Devel

.Rbuildignore

@@ -17,3 +17,4 @@
 ^cran-comments\.md$
 ^bin$
 ^CRAN-SUBMISSION$
+cran-feedback.md

.github/workflows/standard-ci-workflow.yml

@@ -39,13 +39,21 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           use-public-rspm: true
+          extra-repositories: https://bedapub.r-universe.dev
+
+      - name: Install system dependencies (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install jpeg
+          mkdir -p ~/.R
+          echo "CPPFLAGS += -I$(brew --prefix jpeg)/include" >> ~/.R/Makevars
+          echo "LDFLAGS += -L$(brew --prefix jpeg)/lib" >> ~/.R/Makevars
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::testthat, any::Vennerable, any::ribiosArg
           needs: check
-          # Skip ribiosArg (not yet on CRAN) and Vennerable (GitHub only)
-          dependencies: '"hard"'
+          dependencies: '"soft"'
 
       - uses: r-lib/actions/check-r-package@v2
         with:

DESCRIPTION

@@ -2,14 +2,14 @@ Package: ribiosPlot
 Type: Package
 Title: Plotting Module of the 'ribios' Software Suite
 Version: 1.3.0
-Date: 2026-01-24
+Date: 2026-02-20
 Authors@R:
   c(person(given = "Jitao David",
            family = "Zhang",
            role = c("aut", "cre", "ctb"),
            email = "jitao_david.zhang@roche.com",
            comment = c(ORCID="0000-0002-3085-0909")))
-Description: Provides data structures and functions for data transformation and visualization in computational biology in drug discovery. Includes heatmaps, color schemes, PCA plots, and various plotting utilities.
+Description: Provides data structures and functions for data transformation and visualization in computational biology in drug discovery as part of the 'ribios' software suite. Zhang (2025) <https://github.com/bedapub/ribiosPlot>.
 Depends:
     R (>= 3.4.0)
 Imports:

R/cascadePlot.R

@@ -4,6 +4,7 @@
 #' @param x Numeric matrix
 #' @param na.rm Logical. Should missing values (including NaN) be omitted from
 #' the calculations?
+#' @return A numeric vector of length \code{nrow(x)} with the row-wise variances.
 #' @keywords internal
 #' @examples
 #' 

R/colors.R

@@ -39,8 +39,8 @@
 #'   image(z=matrix(1:100, ncol=1), col=col, xaxt="n", yaxt="n")
 #' }
 #'  
-#' par(mfrow=c(3,3))
-#'  
+#' oldpar <- par(mfrow=c(3,3))
+#'
 #' # two colors only:
 #' showpanel(colorpanel(8,low="red",high="green"))
 #'  
@@ -57,7 +57,8 @@
 #' 
 #' showpanel(royalbluered(64))
 #' showpanel(royalredblue(64))
-#' 
+#' par(oldpar)
+#'
 #' @importFrom ribiosUtils isOdd
 #' @export colorpanel
 colorpanel <- function (n, low, mid, high) {

R/pcaPlots.R

@@ -217,7 +217,8 @@ plotPCA <- function(x, choices, ...) UseMethod("plotPCA")
 #' rop <- par(mfrow=c(1,2), pty="s")
 #' plotPCA(testPCA, choices=c(1,2), grid=TRUE, points=pointsList, text=textList)
 #' plotPCA(testPCA, choices=c(2,3), grid=TRUE, points=pointsList, text=textList)
-#' 
+#' par(rop)
+#'
 #' @export
 plotPCA.prcomp <- function(x,
                            choices=c(1,2),

R/utils.R

@@ -244,16 +244,17 @@ intRange <- function(x, na.rm=TRUE) {
 #' limits; if set to 1 the whole range is used.
 #' @param symm logical value; if set to \code{TRUE}, the range will be
 #' symmetric around zero
+#' @return A numeric vector of length 2 giving the lower and upper axis limits.
 #' @examples
-#' 
+#'
 #' myX <- rnorm(100, mean=1)
 #' myY <- rnorm(100)
 #' myLim <- getLims(myX, myY, perc=0.99)
 #' plot(myX, myY, xlim=myLim, ylim=myLim)
 #' mySymmLim <- getLims(myX, myY, perc=0.99, symm=TRUE)
 #' plot(myX, myY, xlim=myLim, ylim=mySymmLim)
-#' 
-#' 
+#'
+#'
 #' @export getLims
 getLims <- function(..., perc=0.99, symm=TRUE) {
     lower <- (1-perc)/2

cran-feedback.md

@@ -0,0 +1,38 @@
+Please always explain all acronyms in the description text. -> PCA
+For more details:
+<https://contributor.r-project.org/cran-cookbook/description_issues.html#explaining-acronyms>
+
+If there are references describing the methods in your package, please
+add these in the description field of your DESCRIPTION file in the form
+authors (year) <doi:...>
+authors (year, ISBN:...)
+or if those are not available: <https:...>
+with no space after 'doi:', 'https:' and angle brackets for
+auto-linking. (If you want to add a title as well please put it in
+quotes: "Title")
+For more details:
+<https://contributor.r-project.org/cran-cookbook/description_issues.html#references>
+
+Please add \value to .Rd files regarding exported methods and explain
+the functions results in the documentation. Please write about the
+structure of the output (class) and also what the output means. (If a
+function does not return a value, please document that too, e.g.
+\value{No return value, called for side effects} or similar)
+For more details:
+<https://contributor.r-project.org/cran-cookbook/docs_issues.html#missing-value-tags-in-.rd-files>
+
+-> Missing Rd-tags:
+      getLims.Rd: \value
+      rowVars.Rd: \value
+
+Please always make sure to reset to user's options(), working directory
+or par() after you changed it in examples and vignettes and demos.
+e.g.:
+oldpar <- par(mfrow = c(1,2))
+...
+par(oldpar)
+
+-> man/colorpanel.Rd, man/plotPCA.prcomp.Rd
+
+For more details:
+<https://contributor.r-project.org/cran-cookbook/code_issues.html#change-of-options-graphical-parameters-and-working-directory>