Log message:
(math/Rigraph) 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
backwardcompatible way, to prepare for upgrading the C core to
0.10. Details are described at
<https://github.com/igraph/rigraph/wiki/Theigraphobjectformat>. 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 nonformula (#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("installationtroubleshooting")`.
 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/Rigraph) 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.
 ARPACKbased 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:
(devel/Rigraph) 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 Rdevel.
 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 ARPACKbased 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 zerobased root vertex indices in the result \
object; this is now fixed and the indices are now 1based.
 `as_graphnel()` does not duplicate loop edges any more.
 `convex_hull()` now returns the vertices of the convex hull with 1based 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 selfloops 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 singlebranch 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 nonpositive
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.
 Singlebracket 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 singlebracket 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 sizezero `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.
