./math/R-igraph, Network analysis and visualization

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Branch: CURRENT, Version:, Package name: R-igraph-, Maintainer: minskim

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.

Required to run:
[textproc/libxml2] [math/R] [devel/R-magrittr] [lang/gcc7] [devel/R-pkgconfig]

Required to build:

Master sites: (Expand)

Version history: (Expand)

CVS history: (Expand)

   2023-08-11 09:11:36 by Makoto Fujiwara | Files touched by this commit (2)
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 \ 

- Prepare migration to igraph/C 0.10 (#781).

- Update generated interface (#765).
   2023-06-11 04:48:20 by Makoto Fujiwara | Files touched by this commit (2)
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.

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

- 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).
   2023-04-19 10:12:01 by Adam Ciarcinski | Files touched by this commit (2359) | Package updated
Log message:
revbump after textproc/icu update
   2023-03-11 12:15:33 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
(math/R-igraph) Adding TEST_DEPENDS+= , but still missing more
   2023-03-11 12:07:54 by Makoto Fujiwara | Files touched by this commit (2) | Package updated
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 \ 
 - `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


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


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

- Package updated to be compatible with Matrix 1.5.


 - Documentation improvements and fixes.

# igraph 1.3.4


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


- `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


- `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.


- 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.


- The length of size-zero `communities` objects is now reported correctly.
- `layout_with_kk()` would fail to produce reasonable results with the default \ 
  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.


 - Documentation improvements and fixes.
   2022-11-23 17:21:30 by Adam Ciarcinski | Files touched by this commit (1878) | Package updated
Log message:
massive revision bump after textproc/icu update
   2022-05-03 02:25:48 by Makoto Fujiwara | Files touched by this commit (1)
Log message:
(math/R-igraph) sorry again, patch-configure not needed anymore
   2022-05-03 02:24:20 by Makoto Fujiwara | Files touched by this commit (3)
Log message:
(math/R-igraph) correct the macro define for expm1l, tks tnn@