chore: Update vendored sources to igraph/igraph@03760a0 (#1470)

igraph · Sep 18, 2024 · c07844d · c07844d
2 parents 2faceb4 + d4b6899
commit c07844d
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diff --git a/R/aaa-auto.R b/R/aaa-auto.R
@@ -644,35 +644,6 @@ are_adjacent_impl <- function(graph, v1, v2) {
   res
 }
 
-distances_impl <- function(graph, from=V(graph), to=V(graph), mode=c("out", "in", "all", "total")) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances, graph, from-1, to-1, mode)
-
-  res
-}
-
-distances_cutoff_impl <- function(graph, from=V(graph), to=V(graph), mode=c("out", "in", "all", "total"), cutoff=-1) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-  cutoff <- as.numeric(cutoff)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_cutoff, graph, from-1, to-1, mode, cutoff)
-
-  res
-}
-
 get_shortest_path_impl <- function(graph, from, to, mode=c("out", "in", "all", "total")) {
   # Argument checks
   ensure_igraph(graph)
@@ -764,116 +735,6 @@ get_shortest_path_dijkstra_impl <- function(graph, from, to, weights=NULL, mode=
   res
 }
 
-distances_dijkstra_impl <- function(graph, from=V(graph), to=V(graph), weights, mode=c("out", "in", "all", "total")) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_dijkstra, graph, from-1, to-1, weights, mode)
-
-  res
-}
-
-distances_dijkstra_cutoff_impl <- function(graph, from=V(graph), to=V(graph), weights, mode=c("out", "in", "all", "total"), cutoff=-1) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-  cutoff <- as.numeric(cutoff)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_dijkstra_cutoff, graph, from-1, to-1, weights, mode, cutoff)
-
-  res
-}
-
-distances_bellman_ford_impl <- function(graph, from=V(graph), to=V(graph), weights, mode=c("out", "in", "all", "total")) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_bellman_ford, graph, from-1, to-1, weights, mode)
-
-  res
-}
-
-distances_johnson_impl <- function(graph, from=V(graph), to=V(graph), weights) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_johnson, graph, from-1, to-1, weights)
-
-  res
-}
-
-distances_floyd_warshall_impl <- function(graph, from=V(graph), to=V(graph), weights=NULL, mode=c("out", "in", "all", "total"), method) {
-  # Argument checks
-  ensure_igraph(graph)
-  from <- as_igraph_vs(graph, from)
-  to <- as_igraph_vs(graph, to)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_distances_floyd_warshall, graph, from-1, to-1, weights, mode, method)
-
-  res
-}
-
 voronoi_impl <- function(graph, generators, ..., weights=NULL, mode=c("out", "in", "all", "total"), tiebreaker=c("random", "first", "last")) {
   # Argument checks
   check_dots_empty()
@@ -3650,6 +3511,23 @@ solve_lsap_impl <- function(c, n) {
   res
 }
 
+find_cycle_impl <- function(graph, mode) {
+  # Argument checks
+  ensure_igraph(graph)
+  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_find_cycle, graph, mode)
+  if (igraph_opt("return.vs.es")) {
+    res$vertices <- create_vs(graph, res$vertices)
+  }
+  if (igraph_opt("return.vs.es")) {
+    res$edges <- create_es(graph, res$edges)
+  }
+  res
+}
+
 is_eulerian_impl <- function(graph) {
   # Argument checks
   ensure_igraph(graph)

diff --git a/revdep/README.md b/revdep/README.md
@@ -1,50 +1,37 @@
 # Revdeps
 
-## Failed to check (34)
+## Failed to check (22)
 
 |package               |version |error |warning |note |
 |:---------------------|:-------|:-----|:-------|:----|
 |bnlearn               |?       |      |        |     |
-|bsub                  |1.1.0   |1     |        |     |
 |CARBayes              |6.1.1   |1     |        |     |
-|chemodiv              |?       |      |        |     |
-|CNVScope              |?       |      |        |     |
 |ConnectednessApproach |1.0.3   |1     |        |     |
-|conos                 |?       |      |        |     |
-|crosstalkr            |?       |      |        |     |
 |datapack              |1.4.1   |1     |        |     |
-|DrugSim2DR            |?       |      |        |     |
-|DRviaSPCN             |?       |      |        |     |
 |easybgm               |0.1.2   |1     |        |     |
 |erah                  |2.0.1   |1     |        |     |
 |evolqg                |0.3-4   |1     |        |     |
 |frechet               |0.3.0   |1     |        |     |
-|GALLO                 |?       |      |        |     |
 |kstMatrix             |?       |      |        |     |
 |manet                 |2.0     |1     |        |     |
 |mlmts                 |1.1.2   |1     |        |     |
-|multinma              |0.7.1   |1     |        |     |
+|multinma              |0.7.2   |1     |        |     |
 |netcmc                |1.0.2   |1     |        |     |
 |NetworkChange         |0.8     |1     |        |     |
-|ohun                  |?       |      |        |     |
-|pagoda2               |?       |      |        |     |
 |PathwaySpace          |?       |      |        |     |
 |pcvr                  |1.0.0   |1     |        |     |
 |piecewiseSEM          |?       |      |        |     |
 |RGraphSpace           |?       |      |        |     |
+|robber                |?       |      |        |     |
 |rTwig                 |1.1.0   |1     |        |     |
-|Seurat                |?       |      |        |     |
-|speakeasyR            |?       |      |        |     |
+|Seurat                |5.1.0   |1     |        |     |
 |streamDAG             |?       |      |        |     |
-|SubtypeDrug           |?       |      |        |     |
-|topologyGSA           |?       |      |        |     |
 
-## New problems (5)
+## New problems (4)
 
 |package   |version |error  |warning  |note |
 |:---------|:-------|:------|:--------|:----|
 |[CePa](problems.md#cepa)|0.8.0   |       |1 __+1__ |     |
-|[manynet](problems.md#manynet)|1.0.5   |__+1__ |         |2    |
 |[MetaNet](problems.md#metanet)|0.1.2   |__+1__ |         |     |
 |[simcausal](problems.md#simcausal)|0.5.6   |__+1__ |         |1    |
 |[skynet](problems.md#skynet)|1.4.3   |__+1__ |         |1    |

diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,9 +1,9 @@
 ## revdepcheck results
 
-We checked 855 reverse dependencies (850 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 858 reverse dependencies (853 from CRAN + 5 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 5 new problems
- * We failed to check 29 packages
+ * We saw 4 new problems
+ * We failed to check 17 packages
 
 Issues with CRAN packages are summarised below.
 
@@ -13,9 +13,6 @@ Issues with CRAN packages are summarised below.
 * CePa
   checking Rd cross-references ... WARNING
 
-* manynet
-  checking examples ... ERROR
-
 * MetaNet
   checking examples ... ERROR
 
@@ -27,32 +24,20 @@ Issues with CRAN packages are summarised below.
 
 ### Failed to check
 
-* bsub                  (NA)
 * CARBayes              (NA)
-* chemodiv              (NA)
-* CNVScope              (NA)
 * ConnectednessApproach (NA)
-* conos                 (NA)
-* crosstalkr            (NA)
 * datapack              (NA)
-* DrugSim2DR            (NA)
-* DRviaSPCN             (NA)
 * easybgm               (NA)
 * erah                  (NA)
 * evolqg                (NA)
 * frechet               (NA)
-* GALLO                 (NA)
 * manet                 (NA)
 * mlmts                 (NA)
 * multinma              (NA)
 * netcmc                (NA)
 * NetworkChange         (NA)
-* ohun                  (NA)
-* pagoda2               (NA)
 * pcvr                  (NA)
+* robber                (NA)
 * rTwig                 (NA)
 * Seurat                (NA)
-* speakeasyR            (NA)
 * streamDAG             (NA)
-* SubtypeDrug           (NA)
-* topologyGSA           (NA)