Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

CRAN release v2.0.0 #1160

Merged
merged 3 commits into from
Jan 24, 2024
Merged

CRAN release v2.0.0 #1160

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6725844
CRAN comments
krlmlr Jan 24, 2024
35fa3f2
Fix LTO bugs
krlmlr Jan 24, 2024
a184217
Fix pkgdown and link
krlmlr Jan 24, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
53 changes: 2 additions & 51 deletions R/aaa-auto.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3228,57 +3228,8 @@ subisomorphic_vf2_impl <- function(graph1, graph2, vertex.color1=NULL, vertex.co
res
}

get_subisomorphisms_vf2_callback_impl <- function(graph1, graph2, vertex.color1=NULL, vertex.color2=NULL, edge.color1=NULL, edge.color2=NULL, ishohandler.fn) {
# Argument checks
ensure_igraph(graph1)
ensure_igraph(graph2)
if (missing(vertex.color1)) {
if ("color" %in% vertex_attr_names(graph1)) {
vertex.color1 <- V(graph1)$color
} else {
vertex.color1 <- NULL
}
}
if (!is.null(vertex.color1)) {
vertex.color1 <- as.numeric(vertex.color1)-1
}
if (missing(vertex.color2)) {
if ("color" %in% vertex_attr_names(graph2)) {
vertex.color2 <- V(graph2)$color
} else {
vertex.color2 <- NULL
}
}
if (!is.null(vertex.color2)) {
vertex.color2 <- as.numeric(vertex.color2)-1
}
if (missing(edge.color1)) {
if ("color" %in% edge_attr_names(graph1)) {
edge.color1 <- E(graph1)$color
} else {
edge.color1 <- NULL
}
}
if (!is.null(edge.color1)) {
edge.color1 <- as.numeric(edge.color1)-1
}
if (missing(edge.color2)) {
if ("color" %in% edge_attr_names(graph2)) {
edge.color2 <- E(graph2)$color
} else {
edge.color2 <- NULL
}
}
if (!is.null(edge.color2)) {
edge.color2 <- as.numeric(edge.color2)-1
}

on.exit( .Call(R_igraph_finalizer) )
# Function call
res <- .Call(R_igraph_get_subisomorphisms_vf2_callback, graph1, graph2, vertex.color1, vertex.color2, edge.color1, edge.color2, ishohandler.fn)

res
}
# get_subisomorphisms_vf2_callback_impl gives LTO warnings
# wrong number of arguments to R_igraph_get_subisomorphisms_vf2_callback()

count_subisomorphisms_vf2_impl <- function(graph1, graph2, vertex.color1, vertex.color2, edge.color1, edge.color2) {
# Argument checks
Expand Down
2 changes: 1 addition & 1 deletion R/community.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -372,7 +372,7 @@ code.length <- function(communities) { # nocov start
#' [igraph.plotting] on how to change the plot.
#'
#' @rdname communities
#' @family Community detection
#' @family community
#' @param communities,x,object A `communities` object, the result of an
#' igraph community detection function.
#' @param graph An igraph graph object, corresponding to `communities`.
Expand Down
2 changes: 1 addition & 1 deletion R/interface.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -537,7 +537,7 @@ get.edge.ids <- function(
on.exit(.Call(R_igraph_finalizer))
.Call(
R_igraph_get_eids, graph, as_igraph_vs(graph, vp) - 1,
as.logical(directed), as.logical(error), as.logical(multi)
as.logical(directed), as.logical(error)
) + 1
}

Expand Down
4 changes: 2 additions & 2 deletions R/layout_drl.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -125,12 +125,12 @@ layout_with_drl <- function(graph, use.seed = FALSE,
if (dim == 2) {
res <- .Call(
R_igraph_layout_drl, graph, seed, use.seed, options,
weights, FALSE
weights
)
} else {
res <- .Call(
R_igraph_layout_drl_3d, graph, seed, use.seed, options,
weights, FALSE
weights
)
}
res
Expand Down
2 changes: 1 addition & 1 deletion R/scg.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -135,7 +135,7 @@ stochastic_matrix <- function(graph, column.wise = FALSE,
res <- .Call(R_igraph_get_stochastic_sparse, graph, column.wise, NULL)
res <- igraph.i.spMatrix(res)
} else {
res <- .Call(R_igraph_get_stochastic, graph, column.wise)
res <- .Call(R_igraph_get_stochastic, graph, column.wise, NULL)
}

if (igraph_opt("add.vertex.names") && is_named(graph)) {
Expand Down
2 changes: 2 additions & 0 deletions cran-comments.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
Resubmission.

igraph 2.0.0

## R CMD check results
Expand Down
1 change: 1 addition & 0 deletions man/as_membership.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_edge_betweenness.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_fast_greedy.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_fluid_communities.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_infomap.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_label_prop.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_leading_eigen.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_leiden.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_louvain.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_optimal.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_spinglass.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/cluster_walktrap.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

22 changes: 21 additions & 1 deletion man/communities.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/compare.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/groups.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/make_clusters.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/modularity.igraph.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/plot_dendrogram.communities.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions man/split_join_distance.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions src/Makevars.in
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ PKG_FFLAGS=$(F_VISIBILITY)
PKG_CPPFLAGS=-DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor @cflags@ \
-DNDEBUG -DNTIMER -DNPRINT -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL= \
-DPRPACK_IGRAPH_SUPPORT \
-DHAVE_GFORTRAN=1 \
-D_GNU_SOURCE=1

PKG_LIBS = -lxml2 -lz -lglpk -lgmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
Expand Down
18 changes: 8 additions & 10 deletions src/cpp11.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -185,7 +185,7 @@ 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 *, 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 *);
Expand All @@ -195,10 +195,9 @@ 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 *);
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_subisomorphisms_vf2_callback(void *, 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_getsphere(void *, void *, void *, void *, void *, void *, void *, void *);
Expand Down Expand Up @@ -282,8 +281,8 @@ extern SEXP R_igraph_lattice(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 *, void *);
extern SEXP R_igraph_layout_drl_3d(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 *);
Expand Down Expand Up @@ -645,7 +644,7 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_get_diameter", (DL_FUNC) &R_igraph_get_diameter, 4},
{"R_igraph_get_edge", (DL_FUNC) &R_igraph_get_edge, 2},
{"R_igraph_get_edgelist", (DL_FUNC) &R_igraph_get_edgelist, 2},
{"R_igraph_get_eids", (DL_FUNC) &R_igraph_get_eids, 5},
{"R_igraph_get_eids", (DL_FUNC) &R_igraph_get_eids, 4},
{"R_igraph_get_graph_id", (DL_FUNC) &R_igraph_get_graph_id, 1},
{"R_igraph_get_isomorphisms_vf2", (DL_FUNC) &R_igraph_get_isomorphisms_vf2, 6},
{"R_igraph_get_k_shortest_paths", (DL_FUNC) &R_igraph_get_k_shortest_paths, 6},
Expand All @@ -655,10 +654,9 @@ static const R_CallMethodDef CallEntries[] = {
{"R_igraph_get_shortest_path_bellman_ford", (DL_FUNC) &R_igraph_get_shortest_path_bellman_ford, 5},
{"R_igraph_get_shortest_path_dijkstra", (DL_FUNC) &R_igraph_get_shortest_path_dijkstra, 5},
{"R_igraph_get_shortest_paths", (DL_FUNC) &R_igraph_get_shortest_paths, 10},
{"R_igraph_get_stochastic", (DL_FUNC) &R_igraph_get_stochastic, 2},
{"R_igraph_get_stochastic", (DL_FUNC) &R_igraph_get_stochastic, 3},
{"R_igraph_get_stochastic_sparse", (DL_FUNC) &R_igraph_get_stochastic_sparse, 3},
{"R_igraph_get_subisomorphisms_vf2", (DL_FUNC) &R_igraph_get_subisomorphisms_vf2, 6},
{"R_igraph_get_subisomorphisms_vf2_callback", (DL_FUNC) &R_igraph_get_subisomorphisms_vf2_callback, 7},
{"R_igraph_get_widest_path", (DL_FUNC) &R_igraph_get_widest_path, 5},
{"R_igraph_get_widest_paths", (DL_FUNC) &R_igraph_get_widest_paths, 5},
{"R_igraph_getsphere", (DL_FUNC) &R_igraph_getsphere, 8},
Expand Down Expand Up @@ -742,8 +740,8 @@ static const R_CallMethodDef CallEntries[] = {
{"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},
{"R_igraph_layout_drl", (DL_FUNC) &R_igraph_layout_drl, 6},
{"R_igraph_layout_drl_3d", (DL_FUNC) &R_igraph_layout_drl_3d, 6},
{"R_igraph_layout_drl", (DL_FUNC) &R_igraph_layout_drl, 5},
{"R_igraph_layout_drl_3d", (DL_FUNC) &R_igraph_layout_drl_3d, 5},
{"R_igraph_layout_fruchterman_reingold", (DL_FUNC) &R_igraph_layout_fruchterman_reingold, 10},
{"R_igraph_layout_fruchterman_reingold_3d", (DL_FUNC) &R_igraph_layout_fruchterman_reingold_3d, 11},
{"R_igraph_layout_gem", (DL_FUNC) &R_igraph_layout_gem, 7},
Expand Down
Loading