[med-svn] [r-cran-igraph] branch upstream updated (6f85dc7 -> ed939d6)

Andreas Tille tille at debian.org
Wed Apr 6 07:41:12 UTC 2016


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  6f85dc7   Imported Upstream version 0.7.1
       new  ed939d6   Imported Upstream version 1.0.1

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:
 AUTHORS                                            |  133 -
 DESCRIPTION                                        |   36 +-
 MD5                                                | 1797 ++--
 NAMESPACE                                          | 1268 ++-
 NEWS                                               | 1036 ---
 R/adjacency.R                                      |  400 +
 R/assortativity.R                                  |  113 +
 R/attributes.R                                     |  790 +-
 R/auto.R                                           | 1317 ++-
 R/basic.R                                          |   70 +-
 R/bipartite.R                                      |  130 +-
 R/centrality.R                                     |  683 +-
 R/centralization.R                                 |  345 +
 R/cliques.R                                        |  242 +-
 R/cocitation.R                                     |   55 +-
 R/cohesive.blocks.R                                |  302 +-
 R/community.R                                      | 1599 +++-
 R/components.R                                     |  134 +-
 R/console.R                                        |  154 +-
 R/conversion.R                                     |  615 +-
 R/data_frame.R                                     |  254 +
 R/decomposition.R                                  |   62 +-
 R/degseq.R                                         |   89 +
 R/demo.R                                           |  106 +-
 R/embedding.R                                      |  347 +
 R/epi.R                                            |   64 +-
 R/fit.R                                            |  119 +-
 R/flow.R                                           |  639 +-
 R/foreign.R                                        |  206 +-
 R/games.R                                          | 1423 ++-
 R/glet.R                                           |   99 +-
 R/hrg.R                                            |  472 +-
 R/igraph-package.R                                 |  190 +
 R/incidence.R                                      |  242 +
 R/indexing.R                                       |  234 +-
 R/interface.R                                      |  415 +-
 R/iterators.R                                      | 1603 +++-
 R/layout.R                                         | 2534 ++++--
 R/layout_drl.R                                     |  275 +
 R/lazyeval.R                                       |  244 +
 R/make.R                                           | 1563 ++++
 R/mgclust.R                                        |  168 +
 R/minimum.spanning.tree.R                          |   47 +-
 R/motifs.R                                         |  172 +-
 R/nexus.R                                          |  214 +-
 R/operators.R                                      |  780 +-
 R/other.R                                          |   98 +-
 R/package.R                                        |    9 -
 R/palette.R                                        |  210 +
 R/par.R                                            |  122 +-
 R/paths.R                                          |  231 +
 R/plot.R                                           |  154 +-
 R/plot.common.R                                    |   83 +-
 R/plot.shapes.R                                    |  268 +-
 R/pp.R                                             |   25 +
 R/print.R                                          |  440 +-
 R/printr.R                                         |  189 +
 R/random_walk.R                                    |   53 +
 R/revolver.R                                       |  493 -
 R/rewire.R                                         |  142 +
 R/scan.R                                           |  424 +
 R/scg.R                                            |  539 +-
 R/sgm.R                                            |  138 +
 R/similarity.R                                     |   65 +
 R/simple.R                                         |   70 +
 R/sir.R                                            |  103 +
 R/socnet.R                                         | 1061 +--
 R/sparsedf.R                                       |    6 +
 R/structural.properties.R                          | 2067 ++++-
 R/structure.generators.R                           |  883 --
 R/structure.info.R                                 |   30 +-
 R/test.R                                           |   50 +-
 R/tkplot.R                                         |  683 +-
 R/topology.R                                       |  895 +-
 R/triangles.R                                      |   73 +
 R/utils.R                                          |   99 +
 R/uuid.R                                           |   13 +
 R/versions.R                                       |  120 +
 R/weakref.R                                        |   41 +
 R/zzz-deprecate.R                                  |  610 ++
 configure                                          |  115 +-
 configure.ac                                       |  146 +
 configure.in                                       |  119 -
 demo/centrality.R                                  |   62 +-
 demo/cohesive.R                                    |   14 +-
 demo/community.R                                   |   66 +-
 demo/crashR.R                                      |   52 +-
 demo/hrg.R                                         |   30 +-
 demo/smallworld.R                                  |   54 +-
 inst/AUTHORS                                       |    5 +
 inst/NEWS.md                                       | 1034 +++
 inst/README.md                                     |   32 +
 inst/benchmarks/correlated.R                       |    8 +
 inst/benchmarks/local.scan.R                       |   57 +
 inst/benchmarks/time_dirSelect.R                   |    7 +
 inst/benchmarks/time_fr_layout.R                   |   12 +
 inst/benchmarks/time_kk_layout.R                   |   17 +
 inst/benchmarks/time_print.R                       |   54 +
 inst/benchmarks/time_sgm.R                         |   11 +
 inst/benchmarks/time_sir.R                         |    2 +-
 inst/tests/dyad.census.R                           |   20 +-
 inst/tests/test-constructor-modifiers.R            |  116 +
 inst/tests/test-index-es.R                         |   40 +
 inst/tests/test-isomorphism.R                      |  121 +
 inst/tests/test-make.R                             |   61 +
 inst/tests/test-make_graph.R                       |   57 +
 inst/tests/test-new-layout-api.R                   |   59 +
 inst/tests/test-notable.R                          |   38 +
 inst/tests/test-old-data-type.R                    |   68 +
 inst/tests/test-random_walk.R                      |   28 +
 inst/tests/test-version.R                          |   20 +
 inst/tests/test-versions.R                         |   25 +
 inst/tests/test-vs-es-printing.R                   |   88 +
 inst/tests/test-vs-es-quirks.R                     |   32 +
 inst/tests/test-vs-es.R                            |  272 +
 inst/tests/test-vs-indexing-lapply.R               |   11 +
 inst/tests/test-vs-operators.R                     |  651 ++
 inst/tests/test-weakref.R                          |  106 +
 inst/tests/test_add.edges.R                        |   43 +-
 inst/tests/test_add.vertices.R                     |   16 +-
 inst/tests/test_adjacency.spectral.embedding.R     |  234 +
 inst/tests/test_all.st.cuts.R                      |   26 +-
 inst/tests/test_alpha.centrality.R                 |   53 +-
 inst/tests/test_are.connected.R                    |   28 +-
 inst/tests/test_arpack.R                           |    2 +-
 inst/tests/test_articulation.points.R              |   12 +-
 inst/tests/test_as.directed.R                      |    8 +-
 inst/tests/test_as.undirected.R                    |    8 +-
 inst/tests/test_assortativity.R                    |   18 +-
 inst/tests/test_attributes.R                       |  164 +-
 inst/tests/test_authority.score.R                  |   34 +-
 inst/tests/test_average.path.length.R              |   28 +-
 inst/tests/test_ba.game.R                          |   50 +-
 inst/tests/test_betweenness.R                      |    6 +-
 inst/tests/test_biconnected.components.R           |   15 +-
 inst/tests/test_bipartite.projection.R             |   78 +-
 inst/tests/test_bipartite.random.game.R            |   40 +-
 inst/tests/test_bonpow.R                           |   12 +-
 inst/tests/test_bug-1019624.R                      |    4 +-
 inst/tests/test_bug-1032819.R                      |    6 +-
 inst/tests/test_bug-1033045.R                      |    6 +-
 inst/tests/test_bug-1073705-indexing.R             |   10 +-
 inst/tests/test_bug-1073800-clique.R               |    7 +-
 inst/tests/test_callbacks.R                        |    2 +-
 inst/tests/test_canonical.permutation.R            |   20 +-
 inst/tests/test_cliques.R                          |   12 +-
 inst/tests/test_closeness.R                        |   42 +-
 inst/tests/test_clusters.R                         |   40 +-
 inst/tests/test_communities.R                      |   52 +-
 inst/tests/test_constraint.R                       |    6 +-
 inst/tests/test_contract.vertices.R                |    8 +-
 inst/tests/test_correlated.R                       |   79 +
 inst/tests/test_count.multiple.R                   |   16 +-
 inst/tests/test_decompose.graph.R                  |   34 +-
 inst/tests/test_degree.R                           |    8 +-
 inst/tests/test_degree.sequence.game.R             |   26 +-
 inst/tests/test_delete.edges.R                     |    8 +-
 inst/tests/test_delete.vertices.R                  |   10 +-
 inst/tests/test_diameter.R                         |   20 +-
 inst/tests/test_dimSelect.R                        |   33 +
 inst/tests/test_dominator.tree.R                   |   16 +-
 inst/tests/test_dot.product.game.R                 |   46 +
 inst/tests/test_dyad.census.R                      |   10 +-
 inst/tests/test_edge.betweenness.R                 |   28 +-
 inst/tests/test_edge.betweenness.community.R       |   19 +-
 inst/tests/test_edge.connectivity.R                |   42 +-
 inst/tests/test_edgenames.R                        |   26 +-
 inst/tests/test_evcent.R                           |   32 +-
 inst/tests/test_fartherst.nodes.R                  |   34 +-
 inst/tests/test_fastgreedy.community.R             |   19 +-
 inst/tests/test_forestfire.R                       |    6 +-
 inst/tests/test_get.adjacency.R                    |   24 +-
 inst/tests/test_get.adjlist.R                      |   36 +-
 inst/tests/test_get.all.shortest.paths.R           |   13 +-
 inst/tests/test_get.diameter.R                     |   14 +-
 inst/tests/test_get.edge.R                         |    8 +-
 inst/tests/test_get.edgelist.R                     |    8 +-
 inst/tests/test_get.incidence.R                    |   10 +-
 inst/tests/test_get.shortest.paths.R               |   12 +-
 inst/tests/test_girth.R                            |    8 +-
 inst/tests/test_graph.adhesion.R                   |   70 +-
 inst/tests/test_graph.adjacency.R                  |   66 +-
 inst/tests/test_graph.adjlist.R                    |   16 +-
 inst/tests/test_graph.bfs.R                        |   10 +-
 inst/tests/test_graph.bipartite.R                  |   10 +-
 inst/tests/test_graph.complementer.R               |   10 +-
 inst/tests/test_graph.compose.R                    |   10 +-
 inst/tests/test_graph.coreness.R                   |   10 +-
 inst/tests/test_graph.data.frame.R                 |   18 +-
 inst/tests/test_graph.de.bruijn.R                  |   10 +-
 inst/tests/test_graph.density.R                    |   12 +-
 inst/tests/test_graph.edgelist.R                   |   22 +-
 inst/tests/test_graph.eigen.R                      |   10 +-
 inst/tests/test_graph.formula.R                    |    6 +-
 inst/tests/test_graph.isoclass.R                   |   14 +-
 inst/tests/test_graph.kautz.R                      |    8 +-
 inst/tests/test_graph.knn.R                        |   24 +-
 inst/tests/test_graph.maxflow.R                    |   16 +-
 inst/tests/test_graph.mincut.R                     |   12 +-
 inst/tests/test_graph.subisomorphic.lad.R          |   67 +-
 inst/tests/test_graph.subisomorphic.vf2.R          |    4 +-
 inst/tests/test_graphNEL.R                         |   14 +-
 inst/tests/test_graphlets.R                        |   39 +-
 inst/tests/test_hrg.R                              |    6 +-
 inst/tests/test_hsbm.R                             |  113 +
 inst/tests/test_igraph.options.R                   |   12 +-
 inst/tests/test_independent.vertex.sets.R          |   10 +-
 inst/tests/test_indexing.R                         |  111 +-
 inst/tests/test_indexing2.R                        |   14 +-
 inst/tests/test_indexing3.R                        |   10 +
 inst/tests/test_is.bipartite.R                     |   12 +-
 inst/tests/test_is.chordal.R                       |   27 +-
 inst/tests/test_iterators.R                        |   40 +-
 inst/tests/test_label.propagation.community.R      |    8 +-
 inst/tests/test_laplacian.spectral.embedding.R     |  442 +
 inst/tests/test_largest.cliques.R                  |   10 +-
 inst/tests/test_largest.independent.vertex.sets.R  |   12 +-
 inst/tests/test_layout.fr.R                        |   25 +
 inst/tests/test_layout.gem.R                       |   12 +
 inst/tests/test_layout.kk.R                        |   53 +
 inst/tests/test_layout.mds.R                       |   18 +-
 inst/tests/test_layout.merge.R                     |   14 +-
 inst/tests/test_leading.eigenvector.community.R    |   27 +-
 inst/tests/test_maximal_cliques.R                  |   30 +-
 inst/tests/test_minimal.st.separators.R            |   10 +-
 inst/tests/test_minimum.size.separators.R          |   32 +-
 inst/tests/test_modularity_matrix.R                |   12 +-
 inst/tests/test_motifs.R                           |   32 +-
 inst/tests/test_multilevel.community.R             |   10 +-
 inst/tests/test_neighborhood.R                     |   52 +-
 inst/tests/test_neighbors.R                        |    6 +-
 inst/tests/test_operators.R                        |   45 +-
 inst/tests/test_operators3.R                       |   16 +-
 inst/tests/test_operators4.R                       |   98 +-
 inst/tests/test_optimal.community.R                |   16 +-
 inst/tests/test_pajek.R                            |    4 +-
 inst/tests/test_print.R                            |   25 +-
 inst/tests/test_sample.R                           |   29 +
 inst/tests/test_sbm.game.R                         |   16 +-
 inst/tests/test_scan.R                             |  188 +
 inst/tests/test_scg.R                              |    6 +-
 inst/tests/test_sdf.R                              |    7 +-
 inst/tests/test_sgm.R                              |   48 +
 inst/tests/test_sir.R                              |    2 +-
 inst/tests/test_sphere.R                           |   40 +
 inst/tests/test_transitivity.R                     |   12 +-
 inst/tests/test_triangles.R                        |   39 +
 inst/tests/test_unfold.tree.R                      |   10 +-
 inst/tests/test_walktrap.community.R               |   19 +-
 inst/tests/test_watts.strogatz.game.R              |    8 +-
 man/E.Rd                                           |  100 +
 man/SCGintro.Rd                                    |  156 -
 man/V.Rd                                           |   93 +
 man/aaa-igraph-package.Rd                          |   69 +-
 man/add_edges.Rd                                   |   55 +
 man/add_layout_.Rd                                 |   69 +
 man/add_vertices.Rd                                |   50 +
 man/adjacent.triangles.Rd                          |   36 -
 man/adjacent_vertices.Rd                           |   41 +
 man/aging.prefatt.game.Rd                          |  120 -
 man/all.st.cuts.Rd                                 |   51 -
 man/all.st.mincuts.Rd                              |   63 -
 man/all_simple_paths.Rd                            |   47 +
 man/alpha.centrality.Rd                            |   73 -
 man/alpha_centrality.Rd                            |   88 +
 man/are_adjacent.Rd                                |   48 +
 man/arpack.Rd                                      |  393 +-
 man/articulation.points.Rd                         |   33 -
 man/articulation_points.Rd                         |   43 +
 man/as.directed.Rd                                 |  104 +-
 man/as.igraph.Rd                                   |   41 +-
 man/as_adj_list.Rd                                 |   50 +
 man/as_adjacency_matrix.Rd                         |   73 +
 man/as_edgelist.Rd                                 |   38 +
 man/as_graphnel.Rd                                 |   52 +
 man/as_ids.Rd                                      |   44 +
 man/as_incidence_matrix.Rd                         |   58 +
 man/as_long_data_frame.Rd                          |   32 +
 man/as_membership.Rd                               |   29 +
 man/assortativity.Rd                               |  173 +-
 man/attribute.combination.Rd                       |  144 -
 man/attributes.Rd                                  |  183 -
 man/authority_score.Rd                             |   67 +
 man/autocurve.edges.Rd                             |   43 -
 man/automorphisms.Rd                               |   63 +
 man/ba.game.Rd                                     |  108 -
 man/betweenness.Rd                                 |  163 +-
 man/bfs.Rd                                         |  116 +
 man/biconnected.components.Rd                      |   48 -
 man/biconnected_components.Rd                      |   52 +
 man/bipartite.projection.Rd                        |   83 -
 man/bipartite.random.game.Rd                       |   58 -
 man/bipartite_mapping.Rd                           |   57 +
 man/bipartite_projection.Rd                        |   87 +
 man/bonpow.Rd                                      |  117 -
 man/c.igraph.es.Rd                                 |   47 +
 man/c.igraph.vs.Rd                                 |   47 +
 man/canonical.permutation.Rd                       |   88 -
 man/canonical_permutation.Rd                       |   86 +
 man/categorical_pal.Rd                             |   43 +
 man/centr_betw.Rd                                  |   61 +
 man/centr_betw_tmax.Rd                             |   53 +
 man/centr_clo.Rd                                   |   57 +
 man/centr_clo_tmax.Rd                              |   54 +
 man/centr_degree.Rd                                |   61 +
 man/centr_degree_tmax.Rd                           |   55 +
 man/centr_eigen.Rd                                 |   71 +
 man/centr_eigen_tmax.Rd                            |   57 +
 man/centralization.Rd                              |  156 -
 man/centralize.Rd                                  |   89 +
 man/cliques.Rd                                     |  143 +-
 man/closeness.Rd                                   |  114 +-
 man/cluster_edge_betweenness.Rd                    |  102 +
 man/cluster_fast_greedy.Rd                         |   66 +
 man/cluster_infomap.Rd                             |   70 +
 man/cluster_label_prop.Rd                          |   72 +
 man/cluster_leading_eigen.Rd                       |  116 +
 man/cluster_louvain.Rd                             |   70 +
 man/cluster_optimal.Rd                             |   75 +
 man/cluster_spinglass.Rd                           |  146 +
 man/cluster_walktrap.Rd                            |   67 +
 man/clusters.Rd                                    |   73 -
 man/cocitation.Rd                                  |   61 +-
 man/cohesive.blocks.Rd                             |  269 -
 man/cohesive_blocks.Rd                             |  282 +
 man/communities.Rd                                 |  465 +-
 man/community.edge.betweenness.Rd                  |   96 -
 man/community.structure.Rd                         |   44 -
 man/compare.Rd                                     |   73 +
 man/compare.communities.Rd                         |   75 -
 man/complementer.Rd                                |   46 +
 man/component_wise.Rd                              |   67 +
 man/components.Rd                                  |  102 +-
 man/compose.Rd                                     |   76 +
 man/consensus_tree.Rd                              |   54 +
 man/console.Rd                                     |   35 +
 man/constraint.Rd                                  |   83 +-
 man/contract.Rd                                    |   49 +
 man/contract.vertices.Rd                           |   51 -
 man/conversion.Rd                                  |   82 -
 man/convex.hull.Rd                                 |   34 -
 man/convex_hull.Rd                                 |   36 +
 man/coreness.Rd                                    |   53 +
 man/count_isomorphisms.Rd                          |   67 +
 man/count_motifs.Rd                                |   43 +
 man/count_subgraph_isomorphisms.Rd                 |  100 +
 man/count_triangles.Rd                             |   63 +
 man/curve_multiple.Rd                              |   49 +
 man/decompose.Rd                                   |   48 +
 man/decompose.graph.Rd                             |   40 -
 man/degree.Rd                                      |   77 +-
 man/degree.sequence.game.Rd                        |   86 -
 man/delete_edge_attr.Rd                            |   70 +
 man/delete_edges.Rd                                |   40 +
 man/delete_graph_attr.Rd                           |   69 +
 man/delete_vertex_attr.Rd                          |   70 +
 man/delete_vertices.Rd                             |   42 +
 man/dendPlot.Rd                                    |   24 -
 man/dendPlot.communities.Rd                        |   95 -
 man/dendPlot.igraphHRG.Rd                          |   94 -
 man/dfs.Rd                                         |  109 +
 man/diameter.Rd                                    |   85 +-
 man/difference.Rd                                  |   24 +
 man/difference.igraph.Rd                           |   64 +
 man/difference.igraph.es.Rd                        |   52 +
 man/difference.igraph.vs.Rd                        |   52 +
 man/dim_select.Rd                                  |   72 +
 man/disjoint_union.Rd                              |   57 +
 man/distances.Rd                                   |  207 +
 man/diverging_pal.Rd                               |   53 +
 man/diversity.Rd                                   |   58 +
 man/dominator.tree.Rd                              |   75 -
 man/dominator_tree.Rd                              |   69 +
 man/dyad.census.Rd                                 |   38 -
 man/dyad_census.Rd                                 |   44 +
 man/each_edge.Rd                                   |   41 +
 man/eccentricity.Rd                                |   73 +-
 man/edge.Rd                                        |   63 +
 man/edge.connectivity.Rd                           |   80 -
 man/edge_attr-set.Rd                               |   79 +
 man/edge_attr.Rd                                   |   75 +
 man/edge_attr_names.Rd                             |   67 +
 man/edge_connectivity.Rd                           |   86 +
 man/edge_density.Rd                                |   53 +
 man/ego.Rd                                         |   92 +
 man/eigen_centrality.Rd                            |   85 +
 man/embed_adjacency_matrix.Rd                      |   88 +
 man/embed_laplacian_matrix.Rd                      |  100 +
 man/ends.Rd                                        |   40 +
 man/erdos.renyi.game.Rd                            |   88 +-
 man/evcent.Rd                                      |   76 -
 man/evolver.Rd                                     |  243 -
 man/fastgreedy.community.Rd                        |   63 -
 man/fit_hrg.Rd                                     |   90 +
 man/fit_power_law.Rd                               |  119 +
 man/forest.fire.game.Rd                            |   79 -
 man/gclust.app.Rd                                  |   29 +
 man/gclust.rsvt.Rd                                 |   33 +
 man/get.adjlist.Rd                                 |   41 -
 man/get.edge.ids.Rd                                |   85 +-
 man/get.incidence.Rd                               |   48 -
 man/getAICc.Rd                                     |   28 +
 man/girth.Rd                                       |   64 +-
 man/gorder.Rd                                      |   35 +
 man/graph.adjacency.Rd                             |  156 -
 man/graph.adjlist.Rd                               |   62 -
 man/graph.automorphisms.Rd                         |   58 -
 man/graph.bfs.Rd                                   |  113 -
 man/graph.bipartite.Rd                             |   54 -
 man/graph.complementer.Rd                          |   40 -
 man/graph.compose.Rd                               |   72 -
 man/graph.constructors.Rd                          |  176 -
 man/graph.data.frame.Rd                            |  110 -
 man/graph.de.bruijn.Rd                             |   38 -
 man/graph.density.Rd                               |   44 -
 man/graph.dfs.Rd                                   |  102 -
 man/graph.difference.Rd                            |   55 -
 man/graph.disjoint.union.Rd                        |   49 -
 man/graph.diversity.Rd                             |   57 -
 man/graph.eigen.Rd                                 |   81 -
 man/graph.famous.Rd                                |  133 -
 man/graph.formula.Rd                               |  125 -
 man/graph.full.bipartite.Rd                        |   39 -
 man/graph.graphdb.Rd                               |   78 -
 man/graph.incidence.Rd                             |   73 -
 man/graph.intersection.Rd                          |   56 -
 man/graph.isomorphism.Rd                           |  329 -
 man/graph.kautz.Rd                                 |   34 -
 man/graph.kcores.Rd                                |   42 -
 man/graph.knn.Rd                                   |   63 -
 man/graph.laplacian.Rd                             |   49 -
 man/graph.lcf.Rd                                   |   31 -
 man/graph.maxflow.Rd                               |  128 -
 man/graph.motifs.Rd                                |   62 -
 man/graph.strength.Rd                              |   44 -
 man/graph.structure.Rd                             |  351 -
 man/graph.union.Rd                                 |   54 -
 man/graphNEL.Rd                                    |   71 -
 man/graph_.Rd                                      |   23 +
 man/graph_attr-set.Rd                              |   76 +
 man/graph_attr.Rd                                  |   70 +
 man/graph_attr_names.Rd                            |   66 +
 man/graph_from_adj_list.Rd                         |   70 +
 man/graph_from_adjacency_matrix.Rd                 |  150 +
 man/graph_from_atlas.Rd                            |   74 +
 man/graph_from_data_frame.Rd                       |  124 +
 man/graph_from_edgelist.Rd                         |   70 +
 man/graph_from_graphdb.Rd                          |   93 +
 man/graph_from_graphnel.Rd                         |   67 +
 man/graph_from_incidence_matrix.Rd                 |   85 +
 man/graph_from_isomorphism_class.Rd                |   50 +
 man/graph_from_lcf.Rd                              |   42 +
 man/graph_from_literal.Rd                          |  153 +
 man/graph_version.Rd                               |   32 +
 man/graphlet_basis.Rd                              |   99 +
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 man/grg.game.Rd                                    |   39 -
 man/groups.Rd                                      |   43 +
 man/growing.random.game.Rd                         |   35 -
 man/gsize.Rd                                       |   40 +
 man/head_of.Rd                                     |   34 +
 man/hrg-methods.Rd                                 |   39 +
 man/hrg.Rd                                         |  241 +-
 man/hrg_tree.Rd                                    |   29 +
 man/hub_score.Rd                                   |   64 +
 man/identical_graphs.Rd                            |   20 +
 man/igraph-attribute-combination.Rd                |  109 +
 man/igraph-dollar.Rd                               |   73 +
 man/igraph-es-attributes.Rd                        |  117 +
 man/igraph-es-indexing.Rd                          |  154 +
 man/igraph-es-indexing2.Rd                         |   85 +
 man/igraph-minus.Rd                                |   69 +
 man/igraph-vs-attributes.Rd                        |  133 +
 man/igraph-vs-indexing.Rd                          |  167 +
 man/igraph-vs-indexing2.Rd                         |   86 +
 man/igraph.console.Rd                              |   28 -
 man/igraph.par.Rd                                  |  108 -
 man/igraph.sample.Rd                               |   29 -
 man/igraph.version.Rd                              |   30 -
 man/igraph.vertex.shapes.Rd                        |  257 -
 man/igraph_demo.Rd                                 |   42 +
 man/igraph_options.Rd                              |  106 +
 man/igraph_test.Rd                                 |   29 +
 man/igraph_version.Rd                              |   34 +
 man/igraphdemo.Rd                                  |   33 -
 man/igraphtest.Rd                                  |   22 -
 man/incident.Rd                                    |   42 +
 man/incident_edges.Rd                              |   41 +
 man/independent.sets.Rd                            |   76 -
 man/infomap.Rd                                     |   64 -
 man/interconnected.islands.Rd                      |   33 -
 man/intersection.Rd                                |   24 +
 man/intersection.igraph.Rd                         |   63 +
 man/intersection.igraph.es.Rd                      |   48 +
 man/intersection.igraph.vs.Rd                      |   48 +
 man/is.bipartite.Rd                                |   56 -
 man/is.chordal.Rd                                  |   71 -
 man/is.dag.Rd                                      |   28 -
 man/is.degree.sequence.Rd                          |   55 -
 man/is.graph.Rd                                    |   24 -
 man/is.multiple.Rd                                 |   76 -
 man/is.mutual.Rd                                   |   39 -
 man/is.named.Rd                                    |   35 -
 man/is.separator.Rd                                |   69 -
 man/is.weighted.Rd                                 |   33 -
 man/is_chordal.Rd                                  |   77 +
 man/is_dag.Rd                                      |   36 +
 man/is_degseq.Rd                                   |   49 +
 man/is_directed.Rd                                 |   38 +
 man/is_graphical.Rd                                |   45 +
 man/is_igraph.Rd                                   |   29 +
 man/is_min_separator.Rd                            |   63 +
 man/is_named.Rd                                    |   44 +
 man/is_separator.Rd                                |   36 +
 man/is_weighted.Rd                                 |   42 +
 man/isomorphic.Rd                                  |  150 +
 man/isomorphism_class.Rd                           |   56 +
 man/isomorphisms.Rd                                |   49 +
 man/iterators.Rd                                   |  234 -
 man/ivs.Rd                                         |   90 +
 man/k.regular.game.Rd                              |   51 -
 man/keeping_degseq.Rd                              |   43 +
 man/kleinberg.Rd                                   |   65 -
 man/knn.Rd                                         |   70 +
 man/label.propagation.community.Rd                 |   70 -
 man/laplacian_matrix.Rd                            |   58 +
 man/layout.Rd                                      |  324 -
 man/layout.bipartite.Rd                            |   48 -
 man/layout.deprecated.Rd                           |   35 +
 man/layout.drl.Rd                                  |  103 -
 man/layout.fruchterman.reingold.grid.Rd            |   20 +
 man/layout.grid.Rd                                 |   47 -
 man/layout.mds.Rd                                  |   52 -
 man/layout.merge.Rd                                |   58 -
 man/layout.spring.Rd                               |   20 +
 man/layout.star.Rd                                 |   36 -
 man/layout.sugiyama.Rd                             |  195 -
 man/layout.svd.Rd                                  |   20 +
 man/layout_.Rd                                     |  107 +
 man/layout_as_bipartite.Rd                         |  104 +
 man/layout_as_star.Rd                              |   90 +
 man/layout_as_tree.Rd                              |  119 +
 man/layout_in_circle.Rd                            |   88 +
 man/layout_nicely.Rd                               |   86 +
 man/layout_on_grid.Rd                              |   99 +
 man/layout_on_sphere.Rd                            |   75 +
 man/layout_randomly.Rd                             |   75 +
 man/layout_with_dh.Rd                              |  173 +
 man/layout_with_drl.Rd                             |  116 +
 man/layout_with_fr.Rd                              |  146 +
 man/layout_with_gem.Rd                             |  105 +
 man/layout_with_graphopt.Rd                        |  108 +
 man/layout_with_kk.Rd                              |  134 +
 man/layout_with_lgl.Rd                             |   94 +
 man/layout_with_mds.Rd                             |  103 +
 man/layout_with_sugiyama.Rd                        |  242 +
 man/leading.eigenvector.Rd                         |  133 -
 man/line.graph.Rd                                  |   38 -
 man/local_scan.Rd                                  |   99 +
 man/make_.Rd                                       |   48 +
 man/make_bipartite_graph.Rd                        |   68 +
 man/make_chordal_ring.Rd                           |   70 +
 man/make_clusters.Rd                               |   35 +
 man/make_de_bruijn_graph.Rd                        |   54 +
 man/make_empty_graph.Rd                            |   63 +
 man/make_full_bipartite_graph.Rd                   |   54 +
 man/make_full_citation_graph.Rd                    |   60 +
 man/make_full_graph.Rd                             |   65 +
 man/make_graph.Rd                                  |  211 +
 man/make_kautz_graph.Rd                            |   49 +
 man/make_lattice.Rd                                |   83 +
 man/make_line_graph.Rd                             |   48 +
 man/make_ring.Rd                                   |   69 +
 man/make_star.Rd                                   |   71 +
 man/make_tree.Rd                                   |   71 +
 man/match_vertices.Rd                              |   80 +
 man/matching.Rd                                    |  156 +-
 man/max_cardinality.Rd                             |   58 +
 man/max_flow.Rd                                    |   77 +
 man/maximum.cardinality.search.Rd                  |   49 -
 man/merge_coords.Rd                                |  106 +
 man/min_cut.Rd                                     |   81 +
 man/min_separators.Rd                              |   81 +
 man/min_st_separators.Rd                           |   48 +
 man/minimal.st.separators.Rd                       |   43 -
 man/minimum.size.separators.Rd                     |   78 -
 man/minimum.spanning.tree.Rd                       |   47 -
 man/modularity.Rd                                  |   79 -
 man/modularity.igraph.Rd                           |   85 +
 man/motifs.Rd                                      |   49 +
 man/mst.Rd                                         |   56 +
 man/multilevel.community.Rd                        |   70 -
 man/neighborhood.Rd                                |   77 -
 man/neighbors.Rd                                   |   43 +
 man/nexus.Rd                                       |  345 +-
 man/norm_coords.Rd                                 |   77 +
 man/normalize.Rd                                   |   66 +
 man/optimal.community.Rd                           |   70 -
 man/page.rank.Rd                                   |  130 -
 man/page_rank.Rd                                   |  142 +
 man/path.Rd                                        |   58 +
 man/permute.Rd                                     |   55 +
 man/permute.vertices.Rd                            |   46 -
 man/pipe.Rd                                        |   28 +
 man/plot.common.Rd                                 |   67 +-
 man/plot.graph.Rd                                  |   64 -
 man/plot.igraph.Rd                                 |   82 +
 man/plot.sir.Rd                                    |  110 +-
 man/plot_dendrogram.communities.Rd                 |  100 +
 man/plot_dendrogram.igraphHRG.Rd                   |   92 +
 man/plus-.igraph.Rd                                |  117 +
 man/power.law.fit.Rd                               |  116 -
 man/power_centrality.Rd                            |  131 +
 man/predict_edges.Rd                               |   85 +
 man/preference.game.Rd                             |   62 -
 man/print.graph.Rd                                 |   82 -
 man/print.igraph.Rd                                |   97 +
 man/print.igraph.es.Rd                             |   83 +
 man/print.igraph.vs.Rd                             |   81 +
 man/print.igraphHRG.Rd                             |   66 +
 man/print.igraphHRGConsensus.Rd                    |   36 +
 man/r_pal.Rd                                       |   24 +
 man/radius.Rd                                      |   49 +
 man/random_walk.Rd                                 |   48 +
 man/read.graph.Rd                                  |  343 -
 man/read_graph.Rd                                  |   60 +
 man/reciprocity.Rd                                 |   63 +-
 man/rep.igraph.Rd                                  |   31 +
 man/rev.igraph.es.Rd                               |   44 +
 man/rev.igraph.vs.Rd                               |   43 +
 man/rewire.Rd                                      |   48 +-
 man/rewire.edges.Rd                                |   33 -
 man/rglplot.Rd                                     |   49 +-
 man/running.mean.Rd                                |   28 -
 man/running_mean.Rd                                |   36 +
 man/sample_.Rd                                     |   30 +
 man/sample_bipartite.Rd                            |   74 +
 man/sample_correlated_gnp.Rd                       |   53 +
 man/sample_correlated_gnp_pair.Rd                  |   54 +
 man/sample_degseq.Rd                               |   99 +
 man/sample_dirichlet.Rd                            |   38 +
 man/sample_dot_product.Rd                          |   58 +
 man/sample_fitness.Rd                              |   79 +
 man/sample_fitness_pl.Rd                           |   86 +
 man/sample_forestfire.Rd                           |   79 +
 man/sample_gnm.Rd                                  |   52 +
 man/sample_gnp.Rd                                  |   51 +
 man/sample_grg.Rd                                  |   53 +
 man/sample_growing.Rd                              |   49 +
 man/sample_hierarchical_sbm.Rd                     |   60 +
 man/sample_hrg.Rd                                  |   30 +
 man/sample_islands.Rd                              |   39 +
 man/sample_k_regular.Rd                            |   54 +
 man/sample_last_cit.Rd                             |   71 +
 man/sample_motifs.Rd                               |   51 +
 man/sample_pa.Rd                                   |  122 +
 man/sample_pa_age.Rd                               |  135 +
 man/sample_pref.Rd                                 |   87 +
 man/sample_sbm.Rd                                  |   57 +
 man/sample_seq.Rd                                  |   42 +
 man/sample_smallworld.Rd                           |   61 +
 man/sample_sphere_surface.Rd                       |   43 +
 man/sample_sphere_volume.Rd                        |   43 +
 man/sample_traits_callaway.Rd                      |   73 +
 man/sbm.game.Rd                                    |   43 -
 man/scan_stat.Rd                                   |   64 +
 man/scg-method.Rd                                  |   52 +
 man/scg.Rd                                         |  293 +-
 man/scg.grouping.Rd                                |  127 -
 man/scg_eps.Rd                                     |   59 +
 man/scg_extra.Rd                                   |   51 -
 man/scg_group.Rd                                   |  133 +
 man/scg_semi_proj.Rd                               |  100 +
 man/semiProjectors.Rd                              |   92 -
 man/sequential_pal.Rd                              |   41 +
 man/set_edge_attr.Rd                               |   75 +
 man/set_graph_attr.Rd                              |   71 +
 man/set_vertex_attr.Rd                             |   75 +
 man/shapes.Rd                                      |  261 +
 man/shortest.paths.Rd                              |  196 -
 man/similarity.Rd                                  |  109 +-
 man/simplified.Rd                                  |   22 +
 man/simplify.Rd                                    |   81 +-
 man/sir.Rd                                         |  172 +-
 man/spectrum.Rd                                    |   79 +
 man/spinglass.community.Rd                         |  144 -
 man/split_join_distance.Rd                         |   44 +
 man/srand.Rd                                       |   35 +-
 man/st_cuts.Rd                                     |   56 +
 man/st_min_cuts.Rd                                 |   66 +
 man/static.fitness.game.Rd                         |   73 -
 man/static.power.law.game.Rd                       |   78 -
 man/stochasticMatrix.Rd                            |   49 -
 man/stochastic_matrix.Rd                           |   55 +
 man/strength.Rd                                    |   56 +
 man/structure.info.Rd                              |   88 -
 man/sub-.igraph.Rd                                 |  130 +
 man/sub-sub-.igraph.Rd                             |   86 +
 man/subcomponent.Rd                                |   44 +
 man/subgraph.Rd                                    |   96 +-
 man/subgraph.centrality.Rd                         |   45 -
 man/subgraph_centrality.Rd                         |   51 +
 man/subgraph_isomorphic.Rd                         |  128 +
 man/subgraph_isomorphisms.Rd                       |   89 +
 man/tail_of.Rd                                     |   34 +
 man/tkigraph.Rd                                    |   29 +-
 man/tkplot.Rd                                      |  288 +-
 man/topo_sort.Rd                                   |   42 +
 man/topological.sort.Rd                            |   39 -
 man/traits.Rd                                      |   53 -
 man/transitivity.Rd                                |  169 +-
 man/triad.census.Rd                                |   56 -
 man/triad_census.Rd                                |   55 +
 man/undocumented.Rd                                |   40 -
 man/unfold.tree.Rd                                 |   48 -
 man/unfold_tree.Rd                                 |   48 +
 man/union.Rd                                       |   24 +
 man/union.igraph.Rd                                |   59 +
 man/union.igraph.es.Rd                             |   49 +
 man/union.igraph.vs.Rd                             |   49 +
 man/unique.igraph.es.Rd                            |   48 +
 man/unique.igraph.vs.Rd                            |   48 +
 man/upgrade_graph.Rd                               |   32 +
 man/vertex.Rd                                      |   50 +
 man/vertex.connectivity.Rd                         |   86 -
 man/vertex.shape.pie.Rd                            |    2 +-
 man/vertex_attr-set.Rd                             |   79 +
 man/vertex_attr.Rd                                 |   76 +
 man/vertex_attr_names.Rd                           |   68 +
 man/vertex_connectivity.Rd                         |  101 +
 man/walktrap.community.Rd                          |   60 -
 man/watts.strogatz.game.Rd                         |   44 -
 man/which_multiple.Rd                              |   82 +
 man/which_mutual.Rd                                |   47 +
 man/with_edge_.Rd                                  |   28 +
 man/with_graph_.Rd                                 |   24 +
 man/with_vertex_.Rd                                |   29 +
 man/without_attr.Rd                                |   25 +
 man/without_loops.Rd                               |   23 +
 man/without_multiples.Rd                           |   22 +
 man/write.graph.Rd                                 |  194 -
 man/write_graph.Rd                                 |   53 +
 src/AMD/Include/amd.h                              |  411 +
 src/AMD/Include/amd_internal.h                     |  347 +
 src/AMD/Makefile                                   |   73 +
 src/AMD/README.txt                                 |  213 +
 src/AMD/Source/amd.f                               | 1214 +++
 src/AMD/Source/amd_1.c                             |  180 +
 src/AMD/Source/amd_2.c                             | 1842 ++++
 src/AMD/Source/amd_aat.c                           |  184 +
 src/AMD/Source/amd_control.c                       |   63 +
 src/AMD/Source/amd_defaults.c                      |   37 +
 src/AMD/Source/amd_dump.c                          |  179 +
 src/AMD/Source/amd_global.c                        |   83 +
 src/AMD/Source/amd_info.c                          |  119 +
 src/AMD/Source/amd_order.c                         |  199 +
 src/AMD/Source/amd_post_tree.c                     |  120 +
 src/AMD/Source/amd_postorder.c                     |  206 +
 src/AMD/Source/amd_preprocess.c                    |  118 +
 src/AMD/Source/amd_valid.c                         |   92 +
 src/AMD/Source/amdbar.f                            | 1206 +++
 src/CHOLMOD.diff                                   |   89 +
 src/CHOLMOD/Check/License.txt                      |   24 +
 src/CHOLMOD/Check/cholmod_check.c                  | 2709 ++++++
 src/CHOLMOD/Check/cholmod_read.c                   | 1319 +++
 src/CHOLMOD/Check/cholmod_write.c                  |  744 ++
 src/CHOLMOD/Check/lesser.txt                       |  504 ++
 src/CHOLMOD/Cholesky/License.txt                   |   24 +
 src/CHOLMOD/Cholesky/cholmod_amd.c                 |  211 +
 src/CHOLMOD/Cholesky/cholmod_analyze.c             |  942 ++
 src/CHOLMOD/Cholesky/cholmod_colamd.c              |  209 +
 src/CHOLMOD/Cholesky/cholmod_etree.c               |  226 +
 src/CHOLMOD/Cholesky/cholmod_factorize.c           |  428 +
 src/CHOLMOD/Cholesky/cholmod_postorder.c           |  291 +
 src/CHOLMOD/Cholesky/cholmod_rcond.c               |  160 +
 src/CHOLMOD/Cholesky/cholmod_resymbol.c            |  608 ++
 src/CHOLMOD/Cholesky/cholmod_rowcolcounts.c        |  536 ++
 src/CHOLMOD/Cholesky/cholmod_rowfac.c              |  735 ++
 src/CHOLMOD/Cholesky/cholmod_solve.c               | 1684 ++++
 src/CHOLMOD/Cholesky/cholmod_spsolve.c             |  396 +
 src/CHOLMOD/Cholesky/lesser.txt                    |  504 ++
 src/CHOLMOD/Cholesky/t_cholmod_lsolve.c            |  850 ++
 src/CHOLMOD/Cholesky/t_cholmod_ltsolve.c           |  849 ++
 src/CHOLMOD/Cholesky/t_cholmod_rowfac.c            |  457 +
 src/CHOLMOD/Cholesky/t_cholmod_solve.c             |  177 +
 src/CHOLMOD/Core/License.txt                       |   25 +
 src/CHOLMOD/Core/cholmod_aat.c                     |  301 +
 src/CHOLMOD/Core/cholmod_add.c                     |  281 +
 src/CHOLMOD/Core/cholmod_band.c                    |  373 +
 src/CHOLMOD/Core/cholmod_change_factor.c           | 1226 +++
 src/CHOLMOD/Core/cholmod_common.c                  |  701 ++
 src/CHOLMOD/Core/cholmod_complex.c                 |  549 ++
 src/CHOLMOD/Core/cholmod_copy.c                    |  406 +
 src/CHOLMOD/Core/cholmod_dense.c                   |  701 ++
 src/CHOLMOD/Core/cholmod_error.c                   |   79 +
 src/CHOLMOD/Core/cholmod_factor.c                  |  936 ++
 src/CHOLMOD/Core/cholmod_memory.c                  |  575 ++
 src/CHOLMOD/Core/cholmod_sparse.c                  |  651 ++
 src/CHOLMOD/Core/cholmod_transpose.c               | 1138 +++
 src/CHOLMOD/Core/cholmod_triplet.c                 |  772 ++
 src/CHOLMOD/Core/cholmod_version.c                 |   37 +
 src/CHOLMOD/Core/lesser.txt                        |  504 ++
 src/CHOLMOD/Core/t_cholmod_change_factor.c         |  660 ++
 src/CHOLMOD/Core/t_cholmod_dense.c                 |  265 +
 src/CHOLMOD/Core/t_cholmod_transpose.c             |  317 +
 src/CHOLMOD/Core/t_cholmod_triplet.c               |  175 +
 src/CHOLMOD/Include/License.txt                    |    8 +
 src/CHOLMOD/Include/README.txt                     |   25 +
 src/CHOLMOD/Include/cholmod.h                      |  125 +
 src/CHOLMOD/Include/cholmod_blas.h                 |  455 +
 src/CHOLMOD/Include/cholmod_camd.h                 |  102 +
 src/CHOLMOD/Include/cholmod_check.h                |  427 +
 src/CHOLMOD/Include/cholmod_cholesky.h             |  565 ++
 src/CHOLMOD/Include/cholmod_complexity.h           |  264 +
 src/CHOLMOD/Include/cholmod_config.h               |   85 +
 src/CHOLMOD/Include/cholmod_core.h                 | 2395 +++++
 src/CHOLMOD/Include/cholmod_internal.h             |  404 +
 src/CHOLMOD/Include/cholmod_io64.h                 |   45 +
 src/CHOLMOD/Include/cholmod_matrixops.h            |  237 +
 src/CHOLMOD/Include/cholmod_modify.h               |  306 +
 src/CHOLMOD/Include/cholmod_partition.h            |  166 +
 src/CHOLMOD/Include/cholmod_supernodal.h           |  172 +
 src/CHOLMOD/Include/cholmod_template.h             |  238 +
 src/CHOLMOD/Makefile                               |   75 +
 src/CHOLMOD/MatrixOps/License.txt                  |   25 +
 src/CHOLMOD/MatrixOps/cholmod_drop.c               |  183 +
 src/CHOLMOD/MatrixOps/cholmod_horzcat.c            |  203 +
 src/CHOLMOD/MatrixOps/cholmod_norm.c               |  452 +
 src/CHOLMOD/MatrixOps/cholmod_scale.c              |  217 +
 src/CHOLMOD/MatrixOps/cholmod_sdmult.c             |  149 +
 src/CHOLMOD/MatrixOps/cholmod_ssmult.c             |  487 +
 src/CHOLMOD/MatrixOps/cholmod_submatrix.c          |  425 +
 src/CHOLMOD/MatrixOps/cholmod_symmetry.c           |  488 +
 src/CHOLMOD/MatrixOps/cholmod_vertcat.c            |  201 +
 src/CHOLMOD/MatrixOps/gpl.txt                      |  340 +
 src/CHOLMOD/MatrixOps/t_cholmod_sdmult.c           |  726 ++
 src/CHOLMOD/Modify/License.txt                     |   25 +
 src/CHOLMOD/Modify/cholmod_rowadd.c                |  678 ++
 src/CHOLMOD/Modify/cholmod_rowdel.c                |  461 +
 src/CHOLMOD/Modify/cholmod_updown.c                | 1570 ++++
 src/CHOLMOD/Modify/gpl.txt                         |  340 +
 src/CHOLMOD/Modify/t_cholmod_updown.c              |  214 +
 src/CHOLMOD/Modify/t_cholmod_updown_numkr.c        |  746 ++
 src/CHOLMOD/Partition/License.txt                  |   25 +
 src/CHOLMOD/Partition/cholmod_camd.c               |  231 +
 src/CHOLMOD/Partition/cholmod_ccolamd.c            |  208 +
 src/CHOLMOD/Partition/cholmod_csymamd.c            |  144 +
 src/CHOLMOD/Partition/cholmod_metis.c              |  795 ++
 src/CHOLMOD/Partition/cholmod_nesdis.c             | 2168 +++++
 src/CHOLMOD/Partition/lesser.txt                   |  504 ++
 src/CHOLMOD/README.txt                             |   81 +
 src/CHOLMOD/Supernodal/License.txt                 |   25 +
 src/CHOLMOD/Supernodal/cholmod_super_numeric.c     |  307 +
 src/CHOLMOD/Supernodal/cholmod_super_solve.c       |  217 +
 src/CHOLMOD/Supernodal/cholmod_super_symbolic.c    |  862 ++
 src/CHOLMOD/Supernodal/gpl.txt                     |  340 +
 src/CHOLMOD/Supernodal/t_cholmod_gpu.c             |  972 ++
 src/CHOLMOD/Supernodal/t_cholmod_super_numeric.c   |  912 ++
 src/CHOLMOD/Supernodal/t_cholmod_super_solve.c     |  450 +
 src/COLAMD/Include/colamd.h                        |  251 +
 src/COLAMD/Makefile                                |   56 +
 src/COLAMD/README.txt                              |  118 +
 src/COLAMD/Source/colamd.c                         | 3604 ++++++++
 src/COLAMD/Source/colamd_global.c                  |   24 +
 src/Makevars.in                                    |   10 +-
 src/Makevars.win                                   |    7 +-
 src/SuiteSparse_config/Makefile                    |   43 +
 src/SuiteSparse_config/README.txt                  |   48 +
 src/SuiteSparse_config/SuiteSparse_config.c        |  191 +
 src/SuiteSparse_config/SuiteSparse_config.h        |  202 +
 src/SuiteSparse_config/SuiteSparse_config.mk       |  393 +
 src/SuiteSparse_config/SuiteSparse_config_GPU.mk   |  393 +
 src/SuiteSparse_config/SuiteSparse_config_Mac.mk   |  395 +
 src/adjlist.c                                      |   44 +-
 src/bigint.c                                       |    6 -
 src/blas.c                                         |    6 +
 src/cattributes.c                                  |  502 +-
 src/centrality.c                                   |   48 +-
 src/community.c                                    |   48 +-
 src/components.c                                   |   91 +-
 src/config.h.in                                    |   32 +-
 src/{ => cs}/cs_add.c                              |    0
 src/{ => cs}/cs_amd.c                              |    0
 src/{ => cs}/cs_chol.c                             |    0
 src/{ => cs}/cs_cholsol.c                          |    0
 src/{ => cs}/cs_compress.c                         |    0
 src/{ => cs}/cs_counts.c                           |    0
 src/{ => cs}/cs_cumsum.c                           |    0
 src/{ => cs}/cs_dfs.c                              |    0
 src/{ => cs}/cs_dmperm.c                           |    0
 src/{ => cs}/cs_droptol.c                          |    0
 src/{ => cs}/cs_dropzeros.c                        |    0
 src/{ => cs}/cs_dupl.c                             |    0
 src/{ => cs}/cs_entry.c                            |    0
 src/{ => cs}/cs_ereach.c                           |    0
 src/{ => cs}/cs_etree.c                            |    0
 src/{ => cs}/cs_fkeep.c                            |    0
 src/{ => cs}/cs_gaxpy.c                            |    0
 src/{ => cs}/cs_happly.c                           |    0
 src/{ => cs}/cs_house.c                            |    0
 src/{ => cs}/cs_ipvec.c                            |    0
 src/{ => cs}/cs_leaf.c                             |    0
 src/{ => cs}/cs_load.c                             |    0
 src/{ => cs}/cs_lsolve.c                           |    0
 src/{ => cs}/cs_ltsolve.c                          |    0
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 src/dotproduct.c                                   |  276 +
 src/dqueue.c                                       |    6 +
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 src/foreign-pajek-parser.c                         |  176 +-
 src/foreign-pajek-parser.h                         |    2 +-
 src/foreign.c                                      |   16 +-
 src/games.c                                        |  270 +-
 src/gengraph_box_list.h                            |    2 +
 src/gengraph_definitions.h                         |    4 +
 src/gengraph_graph_molloy_hash.cpp                 |    4 +-
 src/gengraph_graph_molloy_optimized.cpp            |   16 +-
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 src/gengraph_vertex_cover.h                        |    4 +
 src/glpenv01.c                                     |  234 -
 src/glpk/COPYING                                   |  676 ++
 src/glpk/README                                    |   39 +
 src/glpk/amd/COPYING                               |  502 ++
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 src/{ => glpk/amd}/amd_2.c                         |    0
 src/{ => glpk/amd}/amd_aat.c                       |    0
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 src/heap.pmt                                       |    1 -
 src/igraph.h                                       |   97 -
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 src/igraph_eigen.h                                 |  118 -
 src/igraph_error.h                                 |  721 --
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 src/igraph_sparsemat.h                             |  264 -
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 src/include/igraph_blas.h                          |   74 +
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 src/layout.c                                       |  993 +--
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 src/prpack/prpack_solver.cpp                       |  879 ++
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 src/random.c                                       |  339 +
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 src/revolver_cit.c                                 | 6479 --------------
 src/revolver_grow.c                                | 1284 ---
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 src/rinterface.c                                   | 9398 ++++++++------------
 src/rinterface.h                                   |    6 +
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 src/sbm.c                                          |  387 +
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 src/{ => simpleraytracer}/Color.cpp                |    0
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 src/structural_properties.c                        |   71 +-
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 src/uuid/config.h.in                               |   82 +
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 src/vector.c                                       |  100 +-
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 1279 files changed, 137557 insertions(+), 48676 deletions(-)
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