From 133043dd78b2e9853e86d5f5c5238cf2be40c200 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Fri, 6 Feb 2026 17:23:23 +0100 Subject: [PATCH 1/2] Prepare for CRAN submission - Add NEWS.md - Add R-CMD-check badge to README.md - Remove Remotes field from DESCRIPTION - Update cran-comments.md Co-Authored-By: Claude Opus 4.5 --- DESCRIPTION | 4 -- NEWS.md | 180 +++++++++++++++++++++++++++++++++++++++++++++++ README.md | 2 + cran-comments.md | 10 ++- 4 files changed, 189 insertions(+), 7 deletions(-) create mode 100644 NEWS.md diff --git a/DESCRIPTION b/DESCRIPTION index 5a23ccd..cf25af2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -67,7 +67,3 @@ LazyLoad: yes Encoding: UTF-8 RoxygenNote: 7.3.3 VignetteBuilder: knitr -Remotes: - github::bedapub/ribiosUtils, - github::bedapub/ribiosArg, - github::js229/Vennerable diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..87c9ac0 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,180 @@ +# ribiosPlot 1.3.0 + +* Initial CRAN submission +* Package prepared for CRAN submission with comprehensive documentation +* Depends on ribiosUtils (on CRAN) +* Optional Vennerable integration for users who install it separately + +# ribiosPlot 1.1.30 (2015-08-04) + +* Add `royalredgrayblue` and `royalbluegrayred` color palettes +* `plotPCA`: xlim/ylim parameters auto-adjust for text labels +* Add function `getLims` to get xlim/ylim values from vectors + +# ribiosPlot 1.1.29 (2015-03-13) + +* `compactPar` more flexible to accept and pass parameters to par + +# ribiosPlot 1.1.28 (2015-02-03) + +* Fix bug in heat function: return (n) + +# ribiosPlot 1.1.26 (2015-01-06) + +* Add `compactTrellis()` and `setCompactTrellis()` for compact publication figures +* Add function `p2asterisk` to map p values to asterisk symbols +* Use roxygen2 for documentation + +# ribiosPlot 1.1.25 (2014-07-30) + +* Add function `fcbrewer` for factor-matching colors +* Improved manual pages +* Rename `sqlayout` to `squareLayout` +* Rename `compPar` to `compactPar` + +# ribiosPlot 1.1.24 (2014-07-01) + +* `biosHeatmap`: cex main size better guessed + +# ribiosPlot 1.1.23 (2014-04-28) + +* Add `intRange` and `squareLayout` +* `pdf2png` works on UDIS machine + +# ribiosPlot 1.1.22 (2014-04-22) + +* Add `histMat` to visualize matrices with histograms +* Add `plotPCA` + +# ribiosPlot 1.1.20 (2014-01-28) + +* Add `qHist` and `xclipHist` histogram functions + +# ribiosPlot 1.1.19 (2014-01-23) + +* Add ribiosUtils to dependency list + +# ribiosPlot 1.1.18 (2014-01-22) + +* Add `pdf2png` to convert PDF to PNG + +# ribiosPlot 1.1.17 (2013-08-19) + +* Add `cyanblackyellow` and `yellowblackyan` color combinations +* Add `jitter.xyplot` + +# ribiosPlot 1.1.16 (2013-07-22) + +* `brewer.pal.factor` auto-adjusts color palette size +* PCA plotting functions refactored + +# ribiosPlot 1.1.15 (2013-02-22) + +* Update boxplot.Rscript with improved features + +# ribiosPlot 1.1.14 (2012-10-20) + +* Add `idev` and `ipdf` functions for plotting in Rscripts +* Add `blackyellowred` and `blackgoldred` color panels + +# ribiosPlot 1.1.13 (2012-09-11) + +* exprs-boxplot.Rscript: accepts tab-delimited and gct files + +# ribiosPlot 1.1.12 (2012-09-10) + +* exprs-boxplot.Rscript works with GCT files + +# ribiosPlot 1.1.11 (2012-08-22) + +* Bug fix: `boundNorm` works with NAs + +# ribiosPlot 1.1.10 (2012-06-07) + +* Fix typos in `brewer.pal.factor` and `brewer.pal.factorLevels` + +# ribiosPlot 1.1.9 (2012-06-06) + +* exprs-boxplot.Rscript: handle user-specified ylim values + +# ribiosPlot 1.1.8 (2012-05-23) + +* Distance function changed from dist to `robustDist` +* Add documentation for color functions +* Substantially updated `biosHeatmap` documentation + +# ribiosPlot 1.1.7 (2012-04-30) + +* coverage-plot.Rscript feature file improvements + +# ribiosPlot 1.1.6 (2012-04-15) + +* Add exprs-boxplot.Rscript for command line boxplots + +# ribiosPlot 1.1.5 (2012-04-02) + +* coverage-plot.Rscript supports sequence annotation + +# ribiosPlot 1.1.4 (2012-03-19) + +* Add -featurefile option to coverage-plot.Rscript +* Fix partial matching bug in `biosHeatmap` + +# ribiosPlot 1.1.3 (2012-03-09) + +* Add coverage-plot.Rscript + +# ribiosPlot 1.1.2 (2012-02-14) + +* biosHeatmap.Rscript uses Ward as default clustering method + +# ribiosPlot 1.1.1 (2011-12-08) + +* geneset_xyplot.Rscript improvements + +# ribiosPlot 1.1.0 (2011-12-02) + +* Add `whiteblueblackheat` to three-color palettes + +# ribiosPlot 1.0.9 (2011-11-23) + +* Add `whiteblack` and `blackwhite` to two-color palettes + +# ribiosPlot 1.0.8 (2011-11-22) + +* Add `guessWH` function for auto width/height ratio of heatmaps +* Margins automatically determined based on xlab/ylab + +# ribiosPlot 1.0.7 (2011-11-17) + +* biosHeatmap.Rscript: lwids and lheis options obsolete + +# ribiosPlot 1.0.6 (2011-11-16) + +* Data import taken over by ribiosIO::read_exprs_matrix +* Long titles wrapped in `biosHeatmap` + +# ribiosPlot 1.0.5 (2011-11-15) + +* Add Rscript subdirectory for plotting scripts + +# ribiosPlot 1.0.4 (2011-11-10) + +* Export `colorpanel` function + +# ribiosPlot 1.0.3 (2011-10-10) + +* Add zlim option to `biosHeatmap` + +# ribiosPlot 1.0.2 (2011-10-05) + +* Add `turyeb` color palette + +# ribiosPlot 1.0.1 (2011-10-04) + +* Margins automatically guessed +* Fine tuning of heatmap key plot parameters + +# ribiosPlot 1.0.0 (2011-09-20) + +* Initial release: refactor visualization functions from ribios package diff --git a/README.md b/README.md index 3e6d33e..ddcd179 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,8 @@ *ribiosPlot*: Data transformation and visualisation === +![R-CMD-check badge](https://github.com/bedapub/ribiosPlot/workflows/R-CMD-check/badge.svg) + ## What is *ribiosPlot*? *ribiosPlot* is a R package in the *ribios* suite that assists data transformation and visualization. diff --git a/cran-comments.md b/cran-comments.md index 0be06f6..0ab913a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -8,17 +8,21 @@ ## R CMD check results -0 errors | 0 warnings | 2 notes +0 errors | 0 warnings | 3 notes ### Notes explanation -1. **Unavailable namespace imported from by a ':::' call: 'Vennerable'** +1. **Suggests or Enhances not in mainstream repositories: ribiosArg, Vennerable** + - ribiosArg will be submitted to CRAN after ribiosUtils is accepted + - Vennerable is not on CRAN (maintained on GitHub) + +2. **Unavailable namespace imported from by a ':::' call: 'Vennerable'** The package enhances Vennerable (not on CRAN) with a modified Venn diagram plotting function. This functionality is optional and protected by `if(require("Vennerable"))`. Users who don't have Vennerable installed will simply not have access to this single function. -2. **Possibly unsafe calls: unlockBinding, assignInNamespace** +3. **Possibly unsafe calls: unlockBinding, assignInNamespace** These calls are used solely within the optional `plotVenn()` function to patch a layout issue in the Vennerable package. The function is only called when Vennerable is available and the user explicitly requests From 49753807f7c430ee03e9d2416712b252fc1d5e00 Mon Sep 17 00:00:00 2001 From: Jitao David Zhang Date: Fri, 6 Feb 2026 17:43:26 +0100 Subject: [PATCH 2/2] Use hard dependencies only in CI Skip ribiosArg (not yet on CRAN) and Vennerable (GitHub only) during dependency installation. These are optional Suggests/Enhances packages. Co-Authored-By: Claude Opus 4.5 --- .github/workflows/standard-ci-workflow.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/standard-ci-workflow.yml b/.github/workflows/standard-ci-workflow.yml index b58897d..133d9cb 100644 --- a/.github/workflows/standard-ci-workflow.yml +++ b/.github/workflows/standard-ci-workflow.yml @@ -44,6 +44,8 @@ jobs: with: extra-packages: any::rcmdcheck needs: check + # Skip ribiosArg (not yet on CRAN) and Vennerable (GitHub only) + dependencies: '"hard"' - uses: r-lib/actions/check-r-package@v2 with: