Devel

.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:

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

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

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.

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