Log message:
*: recursive bump for icu 76 shlib major version bump

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).

Log message:
*: revbump for icu downgrade

Log message:
*: recursive bump for icu 76.1 shlib bump

Log message:
revbump after icu and protobuf updates

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.

Log message:
*: recursive bump for icu 74.1

Log message:
(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
<https://github.com/igraph/rigraph/wiki/The-igraph-object-format>. 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
  <https://r.igraph.org/> (#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).

Log message:
(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 <https://igraph.org/> (#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).

Log message:
revbump after textproc/icu update