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  no longer maintained (#946).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

Log message:
(math/R-igraph) Adding TEST_DEPENDS+= , but still missing more

Log message:
(devel/R-igraph) Updated 1.13.1 to 1.14.1

# igraph 1.4.1

## Bug fixes

- `console()` now works again and provides a Tcl/Tk based UI where igraph can \ 
post status messages and progress info (#664).

- Fix errors when printing long vertex names (#677, @ahmohamed).

- Fix regression that broke builds on some systems (e.g., GCC version 5 or \ 
earlier), introduced in igraph 1.4.0 (#670, #671).

- `fit_hrg()` does not crash any more when called with a graph that has less \ 
than three vertices.

## Documentation

- Various improvements (#663, @maelle; #667).

## Internal

- Fix warning about `yyget_leng()` returning wrong type when using LTO (#676).

- Don't mention C++11 or C++17 for best compatibility with both newest R and \ 
older compilers, while still requesting a C++ compiler for linking.

- Don't ignore `build/` when building the package because the vignette index is \ 
built there.

- Skip plot test entirely on R-devel.

- Avoid submodules for building igraph (#674).

- Makevars cleanup (#671).

- Add Zenodo configuration file.

# igraph 1.4.0

## Breaking changes

 - Breaking change: Allow change of attribute type when setting attribute for \ 
all vertices or edges; only attributes of length 1 or the length of the target \ 
set allowed (#633).

## Added

 - `tkplot()` gained a `palette` argument and it is now using the same palette \ 
as `plot()` by default, for sake of consistency.
 - `plot.igraph()` gained a `loop.size` argument that can be used to scale the \ 
common radius of the loop edges.

## Fixed

 - The default maximum number of iterations for ARPACK has been increased to \ 
3000 to match that of the igraph C core.
 - Rare convergence problems have been corrected in `cluster_leading_eigen()`.
 - All ARPACK-based functions now respect random seeds set in R when generating \ 
a random starting vector.
 - `igraph_version()` returned an invalid value in 1.3.4, this is now corrected.
 - The value of `par(xpd=...)` is now restored after plotting a graph.
 - Fixed a bug in `as.dendrogram.communities()` for large dendrograms, thanks
   to @pkharchenko (see PR #292).
 - Fixed two bugs in `graph_from_incidence_matrix()` that prevented the creation \ 
of directed graphs with `mode="all"` from dense or sparse matrices.
 - `dfs()` accidentally returned zero-based root vertex indices in the result \ 
object; this is now fixed and the indices are now 1-based.
 - `as_graphnel()` does not duplicate loop edges any more.
 - `convex_hull()` now returns the vertices of the convex hull with 1-based indexing.
 - Some `rgl.*()` function calls in the codebase were replaced with equivalent \ 
`*3d()` function calls in preparation for upcoming deprecations in `rgl` (see PR \ 
#619)
 - `plot.igraph()` does not use the `frame=...` partial argument any more when \ 
calling `plot.default()`. The default `NULL` value of `frame.plot` is now also \ 
handled correctly.
 - `hub_score()` and `authority_score()` considered self-loops only once on the \ 
diagonal of the adjacency matrix of undirected graphs, thus the result was not \ 
identical to that obtained by `eigen_centrality()` on loopy undirected graphs. \ 
This is now corrected.
 - `distances()` no longer ignores the `mode` parameter when `algorithm='johnson'`.

## Deprecated

 - `automorphisms()` was renamed to `count_automorphisms()`; the old name is \ 
still available, but it is deprecated.

## Other

 - Documentation improvements.
 - The Github repository was now moved to a single-branch setup where the \ 
package can be built from the `main` branch directly.
 - Added igraph extended tutorial as an R vignette (#587).
 - igraph now has a homepage based on `pkgdown` thanks to @maelle (see #645). \ 
This will eventually become the official homepage.

# igraph 1.3.5

Added:

- `mark.groups=...` argument of `plot.igraph()` now accepts `communities`
  objects

Fixed:

- Negative degree exponents are not allowed any more in `sample_pa()` and
  `sample_aging_pa()`.

- Package updated to be compatible with Matrix 1.5.

Other:

 - Documentation improvements and fixes.

# igraph 1.3.4

Added:

- `sample_asym_pref()` now returns the generated types of the vertices in the
  vertex attributes named `outtype` and `intype`.

Fixed:

- `layout_nicely()` does not recurse infinitely any more if it is assigned to
  the `layout` attribute of a graph

- `layout_nicely()` now ignores edge weights when there are non-positive
  edge weights. This is needed because igraph 1.3.3 started validating edge
  weights in `layout_with_fr()` and `layout_with_drl()`, resulting in
  errors when `layout_nicely()` was used on weighted graphs with negative
  weights. Since `layout_nicely()` is the default layout algorithm for
  `plot()`, most users were not even aware that they were using the FR or
  DrL layouts behind the scenes. Now the policy is that `layout_nicely()`
  attempts to get the job done without errors if possible, even if that means
  that edge weights must be ignored. A warning is printed if this is the case.

# igraph 1.3.3

Added:

- `reverse_edges()` reverses specific or all edges in a graph.

- Single-bracket indexing of `V()` and `E()` resolves attribute names in the
  indexing expressions by default (for instance, `E(g)[weight > x]` matches
  edges with a weight larger than a threshold). This can be problematic if the
  attribute masks one of the variables in the local evaluation context.
  We now have a pronoun called `.env` (similarly to `rlang::.env`) that
  allows you to force attribute name lookup to the calling environment. For
  sake of completeness, we also provide `.data` (similarly to `rlang::.data`)
  to force attribute name lookup to the vertex / edge attributes only. These
  pronouns are automatically injected into the environment where the indexing
  expression is evaluated.

Deprecated:

- Names of functions that can be used inside a `V()` or `E()` indexing start
  with a dot since igraph 1.1.1; however, the old dotless names did not print
  a deprecation warning so this may have gone unnoticed for years. We are
  introducting a deprecation warning for `nei()`, `innei()`, `outnei()`,
  `inc()`, `from()` and `to()` inside single-bracket indexing of vertex and
  edge sequences and will remove the old variants soon.

# igraph 1.3.2

The C core is updated to 0.9.9, fixing a range of bugs.

Fixed:

- The length of size-zero `communities` objects is now reported correctly.
- `layout_with_kk()` would fail to produce reasonable results with the default \ 
initial
  coordinates. This has been corrected, however, this function no longer produces
  precisely the same output for a given graph as before. To restore the previous
  behaviour, use `layout_with_kk(g, coord=layout_in_circle(g))` in 2D or
  `layout_with_kk(g, dim=3, coord=layout_on_sphere(g))` in 3D.
- Indexing an `igraph.vs` object with `v[x, na_ok=T]` now correctly handles the
  `na_ok` argument in all cases; previous versions ignored it when `x` was
  a single number.

Other:

 - Documentation improvements and fixes.

Log message:
massive revision bump after textproc/icu update