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Revision 1.19 / (download) - annotate - [select for diffs], Fri Jan 26 21:43:01 2024 UTC (4 weeks, 6 days ago) by mef
Branch: MAIN
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(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  no longer maintained (#946).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.

Revision 1.18 / (download) - annotate - [select for diffs], Wed Nov 8 13:20:01 2023 UTC (3 months, 3 weeks ago) by wiz
Branch: MAIN
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Changes since 1.17: +2 -1 lines
Diff to previous 1.17 (colored)

*: recursive bump for icu 74.1

Revision 1.17 / (download) - annotate - [select for diffs], Fri Aug 11 07:11:36 2023 UTC (6 months, 2 weeks ago) by mef
Branch: MAIN
CVS Tags: pkgsrc-2023Q3-base, pkgsrc-2023Q3
Changes since 1.16: +5 -4 lines
Diff to previous 1.16 (colored)

(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).

Revision 1.16 / (download) - annotate - [select for diffs], Sun Jun 11 02:48:20 2023 UTC (8 months, 3 weeks ago) by mef
Branch: MAIN
CVS Tags: pkgsrc-2023Q2-base, pkgsrc-2023Q2
Changes since 1.15: +4 -4 lines
Diff to previous 1.15 (colored)

(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).

Revision 1.15 / (download) - annotate - [select for diffs], Wed Apr 19 08:10:44 2023 UTC (10 months, 1 week ago) by adam
Branch: MAIN
Changes since 1.14: +2 -1 lines
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revbump after textproc/icu update

Revision 1.14 / (download) - annotate - [select for diffs], Sat Mar 11 11:15:33 2023 UTC (11 months, 3 weeks ago) by mef
Branch: MAIN
CVS Tags: pkgsrc-2023Q1-base, pkgsrc-2023Q1
Changes since 1.13: +12 -1 lines
Diff to previous 1.13 (colored)

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

Revision 1.13 / (download) - annotate - [select for diffs], Sat Mar 11 11:07:54 2023 UTC (11 months, 3 weeks ago) by mef
Branch: MAIN
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(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.

Revision 1.12 / (download) - annotate - [select for diffs], Wed Nov 23 16:20:34 2022 UTC (15 months, 1 week ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2022Q4-base, pkgsrc-2022Q4
Changes since 1.11: +2 -1 lines
Diff to previous 1.11 (colored)

massive revision bump after textproc/icu update

Revision 1.11 / (download) - annotate - [select for diffs], Thu Apr 28 15:44:47 2022 UTC (22 months ago) by mef
Branch: MAIN
CVS Tags: pkgsrc-2022Q3-base, pkgsrc-2022Q3, pkgsrc-2022Q2-base, pkgsrc-2022Q2
Changes since 1.10: +2 -3 lines
Diff to previous 1.10 (colored)

(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.

Revision 1.10 / (download) - annotate - [select for diffs], Mon Apr 18 19:11:34 2022 UTC (22 months, 1 week ago) by adam
Branch: MAIN
Changes since 1.9: +2 -2 lines
Diff to previous 1.9 (colored)

revbump for textproc/icu update

Revision 1.9 / (download) - annotate - [select for diffs], Wed Dec 8 16:05:31 2021 UTC (2 years, 2 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2022Q1-base, pkgsrc-2022Q1, pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored)

revbump for icu and libffi

Revision 1.8 / (download) - annotate - [select for diffs], Wed Apr 21 11:42:09 2021 UTC (2 years, 10 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored)

revbump for textproc/icu

Revision 1.7 / (download) - annotate - [select for diffs], Thu Nov 5 09:08:36 2020 UTC (3 years, 3 months ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1, pkgsrc-2020Q4-base, pkgsrc-2020Q4
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 (colored)

*: Recursive revbump from textproc/icu-68.1

Revision 1.6 / (download) - annotate - [select for diffs], Tue Jun 2 08:24:16 2020 UTC (3 years, 8 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2020Q3-base, pkgsrc-2020Q3, pkgsrc-2020Q2-base, pkgsrc-2020Q2
Changes since 1.5: +2 -1 lines
Diff to previous 1.5 (colored)

Revbump for icu

Revision 1.5 / (download) - annotate - [select for diffs], Wed Sep 25 17:30:08 2019 UTC (4 years, 5 months ago) by brook
Branch: MAIN
CVS Tags: pkgsrc-2020Q1-base, pkgsrc-2020Q1, pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.4: +2 -1 lines
Diff to previous 1.4 (colored)

Add missing dependency on textproc/libxml2.

Revision 1.4 / (download) - annotate - [select for diffs], Thu Aug 8 19:53:50 2019 UTC (4 years, 6 months ago) by brook
Branch: MAIN
Changes since 1.3: +4 -6 lines
Diff to previous 1.3 (colored)

Update all R packages to canonical form.

The canonical form [1] of an R package Makefile includes the
following:

- The first stanza includes R_PKGNAME, R_PKGVER, PKGREVISION (as
  needed), and CATEGORIES.

- HOMEPAGE is not present but defined in math/R/Makefile.extension to
  refer to the CRAN web page describing the package.  Other relevant
  web pages are often linked from there via the URL field.

This updates all current R packages to this form, which will make
regular updates _much_ easier, especially using pkgtools/R2pkg.

[1] http://mail-index.netbsd.org/tech-pkg/2019/08/02/msg021711.html

Revision 1.3 / (download) - annotate - [select for diffs], Wed Jul 31 19:47:01 2019 UTC (4 years, 7 months ago) by brook
Branch: MAIN
Changes since 1.2: +9 -7 lines
Diff to previous 1.2 (colored)

R-igraph: update to version 1.2.4.1.

Update to the canonical form of an R package and fix the LICENSE
field.

Revision 1.2 / (download) - annotate - [select for diffs], Tue Sep 4 00:23:12 2018 UTC (5 years, 5 months ago) by minskim
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

math/R-igraph: Needs a C compiler

Revision 1.1 / (download) - annotate - [select for diffs], Thu May 24 22:25:17 2018 UTC (5 years, 9 months ago) by minskim
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2

math/R-igraph: Import version 1.2.1

Routines for simple graphs and network analysis. It can handle large
graphs very well and provides functions for generating random and
regular graphs, graph visualization, centrality methods and much more.

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