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locks; strict; comment @# @; 1.13 date 2025.02.14.22.59.56; author mef; state Exp; branches; next 1.12; commitid vhgjTXwuPw0muuJF; 1.12 date 2024.11.03.12.40.56; author mef; state Exp; branches; next 1.11; commitid c1LCNj8G7hf8ncwF; 1.11 date 2024.01.26.21.43.01; author mef; state Exp; branches; next 1.10; commitid d0pPMHtgCxLar0WE; 1.10 date 2023.08.11.07.11.36; author mef; state Exp; branches; next 1.9; commitid g9UE7ugIU0BZ0lAE; 1.9 date 2023.06.11.02.48.20; author mef; state Exp; branches; next 1.8; commitid WobKBOLwUu4gwtsE; 1.8 date 2023.03.11.11.07.54; author mef; state Exp; branches; next 1.7; commitid hzewNu7WsS11fHgE; 1.7 date 2022.05.03.00.25.48; author mef; state Exp; branches; next 1.6; commitid TjeLfcuTvmpzIxCD; 1.6 date 2022.05.03.00.24.20; author mef; state Exp; branches; next 1.5; commitid 451i3fChKxQoHxCD; 1.5 date 2022.04.28.15.44.47; author mef; state Exp; branches; next 1.4; commitid vHQAWAPQqoFGXYBD; 1.4 date 2021.10.26.10.55.28; author nia; state Exp; branches; next 1.3; commitid vzl6zVlmjiF3hjeD; 1.3 date 2021.10.07.14.27.50; author nia; state Exp; branches; next 1.2; commitid wLkpKfebF6VS3TbD; 1.2 date 2019.07.31.19.47.01; author brook; state Exp; branches; next 1.1; commitid HzSnsaR8McEIvexB; 1.1 date 2018.05.24.22.25.17; author minskim; state Exp; branches; next ; commitid 115vuWTRMJI0jBDA; desc @@ 1.13 log @(math/R-igraph) Updated 2.1.1 to 2.1.4 # igraph 2.1.4 ## Testing - Tweak tests that use the graph package. # igraph 2.1.3 ## Features - Use `_pv` destroy functions to satisfy ASAN checks (#1630). - Use safe accessor to vector elements (#1633). ## Chore - Replace `graph.isomorphic()` with `isomorphic()` (#1583, #1623). ## Documentation - Convert `plot.common.Rd` to roxygen2 (#1424, #1636). - Remove broken example from `graph_from_graphdb()` manual page (#1622, #1637). - Document argument for NCOL format in `read_graph()` (#1621). - Make documentation of `disjoint_union()` consistent with behavior (#1587, #1641). - Add central note about experimental functions (#1624). # igraph 2.1.2 ## Bug fixes - `adjacent_vertices()` and `incident_edges()` are now correct if the `"return.vs.es"` option is `FALSE` (@@stibu81, #1605, #1606). - Fix protection errors reported by rchk (#1592). - Fix the incorrect handling of the `sample` parameter in `sample_motifs()` and ensure that the default `sample.size` is integer (#1568). ## Documentation - Clarify what type of graph each community detection function supports. - Improve `?read_graph` and `?write_graph` documentation. - Improve `all_simple_paths()` documentation. - `cluster_optimal()` does support directed graphs. ## Testing - Test handling of `"return.vs.es"` in several functions (@@stibu81, #1610). @ text @$NetBSD: distinfo,v 1.12 2024/11/03 12:40:56 mef Exp $ BLAKE2s (R/igraph_2.1.4.tar.gz) = 8a7e26414004ae04b33ee3982df30ac3ba3f09ce851f7c162eb712ffde2777f3 SHA512 (R/igraph_2.1.4.tar.gz) = bbd7aa1edc50c85ffdc1b027bf70f32e0c12754e2baeeda7f7306ff3bf078558fe6fce0144db163d8de6b534d6c8697380b8a719592b42ea5a5ec57a8d74b36e Size (R/igraph_2.1.4.tar.gz) = 4997408 bytes SHA1 (patch-src_vendor_cigraph_vendor_plfit_hzeta.c) = 0f394527fdde6fece01920dd11d9432aaca0d124 @ 1.12 log @(math/R-igraph) Updated 1.6.0 to 2.1.1 (pkgsrc changes) - rename patch file old: patches/patch-src_vendor_plfit_hzeta.c new: patches/patch-src_vendor_cigraph_vendor_plfit_hzeta.c (upstream changes) # igraph 2.1.1 See for a complete changelog, in particular the section "Breaking changes". ## Features - Add `p.value` and `p.precision` arguments to `fit_power_law()` to control the computation of the p-value (#1546). ## Bug fixes - Preserve `as.undirected()` signature thanks to @@jhollway, regression introduced in igraph 2.1.0 (#1536). ## Lifecycle - Deprecate `eigen_centrality(scale = )` (#1543). - Put deprecation message at the beginning not the end of the similarity functions (#1549). ## Documentation - Update allcontributors table (#1552). - Use mathjax for now (#1538). ## Internal - Prepare for libxml2 depending on bcrypt, use pkg-config (#1556, @@kalibera). # igraph 2.1.0 See for a complete changelog, in particular the section "Breaking changes". ## Lifecycle ### Breaking changes - Breaking change: remove tkigraph from {igraph} proper (#1474). - Breaking change: Hard-deprecate `get.edge()` and `layout.grid.3d()` which have been deprecated for 10 years (#1398). - Breaking change: use `rlang::arg_match()` in `igraph.match.arg()` (#1165). ### In-progress deprecations We are working towards a more consistent interface, especially as regards function naming: ultimately we want the igraph functions to use snake case. Please update your scripts and codebases as soon as you can. - Add `independence_number()` as an alias of `ivs_size()` (#1522). - Add `get_edge_ids()` as an alias of `get.edge.ids()` (#1510). - Increase the deprecation signal to a warning for `hub.score()` and `authority.score()` both replaced by `hits_scores()` (#1352). - Soft-deprecate `erdos.renyi.game()` and `random.graph.game()` (#1509). ## Features ### C library - Update vendored C/igraph sources to igraph/igraph@@d2e0f4eb567dfc505227c346a015bef574c4ccd1. ### New functionality - Support `fit_power_law(implementation = "plfit.p")` to compute the P-value (#1386). - Add `max_degree()` (#1403). - Add experimental `sample_chung_lu()` (#1416). - Rename methods available for `sample_degseq()` and add the `"edge.switching.simple"` method (#1376). - Weight support for `eccentricity()` and `radius()` (#1211). - Add some argument checking to `add_shape()` (#1478). ### More informative errors - Export `.from()` etc. with behavior similar to `dplyr::across()` (#1436): functions like `.from()` are meant to be used inside `[` but now if an user misuses them, the error is more informative. ## Bug fixes - Fix including diagonal elements in dense adjacency matrices (#1437). - Align the body of `graph.lattice()` with its replacement `make_lattice()` (#1439). - Use `deprecated()` as default value for `circular` argument to `make_lattice()` (#1431). - `subgraph_centrality()` now ignores edge directions (#1414). - Remove unintended type conversions when using `disjoint_union()` (#1375). - Add missing `PROTECT()` (#1382). - Fix reading of LGL and NCOL files (broken in 2.0.0) (#1347). - Fixed potential memory leak in `R_igraph_community_to_membership2()` (#1367). ## Documentation - Improve the manual page of `sample_()` (#1477). - Improve cross-links from `make_()` manual page (#1476). - Update `is_separator()` documentation based on C docs (#1467). - Add DOI to citation (#1450). - Improve documentation of normalization methods for laplacian_matrix() (#1420). - Fix typos in `?plot.common` (@@gvegayon) (#1413). - Fix `sample_degseq()` example (#1297). - Fix `graph_from_adjacency_matrix()` examples to avoid warnings (#1302). - Replace `\dontrun{}` with `@@examplesIf` (#1307). - Improve `sample_gnp()` examples. - Improve centralization docs. - Further clarifications for `betweenness()` (#1489). - Clarify how betweenness with cutoff is normalized. - Fix `centr_eigen_tmax()` docs. - Make `edge_density()` examples relevant. - Improve `eigen_centrality()` documentation. - Improved `cluster_edge_betweenness()` documentation. - `sample_forestfire()` tests and example (#1318). ### Developer-facing docs - Add slightly tweaked boilerplate `CONTRIBUTING.md` (#1423). - Update troubleshooting document. - Use {devtag} for internal function docs (#1507). - Make `.igraph.progress()` and `.igraph.status()` more internal (#1516). # igraph 2.0.3 See for a complete changelog of the bundled C core, and for the changes since the igraph 2.0.1. (A permanent link to the most recent changelog of the C core used in the R package is .) ## Features - GMP is no longer a dependency (#1256), libxml2 (#1282) and glpk are optional. - Update vendored sources to igraph/igraph@@857a125069c226f266562b3781b82833fe1d59d9. - New `voronoi_cells()` to compute the Voronoi partitioning of a graph (#1173). ## Bug fixes - Fix `rglplot(edge_label = )` (#1267). ## Continuous integration - Run examples with sanitizer (#1288). - Add scheduled builds. ## Documentation - Make `x11()` usage in example happen only in interactive sessions (#1301). - Remove misleading comment about warning given as no warning is given (#1294). - Improve `min_st_separators()` documentation (#1264). - Add link to discussion forum (#1279) and logo (#1280). - Add code finding duplicate `@@seealso`, and use it (#1270). - Remove duplicate `@@seealso` from `?sample_pa` (#1268). - Remove incorrect claim about handling of complete graphs by `is_separator()` and `is_min_separator()` (#1263). - Fix error messages mentioning to mention `upgrade_graph()` instead of the nonexisting `upgrade_version()` (#1252). - Split `is_bipartite()` manual page from other manual page (#1230). - Improve bug report template. - `CITATION.cff` contains only the first three version components. - Install lock workflow to lock stale discussions after one year (#1304). ## Internal - Replace use of deprecated `barabasi.game()` with `sample_pa()` (#1291). - Auto-generate `are_adjacent()`, avoid deprecated `igraph_are_connected()` C function (#1254). # igraph 2.0.2 See for a complete changelog of the bundled C core, and for the changes since the igraph 2.0.1. (A permanent link to the most recent changelog of the C core used in the R package is .) ## Bug fixes - `g + vertices(1, 2, foo = 3)` works again, regression introduced in igraph 2.0.0 (#1247). - `sample_pa()` respects the `out.seq` and `out.dist` arguments again, regression introduced in igraph 2.0.0 (#1226). - `isomorphisms()` and `subgraph_isomorphisims(method = "vf2")` work again, regression introduced in 2.0.0 (#1219). - `biconnected_components()` now returns edge and vertex sequences again, regression introduced in 2.0.0 (#1213). - Remove zeros from the `order` and `order.out` components returned by `dfs()`, regression introduced in 2.0.0 (#1179). - Memory leaks when converting data to C (#1196). ## Features - `realize_bipartite_degseq()` creates a bipartite graph from two degree sequences (#1212). - `is_biconnected()` checks if a graph is biconnected (#1204). - `distances()` now supports the Floyd-Warshall algorithm (#1186). ## Documentation - Use more culturally diverse names in intro vignettes (#1246). - Formatting tweaks in introductory vignettes (#1243). - Recommend {pak} instead of {remotes} (#1228). - Fix typo in `mean_distance()` docs. - Update troubleshooting document, emphasize issues with Anaconda environments (#1209). - Improved docs for shortest path functions (#1201). - Document `"dsatur"` heuristic for `greedy_vertex_coloring()` (#1206). - Remove scg related docs (#1167). - Fix typo in `?articulation_points` (#1191). - Improve installation and troubleshooting instructions (#1184). - Improve docs of assortativity (#1151). ## Testing - Add tests for `isomorphisms()` and `subgraph_isomorphisms()` (#1225). ## Packaging - Always use bundled mini-gmp (#1233). - `config.h` defines `HAVE___UINT128_T` (#1216). - Do not rely on `which` program during configuration (#1232). - `configure` manage libxml multiple include paths (#1197). - Remove empty string in `configure` (#1235). - Link Fortran runtime on Windows as needed by arpack. (#1215). - Workaround for deprecated enum values not being supported with old GCC (#1205). - `HAVE_GFORTRAN` flag for `win` and `ucrt` (#1171). - `make_empty_graph()` is now fully auto-generated (#1068). - Eliminate manual edits from autogenerated files (#1207). - Add read-only comments for RStudio IDE (#1152). ## Internal - Remove unused patch files (#1234). - Update stimulus to 0.21.4 (#1210). - Avoid duplicate objects (#1223). - Eliminate a compiler warning from simpleraytracer (#1185). # igraph 2.0.1.1 ## Bug fixes - Avoid `is.R()` which is deprecated in R 4.4.0. # igraph 2.0.1 ## Bug fixes - Use cpp11 for simpleraytracer glue to avoid `-Wlto` warnings (#1163). # igraph 2.0.0 This major release brings development in line with the C core at . See for a complete changelog, in particular the section "Breaking changes". (A permanent link to the most recent changelog of the C core used in the R package is .) Version 1.6.0 of the R package used version 0.9.9 of the C core. The changes in the 0.10 series of the C core are relevant for version 2.0.0 of the R package, but not all C core functions are exposed in the R interface. Changes to the implementation of some functions in the C core may be reflected in functions in the R package. The change log below is a summary of the additional changes in the R interface. ## Breaking changes - `get.edge.ids(multi = TRUE)` and `as_adjacency_matrix(edges = )` are no longer supported (#1101, #1080). - Remove `NA` padding for `dfs(unreachable = FALSE)$order` and `$order.out` and for `bfs(unreachable = FALSE)$order`, also for `igraph_options(return.vs.es = FALSE)` (#1062, #1124). - `laplacian_matrix(normalized = TRUE)` uses a different normalization method (#1102). - `fit_power_law()` no longer returns a `KS.p` component. - Remove default value for `loops` argument of `centr_degree_tmax()` (#1114). - `as_adjacency_matrix()` no longer supports attributes of type `character` (#1072). - Remove `graph.isomorphic.34()` (#1065, #1067). - Use `lifecycle::deprecate_soft()` for most deprecated functions (#1024, #1025, #1104). - The system libraries GLPK, GMP, and libxml2 are now mandatory for compiling from source. ## Bug fixes - Add scalar conversion checks in a few critical places (#1069). - Check that we receive a scalar when expecting a scalar in C code (#1051). - Check that matrix sizes are in the supported range before passing them to R (#1066). - `transitivity()` now produces a named vector in the local (weighted) case (#1057). - `plot()` correctly computes intersections between edges and rectangle vertices (#1021). - Fix compilation on Windows with spaces in the Rtools path (#1000). ## Features - Use 30 bits of R's RNG (#1079). - Breaking change: Remove `NA` padding for `dfs(unreachable = FALSE)$order` and `$order.out` and for `bfs(unreachable = FALSE)$order`, also for `igraph_options(return.vs.es = FALSE)` (#1062, #1124). - New `k_shortest_paths()` to compute the first k shortest paths between two vertices (#1028). ## Documentation - Add GitHub bug report form. - New `vignette("deprecated-dot-case")` that lists deprecated functions and their alternatives (#1013). - Move deprecation badge to top of doc pages. - Remove usage of `get.adjacency()` from intro vignettes (#1084). - Fix math formatting in `fit_power_law()` docs. - Fix incorrect usage in `subgraph.edges()` example. - Clarify that Infomap considers edge directions. - Improve edge connectivity docs (#1119). - Add some missing diacritics. ## Internal - Use `[]` assignment for converting matrices (#1035). - Move towards autogenerating all bindings (#1043). - Use %\|\|% from rlang (#1112). - Replace loop by `lapply()` when returning vertex and edge sets (#1033). - Do not duplicate prototypes, use a common header for `rinterface.c` and `rinterface_extra.c` (#1055). - Clean up some auto-generation code (#1031), remove unused parts from code generation (#1032), eliminate the use of some deprecated C functions. - Use integers for mode enum in `cluster_label_prop()`. - Standardize the handling of some stimulus enum types (#1064). - Remove unused vectorlist / matrixlist destructors (#1070). - Remove unused stimulus type VERTEXSETLIST_INT (#1049). - Remove unused types (#1060). - Fix Stimulus definitions (#997). - Avoid deprecated `R_igraph_automorphisms()` (#999). - Use new ARPACK_DEFAULTS symbol from C core for default arpack options. - Ignore upstream CITATION file to avoid R CMD check NOTE (#1007). - Add Aviator configuration. ## Testing - Add `as_biadjacency_matrix()` tests for named vectors (#1154, #1155). - Test transferring colors in isomorphism functions (#1050). @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.11 2024/01/26 21:43:01 mef Exp $ d3 3 a5 3 BLAKE2s (R/igraph_2.1.1.tar.gz) = 4c5110449b10f403c8884cfc9d55f260b55e6163da8b1bcaffa4bae7fe774286 SHA512 (R/igraph_2.1.1.tar.gz) = 67704c0c43af9b8c1f89a674bfbbaff28966680984e95a5c3ee33b72011cb8d553365028ba91ebbc0dcbf673718f987916f0a3f7232a6bd185af13df94138874 Size (R/igraph_2.1.1.tar.gz) = 4989066 bytes @ 1.11 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 @d1 1 a1 1 $NetBSD: distinfo,v 1.10 2023/08/11 07:11:36 mef Exp $ d3 4 a6 4 BLAKE2s (R/igraph_1.6.0.tar.gz) = f5a51092ce835dc6de6b2f9f541487448f6bedd5435648416886cc357155f22a SHA512 (R/igraph_1.6.0.tar.gz) = 152878aa21887712a11197726c3d911368da5e2b607c958942087252f95e57c52b45e442b0ca23a74266758f78fe1696d183e5885204b4e2219e54f1233491df Size (R/igraph_1.6.0.tar.gz) = 3510416 bytes SHA1 (patch-src_vendor_plfit_hzeta.c) = 06c895e951bc491bfb26376a4000e4204811748f @ 1.10 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: distinfo,v 1.9 2023/06/11 02:48:20 mef Exp $ d3 3 a5 3 BLAKE2s (R/igraph_1.5.0.1.tar.gz) = 458da4ecc45fb1f52514e040a9e96e40957835f90dd432c1a673235d1d5daf35 SHA512 (R/igraph_1.5.0.1.tar.gz) = 112536df599997c569ffbf83f9d146c359b18cd8bc63769e3da8d75d8f84bfd2395deec8fd058d4508c6ae925320ef628ab1943120158e8d1317bbe23a3b485f Size (R/igraph_1.5.0.1.tar.gz) = 3314208 bytes @ 1.9 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: distinfo,v 1.8 2023/03/11 11:07:54 mef Exp $ d3 3 a5 3 BLAKE2s (R/igraph_1.4.3.tar.gz) = 87f4097f7e13c8aa2f80ae60e1a9ed4ba2007237aad974281ab9264ab7fd33cd SHA512 (R/igraph_1.4.3.tar.gz) = aab982e04630d3064729e3982a2ef3f629bb0d70dd195390cf81a82dade6aa4ac1083f231dd5c9586997862eddcbf90d9ddcecf5526dc603f438b3659aaa98c6 Size (R/igraph_1.4.3.tar.gz) = 3305746 bytes @ 1.8 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: distinfo,v 1.7 2022/05/03 00:25:48 mef Exp $ d3 3 a5 3 BLAKE2s (R/igraph_1.4.1.tar.gz) = c2d4ddcb45eea169ac352b46b665d0199bb3b932b7e67e580a222d2d261ba472 SHA512 (R/igraph_1.4.1.tar.gz) = c3913044b8bf00f6b3e52e20aac3275ffef07a6271b66a93eb1458898e8edfd25a9f35902ecfe8f70b0e3b5cd5e605c5cd2605f38a55ecc42849fd4fb73b1af4 Size (R/igraph_1.4.1.tar.gz) = 2910158 bytes @ 1.7 log @(math/R-igraph) sorry again, patch-configure not needed anymore @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.6 2022/05/03 00:24:20 mef Exp $ d3 3 a5 3 BLAKE2s (R/igraph_1.3.1.tar.gz) = 86dabeb6a382153941acd99b45fc295cfc84dda328de6acc9cbb17f8b20cd412 SHA512 (R/igraph_1.3.1.tar.gz) = 3b725ca47a117501a9902e64cdb29ed5fe59bfba3b056b98a1fb4035fdd9a5f9ea274b87053ebab558e206a9def09af46e957cff0280fe6093dd9638dd3d5f71 Size (R/igraph_1.3.1.tar.gz) = 2489895 bytes @ 1.6 log @(math/R-igraph) correct the macro define for expm1l, tks tnn@@ Ref: http://mail-index.netbsd.org/pkgsrc-users/2022/05/02/msg035568.html @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2022/04/28 15:44:47 mef Exp $ a5 1 SHA1 (patch-configure) = f3f6fc7c3c877f02b9b29c9758f1ac9edb51341c @ 1.5 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: distinfo,v 1.4 2021/10/26 10:55:28 nia Exp $ d6 2 a7 1 SHA1 (patch-src_vendor_plfit_hzeta.c) = b175e674d0c19f45ee2827e573d9afe8b20aa997 @ 1.4 log @math: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2021/10/07 14:27:50 nia Exp $ d3 4 a6 4 BLAKE2s (R/igraph_1.2.4.1.tar.gz) = 88c9e34444b1237bafb24ff9b40e107b52ee1ea55b6103dadeb430fb0cd736b3 SHA512 (R/igraph_1.2.4.1.tar.gz) = f35ed49726aab69d407baececff2d68ce17a750f1cf7ff293f4ecc62de4bc81d544178d86faf1f200359fa83a7410e431e61a2ce2a7a5b360d01c4d310b6f99f Size (R/igraph_1.2.4.1.tar.gz) = 2704004 bytes SHA1 (patch-configure) = f3f6fc7c3c877f02b9b29c9758f1ac9edb51341c @ 1.3 log @math: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.2 2019/07/31 19:47:01 brook Exp $ d3 1 a3 1 RMD160 (R/igraph_1.2.4.1.tar.gz) = 45e9318e5adaabe6dd7340665672a47fa426aa20 @ 1.2 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 $NetBSD$ a2 1 SHA1 (R/igraph_1.2.4.1.tar.gz) = f33e04e37409bc38a218f876942e324feeb780d5 @ 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 @d3 4 a6 4 SHA1 (R/igraph_1.2.1.tar.gz) = 68994ee2f463b5f2ce91621db3a2608798481185 RMD160 (R/igraph_1.2.1.tar.gz) = 43f77e5f0e9cab2fd606a6d8cfd247158203bf73 SHA512 (R/igraph_1.2.1.tar.gz) = 4b4a31f2f2f0fde4c8d8667bd6a6733f1af9e4509570383243d8da0aec918ae0ec63a5be684bb348f56f1a3275d538b59df5534ea1f1214a373323e39fde1789 Size (R/igraph_1.2.1.tar.gz) = 2703426 bytes @