CVS commit: pkgsrc/graphics/R-ggplot2

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Wed Jun  5 12:00:07 UTC 2024

Modified Files:
        pkgsrc/graphics/R-ggplot2: Makefile distinfo

Log Message:
(graphics/R-ggplot2) Updated 3.4.2 to 3.5.1, fix build against R-4.4.0

# ggplot2 3.5.1

This is a small release focusing on fixing regressions from 3.5.0 and
documentation updates.

## Bug fixes

* Fixed bug where discrete scales could not map aesthetics only consisting of
  `NA`s (#5623)
* Fixed spurious warnings from `sec_axis()` with `breaks = NULL` (#5713).
* Patterns and gradients are now also enabled in `geom_sf()`
  (@teunbrand, #5716).
* The default behaviour of `resolution()` has been reverted to pre-3.5.0
  behaviour. Whether mapped discrete vectors should be treated as having
  resolution of 1 is controlled by the new `discrete` argument.
* Fixed bug in `guide_bins()` and `guide_coloursteps()` where discrete breaks,
  such as the levels produced by `cut()`, were ordered incorrectly
  (@teunbrand, #5757).

## Improvements

* When facets coerce the faceting variables to factors, the 'ordered' class
  is dropped (@teunbrand, #5666).
* `coord_map()` and `coord_polar()` throw informative warnings when used
  with the guide system (#5707).
* When passing a function to `stat_contour(breaks)`, that function is used to
  calculate the breaks even if `bins` and `binwidth` are missing
  (@teunbrand, #5686).
* `geom_step()` now supports `lineend`, `linejoin` and `linemitre` parameters
  (@teunbrand, #5705).
* Fixed performance loss when the `.data` pronoun is used in `aes()` (#5730).
* Facet evaluation is better at dealing with inherited errors
  (@teunbrand, #5670).
* `stat_bin()` deals with non-finite breaks better (@teunbrand, #5665).
* While axes in `coord_radial()` don't neatly fit the top/right/bottom/left
  organisation, specifying `position = "top"` or `position = "right"`
  in the scale will flip the placement of the radial axis (#5735)
* Theme elements that do not exist now throw warnings instead of errors (#5719).
* Fixed bug in `coord_radial()` where full circles were not treated as such
  (@teunbrand, #5750).
* When legends detect the presence of values in a layer, `NA` is now detected
  if the data contains values outside the given breaks (@teunbrand, #5749).
* `annotate()` now warns about `stat` or `position` arguments (@teunbrand, #5151)
* `guide_coloursteps(even.steps = FALSE)` now works with discrete data that has
  been formatted by `cut()` (@teunbrand, #3877).

# ggplot2 3.5.0

This is a minor release that turned out quite beefy. It is focused on
overhauling the guide system: the system responsible for displaying information
from scales in the guise of axes and legends. As part of that overhaul, new
guides have been implemented and existing guides have been refined. The look
and feel of guides has been mostly preserved, but their internals and
styling options have changed drastically.

Briefly summarising other highlights, we also welcome `coord_radial()` as a
successor of  `coord_polar()`. Initial support for newer graphical features,
such as pattern fills has been added. The API has changed how `I()`/`<AsIs>`
vectors interact with the scale system, namely: not at all.

## Breaking changes

* The guide system. As a whole. See 'new features' for more information.
  While the S3 guide generics are still in place, the S3 methods for
  `guide_train()`, `guide_merge()`, `guide_geom()`, `guide_transform()`,
  `guide_gengrob()` have been superseded by the respective ggproto methods.
  In practice, this will mean that `NextMethod()` or sub-classing ggplot2's
  guides with the S3 system will no longer work.

* By default, `guide_legend()` now only draws a key glyph for a layer when
  the value is in the layer's data. To revert to the old behaviour, you
  can still set `show.legend = c({aesthetic} = TRUE)` (@teunbrand, #3648).

* In the `scale_{colour/fill}_gradient2()` and
  `scale_{colour/fill}_steps2()` functions, the `midpoint` argument is
  transformed by the scale transformation (#3198).

* The `legend.key` theme element is set to inherit from the `panel.background`
  theme element. The default themes no longer set the `legend.key` element.
  This causes a visual change with the default `theme_gray()` (#5549).

* The `scale_name` argument in `continuous_scale()`, `discrete_scale()` and
  `binned_scale()` is soft-deprecated. If you have implemented custom scales,
  be advised to double-check that unnamed arguments ends up where they should
  (@teunbrand, #1312).

* The `legend.text.align` and `legend.title.align` arguments in `theme()` are
  deprecated. The `hjust` setting of the `legend.text` and `legend.title`
  elements continues to fulfill the role of text alignment (@teunbrand, #5347).

* 'lines' units in `geom_label()`, often used in the `label.padding` argument,
  are now are relative to the text size. This causes a visual change, but fixes
  a misalignment issue between the textbox and text (@teunbrand, #4753)

* `coord_flip()` has been marked as superseded. The recommended alternative is
  to swap the `x` and `y` aesthetic and/or using the `orientation` argument in
  a layer (@teunbrand, #5130).

* The `trans` argument in scales and secondary axes has been renamed to
  `transform`. The `trans` argument itself is deprecated. To access the
  transformation from the scale, a new `get_transformation()` method is
  added to Scale-classes (#5558).

* Providing a numeric vector to `theme(legend.position)` has been deprecated.
  To set the default legend position inside the plot use
  `theme(legend.position = "inside", legend.position.inside = c(...))` instead.

## New features

* Plot scales now ignore `AsIs` objects constructed with `I(x)`, instead of
  invoking the identity scale. This allows these columns to co-exist with other
  layers that need a non-identity scale for the same aesthetic. Also, it makes
  it easy to specify relative positions (@teunbrand, #5142).

* The `fill` aesthetic in many geoms now accepts grid's patterns and gradients.
  For developers of layer extensions, this feature can be enabled by switching
  from `fill = alpha(fill, alpha)` to `fill = fill_alpha(fill, alpha)` when
  providing fills to `grid::gpar()` (@teunbrand, #3997).

* New function `check_device()` for testing the availability of advanced
  graphics features introduced in R 4.1.0 onward (@teunbrand, #5332).

* `coord_radial()` is a successor to `coord_polar()` with more customisation
  options. `coord_radial()` can:

  * integrate with the new guide system via a dedicated `guide_axis_theta()` to
    display the angle coordinate.
  * in addition to drawing full circles, also draw circle sectors by using the
    `end` argument.
  * avoid data vanishing in the center of the plot by setting the `donut`
    argument.
  * adjust the `angle` aesthetic of layers, such as `geom_text()`, to align
    with the coordinate system using the `rotate_angle` argument.

### The guide system

The guide system encompassing axes and legends, as the last remaining chunk of
ggplot2, has been rewritten to use the `<ggproto>` system instead of the S3
system. This change was a necessary step to officially break open the guide
system for extension package developers. The axes and legends now inherit from
a `<Guide>` class, which makes them extensible in the same manner as geoms,
stats, facets and coords (#3329, @teunbrand)

* The most user-facing change is that the styling of guides is rewired through
  the theme system. Guides now have a `theme` argument that can style
  individual guides, while `theme()` has gained additional arguments to style
  guides. Theme elements declared in the guide override theme elements set
  through the plot. The new theme elements for guides are:
  `legend.key.spacing{.x/.y}`, `legend.frame`, `legend.axis.line`,
  `legend.ticks`, `legend.ticks.length`, `legend.text.position` and
  `legend.title.position`. Previous style options in the arguments of
  `guide_*()` functions are soft-deprecated.

* Unfortunately, we could not fully preserve the function of pre-existing
  guide extensions written in the S3 system. A fallback for these old guides
  is encapsulated in the `<GuideOld>` class, which calls the old S3 generics.
  The S3 methods have been removed as part of cleaning up, so the old guides
  will still work if the S3 methods are reimplemented, but we encourage to
  switch to the new system (#2728).

* The `order` argument of guides now strictly needs to be a length-1
  integer (#4958).

#### Axes

* New `guide_axis_stack()` to combine other axis guides on top of one another.

* New `guide_axis_theta()` to draw an axis in a circular arc in
  `coord_radial()`. The guide can be controlled by adding
  `guides(theta = guide_axis_theta(...))` to a plot.

* New `guide_axis_logticks()` can be used to draw logarithmic tick marks as
  an axis. It supersedes the `annotation_logticks()` function
  (@teunbrand, #5325).

* `guide_axis()` gains a `minor.ticks` argument to draw minor ticks (#4387).

* `guide_axis()` gains a `cap` argument that can be used to trim the
      axis line to extreme breaks (#4907).

* Primary axis titles are now placed at the primary guide, so that
  `guides(x = guide_axis(position = "top"))` will display the title at the
  top by default (#4650).

* The default `vjust` for the `axis.title.y.right` element is now 1 instead of
  0.

* Unknown secondary axis guide positions are now inferred as the opposite
  of the primary axis guide when the latter has a known `position` (#4650).

#### Legends

* New `guide_custom()` function for drawing custom graphical objects (grobs)
  unrelated to scales in legend positions (#5416).

* All legends have acquired a `position` argument, that allows individual guides
  to deviate from the `legend.position` set in the `theme()` function. This
  means that legends can now be placed at multiple sides of the plot (#5488).

* The spacing between legend keys and their labels, in addition to legends
  and their titles, is now controlled by the text's `margin` setting. Not
  specifying margins will automatically add appropriate text margins. To
  control the spacing within a legend between keys, the new
  `legend.key.spacing.{x/y}` argument can be used in `theme()`. This leaves the
  `legend.spacing` theme setting dedicated to solely controlling the spacing
  between different guides (#5455).

* `guide_colourbar()` and `guide_coloursteps()` gain an `alpha` argument to
  set the transparency of the bar (#5085).

* New `display` argument in `guide_colourbar()` supplants the `raster` argument.
  In R 4.1.0 and above, `display = "gradient"` will draw a gradient.

* Legend keys that can draw arrows have their size adjusted for arrows.

* When legend titles are larger than the legend, title justification extends
  to the placement of keys and labels (#1903).

* Glyph drawing functions of the `draw_key_*()` family can now set `"width"`
  and `"height"` attributes (in centimetres) to the produced keys to control
  their displayed size in the legend.

* `coord_sf()` now uses customisable guides provided in the scales or
  `guides()` function (@teunbrand).

## Improvements

* `guide_coloursteps(even.steps = FALSE)` now draws one rectangle per interval
  instead of many small ones (#5481).

* `draw_key_label()` now better reflects the appearance of labels (#5561).

* `position_stack()` no longer silently removes missing data, which is now
  handled by the geom instead of position (#3532).

* The `minor_breaks` function argument in scales can now also take a function
  with two arguments: the scale's limits and the scale's major breaks (#3583).

* Failing to fit or predict in `stat_smooth()` now gives a warning and omits
  the failed group, instead of throwing an error (@teunbrand, #5352).

* `labeller()` now handles unspecified entries from lookup tables
  (@92amartins, #4599).

* `fortify.default()` now accepts a data-frame-like object granted the object
  exhibits healthy `dim()`, `colnames()`, and `as.data.frame()` behaviours
  (@hpages, #5390).

* `geom_violin()` gains a `bounds` argument analogous to `geom_density()`s
  (@eliocamp, #5493).

* To apply dodging more consistently in violin plots, `stat_ydensity()` now
  has a `drop` argument to keep or discard groups with 1 observation.

* `geom_boxplot()` gains a new argument, `staplewidth` that can draw staples
  at the ends of whiskers (@teunbrand, #5126)

* `geom_boxplot()` gains an `outliers` argument to switch outliers on or off,
  in a manner that does affects the scale range. For hiding outliers that does
  not affect the scale range, you can continue to use `outlier.shape = NA`
  (@teunbrand, #4892).

* Nicer error messages for xlim/ylim arguments in coord-* functions
  (@92amartins, #4601, #5297).

* You can now omit either `xend` or `yend` from `geom_segment()` as only one
  of these is now required. If one is missing, it will be filled from the `x`
  and `y` aesthetics respectively. This makes drawing horizontal or vertical
  segments a little bit more convenient (@teunbrand, #5140).

* When `geom_path()` has aesthetics varying within groups, the `arrow()` is
  applied to groups instead of individual segments (@teunbrand, #4935).

* `geom_text()` and `geom_label()` gained a `size.unit` parameter that set the
  text size to millimetres, points, centimetres, inches or picas
  (@teunbrand, #3799).

* `geom_label()` now uses the `angle` aesthetic (@teunbrand, #2785)

* The `label.padding` argument in `geom_label()` now supports inputs created
  with the `margin()` function (#5030).

* `ScaleContinuous$get_breaks()` now only calls `scales::zero_range()` on limits
  in transformed space, rather than in data space (#5304).

* Scales throw more informative messages (@teunbrand, #4185, #4258)

* `scale_*_manual()` with a named `values` argument now emits a warning when
  none of those names match the values found in the data (@teunbrand, #5298).

* The `name` argument in most scales is now explicitly the first argument
  (#5535)

* The `translate_shape_string()` internal function is now exported for use in
  extensions of point layers (@teunbrand, #5191).

* To improve `width` calculation in bar plots with empty factor levels,
  `resolution()` considers `mapped_discrete` values as having resolution 1
  (@teunbrand, #5211)

* In `theme()`, some elements can be specified with `rel()` to inherit from
  `unit`-class objects in a relative fashion (@teunbrand, #3951).

* `theme()` now supports splicing a list of arguments (#5542).

* In the theme element hierarchy, parent elements that are a strict subclass
  of child elements now confer their subclass upon the children (#5457).

* New `plot.tag.location` in `theme()` can control placement of the plot tag
  in the `"margin"`, `"plot"` or the new `"panel"` option (#4297).

* `coord_munch()` can now close polygon shapes (@teunbrand, #3271)

* Aesthetics listed in `geom_*()` and `stat_*()` layers now point to relevant
  documentation (@teunbrand, #5123).

* The new argument `axes` in `facet_grid()` and `facet_wrap()` controls the
  display of axes at interior panel positions. Additionally, the `axis.labels`
  argument can be used to only draw tick marks or fully labelled axes
  (@teunbrand, #4064).

* `coord_polar()` can have free scales in facets (@teunbrand, #2815).

* The `get_guide_data()` function can be used to extract position and label
  information from the plot (#5004).

* Improve performance of layers without positional scales (@zeehio, #4990)

* More informative error for mismatched
  `direction`/`theme(legend.direction = ...)` arguments (#4364, #4930).

## Bug fixes

* Fixed regression in `guide_legend()` where the `linewidth` key size
  wasn't adapted to the width of the lines (#5160).

* In `guide_bins()`, the title no longer arbitrarily becomes offset from
  the guide when it has long labels.

* `guide_colourbar()` and `guide_coloursteps()` merge properly when one
  of the aesthetics is dropped (#5324).

* When using `geom_dotplot(binaxis = "x")` with a discrete y-variable, dots are
  now stacked from the y-position rather than from 0 (@teunbrand, #5462)

* `stat_count()` treats `x` as unique in the same manner `unique()` does
  (#4609).

* The plot's title, subtitle and caption now obey horizontal text margins
  (#5533).

* Contour functions will not fail when `options("OutDec")` is not `.` (@eliocamp, #5555).

* Lines where `linewidth = NA` are now dropped in `geom_sf()` (#5204).

* `ggsave()` no longer sometimes creates new directories, which is now
  controlled by the new `create.dir` argument (#5489).

* Legend titles no longer take up space if they've been removed by setting
  `legend.title = element_blank()` (@teunbrand, #3587).

* `resolution()` has a small tolerance, preventing spuriously small resolutions
  due to rounding errors (@teunbrand, #2516).

* `stage()` now works correctly, even with aesthetics that do not have scales
  (#5408)

* `stat_ydensity()` with incomplete groups calculates the default `width`
  parameter more stably (@teunbrand, #5396)

* The `size` argument in `annotation_logticks()` has been deprecated in favour
  of the `linewidth` argument (#5292).

* Binned scales now treat `NA`s in limits the same way continuous scales do
  (#5355).

* Binned scales work better with `trans = "reverse"` (#5355).

* Integers are once again valid input to theme arguments that expect numeric
  input (@teunbrand, #5369)

* Legends in `scale_*_manual()` can show `NA` values again when the `values` is
  a named vector (@teunbrand, #5214, #5286).

* Fixed bug in `coord_sf()` where graticule lines didn't obey
  `panel.grid.major`'s linewidth setting (@teunbrand, #5179)

* Fixed bug in `annotation_logticks()` when no suitable tick positions could
  be found (@teunbrand, #5248).

* The default width of `geom_bar()` is now based on panel-wise resolution of
  the data, rather than global resolution (@teunbrand, #4336).

* `stat_align()` is now applied per panel instead of globally, preventing issues
  when facets have different ranges (@teunbrand, #5227).

* A stacking bug in `stat_align()` was fixed (@teunbrand, #5176).

* `stat_contour()` and `stat_contour_filled()` now warn about and remove
  duplicated coordinates (@teunbrand, #5215).

* `guide_coloursteps()` and `guide_bins()` sort breaks (#5152).

## Internal changes

* The `ScaleContinuous$get_breaks()` method no longer censors
  the computed breaks.

* The ggplot object now contains `$layout` which points to the `Layout` ggproto
  object and will be used by the `ggplot_build.ggplot` method. This was exposed
  so that package developers may extend the behaviour of the `Layout` ggproto
  object without needing to develop an entirely new `ggplot_build` method
  (@jtlandis, #5077).

* Guide building is now part of `ggplot_build()` instead of
  `ggplot_gtable()` to allow guides to observe unmapped data (#5483).

* The `titleGrob()` function has been refactored to be faster and less
  complicated.

* The `scales_*()` functions related to managing the `<ScalesList>` class have
  been implemented as methods in the `<ScalesList>` class, rather than stray
  functions (#1310).

# ggplot2 3.4.4

This hotfix release adapts to a change in r-devel's `base::is.atomic()` and
the upcoming retirement of maptools.

* `fortify()` for sp objects (e.g., `SpatialPolygonsDataFrame`) is now deprecated
  and will be removed soon in support of [the upcoming retirement of rgdal, rgeos,
  and maptools](https://r-spatial.org/r/2023/05/15/evolution4.html). In advance
  of the whole removal, `fortify(<SpatialPolygonsDataFrame>, region = ...)`
  no longer works as of this version (@yutannihilation, #5244).

# ggplot2 3.4.3
This hotfix release addresses a version comparison change in r-devel. There are
no user-facing or breaking changes.


To generate a diff of this commit:
cvs rdiff -u -r1.7 -r1.8 pkgsrc/graphics/R-ggplot2/Makefile \
    pkgsrc/graphics/R-ggplot2/distinfo

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

Modified files:

Index: pkgsrc/graphics/R-ggplot2/Makefile
diff -u pkgsrc/graphics/R-ggplot2/Makefile:1.7 pkgsrc/graphics/R-ggplot2/Makefile:1.8
--- pkgsrc/graphics/R-ggplot2/Makefile:1.7      Sun Jun 11 15:05:51 2023
+++ pkgsrc/graphics/R-ggplot2/Makefile  Wed Jun  5 12:00:07 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.7 2023/06/11 15:05:51 mef Exp $
+# $NetBSD: Makefile,v 1.8 2024/06/05 12:00:07 mef Exp $
 
 R_PKGNAME=     ggplot2
-R_PKGVER=      3.4.2
+R_PKGVER=      3.5.1
 CATEGORIES=    graphics
 
 MAINTAINER=    minskim%NetBSD.org@localhost
Index: pkgsrc/graphics/R-ggplot2/distinfo
diff -u pkgsrc/graphics/R-ggplot2/distinfo:1.7 pkgsrc/graphics/R-ggplot2/distinfo:1.8
--- pkgsrc/graphics/R-ggplot2/distinfo:1.7      Sun Jun 11 15:05:51 2023
+++ pkgsrc/graphics/R-ggplot2/distinfo  Wed Jun  5 12:00:07 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.7 2023/06/11 15:05:51 mef Exp $
+$NetBSD: distinfo,v 1.8 2024/06/05 12:00:07 mef Exp $
 
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-Size (R/ggplot2_3.4.2.tar.gz) = 3153811 bytes
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