Log message:
(graphics/R-ggplot2) Updated 3.3.5 to 3.4.2

# ggplot2 3.4.2
This is a hotfix release anticipating changes in r-devel, but folds in upkeep
changes and a few bug fixes as well.

## Minor improvements

* Various type checks and their messages have been standardised
  (@teunbrand, #4834).

* ggplot2 now uses `scales::DiscreteRange` and `scales::ContinuousRange`, which
  are available to write scale extensions from scratch (@teunbrand, #2710).

* The `layer_data()`, `layer_scales()` and `layer_grob()` now have the default
  `plot = last_plot()` (@teunbrand, #5166).

* The `datetime_scale()` scale constructor is now exported for use in extension
  packages (@teunbrand, #4701).

## Bug fixes

* `update_geom_defaults()` and `update_stat_defaults()` now return properly
  classed objects and have updated docs (@dkahle, #5146).

* For the purposes of checking required or non-missing aesthetics, character
  vectors are no longer considered non-finite (@teunbrand, @4284).

* `annotation_logticks()` skips drawing ticks when the scale range is non-finite
  instead of throwing an error (@teunbrand, #5229).

* Fixed spurious warnings when the `weight` was used in `stat_bin_2d()`,
  `stat_boxplot()`, `stat_contour()`, `stat_bin_hex()` and `stat_quantile()`
  (@teunbrand, #5216).

* To prevent changing the plotting order, `stat_sf()` is now computed per panel
  instead of per group (@teunbrand, #4340).

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

* `geom_text()` drops observations where `angle = NA` instead of throwing an
  error (@teunbrand, #2757).

# ggplot2 3.4.1
This is a small release focusing on fixing regressions in the 3.4.0 release
and minor polishes.

## Breaking changes

* The computed variable `y` in `stat_ecdf()` has been superseded by `ecdf` to
  prevent incorrect scale transformations (@teunbrand, #5113 and #5112).

## New features

* Added `scale_linewidth_manual()` and `scale_linewidth_identity()` to support
  the `linewidth` aesthetic (@teunbrand, #5050).

* `ggsave()` warns when multiple `filename`s are given, and only writes to the
  first file (@teunbrand, #5114).

## Bug fixes

* Fixed a regression in `geom_hex()` where aesthetics were replicated across
  bins (@thomasp85, #5037 and #5044).

* Using two ordered factors as facetting variables in
  `facet_grid(..., as.table = FALSE)` now throws a warning instead of an
  error (@teunbrand, #5109).

* Fixed misbehaviour of `draw_key_boxplot()` and `draw_key_crossbar()` with
  skewed key aspect ratio (@teunbrand, #5082).

* Fixed spurious warning when `weight` aesthetic was used in `stat_smooth()`
  (@teunbrand based on @clauswilke's suggestion, #5053).

* The `lwd` alias is now correctly replaced by `linewidth` instead of `size`
  (@teunbrand based on @clauswilke's suggestion #5051).

* Fixed a regression in `Coord$train_panel_guides()` where names of guides were
  dropped (@maxsutton, #5063).

In binned scales:

* Automatic breaks should no longer be out-of-bounds, and automatic limits are
  adjusted to include breaks (@teunbrand, #5082).

* Zero-range limits no longer throw an error and are treated akin to continuous
  scales with zero-range limits (@teunbrand, #5066).

* The `trans = "date"` and `trans = "time"` transformations \ 
were made compatible
  (@teunbrand, #4217).

# ggplot2 3.4.0
This is a minor release focusing on tightening up the internals and ironing out
some inconsistencies in the API. The biggest change is the addition of the
`linewidth` aesthetic that takes of sizing the width of any line from `size`.
This change, while attempting to be as non-breaking as possible, has the
potential to change the look of some of your plots.

Other notable changes is a complete redo of the error and warning messaging in
ggplot2 using the cli package. Messaging is now better contextualised and it
should be easier to identify which layer an error is coming from. Last, we have
now made the switch to using the vctrs package internally which means that
support for vctrs classes as variables should improve, along with some small
gains in rendering speed.

## Breaking changes

* A `linewidth` aesthetic has been introduced and supersedes the `size`
  aesthetic for scaling the width of lines in line based geoms. `size` will
  remain functioning but deprecated for these geoms and it is recommended to
  update all code to reflect the new aesthetic. For geoms that have _both_ point
  sizing and linewidth sizing (`geom_pointrange()` and `geom_sf`) `size` now
  **only** refers to sizing of points which can leads to a visual change in old
  code (@thomasp85, #3672)

* The default line width for polygons in `geom_sf()` have been decreased to 0.2
  to reflect that this is usually used for demarking borders where a thinner
  line is better suited. This change was made since we already induced a
  visual change in `geom_sf()` with the introduction of the `linewidth`
  aesthetic.

* The dot-dot notation (`..var..`) and `stat()`, which have been superseded by
  `after_stat()`, are now formally deprecated (@yutannihilation, #3693).

* `qplot()` is now formally deprecated (@yutannihilation, #3956).

* `stage()` now properly refers to the values without scale transformations for
  the stage of `after_stat`. If your code requires the scaled version of the
  values for some reason, you have to apply the same transformation by yourself,
  e.g. `sqrt()` for `scale_{x,y}_sqrt()` (@yutannihilation and @teunbrand, #4155).

* Use `rlang::hash()` instead of `digest::digest()`. This update may lead to
  changes in the automatic sorting of legends. In order to enforce a specific
  legend order use the `order` argument in the guide. (@thomasp85, #4458)

* referring to `x` in backquoted expressions with `label_bquote()` is no longer
  possible.

* The `ticks.linewidth` and `frame.linewidth` parameters of `guide_colourbar()`
  are now multiplied with `.pt` like elsewhere in ggplot2. It can cause visual
  changes when these arguments are not the defaults and these changes can be
  restored to their previous behaviour by adding `/ .pt` (@teunbrand #4314).

* `scale_*_viridis_b()` now uses the full range of the viridis scales
  (@gregleleu, #4737)

## New features

* `geom_col()` and `geom_bar()` gain a new `just` argument. This is set to `0.5`
  by default; use `just = 0`/`just = 1` to place columns on the left/right
  of the axis breaks.
  (@wurli, #4899)

* `geom_density()` and `stat_density()` now support `bounds` argument
  to estimate density with boundary correction (@echasnovski, #4013).

* ggplot now checks during statistical transformations whether any data
  columns were dropped and warns about this. If stats intend to drop
  data columns they can declare them in the new field `dropped_aes`.
  (@clauswilke, #3250)

* `...` supports `rlang::list2` dynamic dots in all public functions.
  (@mone27, #4764)

* `theme()` now has a `strip.clip` argument, that can be set to `"off"` to
  prevent the clipping of strip text and background borders (@teunbrand, #4118)

* `geom_contour()` now accepts a function in the `breaks` argument
  (@eliocamp, #4652).

## Minor improvements and bug fixes

* Fix a bug in `position_jitter()` where infinity values were dropped (@javlon,
  #4790).

* `geom_linerange()` now respects the `na.rm` argument (#4927, @thomasp85)

* Improve the support for `guide_axis()` on `coord_trans()`
  (@yutannihilation, #3959)

* Added `stat_align()` to align data without common x-coordinates prior to
  stacking. This is now the default stat for `geom_area()` (@thomasp85, #4850)

* Fix a bug in `stat_contour_filled()` where break value differences below a
  certain number of digits would cause the computations to fail (@thomasp85,
  #4874)

* Secondary axis ticks are now positioned more precisely, removing small visual
  artefacts with alignment between grid and ticks (@thomasp85, #3576)

* Improve `stat_function` documentation regarding `xlim` argument.
  (@92amartins, #4474)

* Fix various issues with how `labels`, `breaks`, `limits`, and `show.limits`
  interact in the different binning guides (@thomasp85, #4831)

* Automatic break calculation now squishes the scale limits to the domain
  of the transformation. This allows `scale_{x/y}_sqrt()` to find breaks at 0
  when appropriate (@teunbrand, #980).

* Using multiple modified aesthetics correctly will no longer trigger warnings.
  If used incorrectly, the warning will now report the duplicated aesthetic
  instead of `NA` (@teunbrand, #4707).

* `aes()` now supports the `!!!` operator in its first two arguments
  (#2675). Thanks to @yutannihilation and @teunbrand for draft
  implementations.

* Require rlang >= 1.0.0 (@billybarc, #4797)

* `geom_violin()` no longer issues "collapsing to unique 'x' values" \ 
warning
  (@bersbersbers, #4455)

* `annotate()` now documents unsupported geoms (`geom_abline()`, `geom_hline()`
  and `geom_vline()`), and warns when they are requested (@mikmart, #4719)

* `presidential` dataset now includes Trump's presidency (@bkmgit, #4703).

* `position_stack()` now works fully with `geom_text()` (@thomasp85, #4367)

* `geom_tile()` now correctly recognises missing data in `xmin`, `xmax`, `ymin`,
  and `ymax` (@thomasp85 and @sigmapi, #4495)

* `geom_hex()` will now use the binwidth from `stat_bin_hex()` if present,
  instead of deriving it (@thomasp85, #4580)

* `geom_hex()` now works on non-linear coordinate systems (@thomasp85)

* Fixed a bug throwing errors when trying to render an empty plot with secondary
  axes (@thomasp85, #4509)

* Axes are now added correctly in `facet_wrap()` when `as.table = FALSE`
  (@thomasp85, #4553)

* Better compatibility of custom device functions in `ggsave()`
  (@thomasp85, #4539)

* Binning scales are now more resilient to calculated limits that ends up being
  `NaN` after transformations (@thomasp85, #4510)

* Strip padding in `facet_grid()` is now only in effect if
  `strip.placement = "outside"` _and_ an axis is present between the \ 
strip and
  the panel (@thomasp85, #4610)

* Aesthetics of length 1 are now recycled to 0 if the length of the data is 0
  (@thomasp85, #4588)

* Setting `size = NA` will no longer cause `guide_legend()` to error
  (@thomasp85, #4559)

* Setting `stroke` to `NA` in `geom_point()` will no longer impair the sizing of
  the points (@thomasp85, #4624)

* `stat_bin_2d()` now correctly recognises the `weight` aesthetic
  (@thomasp85, #4646)

* All geoms now have consistent exposure of linejoin and lineend parameters, and
  the guide keys will now respect these settings (@thomasp85, #4653)

* `geom_sf()` now respects `arrow` parameter for lines (@jakeruss, #4659)

* Updated documentation for `print.ggplot` to reflect that it returns
  the original plot, not the result of `ggplot_build()`. (@r2evans, #4390)

* `scale_*_manual()` no longer displays extra legend keys, or changes their
  order, when a named `values` argument has more items than the data. To display
  all `values` on the legend instead, use
  `scale_*_manual(values = vals, limits = names(vals))`. (@teunbrand, @banfai,
  #4511, #4534)

* Updated documentation for `geom_contour()` to correctly reflect argument
  precedence between `bins` and `binwidth`. (@eliocamp, #4651)

* Dots in `geom_dotplot()` are now correctly aligned to the baseline when
  `stackratio != 1` and `stackdir != "up"` (@mjskay, #4614)

* Key glyphs for `geom_boxplot()`, `geom_crossbar()`, `geom_pointrange()`, and
  `geom_linerange()` are now orientation-aware (@mjskay, #4732)

* Updated documentation for `geom_smooth()` to more clearly describe effects of
  the `fullrange` parameter (@thoolihan, #4399).

# ggplot2 3.3.6
This is a very small release only applying an internal change to comply with
R 4.2 and its deprecation of `default.stringsAsFactors()`. There are no user
facing changes and no breaking changes.

Log message:
graphics: Replace RMD160 checksums with BLAKE2s checksums

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

Log message:
graphics: Remove SHA1 hashes for distfiles

Log message:
(graphics/R-ggplot2) Updated 3.2.0 to 3.3.0

# ggplot2 3.3.3
This is a small patch release mainly intended to address changes in R and CRAN.
It further changes the licensing model of ggplot2 to an MIT license.

* Update the ggplot2 licence to an MIT license (#4231, #4232, #4233, and #4281)
* Use vdiffr conditionally so ggplot2 can be tested on systems without vdiffr
* Update tests to work with the new `all.equal()` defaults in R >4.0.3

# ggplot2 3.3.2
This is a small release focusing on fixing regressions introduced in 3.3.1.

* Added an `outside` option to `annotation_logticks()` that places tick marks
  outside of the plot bounds. (#3783, @kbodwin)

* `annotation_raster()` adds support for native rasters. For large rasters,
  native rasters render significantly faster than arrays (@kent37, #3388)

* Facet strips now have dedicated position-dependent theme elements
  (`strip.text.x.top`, `strip.text.x.bottom`, `strip.text.y.left`,
  `strip.text.y.right`) that inherit from `strip.text.x` and `strip.text.y`,
  respectively. As a consequence, some theme stylings now need to be applied to
  the position-dependent elements rather than to the parent elements. This
  change was already introduced in ggplot2 3.3.0 but not listed in the
  changelog. (@thomasp85, #3683)

* Facets now handle layers containing no data (@yutannihilation, #3853).

* A newly added geom `geom_density_2d_filled()` and associated stat
  `stat_density_2d_filled()` can draw filled density contours
  (@clauswilke, #3846).

* A newly added `geom_function()` is now recommended to use in conjunction
  with/instead of `stat_function()`. In addition, `stat_function()` now
  works with transformed y axes, e.g. `scale_y_log10()`, and in plots
  containing no other data or layers (@clauswilke, #3611, #3905, #3983).

* Fixed a bug in `geom_sf()` that caused problems with legend-type
  autodetection (@clauswilke, #3963).

* Support graphics devices that use the `file` argument instead of `fileneame`
  in `ggsave()` (@bwiernik, #3810)

* Default discrete color scales are now configurable through the `options()` of
  `ggplot2.discrete.colour` and `ggplot2.discrete.fill`. When set to a character
  vector of colour codes (or list of character vectors)  with sufficient length,
  these colours are used for the default scale. See `help(scale_colour_discrete)`
  for more details and examples (@cpsievert, #3833).

* Default continuous colour scales (i.e., the `options()`
  `ggplot2.continuous.colour` and `ggplot2.continuous.fill`, which inform the
  `type` argument of `scale_fill_continuous()` and `scale_colour_continuous()`)
  now accept a function, which allows more control over these default
  `continuous_scale()`s (@cpsievert, #3827).

* A bug was fixed in `stat_contour()` when calculating breaks based on
  the `bins` argument (@clauswilke, #3879, #4004).

* Data columns can now contain `Vector` S4 objects, which are widely used in the
  Bioconductor project. (@teunbrand, #3837)

# ggplot2 3.3.1

This is a small release with no code change. It removes all malicious links to a
site that got hijacked from the readme and pkgdown site.

# ggplot2 3.3.0

This is a minor release but does contain a range of substantial new features,
along with the standard bug fixes. The release contains a few visual breaking
changes, along with breaking changes for extension developers due to a shift in
internal representation of the position scales and their axes. No user breaking
changes are included.

This release also adds Dewey Dunnington (@paleolimbot) to the core team.

## Breaking changes
There are no user-facing breaking changes, but a change in some internal
representations that extension developers may have relied on, along with a few
breaking visual changes which may cause visual tests in downstream packages to
fail.

* The `panel_params` field in the `Layout` now contains a list of list of
  `ViewScale` objects, describing the trained coordinate system scales, instead
  of the list object used before. Any extensions that use this field will likely
  break, as will unit tests that checks aspects of this.

* `element_text()` now issues a warning when vectorized arguments are provided,
  as in `colour = c("red", "green", "blue")`. Such \ 
use is discouraged and not
  officially supported (@clauswilke, #3492).

* Changed `theme_grey()` setting for legend key so that it creates no border
  (`NA`) rather than drawing a white one. (@annennenne, #3180)

* `geom_ribbon()` now draws separate lines for the upper and lower intervals if
  `colour` is mapped. Similarly, `geom_area()` and `geom_density()` now draw
  the upper lines only in the same case by default. If you want old-style full
  stroking, use `outline.type = "full"` (@yutannihilation, #3503 / \ 
@thomasp85, #3708).

## New features

* The evaluation time of aesthetics can now be controlled to a finer degree.
  `after_stat()` supersedes the use of `stat()` and `..var..`-notation, and is
  joined by `after_scale()` to allow for mapping to scaled aesthetic values.
  Remapping of the same aesthetic is now supported with `stage()`, so you can
  map a data variable to a stat aesthetic, and remap the same aesthetic to
  something else after statistical transformation (@thomasp85, #3534)

* All `coord_*()` functions with `xlim` and `ylim` arguments now accept
  vectors with `NA` as a placeholder for the minimum or maximum value
  (e.g., `ylim = c(0, NA)` would zoom the y-axis from 0 to the
  maximum value observed in the data). This mimics the behaviour
  of the `limits` argument in continuous scale functions
  (@paleolimbot, #2907).

* Allowed reversing of discrete scales by re-writing `get_limits()`
  (@AnneLyng, #3115)

* All geoms and stats that had a direction (i.e. where the x and y axes had
  different interpretation), can now freely choose their direction, instead of
  relying on `coord_flip()`. The direction is deduced from the aesthetic
  mapping, but can also be specified directly with the new `orientation`
  argument (@thomasp85, #3506).

* Position guides can now be customized using the new `guide_axis()`, which can
  be passed to position `scale_*()` functions or via `guides()`. The new axis
  guide (`guide_axis()`) comes with arguments `check.overlap` (automatic removal
  of overlapping labels), `angle` (easy rotation of axis labels), and
  `n.dodge` (dodge labels into multiple rows/columns) (@paleolimbot, #3322).

* A new scale type has been added, that allows binning of aesthetics at the
  scale level. It has versions for both position and non-position aesthetics and
  comes with two new guides (`guide_bins` and `guide_coloursteps`)
  (@thomasp85, #3096)

* `scale_x_continuous()` and `scale_y_continuous()` gains an `n.breaks` argument
  guiding the number of automatic generated breaks (@thomasp85, #3102)

* Added `stat_contour_filled()` and `geom_contour_filled()`, which compute
  and draw filled contours of gridded data (@paleolimbot, #3044).
  `geom_contour()` and `stat_contour()` now use the isoband package
  to compute contour lines. The `complete` parameter (which was undocumented
  and has been unused for at least four years) was removed (@paleolimbot, #3044).

* Themes have gained two new parameters, `plot.title.position` and
  `plot.caption.position`, that can be used to customize how plot
  title/subtitle and plot caption are positioned relative to the overall plot
  (@clauswilke, #3252).

## Extensions

* `Geom` now gains a `setup_params()` method in line with the other ggproto
  classes (@thomasp85, #3509)

* The newly added function `register_theme_elements()` now allows developers
  of extension packages to define their own new theme elements and place them
  into the ggplot2 element tree (@clauswilke, #2540).

## Minor improvements and bug fixes

* `coord_trans()` now draws second axes and accepts `xlim`, `ylim`,
  and `expand` arguments to bring it up to feature parity with
  `coord_cartesian()`. The `xtrans` and `ytrans` arguments that were
  deprecated in version 1.0.1 in favour of `x` and `y`
  were removed (@paleolimbot, #2990).

* `coord_trans()` now calculates breaks using the expanded range
  (previously these were calculated using the unexpanded range,
  which resulted in differences between plots made with `coord_trans()`
  and those made with `coord_cartesian()`). The expansion for discrete axes
  in `coord_trans()` was also updated such that it behaves identically
  to that in `coord_cartesian()` (@paleolimbot, #3338).

* `expand_scale()` was deprecated in favour of `expansion()` for setting
  the `expand` argument of `x` and `y` scales (@paleolimbot).

* `geom_abline()`, `geom_hline()`, and `geom_vline()` now issue
  more informative warnings when supplied with set aesthetics
  (i.e., `slope`, `intercept`, `yintercept`, and/or `xintercept`)
  and mapped aesthetics (i.e., `data` and/or `mapping`).

* Fix a bug in `geom_raster()` that squeezed the image when it went outside
  scale limits (#3539, @thomasp85)

* `geom_sf()` now determines the legend type automatically (@microly, #3646).

* `geom_sf()` now removes rows that can't be plotted due to `NA` aesthetics
  (#3546, @thomasp85)

* `geom_sf()` now applies alpha to linestring geometries
  (#3589, @yutannihilation).

* `gg_dep()` was deprecated (@perezp44, #3382).

* Added function `ggplot_add.by()` for lists created with `by()`, allowing such
  lists to be added to ggplot objects (#2734, @Maschette)

* ggplot2 no longer depends on reshape2, which means that it no longer
  (recursively) needs plyr, stringr, or stringi packages.

* Increase the default `nbin` of `guide_colourbar()` to place the ticks more
  precisely (#3508, @yutannihilation).

* `manual_scale()` now matches `values` with the order of `breaks` whenever
  `values` is an unnamed vector. Previously, unnamed `values` would match with
  the limits of the scale and ignore the order of any `breaks` provided. Note
  that this may change the appearance of plots that previously relied on the
  unordered behaviour (#2429, @idno0001).

* `scale_manual_*(limits = ...)` now actually limits the scale (#3262,
  @yutannihilation).

* Fix a bug when `show.legend` is a named logical vector
  (#3461, @yutannihilation).

* Added weight aesthetic option to `stat_density()` and made scaling of
  weights the default (@annennenne, #2902)

* `stat_density2d()` can now take an `adjust` parameter to scale the default
  bandwidth. (#2860, @haleyjeppson)

* `stat_smooth()` uses `REML` by default, if `method = "gam"` and
  `gam`'s method is not specified (@ikosmidis, #2630).

* stacking text when calculating the labels and the y axis with
  `stat_summary()` now works (@ikosmidis, #2709)

* `stat_summary()` and related functions now support rlang-style lambda functions
  (#3568, @dkahle).

* The data mask pronoun, `.data`, is now stripped from default labels.

* Addition of partial themes to plots has been made more predictable;
  stepwise addition of individual partial themes is now equivalent to
  addition of multple theme elements at once (@clauswilke, #3039).

* Facets now don't fail even when some variable in the spec are not available
  in all layers (@yutannihilation, #2963).

# ggplot2 3.2.1

This is a patch release fixing a few regressions introduced in 3.2.0 as well as
fixing some unit tests that broke due to upstream changes.

* `position_stack()` no longer changes the order of the input data. Changes to
  the internal behaviour of `geom_ribbon()` made this reordering problematic
  with ribbons that spanned `y = 0` (#3471)
* Using `qplot()` with a single positional aesthetic will no longer title the
  non-specified scale as `"NULL"` (#3473)
* Fixes unit tests for sf graticule labels caused by chages to sf

Log message:
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

Log message:
Remove MASTER_SITES= from individual R package Makefiles.

Each R package should include ../../math/R/Makefile.extension, which also
defines MASTER_SITES.  Consequently, it is redundant for the individual
packages to do the same.  Package-specific definitions also prevent
redefining MASTER_SITES in a single common place.

Log message:
graphics/R-ggplot2: Import version 2.2.1

A system for 'declaratively' creating graphics, based on "The Grammar
of Graphics". You provide the data, tell 'ggplot2' how to map
variables to aesthetics, what graphical primitives to use, and it
takes care of the details.