[med-svn] [r-cran-igraph] branch upstream updated (ed939d6 -> 87a296f)

Andreas Tille tille at debian.org
Thu Sep 7 08:45:33 UTC 2017


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-cran-igraph.

      from  ed939d6   Imported Upstream version 1.0.1
       new  87a296f   New upstream version 1.1.2

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 DESCRIPTION                                        |   48 +-
 MD5                                                | 1460 ++---
 NAMESPACE                                          |   61 +-
 R/adjacency.R                                      |   12 +-
 R/attributes.R                                     |   63 +-
 R/auto.R                                           |  465 +-
 R/basic.R                                          |    9 +-
 R/bipartite.R                                      |    9 +-
 R/centrality.R                                     |   24 +-
 R/cliques.R                                        |   55 +-
 R/cocitation.R                                     |   10 +-
 R/cohesive.blocks.R                                |    8 +-
 R/community.R                                      |  133 +-
 R/components.R                                     |   19 +-
 R/console.R                                        |    2 +
 R/conversion.R                                     |   49 +-
 R/decomposition.R                                  |    6 +-
 R/embedding.R                                      |   30 +-
 R/epi.R                                            |    4 +-
 R/fit.R                                            |    5 +-
 R/flow.R                                           |   62 +-
 R/foreign.R                                        |  104 +-
 R/games.R                                          |  140 +-
 R/glet.R                                           |   12 +-
 R/hrg.R                                            |   24 +-
 R/igraph-package.R                                 |   11 +-
 R/incidence.R                                      |    5 +-
 R/indexing.R                                       |    2 +-
 R/interface.R                                      |   78 +-
 R/iterators.R                                      |  240 +-
 R/layout.R                                         |  134 +-
 R/layout_drl.R                                     |   14 +-
 R/lazyeval.R                                       |   10 +-
 R/make.R                                           |  104 +-
 R/mgclust.R                                        |   10 +
 R/minimum.spanning.tree.R                          |   13 +-
 R/motifs.R                                         |   21 +-
 R/nexus.R                                          |    9 +-
 R/operators.R                                      |   57 +-
 R/other.R                                          |   12 +-
 R/package.R                                        |    7 -
 R/palette.R                                        |    1 +
 R/par.R                                            |   99 +-
 R/paths.R                                          |    6 +-
 R/plot.R                                           |   55 +-
 R/plot.common.R                                    |   46 +-
 R/plot.shapes.R                                    |   22 +-
 R/pp.R                                             |    2 +-
 R/print.R                                          |   43 +-
 R/printr.R                                         |    7 +-
 R/random_walk.R                                    |    7 +-
 R/rewire.R                                         |   16 +-
 R/scan.R                                           |   55 +-
 R/scg.R                                            |   43 +-
 R/sgm.R                                            |    5 +-
 R/socnet.R                                         |   40 +
 R/structural.properties.R                          |  307 +-
 R/structure.info.R                                 |    7 +-
 R/test.R                                           |    4 +-
 R/tkplot.R                                         |    2 +
 R/topology.R                                       |   36 +-
 R/triangles.R                                      |    2 +-
 R/utils.R                                          |    2 +-
 R/uuid.R                                           |    4 +-
 R/versions.R                                       |    6 +-
 R/weakref.R                                        |   10 +-
 R/zzz-deprecate.R                                  |    2 +
 configure                                          |   18 +-
 configure.ac                                       |    2 +-
 inst/NEWS.md                                       |   70 +
 inst/README.md                                     |    1 +
 inst/benchmarks/time_call.R                        |    4 +-
 inst/tests/test-vs-es-printing.R                   |   88 -
 inst/tests/test-vs-indexing-lapply.R               |   11 -
 inst/tests/test_callbacks.R                        |   10 -
 inst/tests/test_igraph.options.R                   |   14 -
 inst/tests/test_layout.gem.R                       |   12 -
 inst/tests/test_scg.R                              |   66 -
 man/E.Rd                                           |   37 +-
 man/V.Rd                                           |   35 +-
 man/aaa-igraph-package.Rd                          |   11 +-
 man/add_edges.Rd                                   |   18 +-
 man/add_layout_.Rd                                 |   55 +-
 man/add_vertices.Rd                                |   18 +-
 man/adjacent_vertices.Rd                           |   20 +-
 man/all_simple_paths.Rd                            |    5 +-
 man/alpha_centrality.Rd                            |   16 +-
 man/are_adjacent.Rd                                |   22 +-
 man/arpack.Rd                                      |   35 +-
 man/articulation_points.Rd                         |   12 +-
 man/as.directed.Rd                                 |   12 +-
 man/as.igraph.Rd                                   |    5 +-
 man/as_adj_list.Rd                                 |   13 +-
 man/as_adjacency_matrix.Rd                         |    6 +-
 man/as_edgelist.Rd                                 |    5 +-
 man/as_graphnel.Rd                                 |    7 +-
 man/as_ids.Rd                                      |    5 +-
 man/as_incidence_matrix.Rd                         |   11 +-
 man/as_long_data_frame.Rd                          |    3 +-
 man/as_membership.Rd                               |    3 +-
 man/assortativity.Rd                               |   14 +-
 man/authority_score.Rd                             |   12 +-
 man/automorphisms.Rd                               |   14 +-
 man/betweenness.Rd                                 |   18 +-
 man/bfs.Rd                                         |   12 +-
 man/biconnected_components.Rd                      |   12 +-
 man/bipartite_mapping.Rd                           |    6 +-
 man/bipartite_projection.Rd                        |   10 +-
 man/c.igraph.es.Rd                                 |   34 +-
 man/c.igraph.vs.Rd                                 |   34 +-
 man/canonical_permutation.Rd                       |   14 +-
 man/categorical_pal.Rd                             |    7 +-
 man/centr_betw.Rd                                  |   17 +-
 man/centr_betw_tmax.Rd                             |   17 +-
 man/centr_clo.Rd                                   |   19 +-
 man/centr_clo_tmax.Rd                              |   19 +-
 man/centr_degree.Rd                                |   20 +-
 man/centr_degree_tmax.Rd                           |   20 +-
 man/centr_eigen.Rd                                 |   22 +-
 man/centr_eigen_tmax.Rd                            |   22 +-
 man/centralize.Rd                                  |   22 +-
 man/cliques.Rd                                     |   25 +-
 man/closeness.Rd                                   |   15 +-
 man/cluster_edge_betweenness.Rd                    |   17 +-
 man/cluster_fast_greedy.Rd                         |   16 +-
 man/cluster_infomap.Rd                             |   24 +-
 man/cluster_label_prop.Rd                          |   18 +-
 man/cluster_leading_eigen.Rd                       |   18 +-
 man/cluster_louvain.Rd                             |   13 +-
 man/cluster_optimal.Rd                             |   16 +-
 man/cluster_spinglass.Rd                           |   26 +-
 man/cluster_walktrap.Rd                            |   17 +-
 man/cocitation.Rd                                  |    7 +-
 man/cohesive_blocks.Rd                             |   54 +-
 man/communities.Rd                                 |   61 +-
 man/compare.Rd                                     |   11 +-
 man/complementer.Rd                                |    5 +-
 man/component_wise.Rd                              |   61 +-
 man/components.Rd                                  |   25 +-
 man/compose.Rd                                     |   11 +-
 man/consensus_tree.Rd                              |   14 +-
 man/console.Rd                                     |    9 +-
 man/constraint.Rd                                  |   15 +-
 man/contract.Rd                                    |    5 +-
 man/convex_hull.Rd                                 |   12 +-
 man/coreness.Rd                                    |   11 +-
 man/count_isomorphisms.Rd                          |   28 +-
 man/count_motifs.Rd                                |    8 +-
 man/count_subgraph_isomorphisms.Rd                 |   29 +-
 man/count_triangles.Rd                             |   14 +-
 man/curve_multiple.Rd                              |   13 +-
 man/decompose.Rd                                   |   11 +-
 man/degree.Rd                                      |    6 +-
 man/delete_edge_attr.Rd                            |   54 +-
 man/delete_edges.Rd                                |   18 +-
 man/delete_graph_attr.Rd                           |   54 +-
 man/delete_vertex_attr.Rd                          |   54 +-
 man/delete_vertices.Rd                             |   18 +-
 man/dfs.Rd                                         |   12 +-
 man/diameter.Rd                                    |   15 +-
 man/difference.Rd                                  |    3 +-
 man/difference.igraph.Rd                           |    8 +-
 man/difference.igraph.es.Rd                        |   33 +-
 man/difference.igraph.vs.Rd                        |   33 +-
 man/dim_select.Rd                                  |   13 +-
 man/disjoint_union.Rd                              |   13 +-
 man/distances.Rd                                   |   25 +-
 man/diverging_pal.Rd                               |    7 +-
 man/diversity.Rd                                   |   10 +-
 man/dominator_tree.Rd                              |   12 +-
 man/dyad_census.Rd                                 |   12 +-
 man/each_edge.Rd                                   |   14 +-
 man/eccentricity.Rd                                |    3 +-
 man/edge.Rd                                        |   18 +-
 man/edge_attr-set.Rd                               |   55 +-
 man/edge_attr.Rd                                   |   54 +-
 man/edge_attr_names.Rd                             |   53 +-
 man/edge_connectivity.Rd                           |   17 +-
 man/edge_density.Rd                                |   11 +-
 man/ego.Rd                                         |   41 +-
 man/eigen_centrality.Rd                            |   17 +-
 man/embed_adjacency_matrix.Rd                      |   11 +-
 man/embed_laplacian_matrix.Rd                      |   18 +-
 man/ends.Rd                                        |   21 +-
 man/erdos.renyi.game.Rd                            |   12 +-
 man/fit_hrg.Rd                                     |   14 +-
 man/fit_power_law.Rd                               |   13 +-
 man/get.edge.ids.Rd                                |   26 +-
 man/girth.Rd                                       |   11 +-
 man/gorder.Rd                                      |   20 +-
 man/graph_.Rd                                      |    3 +-
 man/graph_attr-set.Rd                              |   54 +-
 man/graph_attr.Rd                                  |   55 +-
 man/graph_attr_names.Rd                            |   54 +-
 man/graph_from_adj_list.Rd                         |   12 +-
 man/graph_from_adjacency_matrix.Rd                 |   15 +-
 man/graph_from_atlas.Rd                            |   42 +-
 man/graph_from_data_frame.Rd                       |   18 +-
 man/graph_from_edgelist.Rd                         |   42 +-
 man/graph_from_graphdb.Rd                          |   12 +-
 man/graph_from_graphnel.Rd                         |    5 +-
 man/graph_from_incidence_matrix.Rd                 |   15 +-
 man/graph_from_isomorphism_class.Rd                |   28 +-
 man/graph_from_lcf.Rd                              |   12 +-
 man/graph_from_literal.Rd                          |   44 +-
 man/graph_id.Rd                                    |   32 +
 man/graph_version.Rd                               |    3 +-
 man/graphlet_basis.Rd                              |   12 +-
 man/groups.Rd                                      |    5 +-
 man/gsize.Rd                                       |   22 +-
 man/head_of.Rd                                     |   20 +-
 man/head_print.Rd                                  |   34 +
 man/hrg-methods.Rd                                 |   14 +-
 man/hrg.Rd                                         |   14 +-
 man/hrg_tree.Rd                                    |   14 +-
 man/hub_score.Rd                                   |   12 +-
 man/identical_graphs.Rd                            |    5 +-
 man/igraph-attribute-combination.Rd                |   13 +-
 man/igraph-dollar.Rd                               |   55 +-
 man/igraph-es-attributes.Rd                        |   61 +-
 man/igraph-es-indexing.Rd                          |   79 +-
 man/igraph-es-indexing2.Rd                         |   70 +-
 man/igraph-minus.Rd                                |   18 +-
 man/igraph-vs-attributes.Rd                        |   87 +-
 man/igraph-vs-indexing.Rd                          |   99 +-
 man/igraph-vs-indexing2.Rd                         |   68 +-
 man/igraph_demo.Rd                                 |   11 +-
 man/igraph_options.Rd                              |   48 +-
 man/igraph_test.Rd                                 |    3 +-
 man/igraph_version.Rd                              |    6 +-
 man/incident.Rd                                    |   20 +-
 man/incident_edges.Rd                              |   20 +-
 man/indent_print.Rd                                |   21 +
 man/intersection.Rd                                |    3 +-
 man/intersection.igraph.Rd                         |   14 +-
 man/intersection.igraph.es.Rd                      |   33 +-
 man/intersection.igraph.vs.Rd                      |   33 +-
 man/is_chordal.Rd                                  |   13 +-
 man/is_dag.Rd                                      |    6 +-
 man/is_degseq.Rd                                   |   14 +-
 man/is_directed.Rd                                 |   22 +-
 man/is_graphical.Rd                                |   14 +-
 man/is_igraph.Rd                                   |    6 +-
 man/is_min_separator.Rd                            |    6 +-
 man/is_named.Rd                                    |    7 +-
 man/is_printer_callback.Rd                         |   17 +
 man/is_separator.Rd                                |    5 +-
 man/is_weighted.Rd                                 |    7 +-
 man/isomorphic.Rd                                  |   28 +-
 man/isomorphism_class.Rd                           |   26 +-
 man/isomorphisms.Rd                                |   28 +-
 man/ivs.Rd                                         |   24 +-
 man/keeping_degseq.Rd                              |   15 +-
 man/knn.Rd                                         |   16 +-
 man/laplacian_matrix.Rd                            |    7 +-
 man/layout.deprecated.Rd                           |    9 +-
 man/layout.fruchterman.reingold.grid.Rd            |    3 +-
 man/layout.spring.Rd                               |    3 +-
 man/layout.svd.Rd                                  |    3 +-
 man/layout_.Rd                                     |   57 +-
 man/layout_as_bipartite.Rd                         |   64 +-
 man/layout_as_star.Rd                              |   66 +-
 man/layout_as_tree.Rd                              |   68 +-
 man/layout_in_circle.Rd                            |   63 +-
 man/layout_nicely.Rd                               |   62 +-
 man/layout_on_grid.Rd                              |   63 +-
 man/layout_on_sphere.Rd                            |   61 +-
 man/layout_randomly.Rd                             |   61 +-
 man/layout_with_dh.Rd                              |   63 +-
 man/layout_with_drl.Rd                             |   22 +-
 man/layout_with_fr.Rd                              |   69 +-
 man/layout_with_gem.Rd                             |   65 +-
 man/layout_with_graphopt.Rd                        |   64 +-
 man/layout_with_kk.Rd                              |   68 +-
 man/layout_with_lgl.Rd                             |   61 +-
 man/layout_with_mds.Rd                             |   66 +-
 man/layout_with_sugiyama.Rd                        |   67 +-
 man/local_scan.Rd                                  |    5 +-
 man/make_.Rd                                       |    3 +-
 man/make_bipartite_graph.Rd                        |   16 +-
 man/make_chordal_ring.Rd                           |   42 +-
 man/make_clusters.Rd                               |    5 +-
 man/make_de_bruijn_graph.Rd                        |   14 +-
 man/make_empty_graph.Rd                            |   43 +-
 man/make_full_bipartite_graph.Rd                   |   15 +-
 man/make_full_citation_graph.Rd                    |   44 +-
 man/make_full_graph.Rd                             |   46 +-
 man/make_graph.Rd                                  |   43 +-
 man/make_kautz_graph.Rd                            |   13 +-
 man/make_lattice.Rd                                |   42 +-
 man/make_line_graph.Rd                             |    7 +-
 man/make_ring.Rd                                   |   47 +-
 man/make_star.Rd                                   |   43 +-
 man/make_tree.Rd                                   |   43 +-
 man/match_vertices.Rd                              |   13 +-
 man/matching.Rd                                    |   20 +-
 man/max_cardinality.Rd                             |   10 +-
 man/max_flow.Rd                                    |   15 +-
 man/merge_coords.Rd                                |   60 +-
 man/min_cut.Rd                                     |    5 +-
 man/min_separators.Rd                              |    3 +-
 man/min_st_separators.Rd                           |   10 +-
 man/modularity.igraph.Rd                           |   17 +-
 man/motifs.Rd                                      |    7 +-
 man/mst.Rd                                         |   16 +-
 man/neighbors.Rd                                   |   20 +-
 man/nexus.Rd                                       |   42 +-
 man/norm_coords.Rd                                 |   68 +-
 man/normalize.Rd                                   |   66 +-
 man/page_rank.Rd                                   |   20 +-
 man/path.Rd                                        |   17 +-
 man/permute.Rd                                     |   10 +-
 man/pipe.Rd                                        |    6 +-
 man/plot.igraph.Rd                                 |   13 +-
 man/plot.sir.Rd                                    |   13 +-
 man/plot_dendrogram.communities.Rd                 |   13 +-
 man/plot_dendrogram.igraphHRG.Rd                   |    7 +-
 man/plus-.igraph.Rd                                |   17 +-
 man/power_centrality.Rd                            |   18 +-
 man/predict_edges.Rd                               |   16 +-
 man/print.igraph.Rd                                |   26 +-
 man/print.igraph.es.Rd                             |   34 +-
 man/print.igraph.vs.Rd                             |   36 +-
 man/print.igraphHRG.Rd                             |   35 +-
 man/print.igraphHRGConsensus.Rd                    |   15 +-
 man/printer_callback.Rd                            |   36 +
 man/printr.Rd                                      |   10 +
 man/r_pal.Rd                                       |    7 +-
 man/radius.Rd                                      |    3 +-
 man/random_walk.Rd                                 |    5 +-
 man/read_graph.Rd                                  |   20 +-
 man/reciprocity.Rd                                 |    5 +-
 man/rep.igraph.Rd                                  |    7 +-
 man/rev.igraph.es.Rd                               |   35 +-
 man/rev.igraph.vs.Rd                               |   35 +-
 man/rewire.Rd                                      |    7 +-
 man/rglplot.Rd                                     |   11 +-
 man/running_mean.Rd                                |    7 +-
 man/sample_.Rd                                     |    3 +-
 man/sample_bipartite.Rd                            |   15 +-
 man/sample_correlated_gnp.Rd                       |    3 +-
 man/sample_correlated_gnp_pair.Rd                  |    3 +-
 man/sample_degseq.Rd                               |   15 +-
 man/sample_dirichlet.Rd                            |    5 +-
 man/sample_dot_product.Rd                          |   12 +-
 man/sample_fitness.Rd                              |   10 +-
 man/sample_fitness_pl.Rd                           |   10 +-
 man/sample_forestfire.Rd                           |   12 +-
 man/sample_gnm.Rd                                  |   12 +-
 man/sample_gnp.Rd                                  |   12 +-
 man/sample_grg.Rd                                  |   15 +-
 man/sample_growing.Rd                              |   15 +-
 man/sample_hierarchical_sbm.Rd                     |   12 +-
 man/sample_hrg.Rd                                  |   15 +-
 man/sample_islands.Rd                              |   12 +-
 man/sample_k_regular.Rd                            |   12 +-
 man/sample_last_cit.Rd                             |   15 +-
 man/sample_motifs.Rd                               |    8 +-
 man/sample_pa.Rd                                   |   15 +-
 man/sample_pa_age.Rd                               |   16 +-
 man/sample_pref.Rd                                 |   20 +-
 man/sample_sbm.Rd                                  |   12 +-
 man/sample_seq.Rd                                  |   13 +-
 man/sample_smallworld.Rd                           |   13 +-
 man/sample_sphere_surface.Rd                       |    5 +-
 man/sample_sphere_volume.Rd                        |    5 +-
 man/sample_traits_callaway.Rd                      |    9 +-
 man/scan_stat.Rd                                   |    3 +-
 man/scg-method.Rd                                  |   12 +-
 man/scg.Rd                                         |   18 +-
 man/scg_eps.Rd                                     |   14 +-
 man/scg_group.Rd                                   |   16 +-
 man/scg_semi_proj.Rd                               |   17 +-
 man/sequential_pal.Rd                              |    7 +-
 man/set_edge_attr.Rd                               |   54 +-
 man/set_graph_attr.Rd                              |   54 +-
 man/set_vertex_attr.Rd                             |   54 +-
 man/shapes.Rd                                      |   15 +-
 man/similarity.Rd                                  |   14 +-
 man/simplified.Rd                                  |    9 +-
 man/simplify.Rd                                    |   13 +-
 man/sir.Rd                                         |   23 +-
 man/spectrum.Rd                                    |   13 +-
 man/split_join_distance.Rd                         |    3 +-
 man/srand.Rd                                       |    3 +-
 man/st_cuts.Rd                                     |   12 +-
 man/st_min_cuts.Rd                                 |   12 +-
 man/stochastic_matrix.Rd                           |   15 +-
 man/strength.Rd                                    |   12 +-
 man/sub-.igraph.Rd                                 |   24 +-
 man/sub-sub-.igraph.Rd                             |   20 +-
 man/subcomponent.Rd                                |   10 +-
 man/subgraph.Rd                                    |   11 +-
 man/subgraph_centrality.Rd                         |   15 +-
 man/subgraph_isomorphic.Rd                         |   31 +-
 man/subgraph_isomorphisms.Rd                       |   26 +-
 man/tail_of.Rd                                     |   20 +-
 man/tkigraph.Rd                                    |    9 +-
 man/tkplot.Rd                                      |   55 +-
 man/topo_sort.Rd                                   |   10 +-
 man/transitivity.Rd                                |   11 +-
 man/triad_census.Rd                                |   12 +-
 man/unfold_tree.Rd                                 |    7 +-
 man/union.Rd                                       |    3 +-
 man/union.igraph.Rd                                |   14 +-
 man/union.igraph.es.Rd                             |   33 +-
 man/union.igraph.vs.Rd                             |   33 +-
 man/unique.igraph.es.Rd                            |   33 +-
 man/unique.igraph.vs.Rd                            |   33 +-
 man/upgrade_graph.Rd                               |    3 +-
 man/vertex.Rd                                      |   19 +-
 man/vertex_attr-set.Rd                             |   54 +-
 man/vertex_attr.Rd                                 |   53 +-
 man/vertex_attr_names.Rd                           |   53 +-
 man/vertex_connectivity.Rd                         |   21 +-
 man/which_multiple.Rd                              |   19 +-
 man/which_mutual.Rd                                |   12 +-
 man/with_edge_.Rd                                  |    9 +-
 man/with_graph_.Rd                                 |    9 +-
 man/with_igraph_opt.Rd                             |   29 +
 man/with_vertex_.Rd                                |    9 +-
 man/without_attr.Rd                                |    9 +-
 man/without_loops.Rd                               |    9 +-
 man/without_multiples.Rd                           |    9 +-
 man/write_graph.Rd                                 |   14 +-
 src/CHOLMOD/Include/cholmod_blas.h                 |    2 +-
 src/DensityGrid.cpp                                |   17 +-
 src/DensityGrid_3d.cpp                             |   18 +-
 src/Makevars.in                                    |    2 +-
 src/Makevars.win                                   |    6 +-
 src/adjlist.c                                      |   46 +
 src/atlas-edges.h                                  |    2 +
 src/attributes.c                                   |   12 +-
 src/bignum.h                                       |    7 +-
 src/bipartite.c                                    |    3 +
 src/bliss.cc                                       |  405 +-
 src/bliss/bignum.hh                                |  133 +
 src/bliss/bliss_heap.cc                            |   99 +
 src/bliss/defs.cc                                  |   42 +
 src/bliss/defs.hh                                  |  128 +
 src/bliss/graph.cc                                 | 5606 ++++++++++++++++++++
 src/bliss/graph.hh                                 |  997 ++++
 src/bliss/heap.hh                                  |   83 +
 src/bliss/igraph-changes.md                        |   36 +
 src/{bliss_kqueue.hh => bliss/kqueue.hh}           |   76 +-
 src/bliss/kstack.hh                                |  141 +
 src/{bliss_orbit.cc => bliss/orbit.cc}             |   59 +-
 src/bliss/orbit.hh                                 |  111 +
 src/bliss/partition.cc                             | 1143 ++++
 src/bliss/partition.hh                             |  308 ++
 src/{bliss_eqrefhash.cc => bliss/uintseqhash.cc}   |   94 +-
 src/bliss/uintseqhash.hh                           |   65 +
 src/bliss/utils.cc                                 |  122 +
 src/bliss/utils.hh                                 |   69 +
 src/bliss_bignum.hh                                |   76 -
 src/bliss_defs.hh                                  |   52 -
 src/bliss_eqrefhash.hh                             |   58 -
 src/bliss_graph.cc                                 | 2495 ---------
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