diff --git a/NAMESPACE b/NAMESPACE
index 22f8159eaf..999714d6bc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -475,6 +475,7 @@ export(head_of)
export(head_print)
export(hierarchical_sbm)
export(hierarchy)
+export(hits_scores)
export(hrg)
export(hrg.consensus)
export(hrg.create)
diff --git a/R/aaa-auto.R b/R/aaa-auto.R
index f5c51172b2..5d8f636bf8 100644
--- a/R/aaa-auto.R
+++ b/R/aaa-auto.R
@@ -298,6 +298,34 @@ turan_impl <- function(n, r) {
res
}
+erdos_renyi_game_gnp_impl <- function(n, p, directed=FALSE, loops=FALSE) {
+ # Argument checks
+ n <- as.numeric(n)
+ p <- as.numeric(p)
+ directed <- as.logical(directed)
+ loops <- as.logical(loops)
+
+ on.exit( .Call(R_igraph_finalizer) )
+ # Function call
+ res <- .Call(R_igraph_erdos_renyi_game_gnp, n, p, directed, loops)
+
+ res
+}
+
+erdos_renyi_game_gnm_impl <- function(n, m, directed=FALSE, loops=FALSE) {
+ # Argument checks
+ n <- as.numeric(n)
+ m <- as.numeric(m)
+ directed <- as.logical(directed)
+ loops <- as.logical(loops)
+
+ on.exit( .Call(R_igraph_finalizer) )
+ # Function call
+ res <- .Call(R_igraph_erdos_renyi_game_gnm, n, m, directed, loops)
+
+ res
+}
+
forest_fire_game_impl <- function(nodes, fw.prob, bw.factor=1, ambs=1, directed=TRUE) {
# Argument checks
nodes <- as.numeric(nodes)
@@ -1411,52 +1439,6 @@ eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weigh
res
}
-hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
- # Argument checks
- ensure_igraph(graph)
- scale <- as.logical(scale)
- if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
- weights <- E(graph)$weight
- }
- if (!is.null(weights) && any(!is.na(weights))) {
- weights <- as.numeric(weights)
- } else {
- weights <- NULL
- }
- options <- modify_list(arpack_defaults(), options)
-
- on.exit( .Call(R_igraph_finalizer) )
- # Function call
- res <- .Call(R_igraph_hub_score, graph, scale, weights, options)
- if (igraph_opt("add.vertex.names") && is_named(graph)) {
- names(res$vector) <- vertex_attr(graph, "name", V(graph))
- }
- res
-}
-
-authority_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
- # Argument checks
- ensure_igraph(graph)
- scale <- as.logical(scale)
- if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
- weights <- E(graph)$weight
- }
- if (!is.null(weights) && any(!is.na(weights))) {
- weights <- as.numeric(weights)
- } else {
- weights <- NULL
- }
- options <- modify_list(arpack_defaults(), options)
-
- on.exit( .Call(R_igraph_finalizer) )
- # Function call
- res <- .Call(R_igraph_authority_score, graph, scale, weights, options)
- if (igraph_opt("add.vertex.names") && is_named(graph)) {
- names(res$vector) <- vertex_attr(graph, "name", V(graph))
- }
- res
-}
-
hub_and_authority_scores_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
# Argument checks
ensure_igraph(graph)
@@ -1475,10 +1457,10 @@ hub_and_authority_scores_impl <- function(graph, scale=TRUE, weights=NULL, optio
# Function call
res <- .Call(R_igraph_hub_and_authority_scores, graph, scale, weights, options)
if (igraph_opt("add.vertex.names") && is_named(graph)) {
- names(res$hub.vector) <- vertex_attr(graph, "name", V(graph))
+ names(res$hub) <- vertex_attr(graph, "name", V(graph))
}
if (igraph_opt("add.vertex.names") && is_named(graph)) {
- names(res$authority.vector) <- vertex_attr(graph, "name", V(graph))
+ names(res$authority) <- vertex_attr(graph, "name", V(graph))
}
res
}
@@ -1986,34 +1968,6 @@ random_walk_impl <- function(graph, start, steps, weights=NULL, mode=c("out", "i
res
}
-random_edge_walk_impl <- function(graph, start, steps, weights=NULL, mode=c("out", "in", "all", "total"), stuck=c("return", "error")) {
- # Argument checks
- ensure_igraph(graph)
- if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
- weights <- E(graph)$weight
- }
- if (!is.null(weights) && any(!is.na(weights))) {
- weights <- as.numeric(weights)
- } else {
- weights <- NULL
- }
- start <- as_igraph_vs(graph, start)
- if (length(start) == 0) {
- stop("No vertex was specified")
- }
- mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
- steps <- as.numeric(steps)
- stuck <- switch(igraph.match.arg(stuck), "error" = 0L, "return" = 1L)
-
- on.exit( .Call(R_igraph_finalizer) )
- # Function call
- res <- .Call(R_igraph_random_edge_walk, graph, weights, start-1, mode, steps, stuck)
- if (igraph_opt("return.vs.es")) {
- res <- create_es(graph, res)
- }
- res
-}
-
global_efficiency_impl <- function(graph, weights=NULL, directed=TRUE) {
# Argument checks
ensure_igraph(graph)
@@ -2197,24 +2151,6 @@ is_bipartite_impl <- function(graph) {
res
}
-bipartite_game_impl <- function(type, n1, n2, p=0.0, m=0, directed=FALSE, mode=c("all", "out", "in", "total")) {
- # Argument checks
- n1 <- as.numeric(n1)
- n2 <- as.numeric(n2)
- p <- as.numeric(p)
- m <- as.numeric(m)
- directed <- as.logical(directed)
- mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
- on.exit( .Call(R_igraph_finalizer) )
- # Function call
- res <- .Call(R_igraph_bipartite_game, type, n1, n2, p, m, directed, mode)
- if (igraph_opt("add.vertex.names") && is_named(graph)) {
- names(res$types) <- vertex_attr(graph, "name", V(graph))
- }
- res
-}
-
get_laplacian_impl <- function(graph, mode=c("out", "in", "all", "total"), normalization=c("unnormalized", "symmetric", "left", "right"), weights=NULL) {
# Argument checks
ensure_igraph(graph)
diff --git a/R/centrality.R b/R/centrality.R
index 645701cb8a..4277020c57 100644
--- a/R/centrality.R
+++ b/R/centrality.R
@@ -40,10 +40,25 @@ page.rank <- function(graph, algo = c("prpack", "arpack"), vids = V(graph), dire
#' @keywords internal
#' @export
hub.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
- lifecycle::deprecate_soft("2.0.0", "hub.score()", "hub_score()")
+ lifecycle::deprecate_warn("2.0.0", "hub.score()", "hits_score()")
hub_score(graph = graph, scale = scale, weights = weights, options = options)
} # nocov end
+#' Kleinberg's hub and authority centrality scores.
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' `authority.score()` was renamed to `authority_score()` to create a more
+#' consistent API.
+#' @inheritParams authority_score
+#' @keywords internal
+#' @export
+authority.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
+ lifecycle::deprecate_warn("2.0.0", "authority.score()", "hits_score()")
+ authority_score(graph = graph, scale = scale, weights = weights, options = options)
+} # nocov end
+
#' Strength or weighted vertex degree
#'
#' @description
@@ -134,21 +149,6 @@ bonpow <- function(graph, nodes = V(graph), loops = FALSE, exponent = 1, rescale
power_centrality(graph = graph, nodes = nodes, loops = loops, exponent = exponent, rescale = rescale, tol = tol, sparse = sparse)
} # nocov end
-#' Kleinberg's hub and authority centrality scores.
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' `authority.score()` was renamed to `authority_score()` to create a more
-#' consistent API.
-#' @inheritParams authority_score
-#' @keywords internal
-#' @export
-authority.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
- lifecycle::deprecate_soft("2.0.0", "authority.score()", "authority_score()")
- authority_score(graph = graph, scale = scale, weights = weights, options = options)
-} # nocov end
-
#' Find Bonacich alpha centrality scores of network positions
#'
#' @description
@@ -1105,6 +1105,7 @@ diversity <- diversity_impl
#' selected by the surfer.
#' @param options A named list, to override some ARPACK options. See
#' [arpack()] for details.
+#' @inheritParams rlang::args_dots_empty
#' @return A named list with members:
#' \item{vector}{The hub or authority scores of the vertices.}
#' \item{value}{The corresponding eigenvalue of the calculated
@@ -1124,36 +1125,66 @@ diversity <- diversity_impl
#' @examples
#' ## An in-star
#' g <- make_star(10)
-#' hub_score(g)$vector
-#' authority_score(g)$vector
+#' hits_scores(g)
#'
#' ## A ring
#' g2 <- make_ring(10)
-#' hub_score(g2)$vector
-#' authority_score(g2)$vector
+#' hits_scores(g2)
#' @family centrality
-hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+hits_scores <- function(graph, ..., scale=TRUE, weights=NULL, options=arpack_defaults()) {
+ rlang::check_dots_empty()
+
+ hub_and_authority_scores_impl(graph = graph,
+ scale = scale,
+ weights = weights,
+ options = options)
+}
+
+#' @title Kleinberg's authority centrality scores.
+#' @rdname hub_score
+#' @param options A named list, to override some ARPACK options. See
+#' [arpack()] for details.
+#' @export
+authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+ lifecycle::deprecate_soft("2.0.4", "authority_score()", "hits_scores()")
if (is.function(options)) {
lifecycle::deprecate_soft(
"1.6.0",
- "hub_score(options = 'must be a list')",
- details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
+ I("arpack_defaults"),
+ "arpack_defaults()",
+ details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
)
- options <- options()
+ options <- arpack_defaults()
}
- hub_score_impl(graph = graph,
- scale = scale,
- weights = weights,
- options = options)
+ scores <- hits_scores(
+ graph = graph,
+ scale = scale,
+ weights = weights,
+ options = options)
+ scores$hub <- NULL
+ rlang::set_names(scores, c("vector", "value", "options"))
}
+#' @title Kleinberg's hub centrality scores.
#' @rdname hub_score
+#' @param graph The input graph.
+#' @param scale Logical scalar, whether to scale the result to have a maximum
+#' score of one. If no scaling is used then the result vector has unit length
+#' in the Euclidean norm.
+#' @param weights Optional positive weight vector for calculating weighted
+#' scores. If the graph has a `weight` edge attribute, then this is used
+#' by default.
+#' This function interprets edge weights as connection strengths. In the
+#' random surfer model, an edge with a larger weight is more likely to be
+#' selected by the surfer.
#' @param options A named list, to override some ARPACK options. See
#' [arpack()] for details.
+#' @family centrality
#' @export
-authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+ lifecycle::deprecate_soft("2.0.3", "hub_score()", "hits_scores()")
if (is.function(options)) {
lifecycle::deprecate_soft(
"1.6.0",
@@ -1164,10 +1195,13 @@ authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defa
options <- arpack_defaults()
}
- authority_score_impl(graph = graph,
- scale = scale,
- weights = weights,
- options = options)
+ scores <- hits_scores(
+ graph = graph,
+ scale = scale,
+ weights = weights,
+ options = options)
+ scores$authority <- NULL
+ rlang::set_names(scores, c("vector", "value", "options"))
}
#' The Page Rank algorithm
diff --git a/R/games.R b/R/games.R
index b290b89a3a..08c5a2eecd 100644
--- a/R/games.R
+++ b/R/games.R
@@ -596,7 +596,7 @@ sample_gnp <- function(n, p, directed = FALSE, loops = FALSE) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
- R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
+ R_igraph_erdos_renyi_game_gnp, as.numeric(n),
as.numeric(p), as.logical(directed), as.logical(loops)
)
@@ -651,7 +651,7 @@ sample_gnm <- function(n, m, directed = FALSE, loops = FALSE) {
on.exit(.Call(R_igraph_finalizer))
res <- .Call(
- R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
+ R_igraph_erdos_renyi_game_gnm, as.numeric(n),
as.numeric(m), as.logical(directed), as.logical(loops)
)
@@ -716,16 +716,19 @@ gnm <- function(...) constructor_spec(sample_gnm, ...)
erdos.renyi.game <- function(n, p.or.m, type = c("gnp", "gnm"),
directed = FALSE, loops = FALSE) {
type <- igraph.match.arg(type)
- type1 <- switch(type,
- "gnp" = 0,
- "gnm" = 1
- )
on.exit(.Call(R_igraph_finalizer))
- res <- .Call(
- R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
- as.numeric(p.or.m), as.logical(directed), as.logical(loops)
- )
+ if (type == "gnp") {
+ res <- .Call(
+ R_igraph_erdos_renyi_game_gnp, as.numeric(n),
+ as.numeric(p.or.m), as.logical(directed), as.logical(loops)
+ )
+ } else if (type == "gnm") {
+ res <- .Call(
+ R_igraph_erdos_renyi_game_gnm, as.numeric(n),
+ as.numeric(p.or.m), as.logical(directed), as.logical(loops)
+ )
+ }
if (igraph_opt("add.params")) {
res$name <- sprintf("Erdos-Renyi (%s) graph", type)
diff --git a/R/make.R b/R/make.R
index 0f75dca76f..28109c92a4 100644
--- a/R/make.R
+++ b/R/make.R
@@ -339,23 +339,28 @@ graph.lcf <- function(n , shifts , repeats = 1) { # nocov start
#' @inheritParams make_lattice
#' @keywords internal
#' @export
-graph.lattice <- function(dimvector = NULL , length = NULL , dim = NULL , nei = 1 , directed = FALSE , mutual = FALSE , circular = FALSE) { # nocov start
- lifecycle::deprecate_soft("2.0.4", "graph.lattice()", "make_lattice()")
- if (is.numeric(length) && length != floor(length)) {
+graph.lattice <- function(dimvector = NULL , length = NULL , dim = NULL , nei = 1 , directed = FALSE , mutual = FALSE , periodic = FALSE, circular) { # nocov start
+ lifecycle::deprecate_soft("2.0.4", "graph.lattice()", "make_lattice()")
+ if (is.numeric(length) && length != floor(length)) {
warning("length was rounded to the nearest integer")
length <- round(length)
}
+ if (lifecycle::is_present(circular)) {
+ lifecycle::deprecate_soft(
+ "2.0.3",
+ "graph.lattice(circular = 'use periodic argument instead')",
+ details = c("`circular` is now deprecated, use `periodic` instead.")
+ )
+ periodic <- circular
+ }
+
if (is.null(dimvector)) {
dimvector <- rep(length, dim)
}
on.exit(.Call(R_igraph_finalizer))
- res <- .Call(
- R_igraph_lattice, as.numeric(dimvector), as.numeric(nei),
- as.logical(directed), as.logical(mutual),
- as.logical(circular)
- )
+ res <- square_lattice_impl(dimvector, nei, directed, mutual, periodic)
if (igraph_opt("add.params")) {
res$name <- "Lattice graph"
res$dimvector <- dimvector
@@ -1654,8 +1659,10 @@ full_graph <- function(...) constructor_spec(make_full_graph, ...)
#' @param directed Whether to create a directed lattice.
#' @param mutual Logical, if `TRUE` directed lattices will be
#' mutually connected.
-#' @param circular Logical, if `TRUE` the lattice or ring will be
-#' circular.
+#' @param periodic Logical vector, Boolean vector, defines whether the generated lattice is
+#' periodic along each dimension. This parameter may also be scalar boolen value which will
+#' be extended to boolean vector with dimvector length.
+#' @param circular Deprecated, use `periodic` instead.
#' @return An igraph graph.
#'
#' @family deterministic constructors
@@ -1665,7 +1672,16 @@ full_graph <- function(...) constructor_spec(make_full_graph, ...)
#' make_lattice(length = 5, dim = 3)
make_lattice <- function(dimvector = NULL, length = NULL, dim = NULL,
nei = 1, directed = FALSE, mutual = FALSE,
- circular = FALSE) {
+ periodic = FALSE, circular) {
+ if (lifecycle::is_present(circular)) {
+ lifecycle::deprecate_soft(
+ "2.0.3",
+ "make_lattice(circular = 'use periodic argument instead')",
+ details = c("`circular` is now deprecated, use `periodic` instead.")
+ )
+ periodic <- circular
+ }
+
if (is.numeric(length) && length != floor(length)) {
warning("length was rounded to the nearest integer")
length <- round(length)
@@ -1675,18 +1691,18 @@ make_lattice <- function(dimvector = NULL, length = NULL, dim = NULL,
dimvector <- rep(length, dim)
}
+ if (length(periodic) == 1) {
+ periodic <- rep(periodic, length(dimvector))
+ }
+
on.exit(.Call(R_igraph_finalizer))
- res <- .Call(
- R_igraph_lattice, as.numeric(dimvector), as.numeric(nei),
- as.logical(directed), as.logical(mutual),
- as.logical(circular)
- )
+ res <- square_lattice_impl(dimvector, nei, directed, mutual, periodic)
if (igraph_opt("add.params")) {
res$name <- "Lattice graph"
res$dimvector <- dimvector
res$nei <- nei
res$mutual <- mutual
- res$circular <- circular
+ res$circular <- periodic
}
res
}
diff --git a/R/random_walk.R b/R/random_walk.R
index c7537528d2..d80df8cca7 100644
--- a/R/random_walk.R
+++ b/R/random_walk.R
@@ -64,4 +64,17 @@ random_walk <- function(
#' @rdname random_walk
#' @export
-random_edge_walk <- random_edge_walk_impl
+random_edge_walk <- function(
+ graph,
+ start,
+ steps,
+ weights = NULL,
+ mode = c("out", "in", "all", "total"),
+ stuck = c("return", "error")) {
+ mode <- match.arg(mode)
+ stuck <- match.arg(stuck)
+ out <- random_walk_impl(graph, start, steps, weights, mode, stuck)
+ # FIXME: Support returning the full structure
+ out$edges
+}
+
diff --git a/R/structural.properties.R b/R/structural.properties.R
index 67ce53568f..adf7f86326 100644
--- a/R/structural.properties.R
+++ b/R/structural.properties.R
@@ -2487,9 +2487,10 @@ unfold_tree <- function(graph, mode = c("all", "out", "in", "total"), roots) {
#' is d\[i\], the degree of vertex i if if i==j, -1 if i!=j and there is an edge
#' between vertices i and j and 0 otherwise.
#'
-#' A normalized version of the Laplacian Matrix is similar: element (i,j) is 1
-#' if i==j, -1/sqrt(d\[i\] d\[j\]) if i!=j and there is an edge between vertices i
-#' and j and 0 otherwise.
+#' The Laplacian matrix can also be normalized, with several
+#' conventional normalization methods. \dQuote{unnormalized} Unnormalized Laplacian.
+#' \dQuote{symmetric} Symmetric normalized Laplacian. \dQuote{left} Left-stochastic normalized Laplacian.
+#' \dQuote{right} Right-stochastic normalized Laplacian.
#'
#' The weighted version of the Laplacian simply works with the weighted degree
#' instead of the plain degree. I.e. (i,j) is d\[i\], the weighted degree of
@@ -2498,8 +2499,9 @@ unfold_tree <- function(graph, mode = c("all", "out", "in", "total"), roots) {
#' of the weights of its adjacent edges.
#'
#' @param graph The input graph.
-#' @param normalized Whether to calculate the normalized Laplacian. See
-#' definitions below.
+#' @param normalization The normalization method to use when calculating the
+#' Laplacian matrix.
+#' @param normalized Deprecated, use `normalization` instead.
#' @param weights An optional vector giving edge weights for weighted Laplacian
#' matrix. If this is `NULL` and the graph has an edge attribute called
#' `weight`, then it will be used automatically. Set this to `NA` if
@@ -2515,14 +2517,30 @@ unfold_tree <- function(graph, mode = c("all", "out", "in", "total"), roots) {
#'
#' g <- make_ring(10)
#' laplacian_matrix(g)
-#' laplacian_matrix(g, norm = TRUE)
-#' laplacian_matrix(g, norm = TRUE, sparse = FALSE)
+#' laplacian_matrix(g, normalization = "unnormalized")
+#' laplacian_matrix(g, normalization = "unnormalized", sparse = FALSE)
#'
-laplacian_matrix <- function(graph, normalized = FALSE, weights = NULL,
- sparse = igraph_opt("sparsematrices")) {
+laplacian_matrix <- function(graph, weights = NULL,
+ sparse = igraph_opt("sparsematrices"), normalization = c("unnormalized", "symmetric", "left", "right"), normalized) {
# Argument checks
+ if (lifecycle::is_present(normalized)) {
+ lifecycle::deprecate_soft(
+ "2.0.3",
+ "make_lattice(normalized = 'provide normalization instead')",
+ details = c("`normalized` is now deprecated, use `normalization` instead.")
+ )
+ normalized <- as.logical(normalized)
+
+ normalization <- "unnormalized"
+ if (normalized) {
+ if (is_directed(graph)) {
+ normalization <- "left"
+ } else {
+ normalization <- "symmetric"
+ }
+ }
+ }
ensure_igraph(graph)
- normalized <- as.logical(normalized)
if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
weights <- E(graph)$weight
}
@@ -2535,7 +2553,11 @@ laplacian_matrix <- function(graph, normalized = FALSE, weights = NULL,
on.exit(.Call(R_igraph_finalizer))
# Function call
- res <- .Call(R_igraph_laplacian, graph, normalized, weights, sparse)
+ if (sparse) {
+ res <- get_laplacian_sparse_impl(graph, "out", normalization, weights)
+ } else {
+ res <- get_laplacian_impl(graph, "out", normalization, weights)
+ }
if (sparse) {
res <- igraph.i.spMatrix(res)
}
diff --git a/man/alpha_centrality.Rd b/man/alpha_centrality.Rd
index bc06658543..b41a3223e0 100644
--- a/man/alpha_centrality.Rd
+++ b/man/alpha_centrality.Rd
@@ -93,12 +93,13 @@ measures of centrality for asymmetric relations'' \emph{Social Networks},
\code{\link[=eigen_centrality]{eigen_centrality()}} and \code{\link[=power_centrality]{power_centrality()}}
Centrality measures
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/betweenness.Rd b/man/betweenness.Rd
index b9145c8fb2..17cdd3661f 100644
--- a/man/betweenness.Rd
+++ b/man/betweenness.Rd
@@ -111,11 +111,12 @@ of Mathematical Sociology} 25(2):163-177, 2001.
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/closeness.Rd b/man/closeness.Rd
index 14912d0d38..0502a7f28f 100644
--- a/man/closeness.Rd
+++ b/man/closeness.Rd
@@ -83,11 +83,12 @@ Conceptual Clarification. \emph{Social Networks}, 1, 215-239.
\seealso{
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/diversity.Rd b/man/diversity.Rd
index 9051ee339e..07fb8e3d71 100644
--- a/man/diversity.Rd
+++ b/man/diversity.Rd
@@ -54,11 +54,12 @@ and Economic Development, \emph{Science} \strong{328}, 1029--1031, 2010.
\seealso{
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/eigen_centrality.Rd b/man/eigen_centrality.Rd
index c8f3ce7874..3e3e5e4001 100644
--- a/man/eigen_centrality.Rd
+++ b/man/eigen_centrality.Rd
@@ -104,11 +104,12 @@ Measures. \emph{American Journal of Sociology}, 92, 1170-1182.
\seealso{
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/graph.laplacian.Rd b/man/graph.laplacian.Rd
index 66471f23ef..4411c53142 100644
--- a/man/graph.laplacian.Rd
+++ b/man/graph.laplacian.Rd
@@ -14,8 +14,7 @@ graph.laplacian(
\arguments{
\item{graph}{The input graph.}
-\item{normalized}{Whether to calculate the normalized Laplacian. See
-definitions below.}
+\item{normalized}{Deprecated, use \code{normalization} instead.}
\item{weights}{An optional vector giving edge weights for weighted Laplacian
matrix. If this is \code{NULL} and the graph has an edge attribute called
diff --git a/man/graph.lattice.Rd b/man/graph.lattice.Rd
index c243b39e41..6c08918146 100644
--- a/man/graph.lattice.Rd
+++ b/man/graph.lattice.Rd
@@ -11,7 +11,8 @@ graph.lattice(
nei = 1,
directed = FALSE,
mutual = FALSE,
- circular = FALSE
+ periodic = FALSE,
+ circular
)
}
\arguments{
@@ -31,8 +32,11 @@ lattice will be connected. This parameter is not used right now.}
\item{mutual}{Logical, if \code{TRUE} directed lattices will be
mutually connected.}
-\item{circular}{Logical, if \code{TRUE} the lattice or ring will be
-circular.}
+\item{periodic}{Logical vector, Boolean vector, defines whether the generated lattice is
+periodic along each dimension. This parameter may also be scalar boolen value which will
+be extended to boolean vector with dimvector length.}
+
+\item{circular}{Deprecated, use \code{periodic} instead.}
}
\description{
\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
diff --git a/man/harmonic_centrality.Rd b/man/harmonic_centrality.Rd
index 8225589484..00fdeaa575 100644
--- a/man/harmonic_centrality.Rd
+++ b/man/harmonic_centrality.Rd
@@ -71,11 +71,12 @@ M. Marchiori and V. Latora, Harmony in the small-world,
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/hits_scores.Rd b/man/hits_scores.Rd
new file mode 100644
index 0000000000..63e7a564d1
--- /dev/null
+++ b/man/hits_scores.Rd
@@ -0,0 +1,90 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/centrality.R
+\name{hits_scores}
+\alias{hits_scores}
+\title{Kleinberg's hub and authority centrality scores.}
+\usage{
+hits_scores(
+ graph,
+ ...,
+ scale = TRUE,
+ weights = NULL,
+ options = arpack_defaults()
+)
+}
+\arguments{
+\item{graph}{The input graph.}
+
+\item{...}{These dots are for future extensions and must be empty.}
+
+\item{scale}{Logical scalar, whether to scale the result to have a maximum
+score of one. If no scaling is used then the result vector has unit length
+in the Euclidean norm.}
+
+\item{weights}{Optional positive weight vector for calculating weighted
+scores. If the graph has a \code{weight} edge attribute, then this is used
+by default.
+This function interprets edge weights as connection strengths. In the
+random surfer model, an edge with a larger weight is more likely to be
+selected by the surfer.}
+
+\item{options}{A named list, to override some ARPACK options. See
+\code{\link[=arpack]{arpack()}} for details.}
+}
+\value{
+A named list with members:
+\item{vector}{The hub or authority scores of the vertices.}
+\item{value}{The corresponding eigenvalue of the calculated
+principal eigenvector.}
+\item{options}{Some information about the ARPACK computation, it has
+the same members as the \code{options} member returned
+by \code{\link[=arpack]{arpack()}}, see that for documentation.}
+}
+\description{
+The hub scores of the vertices are defined as the principal eigenvector
+of \eqn{A A^T}{A*t(A)}, where \eqn{A} is the adjacency matrix of the
+graph.
+}
+\details{
+Similarly, the authority scores of the vertices are defined as the principal
+eigenvector of \eqn{A^T A}{t(A)*A}, where \eqn{A} is the adjacency matrix of
+the graph.
+
+For undirected matrices the adjacency matrix is symmetric and the hub
+scores are the same as authority scores.
+}
+\examples{
+## An in-star
+g <- make_star(10)
+hits_scores(g)
+
+## A ring
+g2 <- make_ring(10)
+hits_scores(g2)
+}
+\references{
+J. Kleinberg. Authoritative sources in a hyperlinked
+environment. \emph{Proc. 9th ACM-SIAM Symposium on Discrete Algorithms},
+1998. Extended version in \emph{Journal of the ACM} 46(1999). Also appears
+as IBM Research Report RJ 10076, May 1997.
+}
+\seealso{
+\code{\link[=eigen_centrality]{eigen_centrality()}} for eigenvector centrality,
+\code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for
+the underlining machinery of the computation.
+
+Centrality measures
+\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
+\code{\link{betweenness}()},
+\code{\link{closeness}()},
+\code{\link{diversity}()},
+\code{\link{eigen_centrality}()},
+\code{\link{harmonic_centrality}()},
+\code{\link{page_rank}()},
+\code{\link{power_centrality}()},
+\code{\link{spectrum}()},
+\code{\link{strength}()},
+\code{\link{subgraph_centrality}()}
+}
+\concept{centrality}
diff --git a/man/hub_score.Rd b/man/hub_score.Rd
index 7e583312a7..cd80422d09 100644
--- a/man/hub_score.Rd
+++ b/man/hub_score.Rd
@@ -1,18 +1,18 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/centrality.R
-\name{hub_score}
-\alias{hub_score}
+\name{authority_score}
\alias{authority_score}
-\title{Kleinberg's hub and authority centrality scores.}
+\alias{hub_score}
+\title{Kleinberg's authority centrality scores.}
\usage{
-hub_score(graph, scale = TRUE, weights = NULL, options = arpack_defaults())
-
authority_score(
graph,
scale = TRUE,
weights = NULL,
options = arpack_defaults()
)
+
+hub_score(graph, scale = TRUE, weights = NULL, options = arpack_defaults())
}
\arguments{
\item{graph}{The input graph.}
@@ -31,50 +31,12 @@ selected by the surfer.}
\item{options}{A named list, to override some ARPACK options. See
\code{\link[=arpack]{arpack()}} for details.}
}
-\value{
-A named list with members:
-\item{vector}{The hub or authority scores of the vertices.}
-\item{value}{The corresponding eigenvalue of the calculated
-principal eigenvector.}
-\item{options}{Some information about the ARPACK computation, it has
-the same members as the \code{options} member returned
-by \code{\link[=arpack]{arpack()}}, see that for documentation.}
-}
\description{
-The hub scores of the vertices are defined as the principal eigenvector
-of \eqn{A A^T}{A*t(A)}, where \eqn{A} is the adjacency matrix of the
-graph.
-}
-\details{
-Similarly, the authority scores of the vertices are defined as the principal
-eigenvector of \eqn{A^T A}{t(A)*A}, where \eqn{A} is the adjacency matrix of
-the graph.
-
-For undirected matrices the adjacency matrix is symmetric and the hub
-scores are the same as authority scores.
-}
-\examples{
-## An in-star
-g <- make_star(10)
-hub_score(g)$vector
-authority_score(g)$vector
+Kleinberg's authority centrality scores.
-## A ring
-g2 <- make_ring(10)
-hub_score(g2)$vector
-authority_score(g2)$vector
-}
-\references{
-J. Kleinberg. Authoritative sources in a hyperlinked
-environment. \emph{Proc. 9th ACM-SIAM Symposium on Discrete Algorithms},
-1998. Extended version in \emph{Journal of the ACM} 46(1999). Also appears
-as IBM Research Report RJ 10076, May 1997.
+Kleinberg's hub centrality scores.
}
\seealso{
-\code{\link[=eigen_centrality]{eigen_centrality()}} for eigenvector centrality,
-\code{\link[=page_rank]{page_rank()}} for the Page Rank scores. \code{\link[=arpack]{arpack()}} for
-the underlining machinery of the computation.
-
Centrality measures
\code{\link{alpha_centrality}()},
\code{\link{betweenness}()},
@@ -82,6 +44,7 @@ Centrality measures
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/laplacian_matrix.Rd b/man/laplacian_matrix.Rd
index f3a0c7c249..241863983f 100644
--- a/man/laplacian_matrix.Rd
+++ b/man/laplacian_matrix.Rd
@@ -6,17 +6,15 @@
\usage{
laplacian_matrix(
graph,
- normalized = FALSE,
weights = NULL,
- sparse = igraph_opt("sparsematrices")
+ sparse = igraph_opt("sparsematrices"),
+ normalization = c("unnormalized", "symmetric", "left", "right"),
+ normalized
)
}
\arguments{
\item{graph}{The input graph.}
-\item{normalized}{Whether to calculate the normalized Laplacian. See
-definitions below.}
-
\item{weights}{An optional vector giving edge weights for weighted Laplacian
matrix. If this is \code{NULL} and the graph has an edge attribute called
\code{weight}, then it will be used automatically. Set this to \code{NA} if
@@ -25,6 +23,11 @@ attribute.}
\item{sparse}{Logical scalar, whether to return the result as a sparse
matrix. The \code{Matrix} package is required for sparse matrices.}
+
+\item{normalization}{The normalization method to use when calculating the
+Laplacian matrix.}
+
+\item{normalized}{Deprecated, use \code{normalization} instead.}
}
\value{
A numeric matrix.
@@ -38,9 +41,10 @@ of rows and columns as the number of vertices in the graph and element (i,j)
is d[i], the degree of vertex i if if i==j, -1 if i!=j and there is an edge
between vertices i and j and 0 otherwise.
-A normalized version of the Laplacian Matrix is similar: element (i,j) is 1
-if i==j, -1/sqrt(d[i] d[j]) if i!=j and there is an edge between vertices i
-and j and 0 otherwise.
+The Laplacian matrix can also be normalized, with several
+conventional normalization methods. \dQuote{unnormalized} Unnormalized Laplacian.
+\dQuote{symmetric} Symmetric normalized Laplacian. \dQuote{left} Left-stochastic normalized Laplacian.
+\dQuote{right} Right-stochastic normalized Laplacian.
The weighted version of the Laplacian simply works with the weighted degree
instead of the plain degree. I.e. (i,j) is d[i], the weighted degree of
@@ -52,8 +56,8 @@ of the weights of its adjacent edges.
g <- make_ring(10)
laplacian_matrix(g)
-laplacian_matrix(g, norm = TRUE)
-laplacian_matrix(g, norm = TRUE, sparse = FALSE)
+laplacian_matrix(g, normalization = "unnormalized")
+laplacian_matrix(g, normalization = "unnormalized", sparse = FALSE)
}
\author{
diff --git a/man/make_lattice.Rd b/man/make_lattice.Rd
index f2d535e204..f5f112d4d4 100644
--- a/man/make_lattice.Rd
+++ b/man/make_lattice.Rd
@@ -12,7 +12,8 @@ make_lattice(
nei = 1,
directed = FALSE,
mutual = FALSE,
- circular = FALSE
+ periodic = FALSE,
+ circular
)
lattice(...)
@@ -34,8 +35,11 @@ lattice will be connected. This parameter is not used right now.}
\item{mutual}{Logical, if \code{TRUE} directed lattices will be
mutually connected.}
-\item{circular}{Logical, if \code{TRUE} the lattice or ring will be
-circular.}
+\item{periodic}{Logical vector, Boolean vector, defines whether the generated lattice is
+periodic along each dimension. This parameter may also be scalar boolen value which will
+be extended to boolean vector with dimvector length.}
+
+\item{circular}{Deprecated, use \code{periodic} instead.}
\item{...}{Passed to \code{make_lattice()}.}
}
diff --git a/man/page_rank.Rd b/man/page_rank.Rd
index 892dd73b09..c7ec98b05d 100644
--- a/man/page_rank.Rd
+++ b/man/page_rank.Rd
@@ -110,12 +110,13 @@ Other centrality scores: \code{\link[=closeness]{closeness()}},
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
\code{\link{strength}()},
diff --git a/man/power_centrality.Rd b/man/power_centrality.Rd
index e046e60d06..b4791e1b35 100644
--- a/man/power_centrality.Rd
+++ b/man/power_centrality.Rd
@@ -136,12 +136,13 @@ Bonacich, P. (1987). ``Power and Centrality: A Family of Measures.''
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{spectrum}()},
\code{\link{strength}()},
diff --git a/man/spectrum.Rd b/man/spectrum.Rd
index ac73ca76c6..de80c18a52 100644
--- a/man/spectrum.Rd
+++ b/man/spectrum.Rd
@@ -79,12 +79,13 @@ spectrum(kite, which = list(pos = "SM", howmany = 2))$values
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{strength}()},
diff --git a/man/strength.Rd b/man/strength.Rd
index ecbc00fbf5..8594af9c02 100644
--- a/man/strength.Rd
+++ b/man/strength.Rd
@@ -57,12 +57,13 @@ Natl. Acad. Sci. USA 101, 3747 (2004)
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/man/subgraph_centrality.Rd b/man/subgraph_centrality.Rd
index 878fa20201..d6fe45ce28 100644
--- a/man/subgraph_centrality.Rd
+++ b/man/subgraph_centrality.Rd
@@ -46,12 +46,13 @@ centrality in Complex Networks. \emph{Physical Review E} 71, 056103 (2005).
Centrality measures
\code{\link{alpha_centrality}()},
+\code{\link{authority_score}()},
\code{\link{betweenness}()},
\code{\link{closeness}()},
\code{\link{diversity}()},
\code{\link{eigen_centrality}()},
\code{\link{harmonic_centrality}()},
-\code{\link{hub_score}()},
+\code{\link{hits_scores}()},
\code{\link{page_rank}()},
\code{\link{power_centrality}()},
\code{\link{spectrum}()},
diff --git a/revdep/README.md b/revdep/README.md
index db372bf3ff..0e86108aed 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,6 +1,6 @@
# Revdeps
-## Failed to check (24)
+## Failed to check (25)
|package |version |error |warning |note |
|:-------------|:-------|:-----|:-------|:----|
@@ -18,6 +18,7 @@
|metadat |? | | | |
|MetaNet |? | | | |
|mlmts |1.1.1 |1 | | |
+|multinma |0.7.1 |1 | | |
|netcmc |1.0.2 |1 | | |
|NetworkChange |0.8 |1 | | |
|pagoda2 |? | | | |
@@ -29,10 +30,11 @@
|streamDAG |? | | | |
|treefit |? | | | |
-## New problems (2)
+## New problems (3)
|package |version |error |warning |note |
|:---------|:-------|:------|:-------|:------|
+|[BCT](problems.md#bct)|1.2 |__+1__ | |1 |
|[netropy](problems.md#netropy)|0.1.0 |__+2__ | |__+1__ |
|[tidygraph](problems.md#tidygraph)|1.3.1 |__+1__ | | |
diff --git a/revdep/cran.md b/revdep/cran.md
index 1a626196a2..1ec3511f29 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,15 +1,18 @@
## revdepcheck results
-We checked 831 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 833 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 2 new problems
- * We failed to check 24 packages
+ * We saw 3 new problems
+ * We failed to check 25 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
+* BCT
+ checking examples ... ERROR
+
* netropy
checking examples ... ERROR
checking running R code from vignettes ... ERROR
@@ -34,6 +37,7 @@ Issues with CRAN packages are summarised below.
* metadat (NA)
* MetaNet (NA)
* mlmts (NA)
+* multinma (NA)
* netcmc (NA)
* NetworkChange (NA)
* pagoda2 (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 9a20736339..ca36596a41 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1 +1,3824 @@
-*Wow, no problems at all. :)*
\ No newline at end of file
+# Canek
+
+
+
+* Version: 0.2.5
+* GitHub: https://github.com/MartinLoza/Canek
+* Source code: https://github.com/cran/Canek
+* Date/Publication: 2023-12-08 05:30:02 UTC
+* Number of recursive dependencies: 225
+
+Run `revdepcheck::cloud_details(, "Canek")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/Canek/new/Canek.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Canek/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘Canek’ version ‘0.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘Canek’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... ERROR
+ Running ‘testthat.R’
+Running the tests in ‘tests/testthat.R’ failed.
+Complete output:
+ > library(testthat)
+ > library(Canek)
+ >
+ > test_check("Canek")
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Error ('test_RunCanek.R:19:1'): (code run outside of `test_that()`) ─────────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test_RunCanek.R:19:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
+ Error: Test failures
+ Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘toy_example.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 ERROR, 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/Canek/old/Canek.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Canek/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘Canek’ version ‘0.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘Canek’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... ERROR
+ Running ‘testthat.R’
+Running the tests in ‘tests/testthat.R’ failed.
+Complete output:
+ > library(testthat)
+ > library(Canek)
+ >
+ > test_check("Canek")
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Error ('test_RunCanek.R:19:1'): (code run outside of `test_that()`) ─────────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test_RunCanek.R:19:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 74 ]
+ Error: Test failures
+ Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘toy_example.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 ERROR, 1 NOTE
+
+
+
+
+
+```
+# CARBayes
+
+
+
+* Version: 6.1.1
+* GitHub: https://github.com/duncanplee/CARBayes
+* Source code: https://github.com/cran/CARBayes
+* Date/Publication: 2024-03-08 13:20:02 UTC
+* Number of recursive dependencies: 136
+
+Run `revdepcheck::cloud_details(, "CARBayes")` for more info
+
+
+
+## In both
+
+* checking whether package ‘CARBayes’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/CARBayes/new/CARBayes.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘CARBayes’ ...
+** package ‘CARBayes’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayes.cpp -o CARBayes.o
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayes.so CARBayes.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/CARBayes/new/CARBayes.Rcheck/00LOCK-CARBayes/00new/CARBayes/libs
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
+ there is no package called ‘quantreg’
+Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: lazy loading failed for package ‘CARBayes’
+* removing ‘/tmp/workdir/CARBayes/new/CARBayes.Rcheck/CARBayes’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘CARBayes’ ...
+** package ‘CARBayes’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c CARBayes.cpp -o CARBayes.o
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o CARBayes.so CARBayes.o RcppExports.o -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/CARBayes/old/CARBayes.Rcheck/00LOCK-CARBayes/00new/CARBayes/libs
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
+ there is no package called ‘quantreg’
+Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: lazy loading failed for package ‘CARBayes’
+* removing ‘/tmp/workdir/CARBayes/old/CARBayes.Rcheck/CARBayes’
+
+
+```
+# ClustAssess
+
+
+
+* Version: 0.3.0
+* GitHub: https://github.com/Core-Bioinformatics/ClustAssess
+* Source code: https://github.com/cran/ClustAssess
+* Date/Publication: 2022-01-26 16:52:46 UTC
+* Number of recursive dependencies: 164
+
+Run `revdepcheck::cloud_details(, "ClustAssess")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/ClustAssess/new/ClustAssess.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ClustAssess/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘ClustAssess’ version ‘0.3.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘ClustAssess’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking compiled code ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... ERROR
+Running examples in ‘ClustAssess-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: get_clustering_difference
+> ### Title: Graph Clustering Method Stability
+> ### Aliases: get_clustering_difference
+>
+> ### ** Examples
+>
+> set.seed(2021)
+> # create an artificial expression matrix
+> expr_matrix = matrix(runif(100*10), nrow = 100)
+> rownames(expr_matrix) = as.character(1:100)
+>
+> adj_matrix = Seurat::FindNeighbors(expr_matrix,
++ k.param = 10,
++ nn.method = "rann",
++ verbose = FALSE,
++ compute.SNN = FALSE)$nn
+Error in loadNamespace(x) : there is no package called ‘Seurat’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... WARNING
+Errors in running code in vignettes:
+when running code in ‘ClustAssess.Rmd’
+ ...
+
+> knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
+
+> set.seed(1001)
+
+> library(Seurat)
+
+ When sourcing ‘ClustAssess.R’:
+Error: there is no package called ‘Seurat’
+Execution halted
+
+ ‘ClustAssess.Rmd’ using ‘UTF-8’... failed
+ ‘comparing-soft-and-hierarchical.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... NOTE
+Error(s) in re-building vignettes:
+--- re-building ‘ClustAssess.Rmd’ using rmarkdown
+
+Quitting from lines 22-27 [setup] (ClustAssess.Rmd)
+Error: processing vignette 'ClustAssess.Rmd' failed with diagnostics:
+there is no package called 'Seurat'
+--- failed re-building ‘ClustAssess.Rmd’
+
+--- re-building ‘comparing-soft-and-hierarchical.Rmd’ using rmarkdown
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/setup-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 31275 bytes
+Input file size = 31389 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24565
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24565
+
+Output IDAT size = 24565 bytes (6710 bytes decrease)
+Output file size = 24643 bytes (6746 bytes = 21.49% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 29856 bytes
+Input file size = 29970 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783
+
+Output IDAT size = 23783 bytes (6073 bytes decrease)
+Output file size = 23861 bytes (6109 bytes = 20.38% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-2.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 31058 bytes
+Input file size = 31172 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24614
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24614
+
+Output IDAT size = 24614 bytes (6444 bytes decrease)
+Output file size = 24692 bytes (6480 bytes = 20.79% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-3.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 21221 bytes
+Input file size = 21323 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17324
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17324
+
+Output IDAT size = 17324 bytes (3897 bytes decrease)
+Output file size = 17402 bytes (3921 bytes = 18.39% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33803 bytes
+Input file size = 33929 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27092
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27092
+
+Output IDAT size = 27092 bytes (6711 bytes decrease)
+Output file size = 27170 bytes (6759 bytes = 19.92% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-2.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33849 bytes
+Input file size = 33975 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27923
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27923
+
+Output IDAT size = 27923 bytes (5926 bytes decrease)
+Output file size = 28001 bytes (5974 bytes = 17.58% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/new/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-3.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33198 bytes
+Input file size = 33324 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27196
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27196
+
+Output IDAT size = 27196 bytes (6002 bytes decrease)
+Output file size = 27274 bytes (6050 bytes = 18.16% decrease)
+
+--- finished re-building ‘comparing-soft-and-hierarchical.Rmd’
+
+SUMMARY: processing the following file failed:
+ ‘ClustAssess.Rmd’
+
+Error: Vignette re-building failed.
+Execution halted
+
+* DONE
+Status: 1 ERROR, 1 WARNING, 2 NOTEs
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/ClustAssess/old/ClustAssess.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘ClustAssess/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘ClustAssess’ version ‘0.3.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘ClustAssess’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking compiled code ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... ERROR
+Running examples in ‘ClustAssess-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: get_clustering_difference
+> ### Title: Graph Clustering Method Stability
+> ### Aliases: get_clustering_difference
+>
+> ### ** Examples
+>
+> set.seed(2021)
+> # create an artificial expression matrix
+> expr_matrix = matrix(runif(100*10), nrow = 100)
+> rownames(expr_matrix) = as.character(1:100)
+>
+> adj_matrix = Seurat::FindNeighbors(expr_matrix,
++ k.param = 10,
++ nn.method = "rann",
++ verbose = FALSE,
++ compute.SNN = FALSE)$nn
+Error in loadNamespace(x) : there is no package called ‘Seurat’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... WARNING
+Errors in running code in vignettes:
+when running code in ‘ClustAssess.Rmd’
+ ...
+
+> knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
+
+> set.seed(1001)
+
+> library(Seurat)
+
+ When sourcing ‘ClustAssess.R’:
+Error: there is no package called ‘Seurat’
+Execution halted
+
+ ‘ClustAssess.Rmd’ using ‘UTF-8’... failed
+ ‘comparing-soft-and-hierarchical.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... NOTE
+Error(s) in re-building vignettes:
+--- re-building ‘ClustAssess.Rmd’ using rmarkdown
+
+Quitting from lines 22-27 [setup] (ClustAssess.Rmd)
+Error: processing vignette 'ClustAssess.Rmd' failed with diagnostics:
+there is no package called 'Seurat'
+--- failed re-building ‘ClustAssess.Rmd’
+
+--- re-building ‘comparing-soft-and-hierarchical.Rmd’ using rmarkdown
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/setup-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 31275 bytes
+Input file size = 31389 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24565
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24565
+
+Output IDAT size = 24565 bytes (6710 bytes decrease)
+Output file size = 24643 bytes (6746 bytes = 21.49% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 29856 bytes
+Input file size = 29970 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783
+
+Output IDAT size = 23783 bytes (6073 bytes decrease)
+Output file size = 23861 bytes (6109 bytes = 20.38% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-2.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 31058 bytes
+Input file size = 31172 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24614
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24614
+
+Output IDAT size = 24614 bytes (6444 bytes decrease)
+Output file size = 24692 bytes (6480 bytes = 20.79% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/clustering-3.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 21221 bytes
+Input file size = 21323 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17324
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 17324
+
+Output IDAT size = 17324 bytes (3897 bytes decrease)
+Output file size = 17402 bytes (3921 bytes = 18.39% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-1.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33803 bytes
+Input file size = 33929 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27092
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27092
+
+Output IDAT size = 27092 bytes (6711 bytes decrease)
+Output file size = 27170 bytes (6759 bytes = 19.92% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-2.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33849 bytes
+Input file size = 33975 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27923
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27923
+
+Output IDAT size = 27923 bytes (5926 bytes decrease)
+Output file size = 28001 bytes (5974 bytes = 17.58% decrease)
+
+** Processing: /tmp/workdir/ClustAssess/old/ClustAssess.Rcheck/vign_test/ClustAssess/vignettes/comparing-soft-and-hierarchical_files/figure-html/ecs-3.png
+672x432 pixels, 3x8 bits/pixel, RGB
+Input IDAT size = 33198 bytes
+Input file size = 33324 bytes
+
+Trying:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27196
+ zc = 9 zm = 8 zs = 1 f = 0
+ zc = 1 zm = 8 zs = 2 f = 0
+ zc = 9 zm = 8 zs = 3 f = 0
+ zc = 9 zm = 8 zs = 0 f = 5
+ zc = 9 zm = 8 zs = 1 f = 5
+ zc = 1 zm = 8 zs = 2 f = 5
+ zc = 9 zm = 8 zs = 3 f = 5
+
+Selecting parameters:
+ zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 27196
+
+Output IDAT size = 27196 bytes (6002 bytes decrease)
+Output file size = 27274 bytes (6050 bytes = 18.16% decrease)
+
+--- finished re-building ‘comparing-soft-and-hierarchical.Rmd’
+
+SUMMARY: processing the following file failed:
+ ‘ClustAssess.Rmd’
+
+Error: Vignette re-building failed.
+Execution halted
+
+* DONE
+Status: 1 ERROR, 1 WARNING, 2 NOTEs
+
+
+
+
+
+```
+# clustree
+
+
+
+* Version: 0.5.1
+* GitHub: https://github.com/lazappi/clustree
+* Source code: https://github.com/cran/clustree
+* Date/Publication: 2023-11-05 19:10:02 UTC
+* Number of recursive dependencies: 191
+
+Run `revdepcheck::cloud_details(, "clustree")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/clustree/new/clustree.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘clustree/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘clustree’ version ‘0.5.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘clustree’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘clustree.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/clustree/old/clustree.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘clustree/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘clustree’ version ‘0.5.1’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘clustree’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘clustree.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# conos
+
+
+
+* Version: 1.5.2
+* GitHub: https://github.com/kharchenkolab/conos
+* Source code: https://github.com/cran/conos
+* Date/Publication: 2024-02-26 19:30:05 UTC
+* Number of recursive dependencies: 238
+
+Run `revdepcheck::cloud_details(, "conos")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/conos/new/conos.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘conos/DESCRIPTION’ ... OK
+* this is package ‘conos’ version ‘1.5.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘conos’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... NOTE
+ installed size is 15.0Mb
+ sub-directories of 1Mb or more:
+ libs 13.1Mb
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking line endings in Makefiles ... OK
+* checking compilation flags in Makevars ... OK
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/conos/old/conos.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘conos/DESCRIPTION’ ... OK
+* this is package ‘conos’ version ‘1.5.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘conos’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... NOTE
+ installed size is 15.0Mb
+ sub-directories of 1Mb or more:
+ libs 13.1Mb
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking line endings in Makefiles ... OK
+* checking compilation flags in Makevars ... OK
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+# countland
+
+
+
+* Version: 0.1.2
+* GitHub: https://github.com/shchurch/countland
+* Source code: https://github.com/cran/countland
+* Date/Publication: 2024-02-01 18:00:02 UTC
+* Number of recursive dependencies: 198
+
+Run `revdepcheck::cloud_details(, "countland")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/countland/new/countland.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘countland/DESCRIPTION’ ... OK
+* this is package ‘countland’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘countland’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking examples ... ERROR
+Running examples in ‘countland-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: Cluster
+> ### Title: Perform spectral clustering on dot products.
+> ### Aliases: Cluster
+>
+> ### ** Examples
+>
+> gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
+> gold.data <- Seurat::Read10X(data.dir = gold_path)
+Error in loadNamespace(x) : there is no package called ‘Seurat’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... ERROR
+ Running ‘testthat.R’
+Running the tests in ‘tests/testthat.R’ failed.
+Complete output:
+ > library(testthat)
+ > library(countland)
+ >
+ > test_check("countland")
+ Performing spectral clustering on dot products...
+ done.
+ Performing spectral embedding on dot products...
+ done.
+ [ FAIL 7 | WARN 2 | SKIP 0 | PASS 13 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Error ('test-countland.R:2:1'): (code run outside of `test_that()`) ─────────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_IMA.R:2:1'): (code run outside of `test_that()`) ─────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_IMA.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_dot.R:2:1'): (code run outside of `test_that()`) ─────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_dot.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_score.R:2:1'): (code run outside of `test_that()`) ───
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_score.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_shared_counts.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_shared_counts.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_subsample.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_subsample.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_subset.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+
+ [ FAIL 7 | WARN 2 | SKIP 0 | PASS 13 ]
+ Error: Test failures
+ Execution halted
+* DONE
+Status: 2 ERRORs, 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/countland/old/countland.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘countland/DESCRIPTION’ ... OK
+* this is package ‘countland’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘countland’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking examples ... ERROR
+Running examples in ‘countland-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: Cluster
+> ### Title: Perform spectral clustering on dot products.
+> ### Aliases: Cluster
+>
+> ### ** Examples
+>
+> gold_path <- system.file("testdata", package = "countland", mustWork = TRUE)
+> gold.data <- Seurat::Read10X(data.dir = gold_path)
+Error in loadNamespace(x) : there is no package called ‘Seurat’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... ERROR
+ Running ‘testthat.R’
+Running the tests in ‘tests/testthat.R’ failed.
+Complete output:
+ > library(testthat)
+ > library(countland)
+ >
+ > test_check("countland")
+ Performing spectral clustering on dot products...
+ done.
+ Performing spectral embedding on dot products...
+ done.
+ [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Error ('test-countland.R:2:1'): (code run outside of `test_that()`) ─────────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_IMA.R:2:1'): (code run outside of `test_that()`) ─────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_IMA.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_dot.R:2:1'): (code run outside of `test_that()`) ─────
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_dot.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_score.R:2:1'): (code run outside of `test_that()`) ───
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_score.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_shared_counts.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_shared_counts.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_subsample.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_subsample.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+ ── Error ('test-countland_subset.R:2:1'): (code run outside of `test_that()`) ──
+
+ Error in `loadNamespace(x)`: there is no package called 'Seurat'
+ Backtrace:
+ ▆
+ 1. └─base::loadNamespace(x) at test-countland_subset.R:2:1
+ 2. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
+ 3. └─base (local) withOneRestart(expr, restarts[[1L]])
+ 4. └─base (local) doWithOneRestart(return(expr), restart)
+
+ [ FAIL 7 | WARN 0 | SKIP 0 | PASS 13 ]
+ Error: Test failures
+ Execution halted
+* DONE
+Status: 2 ERRORs, 1 NOTE
+
+
+
+
+
+```
+# datapack
+
+
+
+* Version: 1.4.1
+* GitHub: https://github.com/ropensci/datapack
+* Source code: https://github.com/cran/datapack
+* Date/Publication: 2022-06-10 19:40:01 UTC
+* Number of recursive dependencies: 67
+
+Run `revdepcheck::cloud_details(, "datapack")` for more info
+
+
+
+## In both
+
+* checking whether package ‘datapack’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/datapack/new/datapack.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘datapack’ ...
+** package ‘datapack’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error in dyn.load(file, DLLpath = DLLpath, ...) :
+ unable to load shared object '/opt/R/4.3.1/lib/R/site-library/redland/libs/redland.so':
+ librdf.so.0: cannot open shared object file: No such file or directory
+Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
+Execution halted
+ERROR: lazy loading failed for package ‘datapack’
+* removing ‘/tmp/workdir/datapack/new/datapack.Rcheck/datapack’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘datapack’ ...
+** package ‘datapack’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error in dyn.load(file, DLLpath = DLLpath, ...) :
+ unable to load shared object '/opt/R/4.3.1/lib/R/site-library/redland/libs/redland.so':
+ librdf.so.0: cannot open shared object file: No such file or directory
+Calls: ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
+Execution halted
+ERROR: lazy loading failed for package ‘datapack’
+* removing ‘/tmp/workdir/datapack/old/datapack.Rcheck/datapack’
+
+
+```
+# DIscBIO
+
+
+
+* Version: 1.2.2
+* GitHub: https://github.com/ocbe-uio/DIscBIO
+* Source code: https://github.com/cran/DIscBIO
+* Date/Publication: 2023-11-06 10:50:02 UTC
+* Number of recursive dependencies: 208
+
+Run `revdepcheck::cloud_details(, "DIscBIO")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/DIscBIO/new/DIscBIO.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘DIscBIO/DESCRIPTION’ ... OK
+* this is package ‘DIscBIO’ version ‘1.2.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘DIscBIO’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/DIscBIO/old/DIscBIO.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘DIscBIO/DESCRIPTION’ ... OK
+* this is package ‘DIscBIO’ version ‘1.2.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘DIscBIO’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# dyngen
+
+
+
+* Version: 1.0.5
+* GitHub: https://github.com/dynverse/dyngen
+* Source code: https://github.com/cran/dyngen
+* Date/Publication: 2022-10-12 15:22:39 UTC
+* Number of recursive dependencies: 208
+
+Run `revdepcheck::cloud_details(, "dyngen")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/dyngen/new/dyngen.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘dyngen/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘dyngen’ version ‘1.0.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘dyngen’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* 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
+ ‘getting_started.html.asis’ using ‘UTF-8’... OK
+ ‘installation.html.asis’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/dyngen/old/dyngen.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘dyngen/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘dyngen’ version ‘1.0.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘dyngen’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* 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
+ ‘getting_started.html.asis’ using ‘UTF-8’... OK
+ ‘installation.html.asis’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# evolqg
+
+
+
+* Version: 0.3-4
+* GitHub: https://github.com/lem-usp/evolqg
+* Source code: https://github.com/cran/evolqg
+* Date/Publication: 2023-12-05 15:20:12 UTC
+* Number of recursive dependencies: 111
+
+Run `revdepcheck::cloud_details(, "evolqg")` for more info
+
+
+
+## In both
+
+* checking whether package ‘evolqg’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘evolqg’ ...
+** package ‘evolqg’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o
+g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/evolqg/new/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs
+** R
+** data
+** inst
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
+ there is no package called ‘quantreg’
+Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: lazy loading failed for package ‘evolqg’
+* removing ‘/tmp/workdir/evolqg/new/evolqg.Rcheck/evolqg’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘evolqg’ ...
+** package ‘evolqg’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c fast_RS.cpp -o fast_RS.o
+g++ -std=gnu++17 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o evolqg.so RcppExports.o fast_RS.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/evolqg/old/evolqg.Rcheck/00LOCK-evolqg/00new/evolqg/libs
+** R
+** data
+** inst
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
+ there is no package called ‘quantreg’
+Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: lazy loading failed for package ‘evolqg’
+* removing ‘/tmp/workdir/evolqg/old/evolqg.Rcheck/evolqg’
+
+
+```
+# frechet
+
+
+
+* Version: 0.3.0
+* GitHub: https://github.com/functionaldata/tFrechet
+* Source code: https://github.com/cran/frechet
+* Date/Publication: 2023-12-09 15:50:08 UTC
+* Number of recursive dependencies: 111
+
+Run `revdepcheck::cloud_details(, "frechet")` for more info
+
+
+
+## In both
+
+* checking whether package ‘frechet’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/frechet/new/frechet.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘frechet’ ...
+** package ‘frechet’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
+ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required
+Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
+Execution halted
+ERROR: lazy loading failed for package ‘frechet’
+* removing ‘/tmp/workdir/frechet/new/frechet.Rcheck/frechet’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘frechet’ ...
+** package ‘frechet’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** byte-compile and prepare package for lazy loading
+Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
+ namespace ‘Matrix’ 1.5-4.1 is already loaded, but >= 1.6.1 is required
+Calls: ... namespaceImportFrom -> asNamespace -> loadNamespace
+Execution halted
+ERROR: lazy loading failed for package ‘frechet’
+* removing ‘/tmp/workdir/frechet/old/frechet.Rcheck/frechet’
+
+
+```
+# manet
+
+
+
+* Version: 2.0
+* GitHub: NA
+* Source code: https://github.com/cran/manet
+* Date/Publication: 2018-08-23 15:02:15 UTC
+* Number of recursive dependencies: 21
+
+Run `revdepcheck::cloud_details(, "manet")` for more info
+
+
+
+## In both
+
+* checking whether package ‘manet’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/manet/new/manet.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘manet’ ...
+** package ‘manet’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘manet’
+* removing ‘/tmp/workdir/manet/new/manet.Rcheck/manet’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘manet’ ...
+** package ‘manet’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘manet’
+* removing ‘/tmp/workdir/manet/old/manet.Rcheck/manet’
+
+
+```
+# metadat
+
+
+
+* Version: 1.2-0
+* GitHub: https://github.com/wviechtb/metadat
+* Source code: https://github.com/cran/metadat
+* Date/Publication: 2022-04-06 11:52:37 UTC
+* Number of recursive dependencies: 126
+
+Run `revdepcheck::cloud_details(, "metadat")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/metadat/new/metadat.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘metadat/DESCRIPTION’ ... OK
+* this is package ‘metadat’ version ‘1.2-0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘rms’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘metadat’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/metadat/old/metadat.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘metadat/DESCRIPTION’ ... OK
+* this is package ‘metadat’ version ‘1.2-0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘rms’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘metadat’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# MetaNet
+
+
+
+* Version: 0.1.2
+* GitHub: https://github.com/Asa12138/MetaNet
+* Source code: https://github.com/cran/MetaNet
+* Date/Publication: 2024-03-25 20:40:07 UTC
+* Number of recursive dependencies: 161
+
+Run `revdepcheck::cloud_details(, "MetaNet")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/MetaNet/new/MetaNet.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘MetaNet/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘MetaNet’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘ggpmisc’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘MetaNet’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... ERROR
+Running examples in ‘MetaNet-Ex.R’ failed
+The error most likely occurred in:
+
+> ### Name: rand_net_par
+> ### Title: Net_pars of many random network
+> ### Aliases: rand_net_par compare_rand
+>
+> ### ** Examples
+>
+> data("c_net")
+> rand_net_par(co_net_rmt, reps = 30) -> randp
+> net_par(co_net_rmt, fast = FALSE) -> pars
+Error in names(res$hub.vector) <- vertex_attr(graph, "name", V(graph)) :
+ attempt to set an attribute on NULL
+Calls: net_par ... -> hits_scores -> hub_and_authority_scores_impl
+Execution halted
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘MetaNet.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 ERROR, 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/MetaNet/old/MetaNet.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘MetaNet/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘MetaNet’ version ‘0.1.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘ggpmisc’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘MetaNet’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘MetaNet.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# mlmts
+
+
+
+* Version: 1.1.1
+* GitHub: NA
+* Source code: https://github.com/cran/mlmts
+* Date/Publication: 2023-01-22 21:30:02 UTC
+* Number of recursive dependencies: 241
+
+Run `revdepcheck::cloud_details(, "mlmts")` for more info
+
+
+
+## In both
+
+* checking whether package ‘mlmts’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘mlmts’ ...
+** package ‘mlmts’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** inst
+** byte-compile and prepare package for lazy loading
+Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
+ there is no package called ‘quantreg’
+Error: unable to load R code in package ‘mlmts’
+Execution halted
+ERROR: lazy loading failed for package ‘mlmts’
+* removing ‘/tmp/workdir/mlmts/new/mlmts.Rcheck/mlmts’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘mlmts’ ...
+** package ‘mlmts’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** inst
+** byte-compile and prepare package for lazy loading
+Error : package or namespace load failed for ‘quantspec’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
+ there is no package called ‘quantreg’
+Error: unable to load R code in package ‘mlmts’
+Execution halted
+ERROR: lazy loading failed for package ‘mlmts’
+* removing ‘/tmp/workdir/mlmts/old/mlmts.Rcheck/mlmts’
+
+
+```
+# netcmc
+
+
+
+* Version: 1.0.2
+* GitHub: NA
+* Source code: https://github.com/cran/netcmc
+* Date/Publication: 2022-11-08 22:30:15 UTC
+* Number of recursive dependencies: 61
+
+Run `revdepcheck::cloud_details(, "netcmc")` for more info
+
+
+
+## In both
+
+* checking whether package ‘netcmc’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘netcmc’ ...
+** package ‘netcmc’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+using C++11
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c eigenValuesRcppConversion.cpp -o eigenValuesRcppConversion.o
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+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorTransposeVectorMultiplicationRcpp.cpp -o vectorTransposeVectorMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o
+g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/netcmc/new/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs
+** R
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘netcmc’
+* removing ‘/tmp/workdir/netcmc/new/netcmc.Rcheck/netcmc’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘netcmc’ ...
+** package ‘netcmc’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+using C++11
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c choleskyDecompositionRcppConversion.cpp -o choleskyDecompositionRcppConversion.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleMatrixMultiplicationRcpp.cpp -o doubleMatrixMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c doubleVectorMultiplicationRcpp.cpp -o doubleVectorMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c eigenValuesRcppConversion.cpp -o eigenValuesRcppConversion.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getDiagonalMatrix.cpp -o getDiagonalMatrix.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getExp.cpp -o getExp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getExpDividedByOnePlusExp.cpp -o getExpDividedByOnePlusExp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMeanCenteredRandomEffects.cpp -o getMeanCenteredRandomEffects.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariateBinomialNetworkLerouxDIC.cpp -o getMultivariateBinomialNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariateGaussianNetworkLerouxDIC.cpp -o getMultivariateGaussianNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariatePoissonNetworkLerouxDIC.cpp -o getMultivariatePoissonNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getNonZeroEntries.cpp -o getNonZeroEntries.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSubvector.cpp -o getSubvector.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSubvectorIndecies.cpp -o getSubvectorIndecies.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumExpNetwork.cpp -o getSumExpNetwork.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumExpNetworkIndecies.cpp -o getSumExpNetworkIndecies.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumExpNetworkLeroux.cpp -o getSumExpNetworkLeroux.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumExpNetworkLerouxIndecies.cpp -o getSumExpNetworkLerouxIndecies.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumLogExp.cpp -o getSumLogExp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumLogExpIndecies.cpp -o getSumLogExpIndecies.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getSumVector.cpp -o getSumVector.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getTripletForm.cpp -o getTripletForm.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariateBinomialNetworkLerouxDIC.cpp -o getUnivariateBinomialNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariateGaussianNetworkLerouxDIC.cpp -o getUnivariateGaussianNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariatePoissonNetworkDIC.cpp -o getUnivariatePoissonNetworkDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariatePoissonNetworkLerouxDIC.cpp -o getUnivariatePoissonNetworkLerouxDIC.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.cpp -o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c getVectorMean.cpp -o getVectorMean.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c matrixInverseRcppConversion.cpp -o matrixInverseRcppConversion.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c matrixMatrixAdditionRcpp.cpp -o matrixMatrixAdditionRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c matrixMatrixSubtractionRcpp.cpp -o matrixMatrixSubtractionRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c matrixVectorMultiplicationRcpp.cpp -o matrixVectorMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c multivariateBinomialNetworkLerouxAllUpdate.cpp -o multivariateBinomialNetworkLerouxAllUpdate.o
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+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariateGaussianNetworkLerouxSingleMHUpdate.cpp -o univariateGaussianNetworkLerouxSingleMHUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.cpp -o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariateGaussianNetworkLerouxTauSquaredUpdate.cpp -o univariateGaussianNetworkLerouxTauSquaredUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariateGaussianNetworkLerouxURandomEffectsUpdate.cpp -o univariateGaussianNetworkLerouxURandomEffectsUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxAllUpdate.cpp -o univariatePoissonNetworkLerouxAllUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxBetaUpdate.cpp -o univariatePoissonNetworkLerouxBetaUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxRhoUpdate.cpp -o univariatePoissonNetworkLerouxRhoUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxSigmaSquaredUpdate.cpp -o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxSingleUpdate.cpp -o univariatePoissonNetworkLerouxSingleUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.cpp -o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxTauSquaredUpdate.cpp -o univariatePoissonNetworkLerouxTauSquaredUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c univariatePoissonNetworkLerouxURandomEffectsUpdate.cpp -o univariatePoissonNetworkLerouxURandomEffectsUpdate.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorTransposeVectorMultiplicationRcpp.cpp -o vectorTransposeVectorMultiplicationRcpp.o
+g++ -std=gnu++11 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppProgress/include' -I/usr/local/include -fpic -g -O2 -c vectorVectorTransposeMultiplicationRcpp.cpp -o vectorVectorTransposeMultiplicationRcpp.o
+g++ -std=gnu++11 -shared -L/opt/R/4.3.1/lib/R/lib -L/usr/local/lib -o netcmc.so RcppExports.o choleskyDecompositionRcppConversion.o doubleMatrixMultiplicationRcpp.o doubleVectorMultiplicationRcpp.o eigenValuesRcppConversion.o getDiagonalMatrix.o getExp.o getExpDividedByOnePlusExp.o getMeanCenteredRandomEffects.o getMultivariateBinomialNetworkLerouxDIC.o getMultivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariateGaussianNetworkLerouxDIC.o getMultivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getMultivariatePoissonNetworkLerouxDIC.o getMultivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getNonZeroEntries.o getSubvector.o getSubvectorIndecies.o getSumExpNetwork.o getSumExpNetworkIndecies.o getSumExpNetworkLeroux.o getSumExpNetworkLerouxIndecies.o getSumLogExp.o getSumLogExpIndecies.o getSumVector.o getTripletForm.o getUnivariateBinomialNetworkLerouxDIC.o getUnivariateBinomialNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariateGaussianNetworkLerouxDIC.o getUnivariateGaussianNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkDIC.o getUnivariatePoissonNetworkFittedValuesAndLikelihoodForDICEveryIteration.o getUnivariatePoissonNetworkLerouxDIC.o getUnivariatePoissonNetworkLerouxFittedValuesAndLikelihoodForDICEveryIteration.o getVectorMean.o matrixInverseRcppConversion.o matrixMatrixAdditionRcpp.o matrixMatrixSubtractionRcpp.o matrixVectorMultiplicationRcpp.o multivariateBinomialNetworkLerouxAllUpdate.o multivariateBinomialNetworkLerouxBetaUpdate.o multivariateBinomialNetworkLerouxRhoUpdate.o multivariateBinomialNetworkLerouxSingleUpdate.o multivariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o multivariateBinomialNetworkLerouxTauSquaredUpdate.o multivariateBinomialNetworkLerouxURandomEffectsUpdate.o multivariateBinomialNetworkLerouxVRandomEffectsUpdate.o multivariateBinomialNetworkLerouxVarianceCovarianceUUpdate.o multivariateBinomialNetworkRandAllUpdate.o multivariateBinomialNetworkRandSingleUpdate.o multivariateGaussianNetworkLerouxAllMHUpdate.o multivariateGaussianNetworkLerouxBetaUpdate.o multivariateGaussianNetworkLerouxRhoUpdate.o multivariateGaussianNetworkLerouxSigmaSquaredEUpdate.o multivariateGaussianNetworkLerouxSingleMHUpdate.o multivariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o multivariateGaussianNetworkLerouxTauSquaredUpdate.o multivariateGaussianNetworkLerouxURandomEffectsUpdate.o multivariateGaussianNetworkLerouxVarianceCovarianceUUpdate.o multivariateGaussianNetworkRandAllUpdate.o multivariateGaussianNetworkRandSingleUpdate.o multivariateGaussianNetworkRandVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxAllUpdate.o multivariatePoissonNetworkLerouxBetaUpdate.o multivariatePoissonNetworkLerouxRhoUpdate.o multivariatePoissonNetworkLerouxSingleUpdate.o multivariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o multivariatePoissonNetworkLerouxTauSquaredUpdate.o multivariatePoissonNetworkLerouxURandomEffectsUpdate.o multivariatePoissonNetworkLerouxVRandomEffectsUpdate.o multivariatePoissonNetworkLerouxVarianceCovarianceUUpdate.o multivariatePoissonNetworkRandAllUpdate.o multivariatePoissonNetworkRandSingleUpdate.o sumMatrix.o univariateBinomialNetworkLerouxAllUpdate.o univariateBinomialNetworkLerouxBetaUpdate.o univariateBinomialNetworkLerouxRhoUpdate.o univariateBinomialNetworkLerouxSigmaSquaredUpdate.o univariateBinomialNetworkLerouxSingleUpdate.o univariateBinomialNetworkLerouxSpatialRandomEffectsUpdate.o univariateBinomialNetworkLerouxTauSquaredUpdate.o univariateBinomialNetworkLerouxURandomEffectsUpdate.o univariateGaussianNetworkLerouxAllMHUpdate.o univariateGaussianNetworkLerouxBetaUpdate.o univariateGaussianNetworkLerouxRhoUpdate.o univariateGaussianNetworkLerouxSigmaSquaredEUpdate.o univariateGaussianNetworkLerouxSigmaSquaredUUpdate.o univariateGaussianNetworkLerouxSingleMHUpdate.o univariateGaussianNetworkLerouxSpatialRandomEffectsMHUpdate.o univariateGaussianNetworkLerouxTauSquaredUpdate.o univariateGaussianNetworkLerouxURandomEffectsUpdate.o univariatePoissonNetworkLerouxAllUpdate.o univariatePoissonNetworkLerouxBetaUpdate.o univariatePoissonNetworkLerouxRhoUpdate.o univariatePoissonNetworkLerouxSigmaSquaredUpdate.o univariatePoissonNetworkLerouxSingleUpdate.o univariatePoissonNetworkLerouxSpatialRandomEffectsUpdate.o univariatePoissonNetworkLerouxTauSquaredUpdate.o univariatePoissonNetworkLerouxURandomEffectsUpdate.o vectorTransposeVectorMultiplicationRcpp.o vectorVectorTransposeMultiplicationRcpp.o -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.3.1/lib/R/lib -lR
+installing to /tmp/workdir/netcmc/old/netcmc.Rcheck/00LOCK-netcmc/00new/netcmc/libs
+** R
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘netcmc’
+* removing ‘/tmp/workdir/netcmc/old/netcmc.Rcheck/netcmc’
+
+
+```
+# NetworkChange
+
+
+
+* Version: 0.8
+* GitHub: https://github.com/jongheepark/NetworkChange
+* Source code: https://github.com/cran/NetworkChange
+* Date/Publication: 2022-03-04 07:30:02 UTC
+* Number of recursive dependencies: 131
+
+Run `revdepcheck::cloud_details(, "NetworkChange")` for more info
+
+
+
+## In both
+
+* checking whether package ‘NetworkChange’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘NetworkChange’ ...
+** package ‘NetworkChange’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘NetworkChange’
+* removing ‘/tmp/workdir/NetworkChange/new/NetworkChange.Rcheck/NetworkChange’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘NetworkChange’ ...
+** package ‘NetworkChange’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+** byte-compile and prepare package for lazy loading
+Error: package or namespace load failed for ‘MCMCpack’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
+ there is no package called ‘quantreg’
+Execution halted
+ERROR: lazy loading failed for package ‘NetworkChange’
+* removing ‘/tmp/workdir/NetworkChange/old/NetworkChange.Rcheck/NetworkChange’
+
+
+```
+# pagoda2
+
+
+
+* Version: 1.0.12
+* GitHub: https://github.com/kharchenkolab/pagoda2
+* Source code: https://github.com/cran/pagoda2
+* Date/Publication: 2024-02-27 00:50:02 UTC
+* Number of recursive dependencies: 162
+
+Run `revdepcheck::cloud_details(, "pagoda2")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/pagoda2/new/pagoda2.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘pagoda2/DESCRIPTION’ ... OK
+* this is package ‘pagoda2’ version ‘1.0.12’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘scde’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘pagoda2’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... NOTE
+ installed size is 10.3Mb
+ sub-directories of 1Mb or more:
+ R 1.5Mb
+ libs 7.6Mb
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking line endings in Makefiles ... OK
+* checking compilation flags in Makevars ... OK
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/pagoda2/old/pagoda2.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘pagoda2/DESCRIPTION’ ... OK
+* this is package ‘pagoda2’ version ‘1.0.12’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘scde’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘pagoda2’ can be installed ... OK
+* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+* checking installed package size ... NOTE
+ installed size is 10.3Mb
+ sub-directories of 1Mb or more:
+ R 1.5Mb
+ libs 7.6Mb
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking line endings in Makefiles ... OK
+* checking compilation flags in Makevars ... OK
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 2 NOTEs
+
+
+
+
+
+```
+# pcutils
+
+
+
+* Version: 0.2.5
+* GitHub: https://github.com/Asa12138/pcutils
+* Source code: https://github.com/cran/pcutils
+* Date/Publication: 2024-03-19 16:50:07 UTC
+* Number of recursive dependencies: 277
+
+Run `revdepcheck::cloud_details(, "pcutils")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/pcutils/new/pcutils.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘pcutils/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘pcutils’ version ‘0.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘ggpmisc’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘pcutils’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking startup messages can be suppressed ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/pcutils/old/pcutils.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘pcutils/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘pcutils’ version ‘0.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘ggpmisc’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘pcutils’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking startup messages can be suppressed ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking examples ... OK
+* DONE
+Status: 1 NOTE
+
+
+
+
+
+```
+# robber
+
+
+
+* Version: 0.2.4
+* GitHub: https://github.com/Chabert-Liddell/robber
+* Source code: https://github.com/cran/robber
+* Date/Publication: 2024-02-07 13:50:02 UTC
+* Number of recursive dependencies: 144
+
+Run `revdepcheck::cloud_details(, "robber")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/robber/new/robber.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘robber/DESCRIPTION’ ... OK
+* this is package ‘robber’ version ‘0.2.4’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘robber’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking startup messages can be suppressed ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘topological-analysis.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: OK
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/robber/old/robber.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘robber/DESCRIPTION’ ... OK
+* this is package ‘robber’ version ‘0.2.4’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘robber’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking startup messages can be suppressed ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking LazyData ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... OK
+ ‘topological-analysis.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: OK
+
+
+
+
+
+```
+# rTwig
+
+
+
+* Version: 1.0.2
+* GitHub: https://github.com/aidanmorales/rTwig
+* Source code: https://github.com/cran/rTwig
+* Date/Publication: 2024-04-08 15:00:02 UTC
+* Number of recursive dependencies: 188
+
+Run `revdepcheck::cloud_details(, "rTwig")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/rTwig/new/rTwig.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘rTwig/DESCRIPTION’ ... OK
+* this is package ‘rTwig’ version ‘1.0.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required and available but unsuitable version: ‘Matrix’
+
+Package suggested but not available for checking: ‘ggpmisc’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/rTwig/old/rTwig.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘rTwig/DESCRIPTION’ ... OK
+* this is package ‘rTwig’ version ‘1.0.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required and available but unsuitable version: ‘Matrix’
+
+Package suggested but not available for checking: ‘ggpmisc’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# scDiffCom
+
+
+
+* Version: 1.0.0
+* GitHub: NA
+* Source code: https://github.com/cran/scDiffCom
+* Date/Publication: 2023-11-03 18:40:02 UTC
+* Number of recursive dependencies: 257
+
+Run `revdepcheck::cloud_details(, "scDiffCom")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/scDiffCom/new/scDiffCom.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘scDiffCom/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘scDiffCom’ version ‘1.0.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘Seurat’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/scDiffCom/old/scDiffCom.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘scDiffCom/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘scDiffCom’ version ‘1.0.0’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘Seurat’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# SignacX
+
+
+
+* Version: 2.2.5
+* GitHub: https://github.com/mathewchamberlain/SignacX
+* Source code: https://github.com/cran/SignacX
+* Date/Publication: 2021-11-18 16:20:03 UTC
+* Number of recursive dependencies: 172
+
+Run `revdepcheck::cloud_details(, "SignacX")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/SignacX/new/SignacX.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘SignacX/DESCRIPTION’ ... OK
+* this is package ‘SignacX’ version ‘2.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘Seurat’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/SignacX/old/SignacX.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘SignacX/DESCRIPTION’ ... OK
+* this is package ‘SignacX’ version ‘2.2.5’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘Seurat’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# streamDAG
+
+
+
+* Version: 1.5
+* GitHub: NA
+* Source code: https://github.com/cran/streamDAG
+* Date/Publication: 2023-10-06 18:50:02 UTC
+* Number of recursive dependencies: 133
+
+Run `revdepcheck::cloud_details(, "streamDAG")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘streamDAG/DESCRIPTION’ ... OK
+* this is package ‘streamDAG’ version ‘1.5’
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘asbio’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘streamDAG/DESCRIPTION’ ... OK
+* this is package ‘streamDAG’ version ‘1.5’
+* checking package namespace information ... OK
+* checking package dependencies ... ERROR
+Package required but not available: ‘asbio’
+
+See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+manual.
+* DONE
+Status: 1 ERROR
+
+
+
+
+
+```
+# treefit
+
+
+
+* Version: 1.0.2
+* GitHub: https://github.com/hayamizu-lab/treefit-r
+* Source code: https://github.com/cran/treefit
+* Date/Publication: 2022-01-18 07:50:02 UTC
+* Number of recursive dependencies: 159
+
+Run `revdepcheck::cloud_details(, "treefit")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+* using log directory ‘/tmp/workdir/treefit/new/treefit.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘treefit/DESCRIPTION’ ... OK
+* this is package ‘treefit’ version ‘1.0.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘treefit’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* 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 ... WARNING
+Errors in running code in vignettes:
+when running code in ‘working-with-seurat.Rmd’
+ ...
+
+
+> trapnell.dynverse <- readRDS(trapnell.path)
+
+> trapnell <- Seurat::CreateSeuratObject(counts = t(trapnell.dynverse$count),
++ min.cells = 3, min.features = 200)
+
+ When sourcing ‘working-with-seurat.R’:
+Error: there is no package called ‘Seurat’
+Execution halted
+
+ ‘treefit.Rmd’ using ‘UTF-8’... OK
+ ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 WARNING, 1 NOTE
+
+
+
+
+
+```
+### CRAN
+
+```
+* using log directory ‘/tmp/workdir/treefit/old/treefit.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+ GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
+* running under: Ubuntu 22.04.4 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘treefit/DESCRIPTION’ ... OK
+* this is package ‘treefit’ version ‘1.0.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... NOTE
+Package suggested but not available for checking: ‘Seurat’
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘treefit’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* checking R code for possible problems ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* 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 ... WARNING
+Errors in running code in vignettes:
+when running code in ‘working-with-seurat.Rmd’
+ ...
+
+
+> trapnell.dynverse <- readRDS(trapnell.path)
+
+> trapnell <- Seurat::CreateSeuratObject(counts = t(trapnell.dynverse$count),
++ min.cells = 3, min.features = 200)
+
+ When sourcing ‘working-with-seurat.R’:
+Error: there is no package called ‘Seurat’
+Execution halted
+
+ ‘treefit.Rmd’ using ‘UTF-8’... OK
+ ‘working-with-seurat.Rmd’ using ‘UTF-8’... failed
+* checking re-building of vignette outputs ... OK
+* DONE
+Status: 1 WARNING, 1 NOTE
+
+
+
+
+
+```
diff --git a/revdep/problems.md b/revdep/problems.md
index c7a91f8651..cd397dc5df 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,3 +1,48 @@
+# BCT
+
+
+
+* Version: 1.2
+* GitHub: NA
+* Source code: https://github.com/cran/BCT
+* Date/Publication: 2022-05-12 14:00:05 UTC
+* Number of recursive dependencies: 13
+
+Run `revdepcheck::cloud_details(, "BCT")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘BCT-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: draw_models
+ > ### Title: Plot the results of the BCT and kBCT functions
+ > ### Aliases: draw_models
+ >
+ > ### ** Examples
+ >
+ >
+ > # Use the pewee dataset as an example:
+ > q <- BCT(pewee, 5) # maximum depth of 5
+ >
+ > draw_models(q)
+ Error in igraph::graph.lattice(length(subwords) + 1, directed = TRUE) :
+ argument "circular" is missing, with no default
+ Calls: draw_models -> show_tree ->
+ Execution halted
+ ```
+
+## In both
+
+* checking C++ specification ... NOTE
+ ```
+ Specified C++11: please drop specification unless essential
+ ```
+
# netropy
@@ -167,7 +212,7 @@ Run `revdepcheck::cloud_details(, "tidygraph")` for more info
Subsetting by nodes
Splitting by nodes
Unfocusing prior to morphing
- [ FAIL 13 | WARN 2 | SKIP 1 | PASS 426 ]
+ [ FAIL 13 | WARN 9 | SKIP 1 | PASS 426 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-random-walk.R:19:3'
@@ -208,7 +253,7 @@ Run `revdepcheck::cloud_details(, "tidygraph")` for more info
── Failure ('test-tidyr-utils.R:18:1'): graph context is empty after test ──────
environment(.graph_context$free)$private$context has length 1, not length 0.
- [ FAIL 13 | WARN 2 | SKIP 1 | PASS 426 ]
+ [ FAIL 13 | WARN 9 | SKIP 1 | PASS 426 ]
Error: Test failures
Execution halted
```
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
index 07ff9ce03a..f029c41d9b 100644
--- a/src/cpp11.cpp
+++ b/src/cpp11.cpp
@@ -22,470 +22,465 @@ extern "C" SEXP _igraph_getsphere(SEXP spos, SEXP sradius, SEXP scolor, SEXP lig
extern "C" {
/* .Call calls */
-extern SEXP R_igraph_add_edges(SEXP, SEXP);
-extern SEXP R_igraph_add_edges_manual(SEXP, SEXP);
-extern SEXP R_igraph_add_env(SEXP);
-extern SEXP R_igraph_add_myid_to_env(SEXP);
-extern SEXP R_igraph_add_version_to_env(SEXP);
-extern SEXP R_igraph_add_vertices(SEXP, SEXP);
-extern SEXP R_igraph_address(SEXP);
-extern SEXP R_igraph_adhesion(SEXP, SEXP);
-extern SEXP R_igraph_adjacency(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_adjacency_spectral_embedding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_adjacent_triangles(SEXP, SEXP);
-extern SEXP R_igraph_adjacent_vertices(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_adjlist(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_all_minimal_st_separators(SEXP);
-extern SEXP R_igraph_all_st_cuts(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_all_st_mincuts(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_are_adjacent(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_arpack(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_arpack_unpack_complex(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_articulation_points(SEXP);
-extern SEXP R_igraph_assortativity(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_assortativity_degree(SEXP, SEXP);
-extern SEXP R_igraph_assortativity_nominal(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_asymmetric_preference_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_atlas(SEXP);
-extern SEXP R_igraph_authority_score(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_automorphism_group(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_average_local_efficiency(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_average_path_length_dijkstra(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_avg_nearest_neighbor_degree(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_barabasi_aging_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_barabasi_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_betweenness_cutoff(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_betweenness_subset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bfs(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bfs_simple(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_biadjacency(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bibcoupling(SEXP, SEXP);
-extern SEXP R_igraph_biconnected_components(SEXP);
-extern SEXP R_igraph_bipartite_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bipartite_game_gnm(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bipartite_game_gnp(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bipartite_projection(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_bipartite_projection_size(SEXP, SEXP);
-extern SEXP R_igraph_bridges(SEXP);
-extern SEXP R_igraph_callaway_traits_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_canonical_permutation(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_betweenness(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_betweenness_tmax(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_closeness(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_closeness_tmax(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_degree(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_degree_tmax(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_eigenvector_centrality(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_centralization_eigenvector_centrality_tmax(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_circulant(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_cited_type_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_citing_cited_type_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_clique_number(SEXP);
-extern SEXP R_igraph_clique_size_hist(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_cliques(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_closeness_cutoff(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_cocitation(SEXP, SEXP);
-extern SEXP R_igraph_cohesion(SEXP, SEXP);
-extern SEXP R_igraph_cohesive_blocks(SEXP);
-extern SEXP R_igraph_community_edge_betweenness(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_fastgreedy(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_fluid_communities(SEXP, SEXP);
-extern SEXP R_igraph_community_infomap(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_label_propagation(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_leading_eigenvector(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_leiden(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_multilevel(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_community_optimal_modularity(SEXP, SEXP);
-extern SEXP R_igraph_community_to_membership2(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_compare_communities(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_complementer(SEXP, SEXP);
-extern SEXP R_igraph_compose(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_connect_neighborhood(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_connected_components(SEXP, SEXP);
-extern SEXP R_igraph_constraint(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_contract_vertices(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_convex_hull(SEXP);
-extern SEXP R_igraph_copy(SEXP);
-extern SEXP R_igraph_copy_env(SEXP);
-extern SEXP R_igraph_copy_from(SEXP);
-extern SEXP R_igraph_copy_to(SEXP);
-extern SEXP R_igraph_coreness(SEXP, SEXP);
-extern SEXP R_igraph_correlated_game(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_correlated_pair_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_count_automorphisms(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_count_isomorphisms_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_count_loops(SEXP);
-extern SEXP R_igraph_count_multiple(SEXP, SEXP);
-extern SEXP R_igraph_count_reachable(SEXP, SEXP);
-extern SEXP R_igraph_count_subisomorphisms_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_create(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_create_bipartite(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_de_bruijn(SEXP, SEXP);
-extern SEXP R_igraph_decompose(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_degree(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_degree_correlation_vector(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_degree_sequence_game(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_delete_edges(SEXP, SEXP);
-extern SEXP R_igraph_delete_vertices(SEXP, SEXP);
-extern SEXP R_igraph_delete_vertices_idx(SEXP, SEXP);
-extern SEXP R_igraph_density(SEXP, SEXP);
-extern SEXP R_igraph_deterministic_optimal_imitation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_dfs(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_diameter(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_difference(SEXP, SEXP);
-extern SEXP R_igraph_dim_select(SEXP);
-extern SEXP R_igraph_disjoint_union(SEXP);
-extern SEXP R_igraph_distances(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_bellman_ford(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_cutoff(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_dijkstra(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_dijkstra_cutoff(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_floyd_warshall(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_distances_johnson(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_diversity(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_dominator_tree(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_dot_product_game(SEXP, SEXP);
-extern SEXP R_igraph_dyad_census(SEXP);
-extern SEXP R_igraph_ecc(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_eccentricity_dijkstra(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_ecount(SEXP);
-extern SEXP R_igraph_edge_betweenness_cutoff(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_edge_betweenness_subset(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_edge_connectivity(SEXP, SEXP);
-extern SEXP R_igraph_edge_disjoint_paths(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_edges(SEXP, SEXP);
-extern SEXP R_igraph_eigen_adjacency(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_eigenvector_centrality(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_empty(SEXP, SEXP);
-extern SEXP R_igraph_erdos_renyi_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_es_adj(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_es_pairs(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_es_path(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_establishment_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_eulerian_cycle(SEXP);
-extern SEXP R_igraph_eulerian_path(SEXP);
-extern SEXP R_igraph_even_tarjan_reduction(SEXP);
-extern SEXP R_igraph_extended_chordal_ring(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_famous(SEXP);
-extern SEXP R_igraph_farthest_points(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_feedback_arc_set(SEXP, SEXP, SEXP);
+extern SEXP R_igraph_add_edges(void *, void *);
+extern SEXP R_igraph_add_edges_manual(void *, void *);
+extern SEXP R_igraph_add_env(void *);
+extern SEXP R_igraph_add_myid_to_env(void *);
+extern SEXP R_igraph_add_version_to_env(void *);
+extern SEXP R_igraph_add_vertices(void *, void *);
+extern SEXP R_igraph_address(void *);
+extern SEXP R_igraph_adhesion(void *, void *);
+extern SEXP R_igraph_adjacency(void *, void *, void *);
+extern SEXP R_igraph_adjacency_spectral_embedding(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_adjacent_triangles(void *, void *);
+extern SEXP R_igraph_adjacent_vertices(void *, void *, void *);
+extern SEXP R_igraph_adjlist(void *, void *, void *);
+extern SEXP R_igraph_all_minimal_st_separators(void *);
+extern SEXP R_igraph_all_st_cuts(void *, void *, void *);
+extern SEXP R_igraph_all_st_mincuts(void *, void *, void *, void *);
+extern SEXP R_igraph_are_adjacent(void *, void *, void *);
+extern SEXP R_igraph_arpack(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_arpack_unpack_complex(void *, void *, void *);
+extern SEXP R_igraph_articulation_points(void *);
+extern SEXP R_igraph_assortativity(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_assortativity_degree(void *, void *);
+extern SEXP R_igraph_assortativity_nominal(void *, void *, void *, void *);
+extern SEXP R_igraph_asymmetric_preference_game(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_atlas(void *);
+extern SEXP R_igraph_automorphism_group(void *, void *, void *);
+extern SEXP R_igraph_average_local_efficiency(void *, void *, void *, void *);
+extern SEXP R_igraph_average_path_length_dijkstra(void *, void *, void *, void *);
+extern SEXP R_igraph_avg_nearest_neighbor_degree(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_barabasi_aging_game(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_barabasi_game(void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_betweenness_cutoff(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_betweenness_subset(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_bfs(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_bfs_simple(void *, void *, void *);
+extern SEXP R_igraph_biadjacency(void *, void *, void *, void *);
+extern SEXP R_igraph_bibcoupling(void *, void *);
+extern SEXP R_igraph_biconnected_components(void *);
+extern SEXP R_igraph_bipartite_game_gnm(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_bipartite_game_gnp(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_bipartite_projection(void *, void *, void *, void *);
+extern SEXP R_igraph_bipartite_projection_size(void *, void *);
+extern SEXP R_igraph_bridges(void *);
+extern SEXP R_igraph_callaway_traits_game(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_canonical_permutation(void *, void *, void *);
+extern SEXP R_igraph_centralization(void *, void *, void *);
+extern SEXP R_igraph_centralization_betweenness(void *, void *, void *);
+extern SEXP R_igraph_centralization_betweenness_tmax(void *, void *, void *);
+extern SEXP R_igraph_centralization_closeness(void *, void *, void *);
+extern SEXP R_igraph_centralization_closeness_tmax(void *, void *, void *);
+extern SEXP R_igraph_centralization_degree(void *, void *, void *, void *);
+extern SEXP R_igraph_centralization_degree_tmax(void *, void *, void *, void *);
+extern SEXP R_igraph_centralization_eigenvector_centrality(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_centralization_eigenvector_centrality_tmax(void *, void *, void *, void *);
+extern SEXP R_igraph_circulant(void *, void *, void *);
+extern SEXP R_igraph_cited_type_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_citing_cited_type_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_clique_number(void *);
+extern SEXP R_igraph_clique_size_hist(void *, void *, void *);
+extern SEXP R_igraph_cliques(void *, void *, void *);
+extern SEXP R_igraph_closeness_cutoff(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_cocitation(void *, void *);
+extern SEXP R_igraph_cohesion(void *, void *);
+extern SEXP R_igraph_cohesive_blocks(void *);
+extern SEXP R_igraph_community_edge_betweenness(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_community_fastgreedy(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_community_fluid_communities(void *, void *);
+extern SEXP R_igraph_community_infomap(void *, void *, void *, void *);
+extern SEXP R_igraph_community_label_propagation(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_community_leading_eigenvector(void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_community_leiden(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_community_multilevel(void *, void *, void *);
+extern SEXP R_igraph_community_optimal_modularity(void *, void *);
+extern SEXP R_igraph_community_to_membership2(void *, void *, void *);
+extern SEXP R_igraph_compare_communities(void *, void *, void *);
+extern SEXP R_igraph_complementer(void *, void *);
+extern SEXP R_igraph_compose(void *, void *, void *);
+extern SEXP R_igraph_connect_neighborhood(void *, void *, void *);
+extern SEXP R_igraph_connected_components(void *, void *);
+extern SEXP R_igraph_constraint(void *, void *, void *);
+extern SEXP R_igraph_contract_vertices(void *, void *, void *);
+extern SEXP R_igraph_convex_hull(void *);
+extern SEXP R_igraph_copy(void *);
+extern SEXP R_igraph_copy_env(void *);
+extern SEXP R_igraph_copy_from(void *);
+extern SEXP R_igraph_copy_to(void *);
+extern SEXP R_igraph_coreness(void *, void *);
+extern SEXP R_igraph_correlated_game(void *, void *, void *, void *);
+extern SEXP R_igraph_correlated_pair_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_count_automorphisms(void *, void *, void *);
+extern SEXP R_igraph_count_isomorphisms_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_count_loops(void *);
+extern SEXP R_igraph_count_multiple(void *, void *);
+extern SEXP R_igraph_count_reachable(void *, void *);
+extern SEXP R_igraph_count_subisomorphisms_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_create(void *, void *, void *);
+extern SEXP R_igraph_create_bipartite(void *, void *, void *);
+extern SEXP R_igraph_de_bruijn(void *, void *);
+extern SEXP R_igraph_decompose(void *, void *, void *, void *);
+extern SEXP R_igraph_degree(void *, void *, void *, void *);
+extern SEXP R_igraph_degree_correlation_vector(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_degree_sequence_game(void *, void *, void *);
+extern SEXP R_igraph_delete_edges(void *, void *);
+extern SEXP R_igraph_delete_vertices(void *, void *);
+extern SEXP R_igraph_delete_vertices_idx(void *, void *);
+extern SEXP R_igraph_density(void *, void *);
+extern SEXP R_igraph_deterministic_optimal_imitation(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_dfs(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_diameter(void *, void *, void *, void *);
+extern SEXP R_igraph_difference(void *, void *);
+extern SEXP R_igraph_dim_select(void *);
+extern SEXP R_igraph_disjoint_union(void *);
+extern SEXP R_igraph_distances(void *, void *, void *, void *);
+extern SEXP R_igraph_distances_bellman_ford(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_distances_cutoff(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_distances_dijkstra(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_distances_dijkstra_cutoff(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_distances_floyd_warshall(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_distances_johnson(void *, void *, void *, void *);
+extern SEXP R_igraph_diversity(void *, void *, void *);
+extern SEXP R_igraph_dominator_tree(void *, void *, void *);
+extern SEXP R_igraph_dot_product_game(void *, void *);
+extern SEXP R_igraph_dyad_census(void *);
+extern SEXP R_igraph_ecc(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_eccentricity_dijkstra(void *, void *, void *, void *);
+extern SEXP R_igraph_ecount(void *);
+extern SEXP R_igraph_edge_betweenness_cutoff(void *, void *, void *, void *);
+extern SEXP R_igraph_edge_betweenness_subset(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_edge_connectivity(void *, void *);
+extern SEXP R_igraph_edge_disjoint_paths(void *, void *, void *);
+extern SEXP R_igraph_edges(void *, void *);
+extern SEXP R_igraph_eigen_adjacency(void *, void *, void *, void *);
+extern SEXP R_igraph_eigenvector_centrality(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_empty(void *, void *);
+extern SEXP R_igraph_erdos_renyi_game_gnm(void *, void *, void *, void *);
+extern SEXP R_igraph_erdos_renyi_game_gnp(void *, void *, void *, void *);
+extern SEXP R_igraph_es_adj(void *, void *, void *, void *);
+extern SEXP R_igraph_es_pairs(void *, void *, void *);
+extern SEXP R_igraph_es_path(void *, void *, void *);
+extern SEXP R_igraph_establishment_game(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_eulerian_cycle(void *);
+extern SEXP R_igraph_eulerian_path(void *);
+extern SEXP R_igraph_even_tarjan_reduction(void *);
+extern SEXP R_igraph_extended_chordal_ring(void *, void *, void *);
+extern SEXP R_igraph_famous(void *);
+extern SEXP R_igraph_farthest_points(void *, void *, void *, void *);
+extern SEXP R_igraph_feedback_arc_set(void *, void *, void *);
extern SEXP R_igraph_finalizer(void);
-extern SEXP R_igraph_forest_fire_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_from_hrg_dendrogram(SEXP);
-extern SEXP R_igraph_from_prufer(SEXP);
-extern SEXP R_igraph_full(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_full_bipartite(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_full_citation(SEXP, SEXP);
-extern SEXP R_igraph_full_multipartite(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_fundamental_cycles(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_generalized_petersen(SEXP, SEXP);
-extern SEXP R_igraph_get_adjacency(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_adjedgelist(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_adjlist(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_all_eids_between(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_all_shortest_paths(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_all_shortest_paths_dijkstra(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_all_simple_paths(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_all_simple_paths_pp(SEXP);
-extern SEXP R_igraph_get_attr_mode(SEXP, SEXP);
-extern SEXP R_igraph_get_biadjacency(SEXP, SEXP);
-extern SEXP R_igraph_get_diameter(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_edge(SEXP, SEXP);
-extern SEXP R_igraph_get_edgelist(SEXP, SEXP);
-extern SEXP R_igraph_get_eids(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_graph_id(SEXP);
-extern SEXP R_igraph_get_isomorphisms_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_k_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_laplacian(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_laplacian_sparse(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_shortest_path(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_shortest_path_bellman_ford(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_shortest_path_dijkstra(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_stochastic(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_stochastic_sparse(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_subisomorphisms_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_widest_path(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_get_widest_paths(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_girth(SEXP, SEXP);
-extern SEXP R_igraph_global_efficiency(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_gomory_hu_tree(SEXP, SEXP);
-extern SEXP R_igraph_graph_center_dijkstra(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_graph_count(SEXP, SEXP);
-extern SEXP R_igraph_graph_power(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_graph_version(SEXP);
-extern SEXP R_igraph_graphlets(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_graphlets_candidate_basis(SEXP, SEXP);
-extern SEXP R_igraph_graphlets_project(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_grg_game(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_growing_random_game(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_harmonic_centrality_cutoff(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_has_loop(SEXP);
-extern SEXP R_igraph_has_multiple(SEXP);
-extern SEXP R_igraph_has_mutual(SEXP, SEXP);
-extern SEXP R_igraph_hrg_consensus(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hrg_create(SEXP, SEXP);
-extern SEXP R_igraph_hrg_fit(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hrg_game(SEXP);
-extern SEXP R_igraph_hrg_predict(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hrg_resize(SEXP, SEXP);
-extern SEXP R_igraph_hrg_sample(SEXP);
-extern SEXP R_igraph_hrg_sample_many(SEXP, SEXP);
-extern SEXP R_igraph_hrg_size(SEXP);
-extern SEXP R_igraph_hsbm_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hsbm_list_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hub_and_authority_scores(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hub_score(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_hypercube(SEXP, SEXP);
-extern SEXP R_igraph_i_levc_arp(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_identical_graphs(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_incident(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_incident_edges(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_independence_number(SEXP);
-extern SEXP R_igraph_independent_vertex_sets(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_induced_subgraph(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_induced_subgraph_map(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_intersection(SEXP, SEXP);
-extern SEXP R_igraph_is_acyclic(SEXP);
-extern SEXP R_igraph_is_biconnected(SEXP);
-extern SEXP R_igraph_is_bipartite(SEXP);
-extern SEXP R_igraph_is_chordal(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_clique(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_complete(SEXP);
-extern SEXP R_igraph_is_connected(SEXP, SEXP);
-extern SEXP R_igraph_is_dag(SEXP);
-extern SEXP R_igraph_is_directed(SEXP);
-extern SEXP R_igraph_is_eulerian(SEXP);
-extern SEXP R_igraph_is_forest(SEXP, SEXP);
-extern SEXP R_igraph_is_graphical(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_independent_vertex_set(SEXP, SEXP);
-extern SEXP R_igraph_is_loop(SEXP, SEXP);
-extern SEXP R_igraph_is_matching(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_maximal_matching(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_minimal_separator(SEXP, SEXP);
-extern SEXP R_igraph_is_multiple(SEXP, SEXP);
-extern SEXP R_igraph_is_mutual(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_is_perfect(SEXP);
-extern SEXP R_igraph_is_separator(SEXP, SEXP);
-extern SEXP R_igraph_is_simple(SEXP);
-extern SEXP R_igraph_is_tree(SEXP, SEXP);
-extern SEXP R_igraph_isoclass(SEXP);
-extern SEXP R_igraph_isoclass_create(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_isoclass_subgraph(SEXP, SEXP);
-extern SEXP R_igraph_isomorphic(SEXP, SEXP);
-extern SEXP R_igraph_isomorphic_bliss(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_isomorphic_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_join(SEXP, SEXP);
-extern SEXP R_igraph_joint_degree_distribution(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_joint_degree_matrix(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_joint_type_distribution(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_k_regular_game(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_kary_tree(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_kautz(SEXP, SEXP);
-extern SEXP R_igraph_laplacian(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_laplacian_spectral_embedding(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_largest_cliques(SEXP);
-extern SEXP R_igraph_largest_independent_vertex_sets(SEXP);
-extern SEXP R_igraph_largest_weighted_cliques(SEXP, SEXP);
-extern SEXP R_igraph_lastcit_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_lattice(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_bipartite(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_circle(SEXP, SEXP);
-extern SEXP R_igraph_layout_davidson_harel(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_drl(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_drl_3d(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_fruchterman_reingold(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_fruchterman_reingold_3d(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_gem(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_graphopt(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_grid(SEXP, SEXP);
-extern SEXP R_igraph_layout_grid_3d(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_kamada_kawai(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_kamada_kawai_3d(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_lgl(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_mds(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_merge_dla(SEXP, SEXP);
-extern SEXP R_igraph_layout_random(SEXP);
-extern SEXP R_igraph_layout_random_3d(SEXP);
-extern SEXP R_igraph_layout_reingold_tilford(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_sphere(SEXP);
-extern SEXP R_igraph_layout_star(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_sugiyama(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_umap(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_umap_3d(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_layout_umap_compute_weights(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_lcf_vector(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_linegraph(SEXP);
-extern SEXP R_igraph_list_triangles(SEXP);
-extern SEXP R_igraph_local_efficiency(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_0(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_0_them(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_1_ecount(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_1_ecount_them(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_k_ecount(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_k_ecount_them(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_neighborhood_ecount(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_local_scan_subset_ecount(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_make_weak_ref(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maxflow(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximal_cliques(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximal_cliques_count(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximal_cliques_file(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximal_cliques_hist(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximal_independent_vertex_sets(SEXP);
-extern SEXP R_igraph_maximum_bipartite_matching(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_maximum_cardinality_search(SEXP);
-extern SEXP R_igraph_mean_degree(SEXP, SEXP);
-extern SEXP R_igraph_mincut(SEXP, SEXP);
-extern SEXP R_igraph_mincut_value(SEXP, SEXP);
-extern SEXP R_igraph_minimum_cycle_basis(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_minimum_size_separators(SEXP);
-extern SEXP R_igraph_minimum_spanning_tree_prim(SEXP, SEXP);
-extern SEXP R_igraph_minimum_spanning_tree_unweighted(SEXP);
-extern SEXP R_igraph_modularity(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_modularity_matrix(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_moran_process(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_motifs_randesu(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_motifs_randesu_estimate(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_motifs_randesu_no(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_mybracket2(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_mybracket2_copy(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_mybracket2_names(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_mybracket2_set(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_mybracket3_set(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_neighborhood(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_neighborhood_graphs(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_neighborhood_size(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_neighbors(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_no_components(SEXP, SEXP);
-extern SEXP R_igraph_path_length_hist(SEXP, SEXP);
-extern SEXP R_igraph_permute_vertices(SEXP, SEXP);
-extern SEXP R_igraph_personalized_pagerank(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_personalized_pagerank_vs(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_power_law_fit(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_preference_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_pseudo_diameter(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_pseudo_diameter_dijkstra(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_radius_dijkstra(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_random_edge_walk(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_random_sample(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_random_spanning_tree(SEXP, SEXP);
-extern SEXP R_igraph_random_walk(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_read_graph_dimacs(SEXP, SEXP);
-extern SEXP R_igraph_read_graph_dl(SEXP, SEXP);
-extern SEXP R_igraph_read_graph_edgelist(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_read_graph_gml(SEXP);
-extern SEXP R_igraph_read_graph_graphdb(SEXP, SEXP);
-extern SEXP R_igraph_read_graph_graphml(SEXP, SEXP);
-extern SEXP R_igraph_read_graph_lgl(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_read_graph_ncol(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_read_graph_pajek(SEXP);
-extern SEXP R_igraph_realize_bipartite_degree_sequence(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_realize_degree_sequence(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_recent_degree_aging_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_reciprocity(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_regular_tree(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_residual_graph(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_reverse_edges(SEXP, SEXP);
-extern SEXP R_igraph_reverse_residual_graph(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_rewire(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_rewire_directed_edges(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_rewire_edges(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_ring(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_roots_for_tree_layout(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_roulette_wheel_imitation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_running_mean(SEXP, SEXP);
-extern SEXP R_igraph_sample_dirichlet(SEXP, SEXP);
-extern SEXP R_igraph_sample_sphere_surface(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_sample_sphere_volume(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_sbm_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_set_verbose(SEXP);
-extern SEXP R_igraph_shortest_paths(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_dice(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_dice_es(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_dice_pairs(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_inverse_log_weighted(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_jaccard(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_jaccard_es(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_similarity_jaccard_pairs(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_simple_interconnected_islands_game(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_simplify(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_simplify_and_colorize(SEXP);
-extern SEXP R_igraph_sir(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_solve_lsap(SEXP, SEXP);
-extern SEXP R_igraph_spanner(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_spinglass_community(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_spinglass_my_community(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_split_join_distance(SEXP, SEXP);
-extern SEXP R_igraph_square_lattice(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_st_edge_connectivity(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_st_mincut(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_st_mincut_value(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_st_vertex_connectivity(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_star(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_static_fitness_game(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_static_power_law_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_stochastic_imitation(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_strength(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_subcomponent(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_subgraph_from_edges(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_subisomorphic(SEXP, SEXP);
-extern SEXP R_igraph_subisomorphic_lad(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_subisomorphic_vf2(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_symmetric_tree(SEXP, SEXP);
-extern SEXP R_igraph_to_directed(SEXP, SEXP);
-extern SEXP R_igraph_to_prufer(SEXP);
-extern SEXP R_igraph_to_undirected(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_topological_sorting(SEXP, SEXP);
-extern SEXP R_igraph_transitive_closure(SEXP);
-extern SEXP R_igraph_transitive_closure_dag(SEXP);
-extern SEXP R_igraph_transitivity_avglocal_undirected(SEXP, SEXP);
-extern SEXP R_igraph_transitivity_barrat(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_transitivity_local_undirected(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_transitivity_local_undirected_all(SEXP, SEXP);
-extern SEXP R_igraph_transitivity_undirected(SEXP, SEXP);
-extern SEXP R_igraph_tree_from_parent_vector(SEXP, SEXP);
-extern SEXP R_igraph_tree_game(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_triad_census(SEXP);
-extern SEXP R_igraph_triangular_lattice(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_trussness(SEXP);
-extern SEXP R_igraph_turan(SEXP, SEXP);
-extern SEXP R_igraph_unfold_tree(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_union(SEXP, SEXP);
-extern SEXP R_igraph_vcount(SEXP);
-extern SEXP R_igraph_vertex_coloring_greedy(SEXP, SEXP);
-extern SEXP R_igraph_vertex_connectivity(SEXP, SEXP);
-extern SEXP R_igraph_vertex_disjoint_paths(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_vertex_path_from_edge_path(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_voronoi(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_vs_adj(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_vs_nei(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_walktrap_community(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_watts_strogatz_game(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_weak_ref_key(SEXP);
-extern SEXP R_igraph_weak_ref_run_finalizer(SEXP);
-extern SEXP R_igraph_weak_ref_value(SEXP);
-extern SEXP R_igraph_weighted_adjacency(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_weighted_clique_number(SEXP, SEXP);
-extern SEXP R_igraph_weighted_cliques(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_wheel(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_widest_path_widths_dijkstra(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_widest_path_widths_floyd_warshall(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_dimacs(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_dot(SEXP, SEXP);
-extern SEXP R_igraph_write_graph_edgelist(SEXP, SEXP);
-extern SEXP R_igraph_write_graph_gml(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_graphml(SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_leda(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_lgl(SEXP, SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_ncol(SEXP, SEXP, SEXP, SEXP);
-extern SEXP R_igraph_write_graph_pajek(SEXP, SEXP);
-extern SEXP UUID_gen(SEXP);
-extern SEXP make_lazy(SEXP, SEXP, SEXP);
-extern SEXP make_lazy_dots(SEXP, SEXP);
-extern SEXP promise_env_(SEXP);
-extern SEXP promise_expr_(SEXP);
+extern SEXP R_igraph_forest_fire_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_from_hrg_dendrogram(void *);
+extern SEXP R_igraph_from_prufer(void *);
+extern SEXP R_igraph_full(void *, void *, void *);
+extern SEXP R_igraph_full_bipartite(void *, void *, void *, void *);
+extern SEXP R_igraph_full_citation(void *, void *);
+extern SEXP R_igraph_full_multipartite(void *, void *, void *);
+extern SEXP R_igraph_fundamental_cycles(void *, void *, void *, void *);
+extern SEXP R_igraph_generalized_petersen(void *, void *);
+extern SEXP R_igraph_get_adjacency(void *, void *, void *, void *);
+extern SEXP R_igraph_get_adjedgelist(void *, void *, void *);
+extern SEXP R_igraph_get_adjlist(void *, void *, void *, void *);
+extern SEXP R_igraph_get_all_eids_between(void *, void *, void *, void *);
+extern SEXP R_igraph_get_all_shortest_paths(void *, void *, void *, void *);
+extern SEXP R_igraph_get_all_shortest_paths_dijkstra(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_all_simple_paths(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_all_simple_paths_pp(void *);
+extern SEXP R_igraph_get_attr_mode(void *, void *);
+extern SEXP R_igraph_get_biadjacency(void *, void *);
+extern SEXP R_igraph_get_diameter(void *, void *, void *, void *);
+extern SEXP R_igraph_get_edge(void *, void *);
+extern SEXP R_igraph_get_edgelist(void *, void *);
+extern SEXP R_igraph_get_eids(void *, void *, void *, void *);
+extern SEXP R_igraph_get_graph_id(void *);
+extern SEXP R_igraph_get_isomorphisms_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_k_shortest_paths(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_laplacian(void *, void *, void *, void *);
+extern SEXP R_igraph_get_laplacian_sparse(void *, void *, void *, void *);
+extern SEXP R_igraph_get_shortest_path(void *, void *, void *, void *);
+extern SEXP R_igraph_get_shortest_path_bellman_ford(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_shortest_path_dijkstra(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_shortest_paths(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_stochastic(void *, void *, void *);
+extern SEXP R_igraph_get_stochastic_sparse(void *, void *, void *);
+extern SEXP R_igraph_get_subisomorphisms_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_widest_path(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_get_widest_paths(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_girth(void *, void *);
+extern SEXP R_igraph_global_efficiency(void *, void *, void *);
+extern SEXP R_igraph_gomory_hu_tree(void *, void *);
+extern SEXP R_igraph_graph_center_dijkstra(void *, void *, void *);
+extern SEXP R_igraph_graph_count(void *, void *);
+extern SEXP R_igraph_graph_power(void *, void *, void *);
+extern SEXP R_igraph_graph_version(void *);
+extern SEXP R_igraph_graphlets(void *, void *, void *);
+extern SEXP R_igraph_graphlets_candidate_basis(void *, void *);
+extern SEXP R_igraph_graphlets_project(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_grg_game(void *, void *, void *, void *);
+extern SEXP R_igraph_growing_random_game(void *, void *, void *, void *);
+extern SEXP R_igraph_harmonic_centrality_cutoff(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_has_loop(void *);
+extern SEXP R_igraph_has_multiple(void *);
+extern SEXP R_igraph_has_mutual(void *, void *);
+extern SEXP R_igraph_hrg_consensus(void *, void *, void *, void *);
+extern SEXP R_igraph_hrg_create(void *, void *);
+extern SEXP R_igraph_hrg_fit(void *, void *, void *, void *);
+extern SEXP R_igraph_hrg_game(void *);
+extern SEXP R_igraph_hrg_predict(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_hrg_resize(void *, void *);
+extern SEXP R_igraph_hrg_sample(void *);
+extern SEXP R_igraph_hrg_sample_many(void *, void *);
+extern SEXP R_igraph_hrg_size(void *);
+extern SEXP R_igraph_hsbm_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_hsbm_list_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_hub_and_authority_scores(void *, void *, void *, void *);
+extern SEXP R_igraph_hypercube(void *, void *);
+extern SEXP R_igraph_i_levc_arp(void *, void *, void *);
+extern SEXP R_igraph_identical_graphs(void *, void *, void *);
+extern SEXP R_igraph_incident(void *, void *, void *);
+extern SEXP R_igraph_incident_edges(void *, void *, void *);
+extern SEXP R_igraph_independence_number(void *);
+extern SEXP R_igraph_independent_vertex_sets(void *, void *, void *);
+extern SEXP R_igraph_induced_subgraph(void *, void *, void *);
+extern SEXP R_igraph_induced_subgraph_map(void *, void *, void *);
+extern SEXP R_igraph_intersection(void *, void *);
+extern SEXP R_igraph_is_acyclic(void *);
+extern SEXP R_igraph_is_biconnected(void *);
+extern SEXP R_igraph_is_bipartite(void *);
+extern SEXP R_igraph_is_chordal(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_is_clique(void *, void *, void *);
+extern SEXP R_igraph_is_complete(void *);
+extern SEXP R_igraph_is_connected(void *, void *);
+extern SEXP R_igraph_is_dag(void *);
+extern SEXP R_igraph_is_directed(void *);
+extern SEXP R_igraph_is_eulerian(void *);
+extern SEXP R_igraph_is_forest(void *, void *);
+extern SEXP R_igraph_is_graphical(void *, void *, void *);
+extern SEXP R_igraph_is_independent_vertex_set(void *, void *);
+extern SEXP R_igraph_is_loop(void *, void *);
+extern SEXP R_igraph_is_matching(void *, void *, void *);
+extern SEXP R_igraph_is_maximal_matching(void *, void *, void *);
+extern SEXP R_igraph_is_minimal_separator(void *, void *);
+extern SEXP R_igraph_is_multiple(void *, void *);
+extern SEXP R_igraph_is_mutual(void *, void *, void *);
+extern SEXP R_igraph_is_perfect(void *);
+extern SEXP R_igraph_is_separator(void *, void *);
+extern SEXP R_igraph_is_simple(void *);
+extern SEXP R_igraph_is_tree(void *, void *);
+extern SEXP R_igraph_isoclass(void *);
+extern SEXP R_igraph_isoclass_create(void *, void *, void *);
+extern SEXP R_igraph_isoclass_subgraph(void *, void *);
+extern SEXP R_igraph_isomorphic(void *, void *);
+extern SEXP R_igraph_isomorphic_bliss(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_isomorphic_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_join(void *, void *);
+extern SEXP R_igraph_joint_degree_distribution(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_joint_degree_matrix(void *, void *, void *, void *);
+extern SEXP R_igraph_joint_type_distribution(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_k_regular_game(void *, void *, void *, void *);
+extern SEXP R_igraph_kary_tree(void *, void *, void *);
+extern SEXP R_igraph_kautz(void *, void *);
+extern SEXP R_igraph_laplacian_spectral_embedding(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_largest_cliques(void *);
+extern SEXP R_igraph_largest_independent_vertex_sets(void *);
+extern SEXP R_igraph_largest_weighted_cliques(void *, void *);
+extern SEXP R_igraph_lastcit_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_bipartite(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_circle(void *, void *);
+extern SEXP R_igraph_layout_davidson_harel(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_drl(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_drl_3d(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_fruchterman_reingold(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_fruchterman_reingold_3d(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_gem(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_graphopt(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_grid(void *, void *);
+extern SEXP R_igraph_layout_grid_3d(void *, void *, void *);
+extern SEXP R_igraph_layout_kamada_kawai(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_kamada_kawai_3d(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_lgl(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_mds(void *, void *, void *);
+extern SEXP R_igraph_layout_merge_dla(void *, void *);
+extern SEXP R_igraph_layout_random(void *);
+extern SEXP R_igraph_layout_random_3d(void *);
+extern SEXP R_igraph_layout_reingold_tilford(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_sphere(void *);
+extern SEXP R_igraph_layout_star(void *, void *, void *);
+extern SEXP R_igraph_layout_sugiyama(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_umap(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_umap_3d(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_layout_umap_compute_weights(void *, void *, void *);
+extern SEXP R_igraph_lcf_vector(void *, void *, void *);
+extern SEXP R_igraph_linegraph(void *);
+extern SEXP R_igraph_list_triangles(void *);
+extern SEXP R_igraph_local_efficiency(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_local_scan_0(void *, void *, void *);
+extern SEXP R_igraph_local_scan_0_them(void *, void *, void *, void *);
+extern SEXP R_igraph_local_scan_1_ecount(void *, void *, void *);
+extern SEXP R_igraph_local_scan_1_ecount_them(void *, void *, void *, void *);
+extern SEXP R_igraph_local_scan_k_ecount(void *, void *, void *, void *);
+extern SEXP R_igraph_local_scan_k_ecount_them(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_local_scan_neighborhood_ecount(void *, void *, void *);
+extern SEXP R_igraph_local_scan_subset_ecount(void *, void *, void *);
+extern SEXP R_igraph_make_weak_ref(void *, void *, void *);
+extern SEXP R_igraph_maxflow(void *, void *, void *, void *);
+extern SEXP R_igraph_maximal_cliques(void *, void *, void *, void *);
+extern SEXP R_igraph_maximal_cliques_count(void *, void *, void *, void *);
+extern SEXP R_igraph_maximal_cliques_file(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_maximal_cliques_hist(void *, void *, void *);
+extern SEXP R_igraph_maximal_independent_vertex_sets(void *);
+extern SEXP R_igraph_maximum_bipartite_matching(void *, void *, void *, void *);
+extern SEXP R_igraph_maximum_cardinality_search(void *);
+extern SEXP R_igraph_mean_degree(void *, void *);
+extern SEXP R_igraph_mincut(void *, void *);
+extern SEXP R_igraph_mincut_value(void *, void *);
+extern SEXP R_igraph_minimum_cycle_basis(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_minimum_size_separators(void *);
+extern SEXP R_igraph_minimum_spanning_tree_prim(void *, void *);
+extern SEXP R_igraph_minimum_spanning_tree_unweighted(void *);
+extern SEXP R_igraph_modularity(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_modularity_matrix(void *, void *, void *, void *);
+extern SEXP R_igraph_moran_process(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_motifs_randesu(void *, void *, void *);
+extern SEXP R_igraph_motifs_randesu_estimate(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_motifs_randesu_no(void *, void *, void *);
+extern SEXP R_igraph_mybracket2(void *, void *, void *);
+extern SEXP R_igraph_mybracket2_copy(void *, void *, void *);
+extern SEXP R_igraph_mybracket2_names(void *, void *, void *);
+extern SEXP R_igraph_mybracket2_set(void *, void *, void *, void *);
+extern SEXP R_igraph_mybracket3_set(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_neighborhood(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_neighborhood_graphs(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_neighborhood_size(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_neighbors(void *, void *, void *);
+extern SEXP R_igraph_no_components(void *, void *);
+extern SEXP R_igraph_path_length_hist(void *, void *);
+extern SEXP R_igraph_permute_vertices(void *, void *);
+extern SEXP R_igraph_personalized_pagerank(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_personalized_pagerank_vs(void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_power_law_fit(void *, void *, void *);
+extern SEXP R_igraph_preference_game(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_pseudo_diameter(void *, void *, void *, void *);
+extern SEXP R_igraph_pseudo_diameter_dijkstra(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_radius_dijkstra(void *, void *, void *);
+extern SEXP R_igraph_random_sample(void *, void *, void *);
+extern SEXP R_igraph_random_spanning_tree(void *, void *);
+extern SEXP R_igraph_random_walk(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_read_graph_dimacs(void *, void *);
+extern SEXP R_igraph_read_graph_dl(void *, void *);
+extern SEXP R_igraph_read_graph_edgelist(void *, void *, void *);
+extern SEXP R_igraph_read_graph_gml(void *);
+extern SEXP R_igraph_read_graph_graphdb(void *, void *);
+extern SEXP R_igraph_read_graph_graphml(void *, void *);
+extern SEXP R_igraph_read_graph_lgl(void *, void *, void *, void *);
+extern SEXP R_igraph_read_graph_ncol(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_read_graph_pajek(void *);
+extern SEXP R_igraph_realize_bipartite_degree_sequence(void *, void *, void *, void *);
+extern SEXP R_igraph_realize_degree_sequence(void *, void *, void *, void *);
+extern SEXP R_igraph_recent_degree_aging_game(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_reciprocity(void *, void *, void *);
+extern SEXP R_igraph_regular_tree(void *, void *, void *);
+extern SEXP R_igraph_residual_graph(void *, void *, void *);
+extern SEXP R_igraph_reverse_edges(void *, void *);
+extern SEXP R_igraph_reverse_residual_graph(void *, void *, void *);
+extern SEXP R_igraph_rewire(void *, void *, void *);
+extern SEXP R_igraph_rewire_directed_edges(void *, void *, void *, void *);
+extern SEXP R_igraph_rewire_edges(void *, void *, void *, void *);
+extern SEXP R_igraph_ring(void *, void *, void *, void *);
+extern SEXP R_igraph_roots_for_tree_layout(void *, void *, void *);
+extern SEXP R_igraph_roulette_wheel_imitation(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_running_mean(void *, void *);
+extern SEXP R_igraph_sample_dirichlet(void *, void *);
+extern SEXP R_igraph_sample_sphere_surface(void *, void *, void *, void *);
+extern SEXP R_igraph_sample_sphere_volume(void *, void *, void *, void *);
+extern SEXP R_igraph_sbm_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_set_verbose(void *);
+extern SEXP R_igraph_shortest_paths(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_dice(void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_dice_es(void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_dice_pairs(void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_inverse_log_weighted(void *, void *, void *);
+extern SEXP R_igraph_similarity_jaccard(void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_jaccard_es(void *, void *, void *, void *);
+extern SEXP R_igraph_similarity_jaccard_pairs(void *, void *, void *, void *);
+extern SEXP R_igraph_simple_interconnected_islands_game(void *, void *, void *, void *);
+extern SEXP R_igraph_simplify(void *, void *, void *, void *);
+extern SEXP R_igraph_simplify_and_colorize(void *);
+extern SEXP R_igraph_sir(void *, void *, void *, void *);
+extern SEXP R_igraph_solve_lsap(void *, void *);
+extern SEXP R_igraph_spanner(void *, void *, void *);
+extern SEXP R_igraph_spinglass_community(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_spinglass_my_community(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_split_join_distance(void *, void *);
+extern SEXP R_igraph_square_lattice(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_st_edge_connectivity(void *, void *, void *);
+extern SEXP R_igraph_st_mincut(void *, void *, void *, void *);
+extern SEXP R_igraph_st_mincut_value(void *, void *, void *, void *);
+extern SEXP R_igraph_st_vertex_connectivity(void *, void *, void *);
+extern SEXP R_igraph_star(void *, void *, void *);
+extern SEXP R_igraph_static_fitness_game(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_static_power_law_game(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_stochastic_imitation(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_strength(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_subcomponent(void *, void *, void *);
+extern SEXP R_igraph_subgraph_from_edges(void *, void *, void *);
+extern SEXP R_igraph_subisomorphic(void *, void *);
+extern SEXP R_igraph_subisomorphic_lad(void *, void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_subisomorphic_vf2(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_symmetric_tree(void *, void *);
+extern SEXP R_igraph_to_directed(void *, void *);
+extern SEXP R_igraph_to_prufer(void *);
+extern SEXP R_igraph_to_undirected(void *, void *, void *);
+extern SEXP R_igraph_topological_sorting(void *, void *);
+extern SEXP R_igraph_transitive_closure(void *);
+extern SEXP R_igraph_transitive_closure_dag(void *);
+extern SEXP R_igraph_transitivity_avglocal_undirected(void *, void *);
+extern SEXP R_igraph_transitivity_barrat(void *, void *, void *, void *);
+extern SEXP R_igraph_transitivity_local_undirected(void *, void *, void *);
+extern SEXP R_igraph_transitivity_local_undirected_all(void *, void *);
+extern SEXP R_igraph_transitivity_undirected(void *, void *);
+extern SEXP R_igraph_tree_from_parent_vector(void *, void *);
+extern SEXP R_igraph_tree_game(void *, void *, void *);
+extern SEXP R_igraph_triad_census(void *);
+extern SEXP R_igraph_triangular_lattice(void *, void *, void *);
+extern SEXP R_igraph_trussness(void *);
+extern SEXP R_igraph_turan(void *, void *);
+extern SEXP R_igraph_unfold_tree(void *, void *, void *);
+extern SEXP R_igraph_union(void *, void *);
+extern SEXP R_igraph_vcount(void *);
+extern SEXP R_igraph_vertex_coloring_greedy(void *, void *);
+extern SEXP R_igraph_vertex_connectivity(void *, void *);
+extern SEXP R_igraph_vertex_disjoint_paths(void *, void *, void *);
+extern SEXP R_igraph_vertex_path_from_edge_path(void *, void *, void *, void *);
+extern SEXP R_igraph_voronoi(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_vs_adj(void *, void *, void *, void *);
+extern SEXP R_igraph_vs_nei(void *, void *, void *, void *);
+extern SEXP R_igraph_walktrap_community(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_watts_strogatz_game(void *, void *, void *, void *, void *, void *);
+extern SEXP R_igraph_weak_ref_key(void *);
+extern SEXP R_igraph_weak_ref_run_finalizer(void *);
+extern SEXP R_igraph_weak_ref_value(void *);
+extern SEXP R_igraph_weighted_adjacency(void *, void *, void *);
+extern SEXP R_igraph_weighted_clique_number(void *, void *);
+extern SEXP R_igraph_weighted_cliques(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_wheel(void *, void *, void *);
+extern SEXP R_igraph_widest_path_widths_dijkstra(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_widest_path_widths_floyd_warshall(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_dimacs(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_dot(void *, void *);
+extern SEXP R_igraph_write_graph_edgelist(void *, void *);
+extern SEXP R_igraph_write_graph_gml(void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_graphml(void *, void *, void *);
+extern SEXP R_igraph_write_graph_leda(void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_lgl(void *, void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_ncol(void *, void *, void *, void *);
+extern SEXP R_igraph_write_graph_pajek(void *, void *);
+extern SEXP UUID_gen(void *);
+extern SEXP make_lazy(void *, void *, void *);
+extern SEXP make_lazy_dots(void *, void *);
+extern SEXP promise_env_(void *);
+extern SEXP promise_expr_(void *);
static const R_CallMethodDef CallEntries[] = {
{"R_igraph_add_edges", (DL_FUNC) &R_igraph_add_edges, 2},
@@ -513,7 +508,6 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_assortativity_nominal", (DL_FUNC) &R_igraph_assortativity_nominal, 4},
{"R_igraph_asymmetric_preference_game", (DL_FUNC) &R_igraph_asymmetric_preference_game, 6},
{"R_igraph_atlas", (DL_FUNC) &R_igraph_atlas, 1},
- {"R_igraph_authority_score", (DL_FUNC) &R_igraph_authority_score, 4},
{"R_igraph_automorphism_group", (DL_FUNC) &R_igraph_automorphism_group, 3},
{"R_igraph_average_local_efficiency", (DL_FUNC) &R_igraph_average_local_efficiency, 4},
{"R_igraph_average_path_length_dijkstra", (DL_FUNC) &R_igraph_average_path_length_dijkstra, 4},
@@ -527,7 +521,6 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_biadjacency", (DL_FUNC) &R_igraph_biadjacency, 4},
{"R_igraph_bibcoupling", (DL_FUNC) &R_igraph_bibcoupling, 2},
{"R_igraph_biconnected_components", (DL_FUNC) &R_igraph_biconnected_components, 1},
- {"R_igraph_bipartite_game", (DL_FUNC) &R_igraph_bipartite_game, 7},
{"R_igraph_bipartite_game_gnm", (DL_FUNC) &R_igraph_bipartite_game_gnm, 5},
{"R_igraph_bipartite_game_gnp", (DL_FUNC) &R_igraph_bipartite_game_gnp, 5},
{"R_igraph_bipartite_projection", (DL_FUNC) &R_igraph_bipartite_projection, 4},
@@ -624,7 +617,8 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_eigen_adjacency", (DL_FUNC) &R_igraph_eigen_adjacency, 4},
{"R_igraph_eigenvector_centrality", (DL_FUNC) &R_igraph_eigenvector_centrality, 5},
{"R_igraph_empty", (DL_FUNC) &R_igraph_empty, 2},
- {"R_igraph_erdos_renyi_game", (DL_FUNC) &R_igraph_erdos_renyi_game, 5},
+ {"R_igraph_erdos_renyi_game_gnm", (DL_FUNC) &R_igraph_erdos_renyi_game_gnm, 4},
+ {"R_igraph_erdos_renyi_game_gnp", (DL_FUNC) &R_igraph_erdos_renyi_game_gnp, 4},
{"R_igraph_es_adj", (DL_FUNC) &R_igraph_es_adj, 4},
{"R_igraph_es_pairs", (DL_FUNC) &R_igraph_es_pairs, 3},
{"R_igraph_es_path", (DL_FUNC) &R_igraph_es_path, 3},
@@ -702,7 +696,6 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_hsbm_game", (DL_FUNC) &R_igraph_hsbm_game, 5},
{"R_igraph_hsbm_list_game", (DL_FUNC) &R_igraph_hsbm_list_game, 5},
{"R_igraph_hub_and_authority_scores", (DL_FUNC) &R_igraph_hub_and_authority_scores, 4},
- {"R_igraph_hub_score", (DL_FUNC) &R_igraph_hub_score, 4},
{"R_igraph_hypercube", (DL_FUNC) &R_igraph_hypercube, 2},
{"R_igraph_i_levc_arp", (DL_FUNC) &R_igraph_i_levc_arp, 3},
{"R_igraph_identical_graphs", (DL_FUNC) &R_igraph_identical_graphs, 3},
@@ -749,13 +742,11 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_k_regular_game", (DL_FUNC) &R_igraph_k_regular_game, 4},
{"R_igraph_kary_tree", (DL_FUNC) &R_igraph_kary_tree, 3},
{"R_igraph_kautz", (DL_FUNC) &R_igraph_kautz, 2},
- {"R_igraph_laplacian", (DL_FUNC) &R_igraph_laplacian, 4},
{"R_igraph_laplacian_spectral_embedding", (DL_FUNC) &R_igraph_laplacian_spectral_embedding, 7},
{"R_igraph_largest_cliques", (DL_FUNC) &R_igraph_largest_cliques, 1},
{"R_igraph_largest_independent_vertex_sets", (DL_FUNC) &R_igraph_largest_independent_vertex_sets, 1},
{"R_igraph_largest_weighted_cliques", (DL_FUNC) &R_igraph_largest_weighted_cliques, 2},
{"R_igraph_lastcit_game", (DL_FUNC) &R_igraph_lastcit_game, 5},
- {"R_igraph_lattice", (DL_FUNC) &R_igraph_lattice, 5},
{"R_igraph_layout_bipartite", (DL_FUNC) &R_igraph_layout_bipartite, 5},
{"R_igraph_layout_circle", (DL_FUNC) &R_igraph_layout_circle, 2},
{"R_igraph_layout_davidson_harel", (DL_FUNC) &R_igraph_layout_davidson_harel, 11},
@@ -834,7 +825,6 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_pseudo_diameter", (DL_FUNC) &R_igraph_pseudo_diameter, 4},
{"R_igraph_pseudo_diameter_dijkstra", (DL_FUNC) &R_igraph_pseudo_diameter_dijkstra, 5},
{"R_igraph_radius_dijkstra", (DL_FUNC) &R_igraph_radius_dijkstra, 3},
- {"R_igraph_random_edge_walk", (DL_FUNC) &R_igraph_random_edge_walk, 6},
{"R_igraph_random_sample", (DL_FUNC) &R_igraph_random_sample, 3},
{"R_igraph_random_spanning_tree", (DL_FUNC) &R_igraph_random_spanning_tree, 2},
{"R_igraph_random_walk", (DL_FUNC) &R_igraph_random_walk, 6},
diff --git a/src/rinterface.c b/src/rinterface.c
index 98b145f4cc..73cb904f07 100644
--- a/src/rinterface.c
+++ b/src/rinterface.c
@@ -966,6 +966,78 @@ SEXP R_igraph_turan(SEXP n, SEXP r) {
return(r_result);
}
+/*-------------------------------------------/
+/ igraph_erdos_renyi_game_gnp /
+/-------------------------------------------*/
+SEXP R_igraph_erdos_renyi_game_gnp(SEXP n, SEXP p, SEXP directed, SEXP loops) {
+ /* Declarations */
+ igraph_t c_graph;
+ igraph_integer_t c_n;
+ igraph_real_t c_p;
+ igraph_bool_t c_directed;
+ igraph_bool_t c_loops;
+ SEXP graph;
+
+ SEXP r_result;
+ /* Convert input */
+ IGRAPH_R_CHECK_INT(n);
+ c_n = (igraph_integer_t) REAL(n)[0];
+ IGRAPH_R_CHECK_REAL(p);
+ c_p = REAL(p)[0];
+ IGRAPH_R_CHECK_BOOL(directed);
+ c_directed = LOGICAL(directed)[0];
+ IGRAPH_R_CHECK_BOOL(loops);
+ c_loops = LOGICAL(loops)[0];
+ /* Call igraph */
+ IGRAPH_R_CHECK(igraph_erdos_renyi_game_gnp(&c_graph, c_n, c_p, c_directed, c_loops));
+
+ /* Convert output */
+ IGRAPH_FINALLY(igraph_destroy, &c_graph);
+ PROTECT(graph=R_igraph_to_SEXP(&c_graph));
+ IGRAPH_I_DESTROY(&c_graph);
+ IGRAPH_FINALLY_CLEAN(1);
+ r_result = graph;
+
+ UNPROTECT(1);
+ return(r_result);
+}
+
+/*-------------------------------------------/
+/ igraph_erdos_renyi_game_gnm /
+/-------------------------------------------*/
+SEXP R_igraph_erdos_renyi_game_gnm(SEXP n, SEXP m, SEXP directed, SEXP loops) {
+ /* Declarations */
+ igraph_t c_graph;
+ igraph_integer_t c_n;
+ igraph_integer_t c_m;
+ igraph_bool_t c_directed;
+ igraph_bool_t c_loops;
+ SEXP graph;
+
+ SEXP r_result;
+ /* Convert input */
+ IGRAPH_R_CHECK_INT(n);
+ c_n = (igraph_integer_t) REAL(n)[0];
+ IGRAPH_R_CHECK_INT(m);
+ c_m = (igraph_integer_t) REAL(m)[0];
+ IGRAPH_R_CHECK_BOOL(directed);
+ c_directed = LOGICAL(directed)[0];
+ IGRAPH_R_CHECK_BOOL(loops);
+ c_loops = LOGICAL(loops)[0];
+ /* Call igraph */
+ IGRAPH_R_CHECK(igraph_erdos_renyi_game_gnm(&c_graph, c_n, c_m, c_directed, c_loops));
+
+ /* Convert output */
+ IGRAPH_FINALLY(igraph_destroy, &c_graph);
+ PROTECT(graph=R_igraph_to_SEXP(&c_graph));
+ IGRAPH_I_DESTROY(&c_graph);
+ IGRAPH_FINALLY_CLEAN(1);
+ r_result = graph;
+
+ UNPROTECT(1);
+ return(r_result);
+}
+
/*-------------------------------------------/
/ igraph_preference_game /
/-------------------------------------------*/
@@ -3902,158 +3974,58 @@ SEXP R_igraph_eigenvector_centrality(SEXP graph, SEXP directed, SEXP scale, SEXP
return(r_result);
}
-/*-------------------------------------------/
-/ igraph_hub_score /
-/-------------------------------------------*/
-SEXP R_igraph_hub_score(SEXP graph, SEXP scale, SEXP weights, SEXP options) {
- /* Declarations */
- igraph_t c_graph;
- igraph_vector_t c_vector;
- igraph_real_t c_value;
- igraph_bool_t c_scale;
- igraph_vector_t c_weights;
- igraph_arpack_options_t c_options;
- SEXP vector;
- SEXP value;
-
- SEXP r_result, r_names;
- /* Convert input */
- R_SEXP_to_igraph(graph, &c_graph);
- if (0 != igraph_vector_init(&c_vector, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_vector_destroy, &c_vector);
- IGRAPH_R_CHECK_BOOL(scale);
- c_scale = LOGICAL(scale)[0];
- if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
- R_SEXP_to_igraph_arpack_options(options, &c_options);
- /* Call igraph */
- IGRAPH_R_CHECK(igraph_hub_score(&c_graph, &c_vector, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
-
- /* Convert output */
- PROTECT(r_result=NEW_LIST(3));
- PROTECT(r_names=NEW_CHARACTER(3));
- PROTECT(vector=R_igraph_vector_to_SEXP(&c_vector));
- igraph_vector_destroy(&c_vector);
- IGRAPH_FINALLY_CLEAN(1);
- PROTECT(value=NEW_NUMERIC(1));
- REAL(value)[0]=c_value;
- PROTECT(options=R_igraph_arpack_options_to_SEXP(&c_options));
- SET_VECTOR_ELT(r_result, 0, vector);
- SET_VECTOR_ELT(r_result, 1, value);
- SET_VECTOR_ELT(r_result, 2, options);
- SET_STRING_ELT(r_names, 0, Rf_mkChar("vector"));
- SET_STRING_ELT(r_names, 1, Rf_mkChar("value"));
- SET_STRING_ELT(r_names, 2, Rf_mkChar("options"));
- SET_NAMES(r_result, r_names);
- UNPROTECT(4);
-
- UNPROTECT(1);
- return(r_result);
-}
-
-/*-------------------------------------------/
-/ igraph_authority_score /
-/-------------------------------------------*/
-SEXP R_igraph_authority_score(SEXP graph, SEXP scale, SEXP weights, SEXP options) {
- /* Declarations */
- igraph_t c_graph;
- igraph_vector_t c_vector;
- igraph_real_t c_value;
- igraph_bool_t c_scale;
- igraph_vector_t c_weights;
- igraph_arpack_options_t c_options;
- SEXP vector;
- SEXP value;
-
- SEXP r_result, r_names;
- /* Convert input */
- R_SEXP_to_igraph(graph, &c_graph);
- if (0 != igraph_vector_init(&c_vector, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_vector_destroy, &c_vector);
- IGRAPH_R_CHECK_BOOL(scale);
- c_scale = LOGICAL(scale)[0];
- if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
- R_SEXP_to_igraph_arpack_options(options, &c_options);
- /* Call igraph */
- IGRAPH_R_CHECK(igraph_authority_score(&c_graph, &c_vector, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
-
- /* Convert output */
- PROTECT(r_result=NEW_LIST(3));
- PROTECT(r_names=NEW_CHARACTER(3));
- PROTECT(vector=R_igraph_vector_to_SEXP(&c_vector));
- igraph_vector_destroy(&c_vector);
- IGRAPH_FINALLY_CLEAN(1);
- PROTECT(value=NEW_NUMERIC(1));
- REAL(value)[0]=c_value;
- PROTECT(options=R_igraph_arpack_options_to_SEXP(&c_options));
- SET_VECTOR_ELT(r_result, 0, vector);
- SET_VECTOR_ELT(r_result, 1, value);
- SET_VECTOR_ELT(r_result, 2, options);
- SET_STRING_ELT(r_names, 0, Rf_mkChar("vector"));
- SET_STRING_ELT(r_names, 1, Rf_mkChar("value"));
- SET_STRING_ELT(r_names, 2, Rf_mkChar("options"));
- SET_NAMES(r_result, r_names);
- UNPROTECT(4);
-
- UNPROTECT(1);
- return(r_result);
-}
-
/*-------------------------------------------/
/ igraph_hub_and_authority_scores /
/-------------------------------------------*/
SEXP R_igraph_hub_and_authority_scores(SEXP graph, SEXP scale, SEXP weights, SEXP options) {
/* Declarations */
igraph_t c_graph;
- igraph_vector_t c_hub_vector;
- igraph_vector_t c_authority_vector;
+ igraph_vector_t c_hub;
+ igraph_vector_t c_authority;
igraph_real_t c_value;
igraph_bool_t c_scale;
igraph_vector_t c_weights;
igraph_arpack_options_t c_options;
- SEXP hub_vector;
- SEXP authority_vector;
+ SEXP hub;
+ SEXP authority;
SEXP value;
SEXP r_result, r_names;
/* Convert input */
R_SEXP_to_igraph(graph, &c_graph);
- if (0 != igraph_vector_init(&c_hub_vector, 0)) {
+ if (0 != igraph_vector_init(&c_hub, 0)) {
igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
}
- IGRAPH_FINALLY(igraph_vector_destroy, &c_hub_vector);
- if (0 != igraph_vector_init(&c_authority_vector, 0)) {
+ IGRAPH_FINALLY(igraph_vector_destroy, &c_hub);
+ if (0 != igraph_vector_init(&c_authority, 0)) {
igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
}
- IGRAPH_FINALLY(igraph_vector_destroy, &c_authority_vector);
+ IGRAPH_FINALLY(igraph_vector_destroy, &c_authority);
IGRAPH_R_CHECK_BOOL(scale);
c_scale = LOGICAL(scale)[0];
if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
R_SEXP_to_igraph_arpack_options(options, &c_options);
/* Call igraph */
- IGRAPH_R_CHECK(igraph_hub_and_authority_scores(&c_graph, &c_hub_vector, &c_authority_vector, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
+ IGRAPH_R_CHECK(igraph_hub_and_authority_scores(&c_graph, &c_hub, &c_authority, &c_value, c_scale, (Rf_isNull(weights) ? 0 : &c_weights), &c_options));
/* Convert output */
PROTECT(r_result=NEW_LIST(4));
PROTECT(r_names=NEW_CHARACTER(4));
- PROTECT(hub_vector=R_igraph_vector_to_SEXP(&c_hub_vector));
- igraph_vector_destroy(&c_hub_vector);
+ PROTECT(hub=R_igraph_vector_to_SEXP(&c_hub));
+ igraph_vector_destroy(&c_hub);
IGRAPH_FINALLY_CLEAN(1);
- PROTECT(authority_vector=R_igraph_vector_to_SEXP(&c_authority_vector));
- igraph_vector_destroy(&c_authority_vector);
+ PROTECT(authority=R_igraph_vector_to_SEXP(&c_authority));
+ igraph_vector_destroy(&c_authority);
IGRAPH_FINALLY_CLEAN(1);
PROTECT(value=NEW_NUMERIC(1));
REAL(value)[0]=c_value;
PROTECT(options=R_igraph_arpack_options_to_SEXP(&c_options));
- SET_VECTOR_ELT(r_result, 0, hub_vector);
- SET_VECTOR_ELT(r_result, 1, authority_vector);
+ SET_VECTOR_ELT(r_result, 0, hub);
+ SET_VECTOR_ELT(r_result, 1, authority);
SET_VECTOR_ELT(r_result, 2, value);
SET_VECTOR_ELT(r_result, 3, options);
- SET_STRING_ELT(r_names, 0, Rf_mkChar("hub_vector"));
- SET_STRING_ELT(r_names, 1, Rf_mkChar("authority_vector"));
+ SET_STRING_ELT(r_names, 0, Rf_mkChar("hub"));
+ SET_STRING_ELT(r_names, 1, Rf_mkChar("authority"));
SET_STRING_ELT(r_names, 2, Rf_mkChar("value"));
SET_STRING_ELT(r_names, 3, Rf_mkChar("options"));
SET_NAMES(r_result, r_names);
@@ -5297,46 +5269,6 @@ SEXP R_igraph_random_walk(SEXP graph, SEXP weights, SEXP start, SEXP mode, SEXP
return(r_result);
}
-/*-------------------------------------------/
-/ igraph_random_edge_walk /
-/-------------------------------------------*/
-SEXP R_igraph_random_edge_walk(SEXP graph, SEXP weights, SEXP start, SEXP mode, SEXP steps, SEXP stuck) {
- /* Declarations */
- igraph_t c_graph;
- igraph_vector_t c_weights;
- igraph_vector_int_t c_edgewalk;
- igraph_integer_t c_start;
- igraph_neimode_t c_mode;
- igraph_integer_t c_steps;
- igraph_random_walk_stuck_t c_stuck;
- SEXP edgewalk;
-
- SEXP r_result;
- /* Convert input */
- R_SEXP_to_igraph(graph, &c_graph);
- if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
- if (0 != igraph_vector_int_init(&c_edgewalk, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_vector_int_destroy, &c_edgewalk);
- c_start = (igraph_integer_t) REAL(start)[0];
- c_mode = (igraph_neimode_t) Rf_asInteger(mode);
- IGRAPH_R_CHECK_INT(steps);
- c_steps = (igraph_integer_t) REAL(steps)[0];
- c_stuck = (igraph_random_walk_stuck_t) Rf_asInteger(stuck);
- /* Call igraph */
- IGRAPH_R_CHECK(igraph_random_edge_walk(&c_graph, (Rf_isNull(weights) ? 0 : &c_weights), &c_edgewalk, c_start, c_mode, c_steps, c_stuck));
-
- /* Convert output */
- PROTECT(edgewalk=R_igraph_vector_int_to_SEXPp1(&c_edgewalk));
- igraph_vector_int_destroy(&c_edgewalk);
- IGRAPH_FINALLY_CLEAN(1);
- r_result = edgewalk;
-
- UNPROTECT(1);
- return(r_result);
-}
-
/*-------------------------------------------/
/ igraph_global_efficiency /
/-------------------------------------------*/
@@ -5961,65 +5893,6 @@ SEXP R_igraph_bipartite_game_gnm(SEXP n1, SEXP n2, SEXP m, SEXP directed, SEXP m
return(r_result);
}
-/*-------------------------------------------/
-/ igraph_bipartite_game /
-/-------------------------------------------*/
-SEXP R_igraph_bipartite_game(SEXP type, SEXP n1, SEXP n2, SEXP p, SEXP m, SEXP directed, SEXP mode) {
- /* Declarations */
- igraph_t c_graph;
- igraph_vector_bool_t c_types;
- igraph_erdos_renyi_t c_type;
- igraph_integer_t c_n1;
- igraph_integer_t c_n2;
- igraph_real_t c_p;
- igraph_integer_t c_m;
- igraph_bool_t c_directed;
- igraph_neimode_t c_mode;
- SEXP graph;
- SEXP types;
-
- SEXP r_result, r_names;
- /* Convert input */
- if (0 != igraph_vector_bool_init(&c_types, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_vector_bool_destroy, &c_types);
- c_type = (igraph_erdos_renyi_t) Rf_asInteger(type);
- IGRAPH_R_CHECK_INT(n1);
- c_n1 = (igraph_integer_t) REAL(n1)[0];
- IGRAPH_R_CHECK_INT(n2);
- c_n2 = (igraph_integer_t) REAL(n2)[0];
- IGRAPH_R_CHECK_REAL(p);
- c_p = REAL(p)[0];
- IGRAPH_R_CHECK_INT(m);
- c_m = (igraph_integer_t) REAL(m)[0];
- IGRAPH_R_CHECK_BOOL(directed);
- c_directed = LOGICAL(directed)[0];
- c_mode = (igraph_neimode_t) Rf_asInteger(mode);
- /* Call igraph */
- IGRAPH_R_CHECK(igraph_bipartite_game(&c_graph, &c_types, c_type, c_n1, c_n2, c_p, c_m, c_directed, c_mode));
-
- /* Convert output */
- PROTECT(r_result=NEW_LIST(2));
- PROTECT(r_names=NEW_CHARACTER(2));
- IGRAPH_FINALLY(igraph_destroy, &c_graph);
- PROTECT(graph=R_igraph_to_SEXP(&c_graph));
- IGRAPH_I_DESTROY(&c_graph);
- IGRAPH_FINALLY_CLEAN(1);
- PROTECT(types=R_igraph_vector_bool_to_SEXP(&c_types));
- igraph_vector_bool_destroy(&c_types);
- IGRAPH_FINALLY_CLEAN(1);
- SET_VECTOR_ELT(r_result, 0, graph);
- SET_VECTOR_ELT(r_result, 1, types);
- SET_STRING_ELT(r_names, 0, Rf_mkChar("graph"));
- SET_STRING_ELT(r_names, 1, Rf_mkChar("types"));
- SET_NAMES(r_result, r_names);
- UNPROTECT(3);
-
- UNPROTECT(1);
- return(r_result);
-}
-
/*-------------------------------------------/
/ igraph_get_laplacian /
/-------------------------------------------*/
diff --git a/src/rinterface_extra.c b/src/rinterface_extra.c
index 7533868b99..374eae67d5 100644
--- a/src/rinterface_extra.c
+++ b/src/rinterface_extra.c
@@ -4291,28 +4291,6 @@ SEXP R_igraph_shortest_paths(SEXP graph, SEXP pvids, SEXP pto,
return result;
}
-SEXP R_igraph_lattice(SEXP pdimvector, SEXP pnei, SEXP pdirected,
- SEXP pmutual, SEXP pcircular) {
-
- igraph_t g;
- igraph_vector_int_t dimvector;
- igraph_integer_t nei=(igraph_integer_t) REAL(pnei)[0];
- igraph_bool_t directed=LOGICAL(pdirected)[0];
- igraph_bool_t mutual=LOGICAL(pmutual)[0];
- igraph_bool_t circular=LOGICAL(pcircular)[0];
- SEXP result;
-
- R_SEXP_to_vector_int_copy(pdimvector, &dimvector);
-
- IGRAPH_R_CHECK(igraph_lattice(&g, &dimvector, nei, directed, mutual, circular));
- PROTECT(result=R_igraph_to_SEXP(&g));
- IGRAPH_I_DESTROY(&g);
- igraph_vector_int_destroy(&dimvector);
-
- UNPROTECT(1);
- return result;
-}
-
SEXP R_igraph_barabasi_game(SEXP pn, SEXP ppower, SEXP pm, SEXP poutseq,
SEXP poutpref, SEXP pA, SEXP pdirected,
SEXP palgo, SEXP pstart) {
@@ -4870,29 +4848,6 @@ SEXP R_igraph_layout_circle(SEXP graph, SEXP porder) {
return result;
}
-SEXP R_igraph_erdos_renyi_game(SEXP pn, SEXP ptype,
- SEXP pporm, SEXP pdirected, SEXP ploops) {
-
- igraph_t g;
- igraph_integer_t n;
- igraph_integer_t type=(igraph_integer_t) REAL(ptype)[0];
- igraph_real_t porm=REAL(pporm)[0];
- igraph_bool_t directed=LOGICAL(pdirected)[0];
- igraph_bool_t loops=LOGICAL(ploops)[0];
- SEXP result;
-
- R_check_int_scalar(pn);
- n=(igraph_integer_t) REAL(pn)[0];
-
- igraph_erdos_renyi_game(&g, (igraph_erdos_renyi_t) type, n, porm, directed,
- loops);
- PROTECT(result=R_igraph_to_SEXP(&g));
- IGRAPH_I_DESTROY(&g);
-
- UNPROTECT(1);
- return result;
-}
-
SEXP R_igraph_full(SEXP pn, SEXP pdirected, SEXP ploops) {
igraph_t g;
@@ -8169,50 +8124,6 @@ SEXP R_igraph_get_eids(SEXP graph, SEXP pvp, SEXP pdirected,
return result;
}
-SEXP R_igraph_laplacian(SEXP graph, SEXP normalized, SEXP weights,
- SEXP psparse) {
- /* Declarations */
- igraph_t c_graph;
- igraph_matrix_t c_res;
- igraph_sparsemat_t c_sparseres;
- igraph_bool_t c_normalized;
- igraph_vector_t c_weights;
- igraph_bool_t c_sparse=LOGICAL(psparse)[0];
- SEXP result;
- /* Convert input */
- R_SEXP_to_igraph(graph, &c_graph);
- if (!c_sparse) {
- if (0 != igraph_matrix_init(&c_res, 0, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_matrix_destroy, &c_res);
- }
- if (c_sparse) {
- if (0 != igraph_sparsemat_init(&c_sparseres, 0, 0, 0)) {
- igraph_error("", __FILE__, __LINE__, IGRAPH_ENOMEM);
- }
- IGRAPH_FINALLY(igraph_sparsemat_destroy, &c_sparseres);
- }
- c_normalized=LOGICAL(normalized)[0];
- if (!Rf_isNull(weights)) { R_SEXP_to_vector(weights, &c_weights); }
- /* Call igraph */
- IGRAPH_R_CHECK(igraph_laplacian(&c_graph, (c_sparse ? 0 : &c_res), (c_sparse ? &c_sparseres : 0), c_normalized, (Rf_isNull(weights) ? 0 : &c_weights)));
-
- /* Convert output */
- if (!c_sparse) {
- PROTECT(result=R_igraph_matrix_to_SEXP(&c_res));
- igraph_matrix_destroy(&c_res);
- IGRAPH_FINALLY_CLEAN(1);
- } else {
- PROTECT(result=R_igraph_sparsemat_to_SEXP(&c_sparseres));
- igraph_sparsemat_destroy(&c_sparseres);
- IGRAPH_FINALLY_CLEAN(1);
- }
-
- UNPROTECT(1);
- return(result);
-}
-
SEXP R_igraph_subisomorphic_lad(SEXP pattern, SEXP target, SEXP domains,
SEXP induced, SEXP time_limit,
SEXP pqmap, SEXP pqall_maps) {
diff --git a/tests/testthat/test-make_lattice.R b/tests/testthat/test-make_lattice.R
index fc7f3fba37..e663806ce1 100644
--- a/tests/testthat/test-make_lattice.R
+++ b/tests/testthat/test-make_lattice.R
@@ -1,5 +1,5 @@
test_that("make_lattice works", {
- g <- make_lattice(dim = 2, length = 3, circular = F)
+ g <- make_lattice(dim = 2, length = 3, periodic = F)
g2 <- make_empty_graph(n = 9) + edges(c(
1, 2,
1, 4,
@@ -16,7 +16,7 @@ test_that("make_lattice works", {
))
expect_equal(as_edgelist(g), as_edgelist(g2))
- g <- make_lattice(dim = 2, length = 3, circular = T)
+ g <- make_lattice(dim = 2, length = 3, periodic = T)
g2 <- make_empty_graph(n = 9) + edges(c(
1, 2,
1, 4,
diff --git a/tools/stimulus/functions-R.yaml b/tools/stimulus/functions-R.yaml
index 1f0d944d4c..6a86213ac6 100644
--- a/tools/stimulus/functions-R.yaml
+++ b/tools/stimulus/functions-R.yaml
@@ -188,12 +188,6 @@ igraph_weighted_sparsemat:
igraph_barabasi_game:
IGNORE: RR, RC
-igraph_erdos_renyi_game_gnp:
- IGNORE: RR, RC, RInit
-
-igraph_erdos_renyi_game_gnm:
- IGNORE: RR, RC, RInit
-
igraph_degree_sequence_game:
IGNORE: RR, RC
@@ -544,25 +538,20 @@ igraph_eigenvector_centrality:
DEPS: weights ON graph, vector ON graph V(graph)
igraph_hub_score:
- # This is a temporary hack; we need to find a way to handle default values
- # for dependencies. The problem is that the VERTEXINDEX type needs two
- # dependencies: the graph and the vertex set, but we only have the graph
- # in the argument list.
- DEPS: weights ON graph, vector ON graph V(graph)
+ IGNORE: RR, RC
igraph_authority_score:
- # This is a temporary hack; we need to find a way to handle default values
- # for dependencies. The problem is that the VERTEXINDEX type needs two
- # dependencies: the graph and the vertex set, but we only have the graph
- # in the argument list.
- DEPS: weights ON graph, vector ON graph V(graph)
+ IGNORE: RR, RC
igraph_hub_and_authority_scores:
# This is a temporary hack; we need to find a way to handle default values
# for dependencies. The problem is that the VERTEXINDEX type needs two
# dependencies: the graph and the vertex set, but we only have the graph
# in the argument list.
- DEPS: weights ON graph, hub_vector ON graph V(graph), authority_vector ON graph V(graph)
+ DEPS: weights ON graph, hub ON graph V(graph), authority ON graph V(graph)
+ PARAMS: GRAPH graph, OUT VERTEX_QTY hub, OUT VERTEX_QTY authority,
+ OUT REAL value, BOOLEAN scale=True, EDGEWEIGHTS weights=NULL,
+ INOUT ARPACKOPT options=ARPACK_DEFAULTS
igraph_unfold_tree:
IGNORE: RR
@@ -652,7 +641,7 @@ igraph_random_walk:
PARAM_ORDER: graph, start, steps, ...
igraph_random_edge_walk:
- PARAM_ORDER: graph, start, steps, ...
+ IGNORE: RR, RC
igraph_global_efficiency:
@@ -717,7 +706,7 @@ igraph_bipartite_game_gnm:
IGNORE: RR
igraph_bipartite_game:
- DEPS: types ON graph V(graph)
+ IGNORE: RR, RC
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