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locks; strict; comment @# @; 1.19 date 2024.01.26.21.43.01; author mef; state Exp; branches; next 1.18; commitid d0pPMHtgCxLar0WE; 1.18 date 2023.11.08.13.20.01; author wiz; state Exp; branches; next 1.17; commitid PsuHTklAIsF4bOLE; 1.17 date 2023.08.11.07.11.36; author mef; state Exp; branches; next 1.16; commitid g9UE7ugIU0BZ0lAE; 1.16 date 2023.06.11.02.48.20; author mef; state Exp; branches; next 1.15; commitid WobKBOLwUu4gwtsE; 1.15 date 2023.04.19.08.10.44; author adam; state Exp; branches; next 1.14; commitid B8gCWhWtMX9vZGlE; 1.14 date 2023.03.11.11.15.33; author mef; state Exp; branches; next 1.13; commitid cRhpADTs3cDGhHgE; 1.13 date 2023.03.11.11.07.54; author mef; state Exp; branches; next 1.12; commitid hzewNu7WsS11fHgE; 1.12 date 2022.11.23.16.20.34; author adam; state Exp; branches; next 1.11; commitid ju2K3LUYlTJKqQ2E; 1.11 date 2022.04.28.15.44.47; author mef; state Exp; branches; next 1.10; commitid vHQAWAPQqoFGXYBD; 1.10 date 2022.04.18.19.11.34; author adam; state Exp; branches; next 1.9; commitid eC9Na3jrfOOUpIAD; 1.9 date 2021.12.08.16.05.31; author adam; state Exp; branches; next 1.8; commitid 2PyWjHx5T8rqARjD; 1.8 date 2021.04.21.11.42.09; author adam; state Exp; branches; next 1.7; commitid fph0Axs0eT3az9QC; 1.7 date 2020.11.05.09.08.36; author ryoon; state Exp; branches; next 1.6; commitid VqGaBtHnBBcd5GuC; 1.6 date 2020.06.02.08.24.16; author adam; state Exp; branches; next 1.5; commitid nisovMpvvZm3RCaC; 1.5 date 2019.09.25.17.30.08; author brook; state Exp; branches; next 1.4; commitid spoqPpR0IQY8XpEB; 1.4 date 2019.08.08.19.53.50; author brook; state Exp; branches; next 1.3; commitid K2VPfA0XCw7xfgyB; 1.3 date 2019.07.31.19.47.01; author brook; state Exp; branches; next 1.2; commitid HzSnsaR8McEIvexB; 1.2 date 2018.09.04.00.23.12; author minskim; state Exp; branches; next 1.1; commitid gVs9oSX2OyHbGIQA; 1.1 date 2018.05.24.22.25.17; author minskim; state Exp; branches; next ; commitid 115vuWTRMJI0jBDA; desc @@ 1.19 log @(math/R-igraph) Updated 1.5.1 to 1.6.0 # igraph 1.6.0 ## Breaking changes - New `arpack_defaults()` replaces `igraph.arpack.default` and `arpack_defaults` lists (#800), with consistent usage checks (#966). - Define methods for `ape::as.phylo()` instead of own `as_phylo()` generic, remove deprecated `asPhylo()` (#763). - `bfs()` with unreachable nodes returns zero instead of `NaN` as `rank` (#956), and negative instead of `NaN` for `dist` (#926). - `random_walk()` adds one more step, the resulting list of vertices is of length `steps + 1` (#934). - `girth()` returns `Inf` for acyclic graphs (#931). - Remove some behaviour / parameters that were deprecated in 1.3 (#842). - Remove `scg_eps()`, `scg_group()` and `scg_semi_proj()`, broken and no longer maintained (#946). ## Bug fixes - Fix `printf()` warning (#975). - Fix calls to `isSymmetric()` for matrix objects with a class (#965). - Reduce frequency of interruption checks (#957). ## Features - Change "incidence matrix" naming to "biadjacency matrix" (#962). - Add aliases using the neighborhood terminology for all ego functions: (#950). - Rename arguments to `assortativity(values, values.in)` from `types1` and `types2` (#952). - Add ellipsis to `cluster_label_prop()` (#954). - Placeholders for `is_acyclic()` and `is_forest()`, to be implemented in igraph 2.0.0 (#945). - `is_tree(details = TRUE)` designates the first vertex as root for non-trees (#935). - `all_shortest_paths()` returns the vertex list in both `res` and `vpaths` components (#930). - Improve symmetry check for adjacency matrices on input (#911). - Warn if non-symmetric undirected adjacency matrix (#904). ## Documentation - Remove duplicate `\seealso{}` (#948). - Update `knnk()` and `sir()` docs. - Fix formula in `reciprocity()` docs. - `strength()` does not give a warning when no weights are given. - Update `sample_smallworld()` manual page (#895). - Correct documentation for weighted cliques. - Update Erdos-Renyi model docs. ## Testing - Clean up tests (#967). - Stabilize tests for `cluster_label_prop()` (#932), `sample_pa()` (#927), `cluster_louvain()` (#933), SIR (#936), `sample_forestfire()` (#929). - Hard-code graph used in test (#928). - Update GML test file (#925). - Improve test for sampling from Dirichlet distribution (#923). - Omit test that no longer holds with igraph 0.10 (#922). - Stabilize test in preparation for upgrade (#920). - Stabilize plot test (#919). - Fix checks. @ text @# $NetBSD: Makefile,v 1.18 2023/11/08 13:20:01 wiz Exp $ R_PKGNAME= igraph R_PKGVER= 1.6.0 CATEGORIES+= graphics MAINTAINER= minskim@@NetBSD.org COMMENT= Network analysis and visualization LICENSE= gnu-gpl-v2 OR gnu-gpl-v3 DEPENDS+= R-cli-[0-9]*:../../devel/R-cli DEPENDS+= R-lifecycle-[0-9]*:../../devel/R-lifecycle DEPENDS+= R-magrittr>=1.5:../../devel/R-magrittr DEPENDS+= R-pkgconfig>=2.0.0:../../devel/R-pkgconfig DEPENDS+= R-rlang-[0-9]*:../../devel/R-rlang # Packages suggested but not available: # 'ape', 'decor', 'graph', 'igraphdata', 'vdiffr' TEST_DEPENDS+= R-knitr-[0-9]*:../../print/R-knitr TEST_DEPENDS+= R-rgl-[0-9]*:../../graphics/R-rgl TEST_DEPENDS+= R-rmarkdown-[0-9]*:../../textproc/R-rmarkdown TEST_DEPENDS+= R-scales-[0-9]*:../../graphics/R-scales TEST_DEPENDS+= R-testthat-[0-9]*:../../devel/R-testthat TEST_DEPENDS+= R-withr-[0-9]*:../../devel/R-withr USE_LANGUAGES= c c++ fortran .include "../../textproc/libxml2/buildlink3.mk" .include "../../lang/R-cpp11/buildlink3.mk" .include "../../math/R/Makefile.extension" .include "../../mk/bsd.pkg.mk" @ 1.18 log @*: recursive bump for icu 74.1 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.17 2023/08/11 07:11:36 mef Exp $ d4 1 a4 1 R_PKGVER= 1.5.0.1 a8 1 PKGREVISION= 1 d12 1 @ 1.17 log @(math/R-igraph) Updated 1.4.3 to 1.5.0 # igraph 1.5.0 ## Breaking changes The internal format of graph objects has changed in a mostly backward-compatible way, to prepare for upgrading the C core to 0.10. Details are described at . Accessing graph objects that have been created with an older igraph version give a clean error message with instructions (#832). The new format cannot be read by igraph 1.4.3 or older, the following error is raised when trying to do so: ``` This graph was created by an old(er) igraph version. Call upgrade_graph() on it to use with the current igraph version For now we convert it on the fly... Error in is_directed(object) : REAL() can only be applied to a 'numeric', not a 'NULL' ``` The only supported remedy is to upgrade the igraph package to version 1.5.0 or later. `graph_version()` now returns an integer scalar (#832, #847), `4` as of igraph 1.5.0 (#835). ## Features - Vertex and edge sequences are converted to numeric vectors when used in attributes (#808). - New `largest_component()` returns the largest connected component (#786, @@ngmaclaren). ## Bug fixes - Fix error message in `make_graph()` when `simplify = ...` is used with a non-formula (#834). ## Testing - Add more tests for `graph_from_literal()` (#826). - Reenable serialization test and tests for `dyad_census()`, stabilize tests (#809, #822, #823). ## Documentation - The documentation for the R package is now hosted at (#780). - Update `vignette("installation-troubleshooting")`. - Fix use of deprecated functions in examples, e.g., replace `gsize()` by `ecount()` (#827). - Fix typos in `?eigen_centrality` docs (@@JJ). - Update CONTRIBUTING.md and ORCID information (#791, #774). - Add DOI to CITATION (#773). ## Internal - Add data for old igraph versions as constructed objects, and tests (#838). - Ensure we're always using named indexes to access the internal data structure (#784). - Prepare migration to igraph/C 0.10 (#781). - Update generated interface (#765). @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.16 2023/06/11 02:48:20 mef Exp $ d9 1 @ 1.16 log @(math/R-igraph) Updated 1.4.1 to 1.4.3 # igraph 1.4.3 ## Internal - Fix tests for dev waldo (#779, @@hadley). - Fix linking on Windows: gfortran needs quadmath. (#778). ## Documentation - Mention limitation of Pajek reader (#776). # igraph 1.4.2 ## Breaking changes - Remove `igraph.eigen.default()` and `eigen_defaults`, introduce internal `eigen_defaults()` as a function (#741). - Remove broken `nexus*()` functions (#705), and `srand()` (#701). ## C core - Update C core. - ARPACK-based calculations are now interruptible. - `shortest_paths()` and `all_shortest_paths()` no longer crash when an invalid `from` vertex is passed and weights are being used. See [diff](https://github.com/igraph/igraph/compare/87c70998344a39b44218f7af903bf62b8bbf3e71...98304787bc811bf709be5aeddea7b570c370988e) for details. ## Printing - Use true vertex names for printing vertex sets. If a vertex set captures a relationship between vertices (e.g., the `father` component of `bfs()`), the vertex set is printed as a named vector (#754). - Suggest restarting R session after fatal error (#745). ## Bug fixes - `as_long_data_frame()` now correctly processes vertex attributes and works with graphs without vertex attributes (#748). - `as.hclust(hrg.fit(g))` works again (#721). ## Documentation - The documentation is now available at (#743). - Reorganize function reference (#662). - Replace `graph()` with `make_graph()` in examples (#738). - Add docs for `as.hclust.igraphHRG()` (#733). - Merged man page of `hub_score()` and `authority_score()` (#698). - Refactor contributors listing (#647). - Improve "family" titles (#679). - Improve docs of ego/neighborhood functions. - Improve `transitivity()` docs. ## Internal - Introduce cpp11 package to improve error handling in the long run (#720). - Avoid longjmp for error handling and interrupts (#751). - `as.hclust.igraphHRG` uses `.Call()` interface (#727). @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.15 2023/04/19 08:10:44 adam Exp $ d4 2 a5 2 R_PKGVER= 1.4.3 CATEGORIES= math graphics d11 1 d17 1 a17 1 # 'ape', 'graph', 'igraphdata', 'vdiffr' @ 1.15 log @revbump after textproc/icu update @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.14 2023/03/11 11:15:33 mef Exp $ d4 1 a4 2 R_PKGVER= 1.4.1 PKGREVISION= 1 d28 2 a30 1 .include "../../textproc/libxml2/buildlink3.mk" @ 1.14 log @(math/R-igraph) Adding TEST_DEPENDS+= , but still missing more @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.13 2023/03/11 11:07:54 mef Exp $ d5 1 @ 1.13 log @(devel/R-igraph) Updated 1.13.1 to 1.14.1 # igraph 1.4.1 ## Bug fixes - `console()` now works again and provides a Tcl/Tk based UI where igraph can post status messages and progress info (#664). - Fix errors when printing long vertex names (#677, @@ahmohamed). - Fix regression that broke builds on some systems (e.g., GCC version 5 or earlier), introduced in igraph 1.4.0 (#670, #671). - `fit_hrg()` does not crash any more when called with a graph that has less than three vertices. ## Documentation - Various improvements (#663, @@maelle; #667). ## Internal - Fix warning about `yyget_leng()` returning wrong type when using LTO (#676). - Don't mention C++11 or C++17 for best compatibility with both newest R and older compilers, while still requesting a C++ compiler for linking. - Don't ignore `build/` when building the package because the vignette index is built there. - Skip plot test entirely on R-devel. - Avoid submodules for building igraph (#674). - Makevars cleanup (#671). - Add Zenodo configuration file. # igraph 1.4.0 ## Breaking changes - Breaking change: Allow change of attribute type when setting attribute for all vertices or edges; only attributes of length 1 or the length of the target set allowed (#633). ## Added - `tkplot()` gained a `palette` argument and it is now using the same palette as `plot()` by default, for sake of consistency. - `plot.igraph()` gained a `loop.size` argument that can be used to scale the common radius of the loop edges. ## Fixed - The default maximum number of iterations for ARPACK has been increased to 3000 to match that of the igraph C core. - Rare convergence problems have been corrected in `cluster_leading_eigen()`. - All ARPACK-based functions now respect random seeds set in R when generating a random starting vector. - `igraph_version()` returned an invalid value in 1.3.4, this is now corrected. - The value of `par(xpd=...)` is now restored after plotting a graph. - Fixed a bug in `as.dendrogram.communities()` for large dendrograms, thanks to @@pkharchenko (see PR #292). - Fixed two bugs in `graph_from_incidence_matrix()` that prevented the creation of directed graphs with `mode="all"` from dense or sparse matrices. - `dfs()` accidentally returned zero-based root vertex indices in the result object; this is now fixed and the indices are now 1-based. - `as_graphnel()` does not duplicate loop edges any more. - `convex_hull()` now returns the vertices of the convex hull with 1-based indexing. - Some `rgl.*()` function calls in the codebase were replaced with equivalent `*3d()` function calls in preparation for upcoming deprecations in `rgl` (see PR #619) - `plot.igraph()` does not use the `frame=...` partial argument any more when calling `plot.default()`. The default `NULL` value of `frame.plot` is now also handled correctly. - `hub_score()` and `authority_score()` considered self-loops only once on the diagonal of the adjacency matrix of undirected graphs, thus the result was not identical to that obtained by `eigen_centrality()` on loopy undirected graphs. This is now corrected. - `distances()` no longer ignores the `mode` parameter when `algorithm='johnson'`. ## Deprecated - `automorphisms()` was renamed to `count_automorphisms()`; the old name is still available, but it is deprecated. ## Other - Documentation improvements. - The Github repository was now moved to a single-branch setup where the package can be built from the `main` branch directly. - Added igraph extended tutorial as an R vignette (#587). - igraph now has a homepage based on `pkgdown` thanks to @@maelle (see #645). This will eventually become the official homepage. # igraph 1.3.5 Added: - `mark.groups=...` argument of `plot.igraph()` now accepts `communities` objects Fixed: - Negative degree exponents are not allowed any more in `sample_pa()` and `sample_aging_pa()`. - Package updated to be compatible with Matrix 1.5. Other: - Documentation improvements and fixes. # igraph 1.3.4 Added: - `sample_asym_pref()` now returns the generated types of the vertices in the vertex attributes named `outtype` and `intype`. Fixed: - `layout_nicely()` does not recurse infinitely any more if it is assigned to the `layout` attribute of a graph - `layout_nicely()` now ignores edge weights when there are non-positive edge weights. This is needed because igraph 1.3.3 started validating edge weights in `layout_with_fr()` and `layout_with_drl()`, resulting in errors when `layout_nicely()` was used on weighted graphs with negative weights. Since `layout_nicely()` is the default layout algorithm for `plot()`, most users were not even aware that they were using the FR or DrL layouts behind the scenes. Now the policy is that `layout_nicely()` attempts to get the job done without errors if possible, even if that means that edge weights must be ignored. A warning is printed if this is the case. # igraph 1.3.3 Added: - `reverse_edges()` reverses specific or all edges in a graph. - Single-bracket indexing of `V()` and `E()` resolves attribute names in the indexing expressions by default (for instance, `E(g)[weight > x]` matches edges with a weight larger than a threshold). This can be problematic if the attribute masks one of the variables in the local evaluation context. We now have a pronoun called `.env` (similarly to `rlang::.env`) that allows you to force attribute name lookup to the calling environment. For sake of completeness, we also provide `.data` (similarly to `rlang::.data`) to force attribute name lookup to the vertex / edge attributes only. These pronouns are automatically injected into the environment where the indexing expression is evaluated. Deprecated: - Names of functions that can be used inside a `V()` or `E()` indexing start with a dot since igraph 1.1.1; however, the old dotless names did not print a deprecation warning so this may have gone unnoticed for years. We are introducting a deprecation warning for `nei()`, `innei()`, `outnei()`, `inc()`, `from()` and `to()` inside single-bracket indexing of vertex and edge sequences and will remove the old variants soon. # igraph 1.3.2 The C core is updated to 0.9.9, fixing a range of bugs. Fixed: - The length of size-zero `communities` objects is now reported correctly. - `layout_with_kk()` would fail to produce reasonable results with the default initial coordinates. This has been corrected, however, this function no longer produces precisely the same output for a given graph as before. To restore the previous behaviour, use `layout_with_kk(g, coord=layout_in_circle(g))` in 2D or `layout_with_kk(g, dim=3, coord=layout_on_sphere(g))` in 3D. - Indexing an `igraph.vs` object with `v[x, na_ok=T]` now correctly handles the `na_ok` argument in all cases; previous versions ignored it when `x` was a single number. Other: - Documentation improvements and fixes. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.12 2022/11/23 16:20:34 adam Exp $ d15 11 @ 1.12 log @massive revision bump after textproc/icu update @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.11 2022/04/28 15:44:47 mef Exp $ d4 1 a4 2 R_PKGVER= 1.3.1 PKGREVISION= 1 d13 1 @ 1.11 log @(devel/R-igraph) Updated 1.2.4.1 to 1.3.1 (pkgsrc) - Add two tentative macro, in patch, log1pl, expm1l. Tks tnn@@ for hint (and correct me if misleading) (upstream) # igraph 1.3.1 Fixed: - `graph_from_adjacency_matrix()` now works with sparse matrices even if the cell values in the sparse matrix are unspecified. - Fixed crash in `cluster_walktrap()` when `modularity=FALSE` and `membership=FALSE` - `edge_attr()` does not ignore its `index=...` argument any more. - `automorphisms()`, `automorphism_group()` and `canonical_permutation()` now allow all possible values supported by the C core in the `sh` argument. Earlier versions supported only `"fm"`. - The `vertex.frame.width` plotting parameter now allows zero and negative values; these will simply remove the outline of the corresponding vertex. - The documentation of the `sh` argument of the BLISS isomorphism algorithm in `isomorphic()` was fixed; earlier versions incorrectly referred to `sh1` and `sh2`. - `dominator_tree()` now conforms to its documentation with respect to the `dom` component of the result: it contains the indices of the dominator vertices for each vertex and -1 for the root of the dominator tree. - Mentions of the `"power"` algorithm of `page_rank()` have been removed from the documentation, as this method is no longer available. - Several other documentation fixes to bring the docs up to date with new behaviours in igraph 1.3. # igraph 1.3.0 The C core is updated to 0.9.7, fixing a range of bugs and introducing a number of new functions. Added: - `has_eulerian_path()` and `has_eulerian_cycle()` decides whether there is an Eulerian path or cycle in the graph. - `eulerian_path()` and `eulerian_cycle()` returns the edges and vertices in an Eulerian path or cycle in the graph. - `any_loop()` checks whether a graph contains at least one loop edge. - `is_tree()` checks whether a graph is a tree and also finds a possible root - `to_prufer()` converts a tree graph into its Prufer sequence - `make_from_prufer()` creates a tree graph from its Prufer sequence - `sample_tree()` to sample labelled trees uniformly at random - `sample_spanning_tree()` to sample spanning trees of an undirected graph uniformly at random - `automorphisms()` and `canonical_permutation()` now supports vertex colors - `random_edge_walk()` to record the edges traversed during a random walk - `harmonic_centrality()` calculates the harmonic centrality of vertices, optionally with a cutoff on path lengths - `mean_distance()` now supports edge weights and it can also return the number of unconnected vertex pairs when `details=TRUE` is passed as an argument - `greedy_vertex_coloring()` finds vertex colorings based on a simple greedy algorithm. - `bridges()` finds the bridges (cut-edges) of a graph - The frame width of circle, rectangle and square vertex shapes can now be adjusted on plots with the `frame.width` vertex attribute or the `vertex.frame.width` keyword argument, thanks to @@simoncarrignon . See PR #500 for more details. - `automorphism_group()` returns a possible (not necessarily minimal) generating set of the automorphism group of a graph. - `global_efficiency()` calculates the global efficiency of the graph. - `local_efficiency()` calculates the local efficiency of each vertex in a graph. - `average_local_efficiency()` calculates the average local efficiency across the set of vertices in a graph. - `rewire(each_edge(...))` now supports rewiring only one endpoint of each edge. - `realize_degseq()` generates graphs from degree sequences in a deterministic manner. It is also available as `make_(degseq(..., deterministic=TRUE))`. - `clique_size_counts()` counts cliques of different sizes without storing them all. - `feedback_arc_set()` finds a minimum-weight feedback arc set in a graph, either with an exact integer programming algorithm or with a linear-time approximation. - `make_bipartite_graph()` now handles vertices with names. - `shortest_paths()` now supports graphs with negative edge weights. - `min_cut()` now supports s-t mincuts even if `value.only=FALSE`. - `as.matrix()` now supports converting an igraph graph to an adjacency or edge list matrix representation. See `as.matrix.igraph()` for more details. This function was migrated from `intergraph`; thanks to Michal Bojanowski. Fixed: - `is_connected()` now returns FALSE for the null graph - Calling `length()` on a graph now returns the number of vertices to make it consistent with indexing the graph with `[[`. - `diameter()` now corrently returns infinity for disconnected graphs when `unconnected=FALSE`. Previous versions returned the number of vertices plus one, which was clearly invalid for weighted graphs. - `mean_distance()` now correctly treats the path length between disconnected vertices as infinite when `unconnected=FALSE`. Previous versions used the number of vertices plus one, adding a bias towards this number, even if the graph was weighted and the number of vertices plus one was not a path length that could safely have been considered as being longer than any "valid" path. - `layout_with_sugiyama()` now handles the case of exactly one extra virtual node correctly; fixes #85 - `bfs()` and `dfs()` callback functions now correctly receive 1-based vertex indices and ranks; it used to be zero-based in earlier versions - Accidentally returning a non-logical value from a `bfs()` or `dfs()` callback does not crash R any more - Calling `print()` on a graph with a small `max.lines` value (smaller than the number of lines needed to print the attribute list and the header) does not raise an error any more; fixes #179 - `as_adjacency_matrix(edges=TRUE, sparse=TRUE)` now consistently returns the last edge ID for each cell in the matrix instead of summing them. - Using the `+` and `-` operators with a `path()` object consisting of two vertices is now handled correctly; fixes #355 - `topo_sort()` now throws an error if the input graph is not acyclic instead of returning an incorrect partial ordering. - Weighted transitivity calculations (i.e. `transitivity(mode="barrat")` now throw an error for multigraphs; the implementation does not work correctly for multigraphs and earlier versions did not warn about this. Changed: - The `neimode` argument of `bfs()` and `dfs()` was renamed to `mode` for sake of consistency with other functions. The old argument name is deprecated and will be removed in 1.4.0. - `bfs()` and `dfs()` callback functions now correctly receive 1-based vertex indices and ranks; it used to be zero-based in earlier versions. (This is actually a bugfix so it's also mentioned in the "Fixed" section). - `closeness()`, `betweenness()` and `edge_betweenness()` now all take a `cutoff` argument on their own. `estimate_closeness()`, `estimate_betweenness()` and `estimate_edge_betweenness()` became aliases, with identical signature. They are _not_ deprecated but their implementation might change in future versions to provide proper estimation schemes instead of a simple cutoff-based approximation. If you explicitly need cutoffs and you want your results to be reproducible with future versions, use `closeness()`, `betweenness()` and `edge_betweenness()` in your code with a `cutoff` argument. - `closeness()` now only considers _reachable_ vertices during the calculation; in other words, closeness centrality is now calculated on a per-component basis for disconnected graphs. Earlier versions considered _all_ vertices. Deprecated: - Using `cutoff=0` for `closeness()`, `betweenness()` and `edge_betweenness()` is deprecated; if you want exact scores, use a negative cutoff. `cutoff=0` will be interpreted literally from igraph 1.4.0. - `centr_degree_tmax()` now prints a warning when it is invoked without an explicit `loops` argument. `loops` will be mandatory from igraph 1.4.0. - The `nexus_list()`, `nexus_info()`, `nexus_get()` and `nexus_search()` functions now return an error informing the user that the Nexus graph repository has been taken offline (actually, several years ago). These functions will be removed in 1.4.0. - The `edges` argument of `as_adjacency_matrix()` is deprecated; it will be removed in igraph 1.4.0. Removed: - The deprecated `page_rank_old()` function and the deprecated `power` method of `page_rank()` were removed. # igraph 1.2.11 Dec 27, 2021 No user visible changes. # igraph 1.2.10 Dec 14, 2021 Fixed: - The macOS versions of `igraph` were accidentally built without GraphML support on CRAN; this should now be fixed. # igraph 1.2.9 Nov 22, 2021 No user visible changes. # igraph 1.2.8 Oct 26, 2021 No user visible changes. # igraph 1.2.7 Oct 15, 2021 The C core is updated to 0.8.5, fixing a range of bugs and introducing a number of new functions. Added: - cluster_leiden added (#399). - cluster_fluid_communities added (#454) Fixed: - `make_lattice()` correctly rounds `length` to the nearest integer while printing a warning (#115). - `make_empty_graph(NULL)` now prints an error instead of producing an invalid graph (#404). - `make_graph(c())` now produces an empty graph instead of printing a misleading error message (#431). - Printing a graph where some edges have NA as the names of both endpoints does not produce a misleading error message any more (#410). - The `types` argument of functions related to bipartite graphs now prints a warning when the types are coerced to booleans (#476). - Betweenness normalisation no longer overflows (#442). - `layout_with_sugiyama()` returns a layout of type matrix even if there is only one vertex in the graph (#408). - Plotting a null graph (i.e. a graph with no vertices) does not throw an error any more (#387). Deprecated: - The `membership` argument of `modularity.matrix()` is now deprecated as the function never needed it anyway. - `modularity()` now prints a warning when it is applied on a directed graph because the implementation in igraph's C core does not support directed graphs as of version 0.8.5. The warning will be turned into an error in the next minor (1.3.0) version of the R interface; the error will be removed later when the C core is updated to a version that supports modularity for directed networks. - `transitivity()` now prints a warning when its local variant (`type="local"`) is called on a directed graph or a graph with multiple edges beecause the implementation in the C core of igraph does not work reliably in these cases as of version 0.8.5. The warning will be turned into an error in the next minor (1.3.0) version of the R interface; the error will be removed later when the C core is updated to a version that supports transitivity for networks with multiple edges. Misc: - Documentation improvements. # igraph 1.2.6 Oct 5, 2020 No user visible changes. # igraph 1.2.5 Mar 27, 2020 No user visible changes. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.10 2022/04/18 19:11:34 adam Exp $ d5 1 @ 1.10 log @revbump for textproc/icu update @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.9 2021/12/08 16:05:31 adam Exp $ d4 1 a4 2 R_PKGVER= 1.2.4.1 PKGREVISION= 5 @ 1.9 log @revbump for icu and libffi @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.8 2021/04/21 11:42:09 adam Exp $ d5 1 a5 1 PKGREVISION= 4 @ 1.8 log @revbump for textproc/icu @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.7 2020/11/05 09:08:36 ryoon Exp $ d5 1 a5 1 PKGREVISION= 3 @ 1.7 log @*: Recursive revbump from textproc/icu-68.1 @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.6 2020/06/02 08:24:16 adam Exp $ d5 1 a5 1 PKGREVISION= 2 @ 1.6 log @Revbump for icu @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.5 2019/09/25 17:30:08 brook Exp $ d5 1 a5 1 PKGREVISION= 1 @ 1.5 log @Add missing dependency on textproc/libxml2. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.4 2019/08/08 19:53:50 brook Exp $ d5 1 @ 1.4 log @Update all R packages to canonical form. The canonical form [1] of an R package Makefile includes the following: - The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as needed), and CATEGORIES. - HOMEPAGE is not present but defined in math/R/Makefile.extension to refer to the CRAN web page describing the package. Other relevant web pages are often linked from there via the URL field. This updates all current R packages to this form, which will make regular updates _much_ easier, especially using pkgtools/R2pkg. [1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.3 2019/07/31 19:47:01 brook Exp $ d17 1 @ 1.3 log @R-igraph: update to version 1.2.4.1. Update to the canonical form of an R package and fix the LICENSE field. @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.2 2018/09/04 00:23:12 minskim Exp $ d3 3 a5 1 CATEGORIES= math graphics R a7 1 HOMEPAGE= http://igraph.org/ a10 3 R_PKGNAME= igraph R_PKGVER= 1.2.4.1 @ 1.2 log @math/R-igraph: Needs a C compiler @ text @d1 1 a1 1 # $NetBSD: Makefile,v 1.1 2018/05/24 22:25:17 minskim Exp $ d3 1 a3 2 DISTNAME= igraph_1.2.1 CATEGORIES= graphics d7 2 a8 2 COMMENT= Network Analysis and Visualization LICENSE= gnu-gpl-v2 d10 4 a13 1 DEPENDS+= R-magrittr-[0-9]*:../../devel/R-magrittr d16 1 a16 1 USE_LANGUAGES= c @ 1.1 log @math/R-igraph: Import version 1.2.1 Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more. @ text @d1 1 a1 1 # $NetBSD$ d14 1 a14 1 USE_LANGUAGES= # none @