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Subject: CVS commit: pkgsrc/math/R-igraph
From: Makoto Fujiwara
Date: 2024-01-26 22:43:01
Message id: 20240126214301.A33F5FA42@cvs.NetBSD.org
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no longer maintained (#946).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.
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