-       2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
-       3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
-       4. └─nat::strahler_order(n)
-       5.   └─nat::segmentgraph(x, weights = F)
-       6.     └─igraph::add.edges(g, elred, segid = segids)
-       7.       └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
-       8.         └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
-       9.           └─igraph:::i_set_edge_attr(...)
+       1. ├─base::suppressWarnings(...) at test-neuroml-io.R:41:2
+       2. │ └─base::withCallingHandlers(...)
+       3. └─testthat::expect_true(...)
       
-      [ FAIL 5 | WARN 414 | SKIP 5 | PASS 774 ]
+      [ FAIL 1 | WARN 424 | SKIP 5 | PASS 787 ]
       Error: Test failures
       Execution halted
     ```
@@ -773,11 +377,11 @@ Run `revdepcheck::cloud_details(, "poppr")` for more info
       Running ‘test-all.R’
     Running the tests in ‘tests/test-all.R’ failed.
     Last 13 lines of output:
-      Attributes: < Modes: list, NULL >
-      Attributes: < Lengths: 3, 0 >
-      Attributes: < names for target but not for current >
-      Attributes: < current is not list-like >
-      target is table, current is numeric
+       3.   │ └─base::eval(...)
+       4.   └─testthat::expect_equal(...)
+      ── Failure ('test-msn.R:439'): nodes are properly scaled ───────────────────────
+      sort(...) not equal to sort(...).
+      names for target but not for current
       Backtrace:
           ▆
        1. └─poppr (local) expect_vertex_size_scale(pmsn, as.integer(table(mll(pc)))) at test-msn.R:439:2
@@ -857,8 +461,8 @@ Run `revdepcheck::cloud_details(, "riverconn")` for more info
     > g <- igraph::graph_from_literal(1-+2, 2-+4, 3-+2, 4-+6, 6-+7, 5-+6, 7-+8, 9-+5, 10-+5 )
     > E(g)$id_dam <- c(NA, NA, "1", NA, NA, "2", NA, NA, NA)
     > E(g)$type <- ifelse(is.na(E(g)$id_barrier), "joint", "dam")
-    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-      strict recycling (2)
+    Error in value_in[seq_along(value_in)] <- value : 
+      replacement has length zero
     Calls: E<- -> i_set_edge_attr
     Execution halted
     ```
@@ -909,53 +513,3 @@ Run `revdepcheck::cloud_details(, "sfnetworks")` for more info
       Execution halted
     ```
 
-# signnet
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/schochastics/signnet
-* Source code: https://github.com/cran/signnet
-* Date/Publication: 2022-12-22 15:10:02 UTC
-* Number of recursive dependencies: 101
-
-Run `revdepcheck::cloud_details(, "signnet")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘signnet-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: triad_census_signed
-    > ### Title: signed triad census
-    > ### Aliases: triad_census_signed
-    > 
-    > ### ** Examples
-    > 
-    > library(igraph)
-    ...
-    The following object is masked from ‘package:base’:
-    
-        union
-    
-    > g <- graph.full(4, directed = TRUE)
-    > E(g)$sign <- c(-1, 1, 1, -1, -1, 1)
-    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-      strict recycling (2)
-    Calls: E<- -> i_set_edge_attr
-    Execution halted
-    ```
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.8Mb
-      sub-directories of 1Mb or more:
-        libs   6.2Mb
-    ```
-

From b053556b7d9d5d9601d9d4d0ce7712a4e8a0131a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 18:39:39 +0100
Subject: [PATCH 13/26] Remove names

---
 R/attributes.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index d195ecdd0a3..ae2dbd619b0 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -275,7 +275,7 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
         stop("strict recycling (1)")
       }
     } else {
-      value_in <- rep(value, length.out = length(index))
+      value_in <- unname(rep(value, length.out = length(index)))
       # Trigger recycling warning
       value_in[seq_along(value_in)] <- value
     }
@@ -479,7 +479,7 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
         stop("strict recycling (2)")
       }
     } else {
-      value_in <- rep(value, length.out = length(index))
+      value_in <- unname(rep(value, length.out = length(index)))
       # Trigger recycling warning
       value_in[seq_along(value_in)] <- value
     }

From 1ed2908d06a6c4ba43a3d1ef613007f809071341 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 19:36:05 +0100
Subject: [PATCH 14/26] revdepcheck

---
 revdep/README.md   |  23 +-
 revdep/cran.md     |  24 +-
 revdep/failures.md | 567 +--------------------------------------------
 revdep/problems.md | 146 ------------
 4 files changed, 7 insertions(+), 753 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index aa61e5319db..410abb29c63 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,31 +1,14 @@
 # Revdeps
 
-## Failed to check (9)
+## New problems (7)
 
-|package   |version |error |warning |note |
-|:---------|:-------|:-----|:-------|:----|
-|DRviaSPCN |?       |      |        |     |
-|genekitr  |?       |      |        |     |
-|immcp     |?       |      |        |     |
-|numbat    |?       |      |        |     |
-|Platypus  |?       |      |        |     |
-|NA        |?       |      |        |     |
-|tidySEM   |?       |      |        |     |
-|vivid     |?       |      |        |     |
-|NA        |?       |      |        |     |
-
-## New problems (10)
-
-|package     |version |error  |warning |note |
-|:-----------|:-------|:------|:-------|:----|
+|package    |version |error  |warning |note |
+|:----------|:-------|:------|:-------|:----|
 |[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
 |[gRbase](problems.md#grbase)|1.8.9   |__+1__ |1       |1    |
-|[metanetwork](problems.md#metanetwork)|0.7.0   |__+1__ |        |     |
-|[nat](problems.md#nat)|1.8.19  |__+1__ |        |     |
 |[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
 |[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
 |[netseg](problems.md#netseg)|1.0-1   |__+2__ |__+1__  |     |
-|[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
 |[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index 05340724044..7bdd93cb2f4 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,9 +1,9 @@
 ## revdepcheck results
 
-We checked 755 reverse dependencies (753 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 10 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 10 new problems
- * We failed to check 7 packages
+ * We saw 7 new problems
+ * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
 
@@ -16,12 +16,6 @@ Issues with CRAN packages are summarised below.
 * gRbase
   checking examples ... ERROR
 
-* metanetwork
-  checking tests ... ERROR
-
-* nat
-  checking tests ... ERROR
-
 * netmeta
   checking examples ... ERROR
 
@@ -33,21 +27,9 @@ Issues with CRAN packages are summarised below.
   checking tests ... ERROR
   checking re-building of vignette outputs ... WARNING
 
-* poppr
-  checking tests ... ERROR
-
 * riverconn
   checking examples ... ERROR
 
 * sfnetworks
   checking tests ... ERROR
 
-### Failed to check
-
-* DRviaSPCN (NA)
-* genekitr  (NA)
-* immcp     (NA)
-* numbat    (NA)
-* Platypus  (NA)
-* tidySEM   (NA)
-* vivid     (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 9daa4c5b6ba..9a207363396 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1,566 +1 @@
-# DRviaSPCN
-
-<details>
-
-* Version: 0.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/DRviaSPCN
-* Date/Publication: 2022-03-03 16:00:02 UTC
-* Number of recursive dependencies: 169
-
-Run `revdepcheck::cloud_details(, "DRviaSPCN")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/DRviaSPCN/new/DRviaSPCN.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘DRviaSPCN’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/DRviaSPCN/old/DRviaSPCN.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘DRviaSPCN’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# genekitr
-
-<details>
-
-* Version: 1.0.8
-* GitHub: https://github.com/GangLiLab/genekitr
-* Source code: https://github.com/cran/genekitr
-* Date/Publication: 2022-11-23 11:30:02 UTC
-* Number of recursive dependencies: 200
-
-Run `revdepcheck::cloud_details(, "genekitr")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.0.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.0.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# immcp
-
-<details>
-
-* Version: 1.0.3
-* GitHub: https://github.com/YuanlongHu/immcp
-* Source code: https://github.com/cran/immcp
-* Date/Publication: 2022-05-12 05:50:02 UTC
-* Number of recursive dependencies: 194
-
-Run `revdepcheck::cloud_details(, "immcp")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# numbat
-
-<details>
-
-* Version: 1.2.1
-* GitHub: https://github.com/kharchenkolab/numbat
-* Source code: https://github.com/cran/numbat
-* Date/Publication: 2023-01-11 00:20:02 UTC
-* Number of recursive dependencies: 132
-
-Run `revdepcheck::cloud_details(, "numbat")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.2.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.2.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# Platypus
-
-<details>
-
-* Version: 3.4.1
-* GitHub: NA
-* Source code: https://github.com/cran/Platypus
-* Date/Publication: 2022-08-15 07:20:20 UTC
-* Number of recursive dependencies: 356
-
-Run `revdepcheck::cloud_details(, "Platypus")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/Platypus/new/Platypus.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘Platypus/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘Platypus’ version ‘3.4.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking package dependencies ... ERROR
-Package required but not available: ‘ggtree’
-
-Packages suggested but not available for checking:
-  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/Platypus/old/Platypus.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘Platypus/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘Platypus’ version ‘3.4.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking package dependencies ... ERROR
-Package required but not available: ‘ggtree’
-
-Packages suggested but not available for checking:
-  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `revdepcheck::cloud_details(, "NA")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# tidySEM
-
-<details>
-
-* Version: 0.2.3
-* GitHub: https://github.com/cjvanlissa/tidySEM
-* Source code: https://github.com/cran/tidySEM
-* Date/Publication: 2022-04-14 17:50:02 UTC
-* Number of recursive dependencies: 170
-
-Run `revdepcheck::cloud_details(, "tidySEM")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK
-  ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK
-  ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK
-  ‘sem_graph.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘Generating_syntax.Rmd’ using ‘UTF-8’... OK
-  ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK
-  ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK
-  ‘sem_graph.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-# vivid
-
-<details>
-
-* Version: 0.2.3
-* GitHub: NA
-* Source code: https://github.com/cran/vivid
-* Date/Publication: 2021-11-20 01:30:02 UTC
-* Number of recursive dependencies: 206
-
-Run `revdepcheck::cloud_details(, "vivid")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking tests ... OK
-  Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘vivid.Rmd’ using ‘UTF-8’... OK
-  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking tests ... OK
-  Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘vivid.Rmd’ using ‘UTF-8’... OK
-  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-# NA
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `revdepcheck::cloud_details(, "NA")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
+*Wow, no problems at all. :)*
\ No newline at end of file
diff --git a/revdep/problems.md b/revdep/problems.md
index a3c5a696739..a44aa669819 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -111,82 +111,6 @@ Run `revdepcheck::cloud_details(, "gRbase")` for more info
         libs  24.3Mb
     ```
 
-# metanetwork
-
-<details>
-
-* Version: 0.7.0
-* GitHub: https://github.com/MarcOhlmann/metanetwork
-* Source code: https://github.com/cran/metanetwork
-* Date/Publication: 2022-12-05 14:10:02 UTC
-* Number of recursive dependencies: 105
-
-Run `revdepcheck::cloud_details(, "metanetwork")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘testthat.R’
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-      Epoch: Iteration #300 error is: 199.570455828093
-      x_max = 1356.85756899361
-      y_max = 349.758686734959
-      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
-      
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-      ── Failure ('test-compute_TL.R:25'): Computation of trophic levels of norway dataset ──
-      V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`).
-      
-      `names(actual)` is a character vector ('Trachurus', 'Sardinella', 'Sciaenidae', 'Ariidae', 'Merluccius', ...)
-      `names(expected)` is absent
-      
-      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-# nat
-
-<details>
-
-* Version: 1.8.19
-* GitHub: https://github.com/natverse/nat
-* Source code: https://github.com/cran/nat
-* Date/Publication: 2022-04-06 11:50:02 UTC
-* Number of recursive dependencies: 86
-
-Run `revdepcheck::cloud_details(, "nat")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘test-all.R’
-    Running the tests in ‘tests/test-all.R’ failed.
-    Last 13 lines of output:
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-      ── Failure ('test-neuroml-io.R:41'): parse neuroml files ───────────────────────
-      myidentical_graph(as.ngraph(read.morphml(nml)[[1]]), as.ngraph(read.neuron(swc))) is not TRUE
-      
-      `actual`:   FALSE
-      `expected`: TRUE 
-      Backtrace:
-          ▆
-       1. ├─base::suppressWarnings(...) at test-neuroml-io.R:41:2
-       2. │ └─base::withCallingHandlers(...)
-       3. └─testthat::expect_true(...)
-      
-      [ FAIL 1 | WARN 424 | SKIP 5 | PASS 787 ]
-      Error: Test failures
-      Execution halted
-    ```
-
 # netmeta
 
 <details>
@@ -356,76 +280,6 @@ Run `revdepcheck::cloud_details(, "netseg")` for more info
     Execution halted
     ```
 
-# poppr
-
-<details>
-
-* Version: 2.9.3
-* GitHub: https://github.com/grunwaldlab/poppr
-* Source code: https://github.com/cran/poppr
-* Date/Publication: 2021-09-07 07:00:02 UTC
-* Number of recursive dependencies: 97
-
-Run `revdepcheck::cloud_details(, "poppr")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘test-all.R’
-    Running the tests in ‘tests/test-all.R’ failed.
-    Last 13 lines of output:
-       3.   │ └─base::eval(...)
-       4.   └─testthat::expect_equal(...)
-      ── Failure ('test-msn.R:439'): nodes are properly scaled ───────────────────────
-      sort(...) not equal to sort(...).
-      names for target but not for current
-      Backtrace:
-          ▆
-       1. └─poppr (local) expect_vertex_size_scale(pmsn, as.integer(table(mll(pc)))) at test-msn.R:439:2
-       2.   ├─base::eval(...) at test-msn.R:105:2
-       3.   │ └─base::eval(...)
-       4.   └─testthat::expect_equal(...)
-      
-      [ FAIL 2 | WARN 0 | SKIP 181 | PASS 378 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘algo.Rnw’ using knitr
-    Error: processing vignette 'algo.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'algo.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `colortbl.sty' not found.
-    
-    Type X to quit or <RETURN> to proceed,
-    or enter new name. (Default extension: sty)
-    ...
-    l.270 \long
-               \def\@secondoffive#1#2#3#4#5{#2}^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘algo.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘algo.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘RClone’
-    ```
-
 # riverconn
 
 <details>

From 343bfc4a4fb3013e2b9d85d448dbdea673adcb5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 20:04:02 +0100
Subject: [PATCH 15/26] Recycle only for complete indexes

---
 R/attributes.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index ae2dbd619b0..bb5f7c34c0a 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -259,7 +259,7 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
 
   vattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_vertex)
 
-  if (!(name %in% names(vattrs))) {
+  if (!complete && !(name %in% names(vattrs))) {
     vattrs[[name]] <- value[rep.int(NA_integer_, vcount(graph))]
   }
 
@@ -463,7 +463,7 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
 
   eattrs <- .Call(C_R_igraph_mybracket2, graph, igraph_t_idx_attr, igraph_attr_idx_edge)
 
-  if (!(name %in% names(eattrs))) {
+  if (!complete && !(name %in% names(eattrs))) {
     eattrs[[name]] <- value[rep.int(NA_integer_, ecount(graph))]
   }
 

From 4f525be65180ba8cada9714b92b5460227831689 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 20:40:23 +0100
Subject: [PATCH 16/26] New results

---
 revdep/README.md   |   6 +-
 revdep/cran.md     |  18 +---
 revdep/problems.md | 244 ---------------------------------------------
 3 files changed, 3 insertions(+), 265 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 410abb29c63..af7fa866919 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,14 +1,10 @@
 # Revdeps
 
-## New problems (7)
+## New problems (3)
 
 |package    |version |error  |warning |note |
 |:----------|:-------|:------|:-------|:----|
 |[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
-|[gRbase](problems.md#grbase)|1.8.9   |__+1__ |1       |1    |
-|[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
-|[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
-|[netseg](problems.md#netseg)|1.0-1   |__+2__ |__+1__  |     |
 |[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index 7bdd93cb2f4..b17eefb507d 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,8 +1,8 @@
 ## revdepcheck results
 
-We checked 10 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 7 new problems
+ * We saw 3 new problems
  * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
@@ -13,20 +13,6 @@ Issues with CRAN packages are summarised below.
 * egor
   checking tests ... ERROR
 
-* gRbase
-  checking examples ... ERROR
-
-* netmeta
-  checking examples ... ERROR
-
-* NetOrigin
-  checking examples ... ERROR
-
-* netseg
-  checking examples ... ERROR
-  checking tests ... ERROR
-  checking re-building of vignette outputs ... WARNING
-
 * riverconn
   checking examples ... ERROR
 
diff --git a/revdep/problems.md b/revdep/problems.md
index a44aa669819..f4449f9444f 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -36,250 +36,6 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       Execution halted
     ```
 
-# gRbase
-
-<details>
-
-* Version: 1.8.9
-* GitHub: NA
-* Source code: https://github.com/cran/gRbase
-* Date/Publication: 2022-11-10 10:40:02 UTC
-* Number of recursive dependencies: 50
-
-Run `revdepcheck::cloud_details(, "gRbase")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘gRbase-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: graph-moralize
-    > ### Title: Moralize a directed acyclic graph
-    > ### Aliases: graph-moralize moralize moralize.default moralizeMAT
-    > ### Keywords: utilities
-    > 
-    > ### ** Examples
-    > 
-    ...
-    
-        decompose, spectrum
-    
-    The following object is masked from ‘package:base’:
-    
-        union
-    
-    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
-    Calls: moralize ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
-    Execution halted
-    ```
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘arrays.Rnw’ using knitr
-    Error: processing vignette 'arrays.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'arrays.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `boxedminipage.sty' not found.
-    
-    Type X to quit or <RETURN> to proceed,
-    or enter new name. (Default extension: sty)
-    
-    ...
-    l.63 ^^M
-            
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘graphs.Rnw’
-    
-    SUMMARY: processing the following files failed:
-      ‘arrays.Rnw’ ‘graphs.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 26.4Mb
-      sub-directories of 1Mb or more:
-        libs  24.3Mb
-    ```
-
-# netmeta
-
-<details>
-
-* Version: 2.7-0
-* GitHub: https://github.com/guido-s/netmeta
-* Source code: https://github.com/cran/netmeta
-* Date/Publication: 2022-12-22 09:30:02 UTC
-* Number of recursive dependencies: 90
-
-Run `revdepcheck::cloud_details(, "netmeta")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘netmeta-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: netcontrib
-    > ### Title: Contribution matrix in network meta-analysis
-    > ### Aliases: netcontrib print.netcontrib
-    > ### Keywords: contribution
-    > 
-    > ### ** Examples
-    > 
-    ...
-    > #
-    > data("Woods2010")
-    > p1 <- pairwise(treatment, event = r, n = N,
-    +   studlab = author, data = Woods2010, sm = "OR")
-    > 
-    > net1 <- netmeta(p1)
-    > cm <- netcontrib(net1)
-    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
-    Calls: netcontrib ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
-    Execution halted
-    ```
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 2 marked UTF-8 strings
-    ```
-
-# NetOrigin
-
-<details>
-
-* Version: 1.1-4
-* GitHub: https://github.com/jmanitz/NetOrigin
-* Source code: https://github.com/cran/NetOrigin
-* Date/Publication: 2022-01-20 08:32:42 UTC
-* Number of recursive dependencies: 77
-
-Run `revdepcheck::cloud_details(, "NetOrigin")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘NetOrigin-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: origin
-    > ### Title: Origin Estimation for Propagation Processes on Complex Networks
-    > ### Aliases: origin origin_edm origin_backtracking origin_centrality
-    > ###   origin_bayesian
-    > 
-    > ### ** Examples
-    > 
-    ...
-    > performance(om, start=1, graph=ptnGoe)
-                      start                         est  hitt rank spj dist
-    1 X.Adolf.Hoyer.Strasse X.Gotthelf.Leimbach.Strasse FALSE    2   2 1332
-    > 
-    > # backtracking origin estimation (Manitz et al., 2016)
-    > ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe)
-    Error in `[.data.frame`(value, rep.int(NA_integer_, vcount(graph))) : 
-      undefined columns selected
-    Calls: origin ... origin_backtracking -> V<- -> i_set_vertex_attr -> [ -> [.data.frame
-    Execution halted
-    ```
-
-# netseg
-
-<details>
-
-* Version: 1.0-1
-* GitHub: https://github.com/mbojan/netseg
-* Source code: https://github.com/cran/netseg
-* Date/Publication: 2022-08-25 12:10:06 UTC
-* Number of recursive dependencies: 59
-
-Run `revdepcheck::cloud_details(, "netseg")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘netseg-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: ssi
-    > ### Title: Spectral Segregation Index for Social Networks
-    > ### Aliases: ssi
-    > 
-    > ### ** Examples
-    > 
-    > if(requireNamespace("igraph", quietly = TRUE)) {
-    ...
-    + vertex.label.family="",
-    + vertex.label=igraph::V(WhiteKinship)$name,
-    + vertex.color= gray(k),
-    + vertex.shape=c("circle", "csquare")[a],
-    + vertex.label.color="black")
-    + legend( "topleft", legend=c("Men", "Women"), pch=c(0,1), col=1)
-    + }
-    Error in simple_vs_index(x, ii, na_ok) : Unknown vertex selected
-    Calls: ssi ... [ -> [.igraph.vs -> lapply -> FUN -> simple_vs_index
-    Execution halted
-    ```
-
-*   checking tests ... ERROR
-    ```
-      Running ‘testthat.R’
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-      Error in `simple_vs_index(x, ii, na_ok)`: Unknown vertex selected
-      Backtrace:
-          ▆
-       1. └─netseg::ssi(EF3, "race") at test-ssi.R:4:2
-       2.   └─igraph::`V<-`(`*tmp*`, value = `*vtmp*`)
-       3.     └─igraph:::i_set_vertex_attr(...)
-       4.       ├─value[rep.int(NA_integer_, vcount(graph))]
-       5.       └─igraph:::`[.igraph.vs`(value, rep.int(NA_integer_, vcount(graph)))
-       6.         └─base::lapply(...)
-       7.           └─igraph (local) FUN(X[[i]], ...)
-       8.             └─igraph:::simple_vs_index(x, ii, na_ok)
-      
-      [ FAIL 2 | WARN 0 | SKIP 0 | PASS 72 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘netseg.Rmd’ using rmarkdown
-    Quitting from lines 252-253 (netseg.Rmd) 
-    Error: processing vignette 'netseg.Rmd' failed with diagnostics:
-    Unknown vertex selected
-    --- failed re-building ‘netseg.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘netseg.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
 # riverconn
 
 <details>

From 1f363f1b345a254f7ecf55e4fe44d353e027d0c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 21:25:26 +0100
Subject: [PATCH 17/26] Add tests from revdepchecks

---
 tests/testthat/test-attributes.R       | 16 ++++++++++++++++
 tests/testthat/test-graph.data.frame.R |  7 +++++++
 2 files changed, 23 insertions(+)

diff --git a/tests/testthat/test-attributes.R b/tests/testthat/test-attributes.R
index 5577dab3a0a..e9bf3a609d7 100644
--- a/tests/testthat/test-attributes.R
+++ b/tests/testthat/test-attributes.R
@@ -229,3 +229,19 @@ test_that("can change type of attributes (#466)", {
   E(g)$foo <- 2
   expect_equal(E(g)$foo, rep(2, 10))
 })
+
+test_that("setting attributes strips names (#466)", {
+  g <- make_ring(10)
+
+  V(g)$foo <- stats::setNames(1:10, letters[1:10])
+  expect_identical(V(g)$foo, 1:10)
+
+  E(g)$foo <- stats::setNames(1:10, letters[1:10])
+  expect_identical(E(g)$foo, 1:10)
+
+  V(g)$bar <- c(a = 1)
+  expect_identical(V(g)$bar, rep(1, 10))
+
+  E(g)$bar <- c(a = 1)
+  expect_identical(E(g)$bar, rep(1, 10))
+})
diff --git a/tests/testthat/test-graph.data.frame.R b/tests/testthat/test-graph.data.frame.R
index 1f8d81f3593..60a1c538035 100644
--- a/tests/testthat/test-graph.data.frame.R
+++ b/tests/testthat/test-graph.data.frame.R
@@ -31,6 +31,13 @@ test_that("graph_from_data_frame works", {
   expect_that(df$edges, equals(relations))
 })
 
+test_that("graph_from_data_frame() creates attributes for zero-row data frames (#466)", {
+  x <- data.frame(from = integer(), to = integer(), foo = integer(), bar = numeric())
+  g <- graph_from_data_frame(x)
+  expect_identical(E(g)$foo, integer())
+  expect_identical(E(g)$bar, numeric())
+})
+
 test_that("graph_from_data_frame works on matrices", {
   el <- cbind(1:5, 5:1, weight = 1:5)
   g <- graph_from_data_frame(el)

From 080ca0cbdb5a9bd8cc645850b34afda8aeb94e92 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 15 Jan 2023 10:44:11 +0100
Subject: [PATCH 18/26] Strict rules

---
 R/attributes.R              | 2 +-
 tests/testthat/test-pajek.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index bb5f7c34c0a..12ddc00376d 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -35,7 +35,7 @@
 
 
 
-ATTRIBUTE_STRICT_RECYCLING <- FALSE
+ATTRIBUTE_STRICT_RECYCLING <- TRUE
 
 #' Graph attributes of a graph
 #'
diff --git a/tests/testthat/test-pajek.R b/tests/testthat/test-pajek.R
index 6a912e8e7a4..ad38f117915 100644
--- a/tests/testthat/test-pajek.R
+++ b/tests/testthat/test-pajek.R
@@ -1,6 +1,6 @@
 test_that("writing Pajek files works", {
   g <- make_ring(9)
-  V(g)$color <- c("red", "green", "yellow")
+  V(g)$color <- rep(c("red", "green", "yellow"), 3)
 
   tc <- rawConnection(raw(0), "w")
   write_graph(g, format = "pajek", file = tc)

From c481cd239097fd85228b869132d5d410a0d52e97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Mon, 16 Jan 2023 05:06:12 +0100
Subject: [PATCH 19/26] revdepcheck

---
 revdep/README.md   |  19 +-
 revdep/cran.md     |  46 +++-
 revdep/problems.md | 644 ++++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 702 insertions(+), 7 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index af7fa866919..ebf149e15f4 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,10 +1,23 @@
 # Revdeps
 
-## New problems (3)
+## New problems (16)
 
-|package    |version |error  |warning |note |
-|:----------|:-------|:------|:-------|:----|
+|package        |version |error  |warning |note |
+|:--------------|:-------|:------|:-------|:----|
+|[backbone](problems.md#backbone)|2.1.1   |__+1__ |        |     |
+|[clustAnalytics](problems.md#clustanalytics)|0.5.2   |       |__+1__  |1    |
+|[deepdep](problems.md#deepdep)|0.4.1   |__+1__ |        |     |
+|[Diderot](problems.md#diderot)|0.13    |__+1__ |        |     |
 |[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
+|[gemtc](problems.md#gemtc)|1.0-1   |__+2__ |        |     |
+|[GREMLINS](problems.md#gremlins)|0.2.0   |__+1__ |__+1__  |1    |
+|[incidentally](problems.md#incidentally)|1.0.1   |       |__+1__  |     |
+|[metanetwork](problems.md#metanetwork)|0.7.0   |__+1__ |        |     |
+|[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
+|[nat](problems.md#nat)|1.8.19  |__+2__ |        |     |
+|[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
+|[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
 |[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
+|[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index b17eefb507d..7565c7222ac 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,8 +1,8 @@
 ## revdepcheck results
 
-We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 19 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 3 new problems
+ * We saw 16 new problems
  * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
@@ -10,12 +10,54 @@ Issues with CRAN packages are summarised below.
 ### New problems
 (This reports the first line of each new failure)
 
+* backbone
+  checking tests ... ERROR
+
+* clustAnalytics
+  checking re-building of vignette outputs ... WARNING
+
+* deepdep
+  checking tests ... ERROR
+
+* Diderot
+  checking examples ... ERROR
+
 * egor
   checking tests ... ERROR
 
+* gemtc
+  checking examples ... ERROR
+  checking tests ... ERROR
+
+* GREMLINS
+  checking examples ... ERROR
+  checking re-building of vignette outputs ... WARNING
+
+* incidentally
+  checking re-building of vignette outputs ... WARNING
+
+* metanetwork
+  checking tests ... ERROR
+
+* mstknnclust
+  checking re-building of vignette outputs ... WARNING
+
+* nat
+  checking examples ... ERROR
+  checking tests ... ERROR
+
+* netmeta
+  checking examples ... ERROR
+
+* poppr
+  checking tests ... ERROR
+
 * riverconn
   checking examples ... ERROR
 
 * sfnetworks
   checking tests ... ERROR
 
+* signnet
+  checking examples ... ERROR
+
diff --git a/revdep/problems.md b/revdep/problems.md
index f4449f9444f..a11e2fe10e9 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,3 +1,171 @@
+# backbone
+
+<details>
+
+* Version: 2.1.1
+* GitHub: https://github.com/zpneal/backbone
+* Source code: https://github.com/cran/backbone
+* Date/Publication: 2022-10-18 17:35:06 UTC
+* Number of recursive dependencies: 36
+
+Run `revdepcheck::cloud_details(, "backbone")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘tinytest.R’
+    Running the tests in ‘tests/tinytest.R’ failed.
+    Last 13 lines of output:
+      test_backbone.R...............   29 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   30 tests OK 
+      test_backbone.R...............   31 tests OK 
+      test_backbone.R...............   32 tests OK 
+      test_backbone.R...............   33 tests OK 
+      test_backbone.R...............   34 tests OK 
+      test_backbone.R...............   35 tests OK 
+      test_backbone.R...............   36 tests OK 
+      test_backbone.R...............   36 tests OK Error in i_set_vertex_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+        strict recycling (1)
+      Calls: <Anonymous> ... FUN -> eval -> eval -> <Anonymous> -> i_set_vertex_attr
+      Execution halted
+    ```
+
+# clustAnalytics
+
+<details>
+
+* Version: 0.5.2
+* GitHub: NA
+* Source code: https://github.com/cran/clustAnalytics
+* Date/Publication: 2022-11-09 11:50:09 UTC
+* Number of recursive dependencies: 69
+
+Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘cluster_stability.Rmd’ using rmarkdown
+    --- finished re-building ‘cluster_stability.Rmd’
+    
+    --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown
+    --- finished re-building ‘graph_rewiring_functions.Rmd’
+    
+    --- re-building ‘other_functions.Rmd’ using rmarkdown
+    --- finished re-building ‘other_functions.Rmd’
+    ...
+    Quitting from lines 109-111 (stability_significance_examples.Rmd) 
+    Error: processing vignette 'stability_significance_examples.Rmd' failed with diagnostics:
+    strict recycling (1)
+    --- failed re-building ‘stability_significance_examples.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘stability_significance_examples.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.6Mb
+      sub-directories of 1Mb or more:
+        libs   6.1Mb
+    ```
+
+# deepdep
+
+<details>
+
+* Version: 0.4.1
+* GitHub: https://github.com/DominikRafacz/deepdep
+* Source code: https://github.com/cran/deepdep
+* Date/Publication: 2021-12-20 16:20:02 UTC
+* Number of recursive dependencies: 144
+
+Run `revdepcheck::cloud_details(, "deepdep")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘spelling.R’
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+        6.     └─ggraph:::create_layout.default(graph, layout, ...)
+        7.       ├─ggraph::create_layout(graph, layout, ...)
+        8.       └─ggraph:::create_layout.tbl_graph(graph, layout, ...)
+        9.         ├─dplyr::mutate(ungroup(activate(graph, "nodes")), .ggraph.orig_index = seq_len(graph_order()))
+       10.         └─tidygraph:::mutate.tbl_graph(...)
+       11.           └─tidygraph::mutate_as_tbl(.data, !!!dot)
+       12.             ├─tidygraph:::set_graph_data(.data, d_tmp)
+       13.             └─tidygraph:::set_graph_data.tbl_graph(.data, d_tmp)
+       14.               └─tidygraph:::set_node_attributes(x, value)
+       15.                 └─igraph::`vertex_attr<-`(`*tmp*`, value = as.list(value))
+       16.                   └─igraph::`vertex.attributes<-`(graph, index = index, value = value)
+      
+      [ FAIL 9 | WARN 0 | SKIP 2 | PASS 25 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# Diderot
+
+<details>
+
+* Version: 0.13
+* GitHub: NA
+* Source code: https://github.com/cran/Diderot
+* Date/Publication: 2020-04-19 11:20:02 UTC
+* Number of recursive dependencies: 15
+
+Run `revdepcheck::cloud_details(, "Diderot")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘Diderot-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: build_graph
+    > ### Title: Builds a citation graph.
+    > ### Aliases: build_graph 'Citation Graph Building'
+    > 
+    > ### ** Examples
+    > 
+    > ## Don't show: 
+    ...
+    > unlink(c(tempfi1, tempfi2))
+    > ## End(Don't show)
+    > 
+    > # Build graph
+    > gr<-build_graph(db=db,small.year.mismatch=TRUE, attrs=c("Corpus","Year","Authors"), nb.cores=1)
+    starting worker pid=11556 on localhost:11592 at 20:54:39.535
+    Error in i_set_vertex_attr(graph = graph, name = name, value = value,  : 
+      strict recycling (1)
+    Calls: build_graph -> set.vertex.attribute -> i_set_vertex_attr
+    Execution halted
+    ```
+
 # egor
 
 <details>
@@ -36,6 +204,428 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       Execution halted
     ```
 
+# gemtc
+
+<details>
+
+* Version: 1.0-1
+* GitHub: https://github.com/gertvv/gemtc
+* Source code: https://github.com/cran/gemtc
+* Date/Publication: 2021-05-14 23:20:02 UTC
+* Number of recursive dependencies: 56
+
+Run `revdepcheck::cloud_details(, "gemtc")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘gemtc-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: atrialFibrillation
+    > ### Title: Prevention of stroke in atrial fibrillation patients
+    > ### Aliases: atrialFibrillation
+    > 
+    > ### ** Examples
+    > 
+    > # Build a model similar to Model 4(b) from Cooper et al. (2009):
+    ...
+    +                   classes=classes)
+    > 
+    > model <- mtc.model(atrialFibrillation,
+    +                    type="regression",
+    +                    regressor=regressor,
+    +                    om.scale=10)
+    Error in i_set_edge_attr(graph = graph, name = name, index = index, value = value) : 
+      strict recycling (2)
+    Calls: mtc.model ... add_edges -> edge_attr<- -> set_edge_attr -> i_set_edge_attr
+    Execution halted
+    ```
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test.R’
+    Running the tests in ‘tests/test.R’ failed.
+    Last 13 lines of output:
+           ▆
+        1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2
+        2.   ├─base::as.matrix(...)
+        3.   └─gemtc::relative.effect(...)
+        4.     └─gemtc:::spanning.tree.mtc.result(result)
+        5.       └─gemtc:::graph.create(...)
+        6.         └─igraph:::`+.igraph`(g, edges.create(e, ...))
+        7.           └─igraph::add_edges(e1, as.igraph.vs(e1, toadd), attr = attr)
+        8.             └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
+        9.               └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
+       10.                 └─igraph:::i_set_edge_attr(...)
+      
+      [ FAIL 35 | WARN 0 | SKIP 0 | PASS 269 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# GREMLINS
+
+<details>
+
+* Version: 0.2.0
+* GitHub: https://github.com/demiperimetre/GREMLINS
+* Source code: https://github.com/cran/GREMLINS
+* Date/Publication: 2020-11-25 13:50:04 UTC
+* Number of recursive dependencies: 62
+
+Run `revdepcheck::cloud_details(, "GREMLINS")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘GREMLINS-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: plotMBM
+    > ### Title: Plot the mesoscopic view of the estimated MBM
+    > ### Aliases: plotMBM
+    > 
+    > ### ** Examples
+    > 
+    > namesFG <- c('A','B')
+    ...
+    [1] "gaussian"  "bernoulli"
+    [1] "-------------------------------------------------------------------"
+    [1] " ------ Searching the numbers of blocks starting from [ 2 2 ] blocks"
+    [1] "ICL : -2028.78 . Nb of blocks: [ 2 2 ]"
+    [1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
+    > plotMBM(res_MBMsimu)
+    Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
+      strict recycling (2)
+    Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
+    Execution halted
+    ```
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
+    Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
+    Error: processing vignette 'EcologicalNetwork.Rmd' failed with diagnostics:
+    strict recycling (2)
+    --- failed re-building ‘EcologicalNetwork.Rmd’
+    
+    --- re-building ‘Introduction.Rmd’ using rmarkdown
+    --- finished re-building ‘Introduction.Rmd’
+    
+    --- re-building ‘SimulatedNetwork.Rmd’ using rmarkdown
+    --- finished re-building ‘SimulatedNetwork.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘EcologicalNetwork.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘mclust’
+      All declared Imports should be used.
+    ```
+
+# incidentally
+
+<details>
+
+* Version: 1.0.1
+* GitHub: https://github.com/zpneal/incidentally
+* Source code: https://github.com/cran/incidentally
+* Date/Publication: 2022-08-05 22:40:09 UTC
+* Number of recursive dependencies: 37
+
+Run `revdepcheck::cloud_details(, "incidentally")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘congress.Rmd’ using rmarkdown
+    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
+    Content type 'application/zip' length 2070239 bytes (2.0 MB)
+    ==================================================
+    downloaded 2.0 MB
+    
+    trying URL 'https://www.govinfo.gov/bulkdata/BILLSTATUS/115/sres/BILLSTATUS-115-sres.zip'
+    Content type 'application/zip' length 2070239 bytes (2.0 MB)
+    ...
+    --- failed re-building ‘congress.Rmd’
+    
+    --- re-building ‘incidentally.Rmd’ using rmarkdown
+    --- finished re-building ‘incidentally.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘congress.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+# metanetwork
+
+<details>
+
+* Version: 0.7.0
+* GitHub: https://github.com/MarcOhlmann/metanetwork
+* Source code: https://github.com/cran/metanetwork
+* Date/Publication: 2022-12-05 14:10:02 UTC
+* Number of recursive dependencies: 105
+
+Run `revdepcheck::cloud_details(, "metanetwork")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘testthat.R’
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+      Epoch: Iteration #300 error is: 199.576452337934
+      x_max = 1356.85756899361
+      y_max = 351.624293301058
+      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
+      
+      ══ Failed tests ════════════════════════════════════════════════════════════════
+      ── Failure ('test-compute_TL.R:25'): Computation of trophic levels of norway dataset ──
+      V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`).
+      
+      `names(actual)` is a character vector ('Trachurus', 'Sardinella', 'Sciaenidae', 'Ariidae', 'Merluccius', ...)
+      `names(expected)` is absent
+      
+      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# mstknnclust
+
+<details>
+
+* Version: 0.3.1
+* GitHub: NA
+* Source code: https://github.com/cran/mstknnclust
+* Date/Publication: 2020-09-17 12:20:03 UTC
+* Number of recursive dependencies: 34
+
+Run `revdepcheck::cloud_details(, "mstknnclust")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘guide.Rmd’ using rmarkdown
+    Quitting from lines 103-110 (guide.Rmd) 
+    Error: processing vignette 'guide.Rmd' failed with diagnostics:
+    strict recycling (1)
+    --- failed re-building ‘guide.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘guide.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+# nat
+
+<details>
+
+* Version: 1.8.19
+* GitHub: https://github.com/natverse/nat
+* Source code: https://github.com/cran/nat
+* Date/Publication: 2022-04-06 11:50:02 UTC
+* Number of recursive dependencies: 86
+
+Run `revdepcheck::cloud_details(, "nat")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘nat-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: prune_strahler
+    > ### Title: Prune a neuron by removing segments with a given Strahler order
+    > ### Aliases: prune_strahler
+    > 
+    > ### ** Examples
+    > 
+    > x=Cell07PNs[[1]]
+    > pruned12=prune_strahler(x)
+    Error in value[[3L]](cond) : 
+      No points left after pruning. Consider lowering orders to prune!
+    Calls: prune_strahler ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
+    Execution halted
+    ```
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test-all.R’
+    Running the tests in ‘tests/test-all.R’ failed.
+    Last 13 lines of output:
+      Backtrace:
+          ▆
+       1. ├─testthat::expect_equal(...) at test-ngraph.R:193:2
+       2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
+       3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
+       4. └─nat::strahler_order(n)
+       5.   └─nat::segmentgraph(x, weights = F)
+       6.     └─igraph::add.edges(g, elred, segid = segids)
+       7.       └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
+       8.         └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
+       9.           └─igraph:::i_set_edge_attr(...)
+      
+      [ FAIL 5 | WARN 414 | SKIP 5 | PASS 774 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+# netmeta
+
+<details>
+
+* Version: 2.7-0
+* GitHub: https://github.com/guido-s/netmeta
+* Source code: https://github.com/cran/netmeta
+* Date/Publication: 2022-12-22 09:30:02 UTC
+* Number of recursive dependencies: 90
+
+Run `revdepcheck::cloud_details(, "netmeta")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘netmeta-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: netcontrib
+    > ### Title: Contribution matrix in network meta-analysis
+    > ### Aliases: netcontrib print.netcontrib
+    > ### Keywords: contribution
+    > 
+    > ### ** Examples
+    > 
+    ...
+    > # Use the Woods dataset
+    > #
+    > data("Woods2010")
+    > p1 <- pairwise(treatment, event = r, n = N,
+    +   studlab = author, data = Woods2010, sm = "OR")
+    > 
+    > net1 <- netmeta(p1)
+    > cm <- netcontrib(net1)
+    Error: C stack usage  9962452 is too close to the limit
+    Execution halted
+    ```
+
+## In both
+
+*   checking data for non-ASCII characters ... NOTE
+    ```
+      Note: found 2 marked UTF-8 strings
+    ```
+
+# poppr
+
+<details>
+
+* Version: 2.9.3
+* GitHub: https://github.com/grunwaldlab/poppr
+* Source code: https://github.com/cran/poppr
+* Date/Publication: 2021-09-07 07:00:02 UTC
+* Number of recursive dependencies: 97
+
+Run `revdepcheck::cloud_details(, "poppr")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking tests ... ERROR
+    ```
+      Running ‘test-all.R’
+    Running the tests in ‘tests/test-all.R’ failed.
+    Last 13 lines of output:
+      Attributes: < Modes: list, NULL >
+      Attributes: < Lengths: 3, 0 >
+      Attributes: < names for target but not for current >
+      Attributes: < current is not list-like >
+      target is table, current is numeric
+      Backtrace:
+          ▆
+       1. └─poppr (local) expect_vertex_size_scale(pmsn, as.integer(table(mll(pc)))) at test-msn.R:439:2
+       2.   ├─base::eval(...) at test-msn.R:105:2
+       3.   │ └─base::eval(...)
+       4.   └─testthat::expect_equal(...)
+      
+      [ FAIL 2 | WARN 0 | SKIP 181 | PASS 378 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+## In both
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error(s) in re-building vignettes:
+      ...
+    --- re-building ‘algo.Rnw’ using knitr
+    Error: processing vignette 'algo.Rnw' failed with diagnostics:
+    Running 'texi2dvi' on 'algo.tex' failed.
+    LaTeX errors:
+    ! LaTeX Error: File `colortbl.sty' not found.
+    
+    Type X to quit or <RETURN> to proceed,
+    or enter new name. (Default extension: sty)
+    ...
+    l.270 \long
+               \def\@secondoffive#1#2#3#4#5{#2}^^M
+    !  ==> Fatal error occurred, no output PDF file produced!
+    --- failed re-building ‘algo.Rnw’
+    
+    SUMMARY: processing the following file failed:
+      ‘algo.Rnw’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘RClone’
+    ```
+
 # riverconn
 
 <details>
@@ -71,8 +661,8 @@ Run `revdepcheck::cloud_details(, "riverconn")` for more info
     > g <- igraph::graph_from_literal(1-+2, 2-+4, 3-+2, 4-+6, 6-+7, 5-+6, 7-+8, 9-+5, 10-+5 )
     > E(g)$id_dam <- c(NA, NA, "1", NA, NA, "2", NA, NA, NA)
     > E(g)$type <- ifelse(is.na(E(g)$id_barrier), "joint", "dam")
-    Error in value_in[seq_along(value_in)] <- value : 
-      replacement has length zero
+    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+      strict recycling (2)
     Calls: E<- -> i_set_edge_attr
     Execution halted
     ```
@@ -123,3 +713,53 @@ Run `revdepcheck::cloud_details(, "sfnetworks")` for more info
       Execution halted
     ```
 
+# signnet
+
+<details>
+
+* Version: 1.0.0
+* GitHub: https://github.com/schochastics/signnet
+* Source code: https://github.com/cran/signnet
+* Date/Publication: 2022-12-22 15:10:02 UTC
+* Number of recursive dependencies: 101
+
+Run `revdepcheck::cloud_details(, "signnet")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘signnet-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: triad_census_signed
+    > ### Title: signed triad census
+    > ### Aliases: triad_census_signed
+    > 
+    > ### ** Examples
+    > 
+    > library(igraph)
+    ...
+    The following object is masked from ‘package:base’:
+    
+        union
+    
+    > g <- graph.full(4, directed = TRUE)
+    > E(g)$sign <- c(-1, 1, 1, -1, -1, 1)
+    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
+      strict recycling (2)
+    Calls: E<- -> i_set_edge_attr
+    Execution halted
+    ```
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  7.8Mb
+      sub-directories of 1Mb or more:
+        libs   6.2Mb
+    ```
+

From 7936460bf30f43b37ae63bd490cb793e9fb6f351 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Mon, 16 Jan 2023 05:31:07 +0100
Subject: [PATCH 20/26] Fix erroneous example

---
 R/conversion.R            | 2 +-
 R/structural.properties.R | 2 +-
 man/as.matrix.igraph.Rd   | 2 +-
 man/matching.Rd           | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/conversion.R b/R/conversion.R
index 9b87b307c88..b8bc17cf321 100644
--- a/R/conversion.R
+++ b/R/conversion.R
@@ -1047,7 +1047,7 @@ as_long_data_frame <- function(graph) {
 #' as.matrix(g, "adjacency")
 #' as.matrix(g, "edgelist")
 #' # use edge attribute "weight"
-#' E(g)$weight <- rep(1:10, each = ecount(g))
+#' E(g)$weight <- rep(1:10, length.out = ecount(g))
 #' as.matrix(g, "adjacency", sparse = FALSE, attr = "weight")
 #'
 as.matrix.igraph <- function(x, matrix.type = c("adjacency", "edgelist"), ...) {
diff --git a/R/structural.properties.R b/R/structural.properties.R
index 73a52370f16..6d30af7d3d5 100644
--- a/R/structural.properties.R
+++ b/R/structural.properties.R
@@ -2118,7 +2118,7 @@ laplacian_matrix <- function(graph, normalized = FALSE, weights = NULL,
 #' is_max_matching(g, m2)
 #' is_max_matching(g, m3)
 #'
-#' V(g)$type <- c(FALSE, TRUE)
+#' V(g)$type <- rep(c(FALSE, TRUE), 3)
 #' print_all(g, v = TRUE)
 #' max_bipartite_match(g)
 #'
diff --git a/man/as.matrix.igraph.Rd b/man/as.matrix.igraph.Rd
index ce464f127a3..c5d97a978f4 100644
--- a/man/as.matrix.igraph.Rd
+++ b/man/as.matrix.igraph.Rd
@@ -41,7 +41,7 @@ g <- make_graph("zachary")
 as.matrix(g, "adjacency")
 as.matrix(g, "edgelist")
 # use edge attribute "weight"
-E(g)$weight <- rep(1:10, each = ecount(g))
+E(g)$weight <- rep(1:10, length.out = ecount(g))
 as.matrix(g, "adjacency", sparse = FALSE, attr = "weight")
 
 }
diff --git a/man/matching.Rd b/man/matching.Rd
index f7396ce136a..6a4ff586073 100644
--- a/man/matching.Rd
+++ b/man/matching.Rd
@@ -103,7 +103,7 @@ is_max_matching(g, m1)
 is_max_matching(g, m2)
 is_max_matching(g, m3)
 
-V(g)$type <- c(FALSE, TRUE)
+V(g)$type <- rep(c(FALSE, TRUE), 3)
 print_all(g, v = TRUE)
 max_bipartite_match(g)
 

From 8f95cc7fda371742a87f34a4b6bf6364678bb97a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sat, 21 Jan 2023 11:01:25 +0100
Subject: [PATCH 21/26] Ignore NULL input

---
 R/attributes.R                   | 12 ++++++++++++
 man/set_edge_attr.Rd             |  3 ++-
 man/set_vertex_attr.Rd           |  3 ++-
 tests/testthat/test-attributes.R |  9 +++++++++
 4 files changed, 25 insertions(+), 2 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index 12ddc00376d..1728445c5f6 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -227,6 +227,7 @@ vertex_attr <- function(graph, name, index = V(graph)) {
 #'   of a subset of vertices.
 #' @param value The new value of the attribute for all (or `index`)
 #'   vertices.
+#'   If `NULL`, the input is returned unchanged.
 #' @return The graph, with the vertex attribute added or set.
 #'
 #' @aliases set.vertex.attribute
@@ -250,6 +251,11 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
+
+  if (is.null(value)) {
+    return(graph)
+  }
+
   single <- is_single_index(index)
   complete <- is_complete_iterator(index)
   if (!missing(index) && check) {
@@ -431,6 +437,7 @@ edge_attr <- function(graph, name, index = E(graph)) {
 #'   a subset of edges.
 #' @param value The new value of the attribute for all (or `index`)
 #'   edges.
+#'   If `NULL`, the input is returned unchanged.
 #' @return The graph, with the edge attribute added or set.
 #'
 #' @aliases set.edge.attribute
@@ -454,6 +461,11 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
   if (!is_igraph(graph)) {
     stop("Not a graph object")
   }
+
+  if (is.null(value)) {
+    return(graph)
+  }
+
   complete <- is_complete_iterator(index)
   single <- is_single_index(index)
   name <- as.character(name)
diff --git a/man/set_edge_attr.Rd b/man/set_edge_attr.Rd
index f38529fddba..8dac8f8fff9 100644
--- a/man/set_edge_attr.Rd
+++ b/man/set_edge_attr.Rd
@@ -16,7 +16,8 @@ set_edge_attr(graph, name, index = E(graph), value)
 a subset of edges.}
 
 \item{value}{The new value of the attribute for all (or \code{index})
-edges.}
+edges.
+If \code{NULL}, the input is returned unchanged.}
 }
 \value{
 The graph, with the edge attribute added or set.
diff --git a/man/set_vertex_attr.Rd b/man/set_vertex_attr.Rd
index 617b83af9af..38ba253b9ec 100644
--- a/man/set_vertex_attr.Rd
+++ b/man/set_vertex_attr.Rd
@@ -16,7 +16,8 @@ set_vertex_attr(graph, name, index = V(graph), value)
 of a subset of vertices.}
 
 \item{value}{The new value of the attribute for all (or \code{index})
-vertices.}
+vertices.
+If \code{NULL}, the input is returned unchanged.}
 }
 \value{
 The graph, with the vertex attribute added or set.
diff --git a/tests/testthat/test-attributes.R b/tests/testthat/test-attributes.R
index e9bf3a609d7..761a1a6ab74 100644
--- a/tests/testthat/test-attributes.R
+++ b/tests/testthat/test-attributes.R
@@ -245,3 +245,12 @@ test_that("setting attributes strips names (#466)", {
   E(g)$bar <- c(a = 1)
   expect_identical(E(g)$bar, rep(1, 10))
 })
+
+test_that("setting NULL attributes works and doesn't change the input (#466)", {
+  g <- make_ring(10)
+
+  expect_identical(set_vertex_attr(g, "foo", value = NULL), g)
+  expect_identical(set_vertex_attr(g, "foo", 1:3, value = NULL), g)
+  expect_identical(set_edge_attr(g, "foo", value = NULL), g)
+  expect_identical(set_edge_attr(g, "foo", 1:3, value = NULL), g)
+})

From 88bf85df4f7cca7b826776d8e531fad71a312478 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sat, 21 Jan 2023 17:53:29 +0100
Subject: [PATCH 22/26] Update results

---
 revdep/README.md   |  13 +-
 revdep/cran.md     |  21 +---
 revdep/problems.md | 300 ++++-----------------------------------------
 3 files changed, 32 insertions(+), 302 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index ebf149e15f4..8db806b5609 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,23 +1,18 @@
 # Revdeps
 
-## New problems (16)
+## New problems (11)
 
-|package        |version |error  |warning |note |
-|:--------------|:-------|:------|:-------|:----|
+|package      |version |error  |warning |note |
+|:------------|:-------|:------|:-------|:----|
 |[backbone](problems.md#backbone)|2.1.1   |__+1__ |        |     |
-|[clustAnalytics](problems.md#clustanalytics)|0.5.2   |       |__+1__  |1    |
 |[deepdep](problems.md#deepdep)|0.4.1   |__+1__ |        |     |
-|[Diderot](problems.md#diderot)|0.13    |__+1__ |        |     |
 |[egor](problems.md#egor)|1.22.12 |__+1__ |        |     |
-|[gemtc](problems.md#gemtc)|1.0-1   |__+2__ |        |     |
 |[GREMLINS](problems.md#gremlins)|0.2.0   |__+1__ |__+1__  |1    |
 |[incidentally](problems.md#incidentally)|1.0.1   |       |__+1__  |     |
-|[metanetwork](problems.md#metanetwork)|0.7.0   |__+1__ |        |     |
 |[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
-|[nat](problems.md#nat)|1.8.19  |__+2__ |        |     |
+|[nat](problems.md#nat)|1.8.19  |__+1__ |1       |     |
 |[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
 |[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
-|[riverconn](problems.md#riverconn)|0.3.22  |__+1__ |        |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
 |[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index 7565c7222ac..98d8aa4bd0f 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,8 +1,8 @@
 ## revdepcheck results
 
-We checked 19 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 16 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 16 new problems
+ * We saw 11 new problems
  * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
@@ -13,22 +13,12 @@ Issues with CRAN packages are summarised below.
 * backbone
   checking tests ... ERROR
 
-* clustAnalytics
-  checking re-building of vignette outputs ... WARNING
-
 * deepdep
   checking tests ... ERROR
 
-* Diderot
-  checking examples ... ERROR
-
 * egor
   checking tests ... ERROR
 
-* gemtc
-  checking examples ... ERROR
-  checking tests ... ERROR
-
 * GREMLINS
   checking examples ... ERROR
   checking re-building of vignette outputs ... WARNING
@@ -36,14 +26,10 @@ Issues with CRAN packages are summarised below.
 * incidentally
   checking re-building of vignette outputs ... WARNING
 
-* metanetwork
-  checking tests ... ERROR
-
 * mstknnclust
   checking re-building of vignette outputs ... WARNING
 
 * nat
-  checking examples ... ERROR
   checking tests ... ERROR
 
 * netmeta
@@ -52,9 +38,6 @@ Issues with CRAN packages are summarised below.
 * poppr
   checking tests ... ERROR
 
-* riverconn
-  checking examples ... ERROR
-
 * sfnetworks
   checking tests ... ERROR
 
diff --git a/revdep/problems.md b/revdep/problems.md
index a11e2fe10e9..e64e25b7cd9 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -36,56 +36,6 @@ Run `revdepcheck::cloud_details(, "backbone")` for more info
       Execution halted
     ```
 
-# clustAnalytics
-
-<details>
-
-* Version: 0.5.2
-* GitHub: NA
-* Source code: https://github.com/cran/clustAnalytics
-* Date/Publication: 2022-11-09 11:50:09 UTC
-* Number of recursive dependencies: 69
-
-Run `revdepcheck::cloud_details(, "clustAnalytics")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘cluster_stability.Rmd’ using rmarkdown
-    --- finished re-building ‘cluster_stability.Rmd’
-    
-    --- re-building ‘graph_rewiring_functions.Rmd’ using rmarkdown
-    --- finished re-building ‘graph_rewiring_functions.Rmd’
-    
-    --- re-building ‘other_functions.Rmd’ using rmarkdown
-    --- finished re-building ‘other_functions.Rmd’
-    ...
-    Quitting from lines 109-111 (stability_significance_examples.Rmd) 
-    Error: processing vignette 'stability_significance_examples.Rmd' failed with diagnostics:
-    strict recycling (1)
-    --- failed re-building ‘stability_significance_examples.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘stability_significance_examples.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.6Mb
-      sub-directories of 1Mb or more:
-        libs   6.1Mb
-    ```
-
 # deepdep
 
 <details>
@@ -125,47 +75,6 @@ Run `revdepcheck::cloud_details(, "deepdep")` for more info
       Execution halted
     ```
 
-# Diderot
-
-<details>
-
-* Version: 0.13
-* GitHub: NA
-* Source code: https://github.com/cran/Diderot
-* Date/Publication: 2020-04-19 11:20:02 UTC
-* Number of recursive dependencies: 15
-
-Run `revdepcheck::cloud_details(, "Diderot")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘Diderot-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: build_graph
-    > ### Title: Builds a citation graph.
-    > ### Aliases: build_graph 'Citation Graph Building'
-    > 
-    > ### ** Examples
-    > 
-    > ## Don't show: 
-    ...
-    > unlink(c(tempfi1, tempfi2))
-    > ## End(Don't show)
-    > 
-    > # Build graph
-    > gr<-build_graph(db=db,small.year.mismatch=TRUE, attrs=c("Corpus","Year","Authors"), nb.cores=1)
-    starting worker pid=11556 on localhost:11592 at 20:54:39.535
-    Error in i_set_vertex_attr(graph = graph, name = name, value = value,  : 
-      strict recycling (1)
-    Calls: build_graph -> set.vertex.attribute -> i_set_vertex_attr
-    Execution halted
-    ```
-
 # egor
 
 <details>
@@ -204,69 +113,6 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       Execution halted
     ```
 
-# gemtc
-
-<details>
-
-* Version: 1.0-1
-* GitHub: https://github.com/gertvv/gemtc
-* Source code: https://github.com/cran/gemtc
-* Date/Publication: 2021-05-14 23:20:02 UTC
-* Number of recursive dependencies: 56
-
-Run `revdepcheck::cloud_details(, "gemtc")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘gemtc-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: atrialFibrillation
-    > ### Title: Prevention of stroke in atrial fibrillation patients
-    > ### Aliases: atrialFibrillation
-    > 
-    > ### ** Examples
-    > 
-    > # Build a model similar to Model 4(b) from Cooper et al. (2009):
-    ...
-    +                   classes=classes)
-    > 
-    > model <- mtc.model(atrialFibrillation,
-    +                    type="regression",
-    +                    regressor=regressor,
-    +                    om.scale=10)
-    Error in i_set_edge_attr(graph = graph, name = name, index = index, value = value) : 
-      strict recycling (2)
-    Calls: mtc.model ... add_edges -> edge_attr<- -> set_edge_attr -> i_set_edge_attr
-    Execution halted
-    ```
-
-*   checking tests ... ERROR
-    ```
-      Running ‘test.R’
-    Running the tests in ‘tests/test.R’ failed.
-    Last 13 lines of output:
-           ▆
-        1. └─gemtc::relative.effect.table(smoking_result) at test-unit-relative.effect.table.R:5:2
-        2.   ├─base::as.matrix(...)
-        3.   └─gemtc::relative.effect(...)
-        4.     └─gemtc:::spanning.tree.mtc.result(result)
-        5.       └─gemtc:::graph.create(...)
-        6.         └─igraph:::`+.igraph`(g, edges.create(e, ...))
-        7.           └─igraph::add_edges(e1, as.igraph.vs(e1, toadd), attr = attr)
-        8.             └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
-        9.               └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
-       10.                 └─igraph:::i_set_edge_attr(...)
-      
-      [ FAIL 35 | WARN 0 | SKIP 0 | PASS 269 ]
-      Error: Test failures
-      Execution halted
-    ```
-
 # GREMLINS
 
 <details>
@@ -380,44 +226,6 @@ Run `revdepcheck::cloud_details(, "incidentally")` for more info
     Execution halted
     ```
 
-# metanetwork
-
-<details>
-
-* Version: 0.7.0
-* GitHub: https://github.com/MarcOhlmann/metanetwork
-* Source code: https://github.com/cran/metanetwork
-* Date/Publication: 2022-12-05 14:10:02 UTC
-* Number of recursive dependencies: 105
-
-Run `revdepcheck::cloud_details(, "metanetwork")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking tests ... ERROR
-    ```
-      Running ‘testthat.R’
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-      Epoch: Iteration #300 error is: 199.576452337934
-      x_max = 1356.85756899361
-      y_max = 351.624293301058
-      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
-      
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-      ── Failure ('test-compute_TL.R:25'): Computation of trophic levels of norway dataset ──
-      V(meta0$metaweb)$TL (`actual`) not equal to V(meta_angola$metaweb)$TL (`expected`).
-      
-      `names(actual)` is a character vector ('Trachurus', 'Sardinella', 'Sciaenidae', 'Ariidae', 'Merluccius', ...)
-      `names(expected)` is absent
-      
-      [ FAIL 1 | WARN 22 | SKIP 0 | PASS 73 ]
-      Error: Test failures
-      Execution halted
-    ```
-
 # mstknnclust
 
 <details>
@@ -467,47 +275,40 @@ Run `revdepcheck::cloud_details(, "nat")` for more info
 
 ## Newly broken
 
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘nat-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: prune_strahler
-    > ### Title: Prune a neuron by removing segments with a given Strahler order
-    > ### Aliases: prune_strahler
-    > 
-    > ### ** Examples
-    > 
-    > x=Cell07PNs[[1]]
-    > pruned12=prune_strahler(x)
-    Error in value[[3L]](cond) : 
-      No points left after pruning. Consider lowering orders to prune!
-    Calls: prune_strahler ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
-    Execution halted
-    ```
-
 *   checking tests ... ERROR
     ```
       Running ‘test-all.R’
     Running the tests in ‘tests/test-all.R’ failed.
     Last 13 lines of output:
-      Backtrace:
-          ▆
-       1. ├─testthat::expect_equal(...) at test-ngraph.R:193:2
-       2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
-       3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
-       4. └─nat::strahler_order(n)
-       5.   └─nat::segmentgraph(x, weights = F)
-       6.     └─igraph::add.edges(g, elred, segid = segids)
-       7.       └─igraph::`edge_attr<-`(`*tmp*`, nam[[i]], idx, value = attrs[[nam[i]]])
-       8.         └─igraph::set_edge_attr(graph, name = name, index = index, value = value)
-       9.           └─igraph:::i_set_edge_attr(...)
+           ▆
+        1. ├─testthat::expect_warning(...) at test-ngraph.R:147:2
+        2. │ └─testthat:::quasi_capture(...)
+        3. │   ├─testthat (local) .capture(...)
+        4. │   │ └─base::withCallingHandlers(...)
+        5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+        6. ├─nat::as.ngraph(testd, graph.attributes = gatts, vertex.attributes = list(X = testd$X[-1]))
+        7. └─nat:::as.ngraph.data.frame(testd, graph.attributes = gatts, vertex.attributes = list(X = testd$X[-1]))
+        8.   └─nat::ngraph(...)
+        9.     └─igraph::set.vertex.attribute(g, name = n, value = vertex.attributes[[n]])
+       10.       └─igraph:::i_set_vertex_attr(...)
       
-      [ FAIL 5 | WARN 414 | SKIP 5 | PASS 774 ]
+      [ FAIL 1 | WARN 420 | SKIP 5 | PASS 787 ]
       Error: Test failures
       Execution halted
     ```
 
+## In both
+
+*   checking examples ... WARNING
+    ```
+    Found the following significant warnings:
+    
+      Warning: 'rgl.close' is deprecated.
+    Deprecated functions may be defunct as soon as of the next release of
+    R.
+    See ?Deprecated.
+    ```
+
 # netmeta
 
 <details>
@@ -545,7 +346,7 @@ Run `revdepcheck::cloud_details(, "netmeta")` for more info
     > 
     > net1 <- netmeta(p1)
     > cm <- netcontrib(net1)
-    Error: C stack usage  9962452 is too close to the limit
+    Error: C stack usage  9965300 is too close to the limit
     Execution halted
     ```
 
@@ -578,7 +379,7 @@ Run `revdepcheck::cloud_details(, "poppr")` for more info
     Running the tests in ‘tests/test-all.R’ failed.
     Last 13 lines of output:
       Attributes: < Modes: list, NULL >
-      Attributes: < Lengths: 3, 0 >
+      Attributes: < Lengths: 2, 0 >
       Attributes: < names for target but not for current >
       Attributes: < current is not list-like >
       target is table, current is numeric
@@ -626,55 +427,6 @@ Run `revdepcheck::cloud_details(, "poppr")` for more info
     Package suggested but not available for checking: ‘RClone’
     ```
 
-# riverconn
-
-<details>
-
-* Version: 0.3.22
-* GitHub: NA
-* Source code: https://github.com/cran/riverconn
-* Date/Publication: 2022-08-06 14:00:07 UTC
-* Number of recursive dependencies: 98
-
-Run `revdepcheck::cloud_details(, "riverconn")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘riverconn-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: d_index_calculation
-    > ### Title: Calculate Reach- and Catchment-scale index improvement for
-    > ###   scenarios of barriers removal
-    > ### Aliases: d_index_calculation
-    > 
-    > ### ** Examples
-    > 
-    ...
-        union
-    
-    > library(igraph)
-    > g <- igraph::graph_from_literal(1-+2, 2-+4, 3-+2, 4-+6, 6-+7, 5-+6, 7-+8, 9-+5, 10-+5 )
-    > E(g)$id_dam <- c(NA, NA, "1", NA, NA, "2", NA, NA, NA)
-    > E(g)$type <- ifelse(is.na(E(g)$id_barrier), "joint", "dam")
-    Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-      strict recycling (2)
-    Calls: E<- -> i_set_edge_attr
-    Execution halted
-    ```
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘markdown’
-      All declared Imports should be used.
-    ```
-
 # sfnetworks
 
 <details>

From f31cc2128d41a1262b0afdafd0f97049c1f0c6d0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Sun, 22 Jan 2023 08:38:05 +0100
Subject: [PATCH 23/26] One new problem

---
 revdep/README.md   |  17 +-
 revdep/cran.md     |  19 +-
 revdep/failures.md | 594 ++++++++++++++++++++++++++++++++++++++++++++-
 revdep/problems.md |  43 +++-
 4 files changed, 667 insertions(+), 6 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 8db806b5609..ab9fbc32e0c 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,6 +1,20 @@
 # Revdeps
 
-## New problems (11)
+## Failed to check (9)
+
+|package   |version |error |warning |note |
+|:---------|:-------|:-----|:-------|:----|
+|DRviaSPCN |?       |      |        |     |
+|genekitr  |?       |      |        |     |
+|immcp     |?       |      |        |     |
+|numbat    |?       |      |        |     |
+|Platypus  |?       |      |        |     |
+|NA        |?       |      |        |     |
+|tidySEM   |?       |      |        |     |
+|vivid     |?       |      |        |     |
+|webSDM    |?       |      |        |     |
+
+## New problems (12)
 
 |package      |version |error  |warning |note |
 |:------------|:-------|:------|:-------|:----|
@@ -12,6 +26,7 @@
 |[mstknnclust](problems.md#mstknnclust)|0.3.1   |       |__+1__  |     |
 |[nat](problems.md#nat)|1.8.19  |__+1__ |1       |     |
 |[netmeta](problems.md#netmeta)|2.7-0   |__+1__ |        |1    |
+|[NetOrigin](problems.md#netorigin)|1.1-4   |__+1__ |        |     |
 |[poppr](problems.md#poppr)|2.9.3   |__+1__ |1       |1    |
 |[sfnetworks](problems.md#sfnetworks)|0.6.1   |__+1__ |        |     |
 |[signnet](problems.md#signnet)|1.0.0   |__+1__ |        |1    |
diff --git a/revdep/cran.md b/revdep/cran.md
index 98d8aa4bd0f..4c1c7a21ef7 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,9 +1,9 @@
 ## revdepcheck results
 
-We checked 16 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 759 reverse dependencies (758 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 11 new problems
- * We failed to check 0 packages
+ * We saw 12 new problems
+ * We failed to check 8 packages
 
 Issues with CRAN packages are summarised below.
 
@@ -35,6 +35,9 @@ Issues with CRAN packages are summarised below.
 * netmeta
   checking examples ... ERROR
 
+* NetOrigin
+  checking examples ... ERROR
+
 * poppr
   checking tests ... ERROR
 
@@ -44,3 +47,13 @@ Issues with CRAN packages are summarised below.
 * signnet
   checking examples ... ERROR
 
+### Failed to check
+
+* DRviaSPCN (NA)
+* genekitr  (NA)
+* immcp     (NA)
+* numbat    (NA)
+* Platypus  (NA)
+* tidySEM   (NA)
+* vivid     (NA)
+* webSDM    (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 9a207363396..f4c5236f2cb 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1 +1,593 @@
-*Wow, no problems at all. :)*
\ No newline at end of file
+# DRviaSPCN
+
+<details>
+
+* Version: 0.1.2
+* GitHub: NA
+* Source code: https://github.com/cran/DRviaSPCN
+* Date/Publication: 2022-03-03 16:00:02 UTC
+* Number of recursive dependencies: 169
+
+Run `revdepcheck::cloud_details(, "DRviaSPCN")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/DRviaSPCN/new/DRviaSPCN.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘DRviaSPCN’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/DRviaSPCN/old/DRviaSPCN.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘DRviaSPCN’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# genekitr
+
+<details>
+
+* Version: 1.1.0
+* GitHub: https://github.com/GangLiLab/genekitr
+* Source code: https://github.com/cran/genekitr
+* Date/Publication: 2023-01-20 03:30:02 UTC
+* Number of recursive dependencies: 200
+
+Run `revdepcheck::cloud_details(, "genekitr")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘genekitr/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘genekitr’ version ‘1.1.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘genekitr/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘genekitr’ version ‘1.1.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# immcp
+
+<details>
+
+* Version: 1.0.3
+* GitHub: https://github.com/YuanlongHu/immcp
+* Source code: https://github.com/cran/immcp
+* Date/Publication: 2022-05-12 05:50:02 UTC
+* Number of recursive dependencies: 194
+
+Run `revdepcheck::cloud_details(, "immcp")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘immcp/DESCRIPTION’ ... OK
+* this is package ‘immcp’ version ‘1.0.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘immcp/DESCRIPTION’ ... OK
+* this is package ‘immcp’ version ‘1.0.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘clusterProfiler’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# numbat
+
+<details>
+
+* Version: 1.2.1
+* GitHub: https://github.com/kharchenkolab/numbat
+* Source code: https://github.com/cran/numbat
+* Date/Publication: 2023-01-11 00:20:02 UTC
+* Number of recursive dependencies: 132
+
+Run `revdepcheck::cloud_details(, "numbat")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘numbat/DESCRIPTION’ ... OK
+* this is package ‘numbat’ version ‘1.2.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Packages required but not available: 'ggtree', 'scistreer'
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘numbat/DESCRIPTION’ ... OK
+* this is package ‘numbat’ version ‘1.2.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Packages required but not available: 'ggtree', 'scistreer'
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# Platypus
+
+<details>
+
+* Version: 3.4.1
+* GitHub: NA
+* Source code: https://github.com/cran/Platypus
+* Date/Publication: 2022-08-15 07:20:20 UTC
+* Number of recursive dependencies: 356
+
+Run `revdepcheck::cloud_details(, "Platypus")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/Platypus/new/Platypus.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Platypus/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘Platypus’ version ‘3.4.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+...
+* checking package dependencies ... ERROR
+Package required but not available: ‘ggtree’
+
+Packages suggested but not available for checking:
+  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/Platypus/old/Platypus.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Platypus/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘Platypus’ version ‘3.4.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+...
+* checking package dependencies ... ERROR
+Package required but not available: ‘ggtree’
+
+Packages suggested but not available for checking:
+  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# NA
+
+<details>
+
+* Version: NA
+* GitHub: NA
+* Source code: https://github.com/cran/NA
+* Number of recursive dependencies: 0
+
+Run `revdepcheck::cloud_details(, "NA")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
+```
+# tidySEM
+
+<details>
+
+* Version: 0.2.3
+* GitHub: https://github.com/cjvanlissa/tidySEM
+* Source code: https://github.com/cran/tidySEM
+* Date/Publication: 2022-04-14 17:50:02 UTC
+* Number of recursive dependencies: 170
+
+Run `revdepcheck::cloud_details(, "tidySEM")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘tidySEM/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘tidySEM’ version ‘0.2.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘blavaan’
+
+Package suggested but not available for checking: ‘umx’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘tidySEM/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘tidySEM’ version ‘0.2.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘blavaan’
+
+Package suggested but not available for checking: ‘umx’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# vivid
+
+<details>
+
+* Version: 0.2.3
+* GitHub: NA
+* Source code: https://github.com/cran/vivid
+* Date/Publication: 2021-11-20 01:30:02 UTC
+* Number of recursive dependencies: 206
+
+Run `revdepcheck::cloud_details(, "vivid")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘vivid/DESCRIPTION’ ... OK
+* this is package ‘vivid’ version ‘0.2.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+...
+* checking tests ... OK
+  Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+  ‘vivid.Rmd’ using ‘UTF-8’... OK
+  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘vivid/DESCRIPTION’ ... OK
+* this is package ‘vivid’ version ‘0.2.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+...
+* checking tests ... OK
+  Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+  ‘vivid.Rmd’ using ‘UTF-8’... OK
+  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+# webSDM
+
+<details>
+
+* Version: 1.1-1
+* GitHub: https://github.com/giopogg/webSDM
+* Source code: https://github.com/cran/webSDM
+* Date/Publication: 2022-11-25 12:40:02 UTC
+* Number of recursive dependencies: 189
+
+Run `revdepcheck::cloud_details(, "webSDM")` for more info
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/webSDM/new/webSDM.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘webSDM/DESCRIPTION’ ... OK
+* this is package ‘webSDM’ version ‘1.1-1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘rstanarm’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/webSDM/old/webSDM.Rcheck’
+* using R version 4.1.1 (2021-08-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘webSDM/DESCRIPTION’ ... OK
+* this is package ‘webSDM’ version ‘1.1-1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘rstanarm’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
diff --git a/revdep/problems.md b/revdep/problems.md
index e64e25b7cd9..d8542b472dd 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -346,7 +346,7 @@ Run `revdepcheck::cloud_details(, "netmeta")` for more info
     > 
     > net1 <- netmeta(p1)
     > cm <- netcontrib(net1)
-    Error: C stack usage  9965300 is too close to the limit
+    Error: C stack usage  9966612 is too close to the limit
     Execution halted
     ```
 
@@ -357,6 +357,47 @@ Run `revdepcheck::cloud_details(, "netmeta")` for more info
       Note: found 2 marked UTF-8 strings
     ```
 
+# NetOrigin
+
+<details>
+
+* Version: 1.1-4
+* GitHub: https://github.com/jmanitz/NetOrigin
+* Source code: https://github.com/cran/NetOrigin
+* Date/Publication: 2022-01-20 08:32:42 UTC
+* Number of recursive dependencies: 77
+
+Run `revdepcheck::cloud_details(, "NetOrigin")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘NetOrigin-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: origin
+    > ### Title: Origin Estimation for Propagation Processes on Complex Networks
+    > ### Aliases: origin origin_edm origin_backtracking origin_centrality
+    > ###   origin_bayesian
+    > 
+    > ### ** Examples
+    > 
+    ...
+    > performance(om, start=1, graph=ptnGoe)
+                      start                         est  hitt rank spj dist
+    1 X.Adolf.Hoyer.Strasse X.Gotthelf.Leimbach.Strasse FALSE    2   2 1332
+    > 
+    > # backtracking origin estimation (Manitz et al., 2016)
+    > ob <- origin(events=delayGoe[10,-c(1:2)], type='backtracking', graph=ptnGoe)
+    Error in if (V(graph)[current_node]$events > 0 | !start_with_event_node) { : 
+      argument is of length zero
+    Calls: origin -> origin_backtracking
+    Execution halted
+    ```
+
 # poppr
 
 <details>

From 882eeaa85f2ec1b1bba796ebaa96ef4804ac2362 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Tue, 24 Jan 2023 10:05:38 +0100
Subject: [PATCH 24/26] Finalize behavior, tweak error messages

---
 R/attributes.R | 46 ++++++++++++++++++++++------------------------
 1 file changed, 22 insertions(+), 24 deletions(-)

diff --git a/R/attributes.R b/R/attributes.R
index 1728445c5f6..1c0c7f7722e 100644
--- a/R/attributes.R
+++ b/R/attributes.R
@@ -35,8 +35,6 @@
 
 
 
-ATTRIBUTE_STRICT_RECYCLING <- TRUE
-
 #' Graph attributes of a graph
 #'
 #' @param graph Input graph.
@@ -272,18 +270,18 @@ i_set_vertex_attr <- function(graph, name, index = V(graph), value, check = TRUE
   if (single) {
     vattrs[[name]][[index]] <- value
   } else {
-    if (ATTRIBUTE_STRICT_RECYCLING) {
-      if (length(value) == 1) {
-        value_in <- rep(unname(value), length(index))
-      } else if (length(value) == length(index)) {
-        value_in <- unname(value)
-      } else {
-        stop("strict recycling (1)")
-      }
+    if (length(value) == 1) {
+      value_in <- rep(unname(value), length(index))
+    } else if (length(value) == length(index)) {
+      value_in <- unname(value)
     } else {
-      value_in <- unname(rep(value, length.out = length(index)))
-      # Trigger recycling warning
-      value_in[seq_along(value_in)] <- value
+      stop(
+        "Length of new attribute value must be ",
+        if (length(index) != 1) "1 or ",
+        length(index),
+        ", the number of target vertices, not ",
+        length(value)
+      )
     }
 
     if (complete) {
@@ -482,18 +480,18 @@ i_set_edge_attr <- function(graph, name, index = E(graph), value, check = TRUE)
   if (single) {
     eattrs[[name]][[index]] <- value
   } else {
-    if (ATTRIBUTE_STRICT_RECYCLING) {
-      if (length(value) == 1) {
-        value_in <- rep(unname(value), length(index))
-      } else if (length(value) == length(index)) {
-        value_in <- unname(value)
-      } else {
-        stop("strict recycling (2)")
-      }
+    if (length(value) == 1) {
+      value_in <- rep(unname(value), length(index))
+    } else if (length(value) == length(index)) {
+      value_in <- unname(value)
     } else {
-      value_in <- unname(rep(value, length.out = length(index)))
-      # Trigger recycling warning
-      value_in[seq_along(value_in)] <- value
+      stop(
+        "Length of new attribute value must be ",
+        if (length(index) != 1) "1 or ",
+        length(index),
+        ", the number of target edges, not ",
+        length(value)
+      )
     }
 
     if (complete) {

From ce32250d55050aea159c9bc637f16ad944b11c64 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Thu, 26 Jan 2023 08:26:34 +0100
Subject: [PATCH 25/26] Iterators created with E(P = ...) or E(path = ...) are
 incomplete

---
 R/iterators.R                   | 2 +-
 tests/testthat/test-iterators.R | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/iterators.R b/R/iterators.R
index daa379fe6da..c5cae425fec 100644
--- a/R/iterators.R
+++ b/R/iterators.R
@@ -317,6 +317,7 @@ E <- function(graph, P = NULL, path = NULL, directed = TRUE) {
   if (is.null(P) && is.null(path)) {
     ec <- ecount(graph)
     res <- seq_len(ec)
+    res <- set_complete_iterator(res)
   } else if (!is.null(P)) {
     on.exit(.Call(C_R_igraph_finalizer))
     res <- .Call(
@@ -340,7 +341,6 @@ E <- function(graph, P = NULL, path = NULL, directed = TRUE) {
   }
 
   class(res) <- "igraph.es"
-  res <- set_complete_iterator(res)
   add_vses_graph_ref(res, graph)
 }
 
diff --git a/tests/testthat/test-iterators.R b/tests/testthat/test-iterators.R
index c39cdbd2952..b3370848aad 100644
--- a/tests/testthat/test-iterators.R
+++ b/tests/testthat/test-iterators.R
@@ -93,9 +93,11 @@ test_that("V(g) returns complete iterator, completeness is lost with next subset
 })
 
 test_that("E(g) returns complete iterator, completeness is lost with next subsetting", {
-  g <- make_star(4)
+  g <- make_full_graph(4)
   iter <- E(g)
   expect_true(is_complete_iterator(iter))
   expect_false(is_complete_iterator(iter[1]))
   expect_false(is_complete_iterator(iter[1:3]))
+  expect_false(is_complete_iterator(E(g, P = 1:4)))
+  expect_false(is_complete_iterator(E(g, path = 1:4)))
 })

From e1a8366d8cdff100d1440a3f4b7ea5cc1c3ebabb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kirill=20M=C3=BCller?= <krlmlr+r@mailbox.org>
Date: Thu, 26 Jan 2023 09:26:50 +0100
Subject: [PATCH 26/26] No substantial change

---
 revdep/README.md   |  14 --
 revdep/cran.md     |  14 +-
 revdep/failures.md | 594 +--------------------------------------------
 revdep/problems.md |  20 +-
 4 files changed, 13 insertions(+), 629 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index ab9fbc32e0c..4bd01ab14be 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,19 +1,5 @@
 # Revdeps
 
-## Failed to check (9)
-
-|package   |version |error |warning |note |
-|:---------|:-------|:-----|:-------|:----|
-|DRviaSPCN |?       |      |        |     |
-|genekitr  |?       |      |        |     |
-|immcp     |?       |      |        |     |
-|numbat    |?       |      |        |     |
-|Platypus  |?       |      |        |     |
-|NA        |?       |      |        |     |
-|tidySEM   |?       |      |        |     |
-|vivid     |?       |      |        |     |
-|webSDM    |?       |      |        |     |
-
 ## New problems (12)
 
 |package      |version |error  |warning |note |
diff --git a/revdep/cran.md b/revdep/cran.md
index 4c1c7a21ef7..793c3275f52 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,9 +1,9 @@
 ## revdepcheck results
 
-We checked 759 reverse dependencies (758 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 12 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 12 new problems
- * We failed to check 8 packages
+ * We failed to check 0 packages
 
 Issues with CRAN packages are summarised below.
 
@@ -47,13 +47,3 @@ Issues with CRAN packages are summarised below.
 * signnet
   checking examples ... ERROR
 
-### Failed to check
-
-* DRviaSPCN (NA)
-* genekitr  (NA)
-* immcp     (NA)
-* numbat    (NA)
-* Platypus  (NA)
-* tidySEM   (NA)
-* vivid     (NA)
-* webSDM    (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index f4c5236f2cb..9a207363396 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1,593 +1 @@
-# DRviaSPCN
-
-<details>
-
-* Version: 0.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/DRviaSPCN
-* Date/Publication: 2022-03-03 16:00:02 UTC
-* Number of recursive dependencies: 169
-
-Run `revdepcheck::cloud_details(, "DRviaSPCN")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/DRviaSPCN/new/DRviaSPCN.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘DRviaSPCN’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/DRviaSPCN/old/DRviaSPCN.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘DRviaSPCN/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘DRviaSPCN’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# genekitr
-
-<details>
-
-* Version: 1.1.0
-* GitHub: https://github.com/GangLiLab/genekitr
-* Source code: https://github.com/cran/genekitr
-* Date/Publication: 2023-01-20 03:30:02 UTC
-* Number of recursive dependencies: 200
-
-Run `revdepcheck::cloud_details(, "genekitr")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# immcp
-
-<details>
-
-* Version: 1.0.3
-* GitHub: https://github.com/YuanlongHu/immcp
-* Source code: https://github.com/cran/immcp
-* Date/Publication: 2022-05-12 05:50:02 UTC
-* Number of recursive dependencies: 194
-
-Run `revdepcheck::cloud_details(, "immcp")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# numbat
-
-<details>
-
-* Version: 1.2.1
-* GitHub: https://github.com/kharchenkolab/numbat
-* Source code: https://github.com/cran/numbat
-* Date/Publication: 2023-01-11 00:20:02 UTC
-* Number of recursive dependencies: 132
-
-Run `revdepcheck::cloud_details(, "numbat")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.2.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.2.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# Platypus
-
-<details>
-
-* Version: 3.4.1
-* GitHub: NA
-* Source code: https://github.com/cran/Platypus
-* Date/Publication: 2022-08-15 07:20:20 UTC
-* Number of recursive dependencies: 356
-
-Run `revdepcheck::cloud_details(, "Platypus")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/Platypus/new/Platypus.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘Platypus/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘Platypus’ version ‘3.4.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking package dependencies ... ERROR
-Package required but not available: ‘ggtree’
-
-Packages suggested but not available for checking:
-  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/Platypus/old/Platypus.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘Platypus/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘Platypus’ version ‘3.4.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking package dependencies ... ERROR
-Package required but not available: ‘ggtree’
-
-Packages suggested but not available for checking:
-  'Matrix.utils', 'monocle3', 'ProjecTILs', 'SeuratWrappers'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-<details>
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `revdepcheck::cloud_details(, "NA")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# tidySEM
-
-<details>
-
-* Version: 0.2.3
-* GitHub: https://github.com/cjvanlissa/tidySEM
-* Source code: https://github.com/cran/tidySEM
-* Date/Publication: 2022-04-14 17:50:02 UTC
-* Number of recursive dependencies: 170
-
-Run `revdepcheck::cloud_details(, "tidySEM")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘blavaan’
-
-Package suggested but not available for checking: ‘umx’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘blavaan’
-
-Package suggested but not available for checking: ‘umx’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# vivid
-
-<details>
-
-* Version: 0.2.3
-* GitHub: NA
-* Source code: https://github.com/cran/vivid
-* Date/Publication: 2021-11-20 01:30:02 UTC
-* Number of recursive dependencies: 206
-
-Run `revdepcheck::cloud_details(, "vivid")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking tests ... OK
-  Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘vivid.Rmd’ using ‘UTF-8’... OK
-  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking tests ... OK
-  Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
-  ‘vivid.Rmd’ using ‘UTF-8’... OK
-  ‘vividQStart.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-# webSDM
-
-<details>
-
-* Version: 1.1-1
-* GitHub: https://github.com/giopogg/webSDM
-* Source code: https://github.com/cran/webSDM
-* Date/Publication: 2022-11-25 12:40:02 UTC
-* Number of recursive dependencies: 189
-
-Run `revdepcheck::cloud_details(, "webSDM")` for more info
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/webSDM/new/webSDM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘webSDM/DESCRIPTION’ ... OK
-* this is package ‘webSDM’ version ‘1.1-1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘rstanarm’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/webSDM/old/webSDM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘webSDM/DESCRIPTION’ ... OK
-* this is package ‘webSDM’ version ‘1.1-1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘rstanarm’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
+*Wow, no problems at all. :)*
\ No newline at end of file
diff --git a/revdep/problems.md b/revdep/problems.md
index d8542b472dd..158821a8ccd 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -31,7 +31,7 @@ Run `revdepcheck::cloud_details(, "backbone")` for more info
       test_backbone.R...............   35 tests OK 
       test_backbone.R...............   36 tests OK 
       test_backbone.R...............   36 tests OK Error in i_set_vertex_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-        strict recycling (1)
+        Length of new attribute value must be 1 or 110, the number of target vertices, not 10
       Calls: <Anonymous> ... FUN -> eval -> eval -> <Anonymous> -> i_set_vertex_attr
       Execution halted
     ```
@@ -96,7 +96,7 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       Running ‘testthat.R’
     Running the tests in ‘tests/testthat.R’ failed.
     Last 13 lines of output:
-      Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Filtering out empty alter entries using provided network size values: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: [ FAIL 1 | WARN 4 | SKIP 15 | PASS 205 ]
+      Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: Filtering out empty alter entries using provided network size values: Sorting data by egoID: Transforming alters data to long format: Transforming wide dyad data to edgelist: [ FAIL 1 | WARN 7 | SKIP 15 | PASS 205 ]
       
       ══ Skipped tests ═══════════════════════════════════════════════════════════════
       • On CRAN (15)
@@ -108,7 +108,7 @@ Run `revdepcheck::cloud_details(, "egor")` for more info
       `actual` is a double vector ()
       `expected` is NULL
       
-      [ FAIL 1 | WARN 4 | SKIP 15 | PASS 205 ]
+      [ FAIL 1 | WARN 7 | SKIP 15 | PASS 205 ]
       Error: Test failures
       Execution halted
     ```
@@ -149,7 +149,7 @@ Run `revdepcheck::cloud_details(, "GREMLINS")` for more info
     [1] "Best model------ ICL : -2028.78 . Nb of clusters: [ 2 2 ] for [ A , B ] respectively"
     > plotMBM(res_MBMsimu)
     Error in i_set_edge_attr(graph = graph, name = name, value = value, check = FALSE) : 
-      strict recycling (2)
+      Length of new attribute value must be 1 or 0, the number of target edges, not 8
     Calls: plotMBM -> %>% -> set_edge_attr -> i_set_edge_attr
     Execution halted
     ```
@@ -161,7 +161,7 @@ Run `revdepcheck::cloud_details(, "GREMLINS")` for more info
     --- re-building ‘EcologicalNetwork.Rmd’ using rmarkdown
     Quitting from lines 130-131 (EcologicalNetwork.Rmd) 
     Error: processing vignette 'EcologicalNetwork.Rmd' failed with diagnostics:
-    strict recycling (2)
+    Length of new attribute value must be 1 or 0, the number of target edges, not 14
     --- failed re-building ‘EcologicalNetwork.Rmd’
     
     --- re-building ‘Introduction.Rmd’ using rmarkdown
@@ -249,7 +249,7 @@ Run `revdepcheck::cloud_details(, "mstknnclust")` for more info
     --- re-building ‘guide.Rmd’ using rmarkdown
     Quitting from lines 103-110 (guide.Rmd) 
     Error: processing vignette 'guide.Rmd' failed with diagnostics:
-    strict recycling (1)
+    Length of new attribute value must be 1 or 84, the number of target vertices, not 2
     --- failed re-building ‘guide.Rmd’
     
     SUMMARY: processing the following file failed:
@@ -267,7 +267,7 @@ Run `revdepcheck::cloud_details(, "mstknnclust")` for more info
 * GitHub: https://github.com/natverse/nat
 * Source code: https://github.com/cran/nat
 * Date/Publication: 2022-04-06 11:50:02 UTC
-* Number of recursive dependencies: 86
+* Number of recursive dependencies: 87
 
 Run `revdepcheck::cloud_details(, "nat")` for more info
 
@@ -346,7 +346,7 @@ Run `revdepcheck::cloud_details(, "netmeta")` for more info
     > 
     > net1 <- netmeta(p1)
     > cm <- netcontrib(net1)
-    Error: C stack usage  9966612 is too close to the limit
+    Error: C stack usage  9968708 is too close to the limit
     Execution halted
     ```
 
@@ -542,7 +542,7 @@ Run `revdepcheck::cloud_details(, "signnet")` for more info
     > g <- graph.full(4, directed = TRUE)
     > E(g)$sign <- c(-1, 1, 1, -1, -1, 1)
     Error in i_set_edge_attr(x, attr(value, "name"), index = value, value = attr(value,  : 
-      strict recycling (2)
+      Length of new attribute value must be 1 or 12, the number of target edges, not 6
     Calls: E<- -> i_set_edge_attr
     Execution halted
     ```
@@ -553,6 +553,6 @@ Run `revdepcheck::cloud_details(, "signnet")` for more info
     ```
       installed size is  7.8Mb
       sub-directories of 1Mb or more:
-        libs   6.2Mb
+        libs   6.1Mb
     ```