CVS commit: pkgsrc/math/R-igraph

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Fri Jan 26 21:43:01 UTC 2024

Modified Files:
        pkgsrc/math/R-igraph: Makefile distinfo

Log Message:
(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  no longer maintained (#946).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.


To generate a diff of this commit:
cvs rdiff -u -r1.18 -r1.19 pkgsrc/math/R-igraph/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/math/R-igraph/distinfo

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:1.18 pkgsrc/math/R-igraph/Makefile:1.19
--- pkgsrc/math/R-igraph/Makefile:1.18  Wed Nov  8 13:20:01 2023
+++ pkgsrc/math/R-igraph/Makefile       Fri Jan 26 21:43:01 2024
@@ -1,15 +1,15 @@
-# $NetBSD: Makefile,v 1.18 2023/11/08 13:20:01 wiz Exp $
+# $NetBSD: Makefile,v 1.19 2024/01/26 21:43:01 mef Exp $
 
 R_PKGNAME=     igraph
-R_PKGVER=      1.5.0.1
+R_PKGVER=      1.6.0
 CATEGORIES+=   graphics
 
 MAINTAINER=    minskim%NetBSD.org@localhost
 COMMENT=       Network analysis and visualization
-PKGREVISION=   1
 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

Index: pkgsrc/math/R-igraph/distinfo
diff -u pkgsrc/math/R-igraph/distinfo:1.10 pkgsrc/math/R-igraph/distinfo:1.11
--- pkgsrc/math/R-igraph/distinfo:1.10  Fri Aug 11 07:11:36 2023
+++ pkgsrc/math/R-igraph/distinfo       Fri Jan 26 21:43:01 2024
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.10 2023/08/11 07:11:36 mef Exp $
+$NetBSD: distinfo,v 1.11 2024/01/26 21:43:01 mef Exp $
 
-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
+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