igraph · aviator-app · Jan 16, 2024 · Dec 18, 2023 · Jan 11, 2024 · Jan 11, 2024
diff --git a/.github/workflows/build-and-check.yml b/.github/workflows/build-and-check.yml
@@ -172,7 +172,7 @@ jobs:
       - name: Check R package
         uses: r-lib/actions/check-r-package@v2
         with:
-          error-on: '"error"'
+          error-on: '"note"'
 
   coverage:
     runs-on: ubuntu-20.04

diff --git a/R/aaa-auto.R b/R/aaa-auto.R
@@ -969,7 +969,7 @@ edge_betweenness_subset_impl <- function(graph, eids=E(graph), directed=TRUE, so
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
   res <- .Call(R_igraph_edge_betweenness_subset, graph, eids-1, directed, sources-1, targets-1, weights)
-  if (igraph_opt("add.vertex.names") && is_named(graph)) {
+if (igraph_opt("add.vertex.names") && is_named(graph)) {
     names(res) <- vertex_attr(graph, "name", V(graph))
   }
   res
@@ -2297,25 +2297,6 @@ largest_cliques_impl <- function(graph) {
   res
 }
 
-maximal_cliques_subset_impl <- function(graph, subset, outfile=NULL, min.size=0, max.size=0, details=FALSE) {
-  # Argument checks
-  ensure_igraph(graph)
-  subset <- as_igraph_vs(graph, subset)
-  min.size <- as.numeric(min.size)
-  max.size <- as.numeric(max.size)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_maximal_cliques_subset, graph, subset-1, outfile, min.size, max.size)
-  if (igraph_opt("return.vs.es")) {
-    res$res <- lapply(res$res, unsafe_create_vs, graph = graph, verts = V(graph))
-  }
-  if (!details) {
-    res <- res$res
-  }
-  res
-}
-
 maximal_cliques_hist_impl <- function(graph, min.size=0, max.size=0) {
   # Argument checks
   ensure_igraph(graph)
@@ -2703,26 +2684,6 @@ from_hrg_dendrogram_impl <- function(hrg) {
   res
 }
 
-get_adjacency_sparse_impl <- function(graph, type=c("both", "upper", "lower"), weights=NULL, loops=ONCE) {
-  # Argument checks
-  ensure_igraph(graph)
-  type <- switch(igraph.match.arg(type), "upper"=0L, "lower"=1L, "both"=2L)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_get_adjacency_sparse, graph, type, weights, loops)
-
-  res
-}
-
 get_stochastic_sparse_impl <- function(graph, column.wise=FALSE, weights=NULL) {
   # Argument checks
   ensure_igraph(graph)
@@ -2755,17 +2716,6 @@ to_directed_impl <- function(graph, mode=c("mutual", "arbitrary", "random", "acy
   res
 }
 
-read_graph_dimacs_flow_impl <- function(instream, directed=TRUE) {
-  # Argument checks
-  directed <- as.logical(directed)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_read_graph_dimacs_flow, instream, directed)
-
-  res
-}
-
 dyad_census_impl <- function(graph) {
   # Argument checks
   ensure_igraph(graph)
@@ -3615,30 +3565,6 @@ dim_select_impl <- function(sv) {
   res
 }
 
-almost_equals_impl <- function(a, b, eps) {
-  # Argument checks
-
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_almost_equals, a, b, eps)
-
-
-  res
-}
-
-cmp_epsilon_impl <- function(a, b, eps) {
-  # Argument checks
-
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_cmp_epsilon, a, b, eps)
-
-
-  res
-}
-
 solve_lsap_impl <- function(c, n) {
   # Argument checks
   c[] <- as.numeric(c)
@@ -3938,41 +3864,6 @@ stochastic_imitation_impl <- function(graph, vid, algo, quantities, strategies,
   res
 }
 
-progress_impl <- function(message, percent) {
-  # Argument checks
-  percent <- as.numeric(percent)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_progress, message, percent)
-
-
-  res
-}
-
-status_impl <- function(message) {
-  # Argument checks
-
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_status, message)
-
-
-  res
-}
-
-strerror_impl <- function(igraph.errno) {
-  # Argument checks
-
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_strerror, igraph.errno)
-
-
-  res
-}
 
 vertex_path_from_edge_path_impl <- function(graph, start, edge.path, mode=c("out", "in", "all", "total")) {
   # Argument checks

diff --git a/R/structural.properties.R b/R/structural.properties.R
@@ -1067,6 +1067,7 @@ all_shortest_paths <- function(graph, from,
 #' @param to The target vertex of the shortest paths.
 #' @param k The number of paths to find. They will be returned in order of
 #' increasing length.
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams shortest_paths
 #' @return A named list with two components is returned:
 #' \item{vpaths}{The list of \eqn{k} shortest paths in terms of vertices}

diff --git a/configure b/configure
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 # Use pkg-config or xml2-config to get the include directory for libxml-2.0
 xml2_include_dir=""
@@ -11,7 +11,7 @@ else
     exit 1
 fi
 
-if [[ -n "$xml2_include_dir" ]]; then
+if [ -n "$xml2_include_dir" ]; then
     PKG_CFLAGS="-I\"$xml2_include_dir\""
     echo "libxml2 include directory: $xml2_include_dir"
 else

diff --git a/man/k_shortest_paths.Rd b/man/k_shortest_paths.Rd
diff --git a/src/Makevars.in b/src/Makevars.in
@@ -4,12 +4,11 @@ PKG_CFLAGS=$(C_VISIBILITY)
 PKG_CXXFLAGS=$(CXX_VISIBILITY)
 PKG_FFLAGS=$(F_VISIBILITY)
 
-PKG_CPPFLAGS=@cflags@ -DUSING_R -I. -Ivendor -Ivendor/cigraph/src -Ivendor/cigraph/include -Ivendor/cigraph/vendor \
+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 \
 	-D_GNU_SOURCE=1
 
-PKG_LIBS = -L"${LIB_XML}/lib" -lxml2 -lz -L"${GLPK_HOME}/lib" \
-  -lglpk -lgmp -L"${LIB_GMP}/lib" $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_LIBS = -lxml2 -lz -lglpk -lgmp $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
 
 OBJECTS=${SOURCES}
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
@@ -30,7 +30,6 @@ 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_almost_equals(void *, void *, void *);
 extern SEXP R_igraph_are_connected(void *, void *, void *);
 extern SEXP R_igraph_arpack(void *, void *, void *, void *, void *);
 extern SEXP R_igraph_arpack_unpack_complex(void *, void *, void *);
@@ -78,7 +77,6 @@ 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_cmp_epsilon(void *, void *, void *);
 extern SEXP R_igraph_cocitation(void *, void *);
 extern SEXP R_igraph_cohesion(void *, void *);
 extern SEXP R_igraph_cohesive_blocks(void *);
@@ -175,7 +173,6 @@ 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_adjacency_sparse(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 *);
@@ -325,7 +322,6 @@ 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_cliques_subset(void *, void *, 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 *);
@@ -357,7 +353,6 @@ extern SEXP R_igraph_personalized_pagerank(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_progress(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(void *, void *);
@@ -367,7 +362,6 @@ 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_dimacs_flow(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 *);
@@ -420,10 +414,8 @@ 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_status(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_strerror(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 *);
@@ -498,7 +490,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_all_minimal_st_separators",                  (DL_FUNC) &R_igraph_all_minimal_st_separators,                   1},
     {"R_igraph_all_st_cuts",                                (DL_FUNC) &R_igraph_all_st_cuts,                                 3},
     {"R_igraph_all_st_mincuts",                             (DL_FUNC) &R_igraph_all_st_mincuts,                              4},
-    {"R_igraph_almost_equals",                              (DL_FUNC) &R_igraph_almost_equals,                               3},
     {"R_igraph_are_connected",                              (DL_FUNC) &R_igraph_are_connected,                               3},
     {"R_igraph_arpack",                                     (DL_FUNC) &R_igraph_arpack,                                      5},
     {"R_igraph_arpack_unpack_complex",                      (DL_FUNC) &R_igraph_arpack_unpack_complex,                       3},
@@ -546,7 +537,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_clique_size_hist",                           (DL_FUNC) &R_igraph_clique_size_hist,                            3},
     {"R_igraph_cliques",                                    (DL_FUNC) &R_igraph_cliques,                                     3},
     {"R_igraph_closeness_cutoff",                           (DL_FUNC) &R_igraph_closeness_cutoff,                            6},
-    {"R_igraph_cmp_epsilon",                                (DL_FUNC) &R_igraph_cmp_epsilon,                                 3},
     {"R_igraph_cocitation",                                 (DL_FUNC) &R_igraph_cocitation,                                  2},
     {"R_igraph_cohesion",                                   (DL_FUNC) &R_igraph_cohesion,                                    2},
     {"R_igraph_cohesive_blocks",                            (DL_FUNC) &R_igraph_cohesive_blocks,                             1},
@@ -643,7 +633,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_fundamental_cycles",                         (DL_FUNC) &R_igraph_fundamental_cycles,                          4},
     {"R_igraph_generalized_petersen",                       (DL_FUNC) &R_igraph_generalized_petersen,                        2},
     {"R_igraph_get_adjacency",                              (DL_FUNC) &R_igraph_get_adjacency,                               4},
-    {"R_igraph_get_adjacency_sparse",                       (DL_FUNC) &R_igraph_get_adjacency_sparse,                        4},
     {"R_igraph_get_adjedgelist",                            (DL_FUNC) &R_igraph_get_adjedgelist,                             3},
     {"R_igraph_get_adjlist",                                (DL_FUNC) &R_igraph_get_adjlist,                                 4},
     {"R_igraph_get_all_eids_between",                       (DL_FUNC) &R_igraph_get_all_eids_between,                        4},
@@ -793,7 +782,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_maximal_cliques_count",                      (DL_FUNC) &R_igraph_maximal_cliques_count,                       4},
     {"R_igraph_maximal_cliques_file",                       (DL_FUNC) &R_igraph_maximal_cliques_file,                        5},
     {"R_igraph_maximal_cliques_hist",                       (DL_FUNC) &R_igraph_maximal_cliques_hist,                        3},
-    {"R_igraph_maximal_cliques_subset",                     (DL_FUNC) &R_igraph_maximal_cliques_subset,                      5},
     {"R_igraph_maximal_independent_vertex_sets",            (DL_FUNC) &R_igraph_maximal_independent_vertex_sets,             1},
     {"R_igraph_maximum_bipartite_matching",                 (DL_FUNC) &R_igraph_maximum_bipartite_matching,                  4},
     {"R_igraph_maximum_cardinality_search",                 (DL_FUNC) &R_igraph_maximum_cardinality_search,                  1},
@@ -825,7 +813,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_personalized_pagerank_vs",                   (DL_FUNC) &R_igraph_personalized_pagerank_vs,                    8},
     {"R_igraph_power_law_fit",                              (DL_FUNC) &R_igraph_power_law_fit,                               3},
     {"R_igraph_preference_game",                            (DL_FUNC) &R_igraph_preference_game,                             7},
-    {"R_igraph_progress",                                   (DL_FUNC) &R_igraph_progress,                                    2},
     {"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",                                     (DL_FUNC) &R_igraph_radius,                                      2},
@@ -835,7 +822,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_random_spanning_tree",                       (DL_FUNC) &R_igraph_random_spanning_tree,                        2},
     {"R_igraph_random_walk",                                (DL_FUNC) &R_igraph_random_walk,                                 6},
     {"R_igraph_read_graph_dimacs",                          (DL_FUNC) &R_igraph_read_graph_dimacs,                           2},
-    {"R_igraph_read_graph_dimacs_flow",                     (DL_FUNC) &R_igraph_read_graph_dimacs_flow,                      2},
     {"R_igraph_read_graph_dl",                              (DL_FUNC) &R_igraph_read_graph_dl,                               2},
     {"R_igraph_read_graph_edgelist",                        (DL_FUNC) &R_igraph_read_graph_edgelist,                         3},
     {"R_igraph_read_graph_gml",                             (DL_FUNC) &R_igraph_read_graph_gml,                              1},
@@ -888,10 +874,8 @@ static const R_CallMethodDef CallEntries[] = {
     {"R_igraph_star",                                       (DL_FUNC) &R_igraph_star,                                        3},
     {"R_igraph_static_fitness_game",                        (DL_FUNC) &R_igraph_static_fitness_game,                         5},
     {"R_igraph_static_power_law_game",                      (DL_FUNC) &R_igraph_static_power_law_game,                       7},
-    {"R_igraph_status",                                     (DL_FUNC) &R_igraph_status,                                      1},
     {"R_igraph_stochastic_imitation",                       (DL_FUNC) &R_igraph_stochastic_imitation,                        6},
     {"R_igraph_strength",                                   (DL_FUNC) &R_igraph_strength,                                    5},
-    {"R_igraph_strerror",                                   (DL_FUNC) &R_igraph_strerror,                                    1},
     {"R_igraph_subcomponent",                               (DL_FUNC) &R_igraph_subcomponent,                                3},
     {"R_igraph_subgraph_from_edges",                        (DL_FUNC) &R_igraph_subgraph_from_edges,                         3},
     {"R_igraph_subisomorphic",                              (DL_FUNC) &R_igraph_subisomorphic,                               2},