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CVS commit: pkgsrc/math/R-igraph
Module Name: pkgsrc
Committed By: mef
Date: Sun Nov 3 12:40:56 UTC 2024
Modified Files:
pkgsrc/math/R-igraph: Makefile distinfo
Added Files:
pkgsrc/math/R-igraph/patches:
patch-src_vendor_cigraph_vendor_plfit_hzeta.c
Removed Files:
pkgsrc/math/R-igraph/patches: patch-src_vendor_plfit_hzeta.c
Log Message:
(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 <https://github.com/igraph/rigraph/blob/9828d7b11be330f994f07ae93a071b356eced903/src/vendor/cigraph/CHANGELOG.md> 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 <https://github.com/igraph/rigraph/blob/05973441b83decdeab8cc9c500a642c00b924770/src/vendor/cigraph/CHANGELOG.md> 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 <https://github.com/igraph/rigraph/blob/3299d31/src/vendor/cigraph/CHANGELOG.md> for a complete changelog of the bundled C core, and
<https://github.com/igraph/rigraph/compare/f3fa58b..3299d31#diff-aeb78e0159780a9b26daabaf6f95f450b0cfec7161fc735f27ad69145a57dc84> 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
<https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md>.)
## 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 <https://github.com/igraph/rigraph/blob/f3fa58b/src/vendor/cigraph/CHANGELOG.md> for a complete changelog of the bundled C core, and
<https://github.com/igraph/rigraph/compare/1bd2bf79..f3fa58b#diff-aeb78e0159780a9b26daabaf6f95f450b0cfec7161fc735f27ad69145a57dc84> 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
<https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md>.)
## 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 <https://github.com/igraph/igraph>.
See <https://github.com/igraph/rigraph/blob/1bd2bf79/src/vendor/cigraph/CHANGELOG.md> 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
<https://github.com/igraph/rigraph/blob/main/src/vendor/cigraph/CHANGELOG.md>.)
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).
To generate a diff of this commit:
cvs rdiff -u -r1.22 -r1.23 pkgsrc/math/R-igraph/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/math/R-igraph/distinfo
cvs rdiff -u -r0 -r1.1 \
pkgsrc/math/R-igraph/patches/patch-src_vendor_cigraph_vendor_plfit_hzeta.c
cvs rdiff -u -r1.2 -r0 \
pkgsrc/math/R-igraph/patches/patch-src_vendor_plfit_hzeta.c
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/math/R-igraph/Makefile
diff -u pkgsrc/math/R-igraph/Makefile:1.22 pkgsrc/math/R-igraph/Makefile:1.23
--- pkgsrc/math/R-igraph/Makefile:1.22 Fri Nov 1 12:53:25 2024
+++ pkgsrc/math/R-igraph/Makefile Sun Nov 3 12:40:56 2024
@@ -1,12 +1,11 @@
-# $NetBSD: Makefile,v 1.22 2024/11/01 12:53:25 wiz Exp $
+# $NetBSD: Makefile,v 1.23 2024/11/03 12:40:56 mef Exp $
R_PKGNAME= igraph
-R_PKGVER= 1.6.0
+R_PKGVER= 2.1.1
CATEGORIES+= graphics
MAINTAINER= minskim%NetBSD.org@localhost
COMMENT= Network analysis and visualization
-PKGREVISION= 3
LICENSE= gnu-gpl-v2 OR gnu-gpl-v3
DEPENDS+= R-cli-[0-9]*:../../devel/R-cli
@@ -14,9 +13,10 @@ DEPENDS+= R-lifecycle-[0-9]*:../../devel
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
+DEPENDS+= R-vctrs-[0-9]*:../../math/R-vctrs
# Packages suggested but not available:
-# 'ape', 'decor', 'graph', 'igraphdata', 'vdiffr'
+# 'ape', 'decor', 'igraphdata', 'vdiffr'
TEST_DEPENDS+= R-knitr-[0-9]*:../../print/R-knitr
TEST_DEPENDS+= R-rgl-[0-9]*:../../graphics/R-rgl
Index: pkgsrc/math/R-igraph/distinfo
diff -u pkgsrc/math/R-igraph/distinfo:1.11 pkgsrc/math/R-igraph/distinfo:1.12
--- pkgsrc/math/R-igraph/distinfo:1.11 Fri Jan 26 21:43:01 2024
+++ pkgsrc/math/R-igraph/distinfo Sun Nov 3 12:40:56 2024
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.11 2024/01/26 21:43:01 mef Exp $
+$NetBSD: distinfo,v 1.12 2024/11/03 12:40:56 mef Exp $
-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
+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
+SHA1 (patch-src_vendor_cigraph_vendor_plfit_hzeta.c) = 0f394527fdde6fece01920dd11d9432aaca0d124
Added files:
Index: pkgsrc/math/R-igraph/patches/patch-src_vendor_cigraph_vendor_plfit_hzeta.c
diff -u /dev/null pkgsrc/math/R-igraph/patches/patch-src_vendor_cigraph_vendor_plfit_hzeta.c:1.1
--- /dev/null Sun Nov 3 12:40:56 2024
+++ pkgsrc/math/R-igraph/patches/patch-src_vendor_cigraph_vendor_plfit_hzeta.c Sun Nov 3 12:40:56 2024
@@ -0,0 +1,20 @@
+$NetBSD: patch-src_vendor_cigraph_vendor_plfit_hzeta.c,v 1.1 2024/11/03 12:40:56 mef Exp $
+
+/* tweak the macro, not found in NetBSD as of 9.99.96 */
+/* corrected by tnn. thanks */
+
+--- src/vendor/cigraph/vendor/plfit/hzeta.c.orig 2024-09-26 20:28:57.000000000 +0900
++++ src/vendor/cigraph/vendor/plfit/hzeta.c 2024-11-03 15:49:13.010904356 +0900
+@@ -65,6 +65,12 @@
+ #define M_LOG2E 1.44269504088896340735992468100189214
+ #endif
+
++/* tweak the macro, not found in NetBSD as of 9.99.96 */
++#ifdef __NetBSD__
++#define log1pl(x) logl(1.0f+(x))
++#define expm1l(x) (expl(x) - 1.0f)
++#endif
++
+ #ifndef M_LN2
+ #define M_LN2 0.693147180559945309417232121458176568
+ #endif
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