CVS commit: pkgsrc/math/R-igraph

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/R-igraph
From: "Makoto Fujiwara" <mef%netbsd.org@localhost>
Date: Sat, 11 Mar 2023 11:07:54 +0000

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Mar 11 11:07:54 UTC 2023

Modified Files:
        pkgsrc/math/R-igraph: Makefile distinfo

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.


To generate a diff of this commit:
cvs rdiff -u -r1.12 -r1.13 pkgsrc/math/R-igraph/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/R-igraph/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-igraph/Makefile
diff -u pkgsrc/math/R-igraph/Makefile:1.12 pkgsrc/math/R-igraph/Makefile:1.13
--- pkgsrc/math/R-igraph/Makefile:1.12  Wed Nov 23 16:20:34 2022
+++ pkgsrc/math/R-igraph/Makefile       Sat Mar 11 11:07:54 2023
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.12 2022/11/23 16:20:34 adam Exp $
+# $NetBSD: Makefile,v 1.13 2023/03/11 11:07:54 mef Exp $
 
 R_PKGNAME=     igraph
-R_PKGVER=      1.3.1
-PKGREVISION=   1
+R_PKGVER=      1.4.1
 CATEGORIES=    math graphics
 
 MAINTAINER=    minskim%NetBSD.org@localhost
@@ -11,6 +10,7 @@ LICENSE=      gnu-gpl-v2 OR gnu-gpl-v3
 
 DEPENDS+=      R-magrittr>=1.5:../../devel/R-magrittr
 DEPENDS+=      R-pkgconfig>=2.0.0:../../devel/R-pkgconfig
+DEPENDS+=      R-rlang-[0-9]*:../../devel/R-rlang
 
 USE_LANGUAGES= c c++ fortran
 

Index: pkgsrc/math/R-igraph/distinfo
diff -u pkgsrc/math/R-igraph/distinfo:1.7 pkgsrc/math/R-igraph/distinfo:1.8
--- pkgsrc/math/R-igraph/distinfo:1.7   Tue May  3 00:25:48 2022
+++ pkgsrc/math/R-igraph/distinfo       Sat Mar 11 11:07:54 2023
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.7 2022/05/03 00:25:48 mef Exp $
+$NetBSD: distinfo,v 1.8 2023/03/11 11:07:54 mef Exp $
 
-BLAKE2s (R/igraph_1.3.1.tar.gz) = 86dabeb6a382153941acd99b45fc295cfc84dda328de6acc9cbb17f8b20cd412
-SHA512 (R/igraph_1.3.1.tar.gz) = 3b725ca47a117501a9902e64cdb29ed5fe59bfba3b056b98a1fb4035fdd9a5f9ea274b87053ebab558e206a9def09af46e957cff0280fe6093dd9638dd3d5f71
-Size (R/igraph_1.3.1.tar.gz) = 2489895 bytes
+BLAKE2s (R/igraph_1.4.1.tar.gz) = c2d4ddcb45eea169ac352b46b665d0199bb3b932b7e67e580a222d2d261ba472
+SHA512 (R/igraph_1.4.1.tar.gz) = c3913044b8bf00f6b3e52e20aac3275ffef07a6271b66a93eb1458898e8edfd25a9f35902ecfe8f70b0e3b5cd5e605c5cd2605f38a55ecc42849fd4fb73b1af4
+Size (R/igraph_1.4.1.tar.gz) = 2910158 bytes
 SHA1 (patch-src_vendor_plfit_hzeta.c) = 06c895e951bc491bfb26376a4000e4204811748f

Prev by Date: CVS commit: pkgsrc/doc
Next by Date: CVS commit: pkgsrc/math/R-igraph
Previous by Thread: CVS commit: pkgsrc/doc
Next by Thread: CVS commit: pkgsrc/math/R-igraph
Indexes:

Home | Main Index | Thread Index | Old Index