gggenomes 1.1.0 release - ggplot 4.0.0 compatibilty

Author: thackl

.Rbuildignore

@@ -9,4 +9,8 @@
 ^data-raw$
 ^pkgdown$
 ^LICENSE.md$
-^\.vscode$
+^\.vscode$
+^issues(/|$)
+^vignettes-manual-export$
+^cran-comments.md$
+^CRAN-SUBMISSION$

.github/workflows/main.yml

@@ -1,18 +1,18 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 on:
   push:
-    branches:
-      - main
-      - master
-      - develop
+    branches: [main, master, develop]
   pull_request:
-    branches:
-      - main
-      - master
-      - develop
+    branches: [main, master, develop]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -27,18 +27,23 @@ jobs:
           - {os: macos-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-latest, r: 'oldrel-4'}
+          
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      _R_CHECK_FORCE_SUGGESTS_: false
+      # Some packages might unavailable on the older versions, so let's ignore xref warnings
+      _R_CHECK_RD_XREFS_: false
+      # Runs vdiffr test only on the latest version of R
+      VDIFFR_RUN_TESTS: ${{ matrix.config.r == 'release' }}
+      VDIFFR_LOG_PATH: "../vdiffr.Rout.fail"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -50,9 +55,15 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck, doMC=?ignore
+          cache-version: 3
+          extra-packages: >
+            any::rcmdcheck,
+            any::Hmisc,
+            any::quantreg
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-build-vignettes","--no-manual")'
+          args: 'c("--ignore-vignettes","--no-manual")'

.gitignore

@@ -2,7 +2,7 @@
 .Rhistory
 .RData
 docs/
-org/
+issues/
 R-deprecated/
 data-raw/
 tests/

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.1.0
+Date: 2025-10-13 07:11:50 UTC
+SHA: 9d50a47e7bdeca13941100df7488fb8134ceb768

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gggenomes
 Title: A Grammar of Graphics for Comparative Genomics
-Version: 1.0.1
+Version: 1.1.0
 Authors@R: c(
   person("Thomas", "Hackl", email = "t.hackl@rug.nl", role = c("aut", "cre")),
   person("Markus J.", "Ankenbrand", email = "iimog@iimog.org", role = c("aut")),
@@ -16,11 +16,11 @@ URL: https://thackl.github.io/gggenomes/, https://github.com/thackl/gggenomes
 BugReports: https://github.com/thackl/gggenomes/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Depends:
-    R (>= 3.5.0),
+    R (>= 4.1.0),
     ggplot2 (>= 3.5.0),
 Imports:
     vctrs,
@@ -48,3 +48,4 @@ Suggests:
     knitr,
     ggrepel,
     IRanges,
+    rmarkdown

NAMESPACE

@@ -39,7 +39,6 @@ S3method(flip_strand,logical)
 S3method(flip_strand,numeric)
 S3method(get_seqs,gggenomes)
 S3method(get_seqs,gggenomes_layout)
-S3method(ggplot,gggenomes_layout)
 S3method(layout,gggenomes)
 S3method(layout,gggenomes_layout)
 S3method(makeContent,genetree)

News.md

@@ -0,0 +1,9 @@
+# gggenomes 1.1.0
+
+* Updated for **ggplot2 4.0** layout changes — restores full compatibility
+* Requires **R ≥ 4.1.0** (native pipe `|>` support)
+* Replaced deprecated `size` aesthetic in line geoms with `linewidth`
+* CI configuration refreshed for multi-platform testing
+* Examples guarded for missing optional packages in Windows oldrel builds (**Hmisc**, **ggtree**)
+* CITATION file updated (`bibentry()`/`person()`)
+* Minor typo and code clean-ups