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

Log message:
(math/R-igraph) sorry again, patch-configure not needed anymore

Log message:
(math/R-igraph) correct the macro define for expm1l, tks tnn@

Ref:
http://mail-index.netbsd.org/pkgsrc-users/2022/05/02/msg035568.html

Log message:
(devel/R-igraph) Updated 1.2.4.1 to 1.3.1

(pkgsrc)
 - Add two tentative macro, in patch, log1pl, expm1l. Tks tnn@ for hint
   (and correct me if misleading)

(upstream)
# igraph 1.3.1

Fixed:

- `graph_from_adjacency_matrix()` now works with sparse matrices even if the
  cell values in the sparse matrix are unspecified.
- Fixed crash in `cluster_walktrap()` when `modularity=FALSE` and `membership=FALSE`
- `edge_attr()` does not ignore its `index=...` argument any more.
- `automorphisms()`, `automorphism_group()` and `canonical_permutation()` now
  allow all possible values supported by the C core in the `sh` argument.
  Earlier versions supported only `"fm"`.
- The `vertex.frame.width` plotting parameter now allows zero and negative
  values; these will simply remove the outline of the corresponding vertex.
- The documentation of the `sh` argument of the BLISS isomorphism algorithm in
  `isomorphic()` was fixed; earlier versions incorrectly referred to `sh1` and
  `sh2`.
- `dominator_tree()` now conforms to its documentation with respect to the
  `dom` component of the result: it contains the indices of the dominator
  vertices for each vertex and -1 for the root of the dominator tree.
- Mentions of the `"power"` algorithm of `page_rank()` have been \ 
removed from
  the documentation, as this method is no longer available.
- Several other documentation fixes to bring the docs up to date with new behaviours
  in igraph 1.3.

# igraph 1.3.0

The C core is updated to 0.9.7, fixing a range of bugs and introducing a number
of new functions.

Added:

- `has_eulerian_path()` and `has_eulerian_cycle()` decides whether there is an
  Eulerian path or cycle in the graph.
- `eulerian_path()` and `eulerian_cycle()` returns the edges and vertices in an
  Eulerian path or cycle in the graph.
- `any_loop()` checks whether a graph contains at least one loop edge.
- `is_tree()` checks whether a graph is a tree and also finds a possible root
- `to_prufer()` converts a tree graph into its Prufer sequence
- `make_from_prufer()` creates a tree graph from its Prufer sequence
- `sample_tree()` to sample labelled trees uniformly at random
- `sample_spanning_tree()` to sample spanning trees of an undirected graph
  uniformly at random
- `automorphisms()` and `canonical_permutation()` now supports vertex colors
- `random_edge_walk()` to record the edges traversed during a random walk
- `harmonic_centrality()` calculates the harmonic centrality of vertices,
  optionally with a cutoff on path lengths
- `mean_distance()` now supports edge weights and it can also return the number
  of unconnected vertex pairs when `details=TRUE` is passed as an argument
- `greedy_vertex_coloring()` finds vertex colorings based on a simple greedy
  algorithm.
- `bridges()` finds the bridges (cut-edges) of a graph
- The frame width of circle, rectangle and square vertex shapes can now be
  adjusted on plots with the `frame.width` vertex attribute or the
  `vertex.frame.width` keyword argument, thanks to @simoncarrignon .
  See PR #500 for more details.
- `automorphism_group()` returns a possible (not necessarily minimal)
  generating set of the automorphism group of a graph.
- `global_efficiency()` calculates the global efficiency of the graph.
- `local_efficiency()` calculates the local efficiency of each vertex in a graph.
- `average_local_efficiency()` calculates the average local efficiency across
  the set of vertices in a graph.
- `rewire(each_edge(...))` now supports rewiring only one endpoint of each edge.
- `realize_degseq()` generates graphs from degree sequences in a deterministic
  manner. It is also available as `make_(degseq(..., deterministic=TRUE))`.
- `clique_size_counts()` counts cliques of different sizes without storing them all.
- `feedback_arc_set()` finds a minimum-weight feedback arc set in a graph, either
  with an exact integer programming algorithm or with a linear-time approximation.
- `make_bipartite_graph()` now handles vertices with names.
- `shortest_paths()` now supports graphs with negative edge weights.
- `min_cut()` now supports s-t mincuts even if `value.only=FALSE`.
- `as.matrix()` now supports converting an igraph graph to an adjacency or edge
  list matrix representation. See `as.matrix.igraph()` for more details. This
  function was migrated from `intergraph`; thanks to Michal Bojanowski.

Fixed:

- `is_connected()` now returns FALSE for the null graph
- Calling `length()` on a graph now returns the number of vertices to make it
  consistent with indexing the graph with `[[`.
- `diameter()` now corrently returns infinity for disconnected graphs when
  `unconnected=FALSE`. Previous versions returned the number of vertices plus
  one, which was clearly invalid for weighted graphs.
- `mean_distance()` now correctly treats the path length between disconnected
  vertices as infinite when `unconnected=FALSE`. Previous versions used the
  number of vertices plus one, adding a bias towards this number, even if the
  graph was weighted and the number of vertices plus one was not a path length
  that could safely have been considered as being longer than any \ 
"valid" path.
- `layout_with_sugiyama()` now handles the case of exactly one extra virtual
  node correctly; fixes #85
- `bfs()` and `dfs()` callback functions now correctly receive 1-based vertex
  indices and ranks; it used to be zero-based in earlier versions
- Accidentally returning a non-logical value from a `bfs()` or `dfs()` callback
  does not crash R any more
- Calling `print()` on a graph with a small `max.lines` value (smaller than the
  number of lines needed to print the attribute list and the header) does not
  raise an error any more; fixes #179
- `as_adjacency_matrix(edges=TRUE, sparse=TRUE)` now consistently returns the
  last edge ID for each cell in the matrix instead of summing them.
- Using the `+` and `-` operators with a `path()` object consisting of two
  vertices is now handled correctly; fixes #355
- `topo_sort()` now throws an error if the input graph is not acyclic instead
  of returning an incorrect partial ordering.
- Weighted transitivity calculations (i.e. \ 
`transitivity(mode="barrat")` now
  throw an error for multigraphs; the implementation does not work correctly
  for multigraphs and earlier versions did not warn about this.

Changed:

- The `neimode` argument of `bfs()` and `dfs()` was renamed to `mode` for sake
  of consistency with other functions. The old argument name is deprecated and
  will be removed in 1.4.0.
- `bfs()` and `dfs()` callback functions now correctly receive 1-based vertex
  indices and ranks; it used to be zero-based in earlier versions. (This is
  actually a bugfix so it's also mentioned in the "Fixed" section).
- `closeness()`, `betweenness()` and `edge_betweenness()` now all take a
  `cutoff` argument on their own. `estimate_closeness()`, `estimate_betweenness()`
  and `estimate_edge_betweenness()` became aliases, with identical signature.
  They are _not_ deprecated but their implementation might change in future
  versions to provide proper estimation schemes instead of a simple cutoff-based
  approximation. If you explicitly need cutoffs and you want your results to be
  reproducible with future versions, use `closeness()`, `betweenness()` and
  `edge_betweenness()` in your code with a `cutoff` argument.
- `closeness()` now only considers _reachable_ vertices during the calculation;
  in other words, closeness centrality is now calculated on a per-component
  basis for disconnected graphs. Earlier versions considered _all_ vertices.

Deprecated:

- Using `cutoff=0` for `closeness()`, `betweenness()` and `edge_betweenness()`
  is deprecated; if you want exact scores, use a negative cutoff. `cutoff=0`
  will be interpreted literally from igraph 1.4.0.
- `centr_degree_tmax()` now prints a warning when it is invoked without an
  explicit `loops` argument. `loops` will be mandatory from igraph 1.4.0.
- The `nexus_list()`, `nexus_info()`, `nexus_get()` and `nexus_search()`
  functions now return an error informing the user that the Nexus graph
  repository has been taken offline (actually, several years ago). These
  functions will be removed in 1.4.0.
- The `edges` argument of `as_adjacency_matrix()` is deprecated; it will be
  removed in igraph 1.4.0.

Removed:

- The deprecated `page_rank_old()` function and the deprecated `power` method of
  `page_rank()` were removed.

# igraph 1.2.11

Dec 27, 2021

No user visible changes.

# igraph 1.2.10

Dec 14, 2021

Fixed:

- The macOS versions of `igraph` were accidentally built without GraphML
  support on CRAN; this should now be fixed.

# igraph 1.2.9

Nov 22, 2021

No user visible changes.

# igraph 1.2.8

Oct 26, 2021

No user visible changes.

# igraph 1.2.7

Oct 15, 2021

The C core is updated to 0.8.5, fixing a range of bugs and introducing a number \ 
of new functions.

Added:

- cluster_leiden added (#399).
- cluster_fluid_communities added (#454)

Fixed:

- `make_lattice()` correctly rounds `length` to the nearest integer while
  printing a warning (#115).
- `make_empty_graph(NULL)` now prints an error instead of producing an
  invalid graph (#404).
- `make_graph(c())` now produces an empty graph instead of printing a
  misleading error message (#431).
- Printing a graph where some edges have NA as the names of both endpoints
  does not produce a misleading error message any more (#410).
- The `types` argument of functions related to bipartite graphs now prints
  a warning when the types are coerced to booleans (#476).
- Betweenness normalisation no longer overflows (#442).
- `layout_with_sugiyama()` returns a layout of type matrix even if there is
  only one vertex in the graph (#408).
- Plotting a null graph (i.e. a graph with no vertices) does not throw an error
  any more (#387).

Deprecated:

- The `membership` argument of `modularity.matrix()` is now deprecated as the
  function never needed it anyway.
- `modularity()` now prints a warning when it is applied on a directed graph
  because the implementation in igraph's C core does not support directed
  graphs as of version 0.8.5. The warning will be turned into an error in
  the next minor (1.3.0) version of the R interface; the error will be removed
  later when the C core is updated to a version that supports modularity for
  directed networks.
- `transitivity()` now prints a warning when its local variant \ 
(`type="local"`)
  is called on a directed graph or a graph with multiple edges beecause the
  implementation in the C core of igraph does not work reliably in these cases
  as of version 0.8.5. The warning will be turned into an error in the next
  minor (1.3.0) version of the R interface; the error will be removed later
  when the C core is updated to a version that supports transitivity for
  networks with multiple edges.

Misc:

- Documentation improvements.

# igraph 1.2.6

Oct 5, 2020

No user visible changes.

# igraph 1.2.5

Mar 27, 2020

No user visible changes.

Log message:
revbump for textproc/icu update

Log message:
revbump for icu and libffi

Log message:
math: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

Log message:
math: Remove SHA1 hashes for distfiles