CVS commit: pkgsrc/math/R-igraph

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Mon Jun 15 14:23:38 UTC 2026

Modified Files:
        pkgsrc/math/R-igraph: Makefile distinfo
Added Files:
        pkgsrc/math/R-igraph/patches: patch-src_Makevars.in

Log Message:
(math/R-igraph) Updated 2.1.4 to 2.3.2, Fix Build against R-4.6.0

# igraph 2.3.2
--------------
## Bug fixes

- Fix obsolete Fortran syntax (#2644).

# igraph 2.3.1
--------------
## Bug fixes

- Fix mismatches between C function signatures and function
  calls. This only affects private functions that are defined but not
  yet used (#2620).

# igraph 2.3.0
--------------
## New features

- Add `make_wheel()` to expose `igraph_wheel()` (#1561, #2409).

- Add `transitive_closure()` function to compute the transitive
  closure of a graph (#1350, #2413).

- Add `make_full_multipartite()` and `make_turan()` graph constructors
  (#1562, #2406).

- Add `count_loops()` (#1379, #2414).

- Add `make_circulant()` to expose `igraph_circulant()` (#1563,
  #2407).

- Add `mean_degree()` (#1380, #2415).

- Add `count_reachable()` function (#1349, #2412).

- Add `invalidate_cache()` (#1387, #2416).

- `graphlet_basis()` returns a list of vertices in the `"cliques"`
  component instead of a raw integer matrix (#2470, #2472).

- `vertices()` now errors on duplicate attribute names (#1248, #2430).

- Implement generic mechanism for `layout_()` modifiers, allowing
  layout algorithms to be composed and adjusted uniformly (#1473,
  #2435).

- Change graph constructors to use explicit named arguments instead of
  positional ones (#2466, #2467).

- Improve formatting of error messages originating from the C library
  (#2202, #2515).

- Functions that accept a single vertex now check that exactly one
  vertex is passed (#2556).

## Bug fixes

- Error call in `with_vertex_()`/`with_edge_()` should report the
  public `make_()` function, not the internal helper (#2609).

- Not all loops are plotted when a graph has multiple loops at the
  same vertex (#2594, #2595).

- Fix `hrg_game_impl()` which produced incorrect results (#2577,
  #2578).

- `graphlet_proj()` no longer erroneously assigns class `"igraphHRG"`
  to the returned graph.

- Support character labels in `assortativity_nominal()` in addition to
  integer type codes (#1283, #2432).

- Fix uninitialized variable warnings when building with R 4.5 on
  Windows (#2526, #2527).

- `modularity()` now uses the `"weights"` edge attribute automatically
  when no `weights` argument is supplied.

- Fix `alpha_centrality()` crash when `weights` is set to a custom
  edge attribute name rather than a numeric vector (#915, #2403).

- Fix matrix lists for output when returning multiple matrices from C.

## Documentation

- Error messages throughout the package now use the `cli` package for
  consistent, styled output instead of base R `stop()` (#731, #2588).

- The R Consortium is listed as a funder with its ROR ID in the
  package metadata (#2587).

- Fixes to the pkgdown reference index (#2590, #2592).

- Documentation pages for R functions now automatically link to the
  corresponding C library documentation (#2518).

## Testing

- Structured unit tests alongside snapshot tests have been added for
  all autogenerated `_impl` functions in `test-aaa-auto.R`, verifying
  argument passing and return values (#2448, #2449).

## Internal

- The R interface for most C library functions is now autogenerated
  using the py-stimulus framework, covering 108+ functions including
  BFS and DFS callbacks, leading-eigenvector community detection,
  motif callbacks, sparse matrix operations, and graph-list
  constructors. Arguments use snake_case naming throughout for
  consistency (#2152, #2424, #2442, #2461, #2462, #2464, #2465, #2484,
  #2485, #2531, #2532, #2533, #2534, #2540, #2550, #2551, #2552,
  #2553, #2554, #2555).

- Most direct `.Call()` invocations to C library functions have been
  replaced with autogenerated `_impl()` wrapper functions that use
  explicit named arguments, covering all R source files
  (`R/assortativity.R`, `R/bipartite.R`, `R/centrality.R`,
  `R/centralization.R`, `R/cliques.R`, `R/coloring.R`,
  `R/embedding.R`, `R/flow.R`, `R/games.R`, `R/layout.R`, `R/make.R`,
  `R/other.R`, `R/simple.R`, `R/structural-properties.R`,
  `R/topology.R`, `R/trees.R`, `R/triangles.R`, and others) (#2332,
  #2334, #2345, #2347, #2348, #2351, #2352, #2355, #2357, #2358,
  #2359, #2361, #2362, #2363, #2364, #2365, #2366, #2367, #2368,
  #2369, #2370, #2372, #2373, #2374, #2379, #2380, #2382, #2383,
  #2384, #2386, #2388, #2398, #2422, #2423, #2428, #2429, #2434,
  #2443, #2471, #2476, #2477, #2478, #2539, #2541, #2545, #2546).

# igraph 2.2.3
--------------
## Chore

- Remove calls to non-API functions.

# igraph 2.2.2
--------------
## Chore

- Remove calls to unused APIs only used in the conversion of very old
  graph objects.

# igraph 2.2.1
--------------
## Chore

- Fix ASAN checks.

- Add protection to fix rchk error.

## Testing

- Improve centralitystress test (#2214).

- Fix flaky test.

# igraph 2.2.0
--------------
Update C core to version 0.10.17. See
<https://github.com/igraph/rigraph/blob/20552ef94aed6ae4b23465ae8c7e4d3b0e558c71/src/vendor/cigraph/CHANGELOG.md>
for a complete changelog, in particular the section "Breaking
changes".

## Features

- Generate almost all R implementations (#2047).

- Expose `align_layout()` and add to `layout_nicely()` to align layout
  with axis automatically (#1907, #1957, #1958).

- Expose `simple_cycles()` which lists all simple cycles (#1573, #1580).

- Expose `is_complete()`, `is_clique()` and `is_ivs()` (#1316, #1388, #1581).

- Expose `find_cycle()` (#1471, #1571).

- Expose `feedback_vertex_set()` to find a minimum feedback vertex set
  in a graph (#1446, #1447, #1560).

- Add `weights` parameter to `local_scan()` (#1082, #1448, #1982).

- Add more layouts to `tkplot()` (#160, #1967).

- Add `plot(mark.lwd = )` to change line width of mark.groups (#306, #1898).

- Add `plot(vertex.label.angle = , vertex.label.adj = )` arguments to
  rotate vertex labels (#106, #1899).

- Add relative size scaling to vertices in `plot()` (@gvegayon, #172).

- Split `sample_bipartite()` into two functions for the G(n, m) and
  G(n, p) case (#630, #1692).

- Implement multi attribute assignment (#55, #1916) and adding
  attributes via data frames (#1373, #1669, #1716). Support factors in
  `graph_from_data_frame()` (#34, #1829).

- All `_hrg()` functions check their argument (#1074, #1699).

- HRG printing with `type = "auto"` uses `"plain"` for large trees
  (#1879).

- `get_edge_ids()` accepts data frames and matrices (#1663).

- `igraph_version()` returns version of C core in an attribute (#1208,
  #1781).

## Breaking changes

- Breaking change: change arguments default and order for
  `graph_from_lcf()` (#1858, #1872).

- Breaking change: Subset assignment of a graph avoids addition of
  double edges and ignores loops unless the new `loops` argument is
  set to `TRUE` (#1662, #1661).

- Breaking change: remove deprecated `neimode` parameter from `bfs()`
  and `dfs()` (#1105, #1526).

- Breaking change: stricter deprecation of non-functional parameters
  of `layout_with_kk()` and `layout_with_fr()` (#1108, #1628).

## Bug fixes

- `NA` attribute values are replaced with default values in `plot()`
  (#293, #1707).

- `NA` checking only in from/to columns of edge data frame (#1906).

- Keep vertex attribute type for `disjoint_union()` (#1640, #1909).

- Error in bipartite projection if `type` is not a vertex attribute
  (#898, #1889).

- Do not try to destroy non-initialized SIR objects upon error (#1888).

- Added proper `NA` handling for matrix inputs (#917, #918, #1828).

- Remove string matrix support from functions operating on biadjacency
  matrices (#1540, #1542, #1803).

- Integer vectors are validated before transferring them to the C
  library (#1434, #1582).

- Changed base location for `graph_from_graphdb()` and added tests
  (#1712, #1732).

- Recycling of logical vectors when indexing into edge/vertex
  selectors now throws an error (#848, #1731).

- Use `function()` instead of `(x)` in `arrow.mode` (#1722).

- Temporarily disable generating an interface for
  `igraph_simple_cycles_callback()` as the framework for handling
  callback functions is not yet present.

## Plotting bug fixes

- Adjust loop position to vertex size in `plot()` (#1980).

- Don't rescale plot coordinates to `[-1,1] x [-1,1]` by default
  (#1492, #1956, #1962).

- Fail if `"layout"` attribute doesn't match the number of vertices
  (#1880).

- Automatically arrange loops in `plot()` (#407, #556, #1881).

- Vectorized drawing of arrows in `plot()` (#257, #1904).

- Allow more than one edge label font family in `plot()` (#37, #1896).

- Pie shapes now work as intended (#1882, #1883).

- Loops not plotted on canvas (#1799, #1800).

- Replace `NA` values in `label` attributes in `plot()` with default
  values (#1796, #1797).

- Removed duplicated plotting of arrow heads (#640, #1709).

- Correct mapping of edge label properties in plots when loops are
  present (#157, #1706).

## Documentation

- Welcome Maëlle Salmon and David Schoch as authors (#1733), add
  author links (#1821).

- Remove demos (#2008).

- Add 2023 preprint (#1240, #1984).

- Update allcontributors info (#1975).

- Link to replacements of deprecated functions (#1823).

- Add documentation of all file formats to `read_graph()` and
  `write_graph()` (#777, #1969). Recommend `saveRDS()` and `readRDS()`
  for saving and loading graphs (#1242, #1700).

- Document return value of `make_clusters()` (#1794).

- Clarify that `girth()` returns `Inf` for acyclic graphs (@eqmooring,
  #1831).

- Clarify the use of weights in `layout_with_kk()`.

- Refer to current latest version of R in troubleshooting page.

- Fix typos in `laplacian_matrix()` documentation.

- Document ellipsis in `cohesion()` (#971, #1985).

- Correct the description of the `weights` parameter of `hits_scores()`.

- Better describe output of `all_shortest_paths()` (#1029, #1778).

- `make_graph()` now supports `"Groetzsch"` as an alias of
  `"Grotzsch"`. This change was implemented in the C core.

- Update description of `order` parameter of `ego()` and related
  functions (#1746).

- Added lifecycle table (#1525).

- Add more about igraph.r2cdocs in the contributing guide (#1686,
  #1697).

## Performance

- Accelerate check if an index sequence corresponds to the entire list
  of vertices (#1427, #1818).

- Faster single bracket querying of a graph (#1465, #1658).


To generate a diff of this commit:
cvs rdiff -u -r1.28 -r1.29 pkgsrc/math/R-igraph/Makefile
cvs rdiff -u -r1.13 -r1.14 pkgsrc/math/R-igraph/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/math/R-igraph/patches/patch-src_Makevars.in

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:1.28 pkgsrc/math/R-igraph/Makefile:1.29
--- pkgsrc/math/R-igraph/Makefile:1.28  Wed Jan  7 08:47:51 2026
+++ pkgsrc/math/R-igraph/Makefile       Mon Jun 15 14:23:37 2026
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.28 2026/01/07 08:47:51 wiz Exp $
+# $NetBSD: Makefile,v 1.29 2026/06/15 14:23:37 mef Exp $
 
 R_PKGNAME=     igraph
-R_PKGVER=      2.1.4
+R_PKGVER=      2.3.2
 CATEGORIES+=   graphics
 
 MAINTAINER=    minskim%NetBSD.org@localhost

Index: pkgsrc/math/R-igraph/distinfo
diff -u pkgsrc/math/R-igraph/distinfo:1.13 pkgsrc/math/R-igraph/distinfo:1.14
--- pkgsrc/math/R-igraph/distinfo:1.13  Fri Feb 14 22:59:56 2025
+++ pkgsrc/math/R-igraph/distinfo       Mon Jun 15 14:23:37 2026
@@ -1,6 +1,7 @@
-$NetBSD: distinfo,v 1.13 2025/02/14 22:59:56 mef Exp $
+$NetBSD: distinfo,v 1.14 2026/06/15 14:23:37 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
+BLAKE2s (R/igraph_2.3.2.tar.gz) = aba0888fa65b0320235d51623a1e9eb9558f05aa3a2ecef23d33557f52025c6f
+SHA512 (R/igraph_2.3.2.tar.gz) = 9ffd4ce1e11387cfce807b4852257356579eab53152450daa082e71b7d3312707f423c152fc7891500860b2511f668c4d9690c6e4657e2e86ba312f294d3a609
+Size (R/igraph_2.3.2.tar.gz) = 5209216 bytes
+SHA1 (patch-src_Makevars.in) = 0d5a823d0607400f975e37d37f1065bd02dda0a2
 SHA1 (patch-src_vendor_cigraph_vendor_plfit_hzeta.c) = 0f394527fdde6fece01920dd11d9432aaca0d124

Added files:

Index: pkgsrc/math/R-igraph/patches/patch-src_Makevars.in
diff -u /dev/null pkgsrc/math/R-igraph/patches/patch-src_Makevars.in:1.1
--- /dev/null   Mon Jun 15 14:23:38 2026
+++ pkgsrc/math/R-igraph/patches/patch-src_Makevars.in  Mon Jun 15 14:23:38 2026
@@ -0,0 +1,15 @@
+$NetBSD: patch-src_Makevars.in,v 1.1 2026/06/15 14:23:38 mef Exp $
+
+deps.mk has been removed ?
+
+--- src/Makevars.in.orig       2026-06-15 23:05:22.168262449 +0900
++++ src/Makevars.in    2026-06-15 23:05:39.955157560 +0900
+@@ -16,7 +16,7 @@ all: symbols.rds $(SHLIB)
+ deps.mk:
+       touch -r $$(ls -t *.cpp | head -n 1) "$@"
+ 
+-include deps.mk
++## include deps.mk
+ 
+ PKG_CFLAGS=$(C_VISIBILITY)
+ PKG_CXXFLAGS=$(CXX_VISIBILITY)