[willgearty]

Bumps the minimum ggplot2 version in DESCRIPTION from 3.5.0 to 3.5.2, and adds a CI job that actually tests it.

deeptime imports ggh4x, and ggh4x 0.3.1 already has Depends: ggplot2 (>= 3.5.2). It also calls ggplot2::is_theme_element(), which doesn't exist before 3.5.2, so deeptime couldn't actually be used with ggplot2 3.5.0 or 3.5.1. This makes that requirement explicit.

• DESCRIPTION: ggplot2 (>= 3.5.0) → ggplot2 (>= 3.5.2)
• NEWS.md: notes the new requirement, in the same style as the previous ggplot2 bump in 2.0.0
• R-CMD-check.yaml:
  • Renames the ">= 3.5.2" matrix entry to release, which is what it installed in practice (the latest ggplot2, 4.0.3 in recent runs), so ggplot2 3.5.x was never tested.
  • Adds one job pinned to ggplot2 3.5.2 on ubuntu-latest with R release, via include:. It installs that exact version with remotes::install_version(), so the pre-4.0 test snapshots now run in CI.
  • The install step now only runs for pinned versions; for release, setup-r-dependencies already installs the current ggplot2.
  • The 3.5.2 job builds and checks without vignettes (--no-build-vignettes / --ignore-vignettes) and only fails on errors. Current versions of two suggested packages used in the vignettes require ggplot2 4.x: ggtree (Bioconductor 3.22) needs >= 4.0.0 and ggpattern needs >= 4.0.2. Skipping vignettes only produces a NOTE. Docs inherited from ggplot2 4.x also link to annotation_borders(), which 3.5.2 doesn't have, giving a Rd cross-reference WARNING. All other jobs keep the previous build options and still fail on warnings.
• Tests, so the 3.5.2 job only fails on known issues:
  • test-guides.R: adds skip_if_not_installed("ggtree") to the two tests that used ggtree without it ("guide_geo works with coord_geo_radial" and the second "ggtree scale works with only fossil taxa"). With ggplot2 3.5.2, ggtree can't load, so these errored instead of skipping.
  • coord_geo pre-4.0 snapshots (_snaps/coord_geo/): updates "stacked scales with single pos" and adds the missing "stacked scales on top/bottom" and "on left/right". The updated snapshot only gains empty clip-path groups; its text, positions and shapes are unchanged. The two new ones match their ggplot4/ counterparts in label text, positions and shapes.

No package code changes were needed: all existing version checks are packageVersion("ggplot2") > "3.5.2". I checked that the package installs with ggplot2 3.5.2, and that installing with ggplot2 3.5.0 now fails with "namespace 'ggplot2' 3.5.0 is already loaded, but >= 3.5.2 is required". Locally, test-coord_geo.R and test-guides.R pass with ggplot2 3.5.2 (with and without ggtree available) and with 4.0.3.

Things to know:

• The 3.5.2 job should only fail on the coord_trans_xy pre-4.0 snapshots until Fix coord_trans_xy() axis labels with ggplot2 < 4.0.0 #117 is merged (2 outdated and 3 missing; on CI a missing snapshot counts as a failure). The geom_text_clade tests are skipped in this job because ggtree can't load, so they don't depend on Fix geom_text_clade(text_geom = "label") with ggplot2 < 4.0.0 #120.
• Job names change, e.g. ubuntu-latest (release, ggplot2 >= 3.5.2) → ubuntu-latest (release, ggplot2 release). If branch protection on main requires checks by name, those settings will need updating.
• This touches the top of NEWS.md, as do Fix coord_trans_xy() gridlines #116, Fix coord_trans_xy() axis labels with ggplot2 < 4.0.0 #117 and Fix geom_text_clade(text_geom = "label") with ggplot2 < 4.0.0 #120, so whichever of them merges later will need a small merge of NEWS.md.

AI disclosure: Claude identified the problem and drafted the change.

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https://claude.ai/code/session_01A7zDoJJQSEuNmyB6xR3njB

[willgearty]

The new ubuntu-latest (release, ggplot2 3.5.2) job fails while building the vignettes, before any tests run. Current versions of two suggested packages already require ggplot2 4.x:

• ggtree (Bioconductor 3.22) requires ggplot2 >= 4.0.0, which breaks the ggarrange2 and phylogenies vignettes.
• ggpattern requires ggplot2 >= 4.0.2, which breaks the geo vignette.

I reproduced the rest of the check locally with ggplot2 3.5.2, without vignettes and with ggtree/ggpattern unavailable. Getting this job green would also need:

1. Building and checking without vignettes for this job, which only produces a NOTE.
2. error-on: "error" for this job. Docs inherited from ggplot2 4.x link to annotation_borders(), which ggplot2 3.5.2 doesn't have, so Rd cross-references give a WARNING.
3. The coord_trans_xy pre-4.0 snapshot fix from Fix coord_trans_xy() axis labels with ggplot2 < 4.0.0 #117 (2 failures).
4. skip_if_not_installed("ggtree") in two guides tests that use ggtree without it (test-guides.R:184 and :200).
5. A look at the pre-4.0 coord_geo "stacked scales with single pos" snapshot, and possibly the pre-4.0 pattern snapshots.

That's more than a version bump, so I'm checking with the maintainer before widening this PR.

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[willgearty]

Update after 2868b97: the ggplot2 3.5.2 job now gets past the vignettes and docs (the Rd cross-reference WARNING is reported but no longer fails the job), and only the tests fail. That's expected, since test fixes are being left to separate PRs. CI shows 10 failures, and on CI a missing snapshot counts as a failure:

• test-coord_trans_xy.R (5): 2 outdated and 3 missing pre-4.0 snapshots. All are fixed by Fix coord_trans_xy() axis labels with ggplot2 < 4.0.0 #117.
• test-coord_geo.R (3): the pre-4.0 "stacked scales with single pos" snapshot is outdated (line 88), and the "stacked scales on top/bottom" and "on left/right" snapshots only exist under ggplot4/ (lines 120 and 129). No PR covers these yet.
• test-guides.R (2, lines 184 and 200): these use ggtree without skip_if_not_installed("ggtree"), and ggtree can't load with ggplot2 3.5.2. No PR covers these yet.

The pattern snapshots pass on CI, so their earlier local failures were specific to my environment. The geom_text_clade tests are skipped in this job because ggtree can't load.

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