Merge pull request #48 from m-jahn/dev

various fixes for CRAN release 0.1.2

Author: m-jahn

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: WeightedTreemaps
 Title: Generate and Plot Voronoi or Sunburst Treemaps from Hierarchical
     Data
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
     person("Michael", "Jahn", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-3913-153X")),

NEWS.md

@@ -1,5 +1,7 @@
+# WeightedTreemaps 0.1.2
+
 # WeightedTreemaps 0.1.1
 
 - The package was prepared for release on CRAN
 - A Shiny app for generating treemaps from custom data is now
-available at [Shinyapps.io](https://m-jahn.shinyapps.io/ShinyTreemaps/)
+available at [Shinyapps.io](https://m-jahn.shinyapps.io/ShinyTreemaps/)

R/drawTreemap.R

@@ -75,41 +75,44 @@
 #'   the input for the drawing function
 #'
 #' @examples
-#' # load example data
-#' data(mtcars)
-#' mtcars$car_name = gsub(" ", "\n", row.names(mtcars))
+#' # load package
+#' library(WeightedTreemaps)
 #'
-#' # generate treemap; set seed to obtain same pattern every time
+#' # generate dummy data
+#' df <- data.frame(
+#'   A = rep(c("abcd", "efgh"), each = 4),
+#'   B = letters[1:8],
+#'   size = c(37, 52, 58, 27, 49, 44, 34, 45)
+#' )
+#'
+#' # compute treemap
 #' tm <- voronoiTreemap(
-#'   data = mtcars,
-#'   levels = c("gear", "car_name"),
-#'   cell_size = "wt",
-#'   shape = "rounded_rect",
+#'   data = df,
+#'   levels = c("B"),
+#'   cell_size = "size",
+#'   shape = "circle",
+#'   positioning = "regular",
 #'   seed = 123
 #' )
 #'
-#' # draw treemap
-#' drawTreemap(tm, label_size = 2)
+#' # plot treemap with each cell colored by name (default)
+#' drawTreemap(tm, label_size = 1, color_type = "categorical")
 #'
-#' # draw different variants of the same treemap on one page using
-#' # the 'layout' and 'position' arguments (indicating rows and columns)
-#' drawTreemap(tm, title = "treemap 1", label_size = 2,
-#'   color_type = "categorical", color_level = 1,
-#'   layout = c(1,3), position = c(1, 1))
+#' # plot treemap with each cell colored by name, but larger cells
+#' # lighter and smaller cells darker
+#' drawTreemap(tm, label_size = 1, color_type = "both")
 #'
-#' drawTreemap(tm, title = "treemap 2", label_size = 2,
-#'   color_type = "categorical", color_level = 2, border_size = 3,
-#'   add = TRUE, layout = c(1,3), position = c(1, 2))
-#'
-#' drawTreemap(tm, title = "treemap 3", label_size = 2,
-#'   color_type = "cell_size", color_level = 2,
-#'   color_palette = heat.colors(10),
-#'   border_color = grey(0.4), label_color = grey(0.4),
-#'   add = TRUE, layout = c(1,3), position = c(1, 3),
-#'   title_color = "black")
+#' # plot treemap with different color palette and style
+#' drawTreemap(tm, label_size = 1, label_color = grey(0.3),
+#'             border_color = grey(0.3), color_palette = heat.colors(6)
+#' )
 #'
 #' # ---------------------------------------------
 #'
+#' # load example data
+#' data(mtcars)
+#' mtcars$car_name = gsub(" ", "\n", row.names(mtcars))
+#'
 #' # generate sunburst treemap
 #' tm <- sunburstTreemap(
 #'   data = mtcars,

R/voronoiTreemap.R

@@ -81,38 +81,37 @@
 #' @seealso \code{\link{drawTreemap}} for drawing the treemap.
 #'
 #' @examples
-#' # load example data
-#' data(mtcars)
-#' mtcars$car_name = gsub(" ", "\n", row.names(mtcars))
+#' # load package
+#' library(WeightedTreemaps)
 #'
-#' # generate treemap; set seed to obtain same pattern every time
+#' # generate dummy data
+#' df <- data.frame(
+#'   A = rep(c("abcd", "efgh"), each = 4),
+#'   B = letters[1:8],
+#'   size = c(37, 52, 58, 27, 49, 44, 34, 45)
+#' )
+#'
+#' # compute treemap
 #' tm <- voronoiTreemap(
-#'   data = mtcars,
-#'   levels = c("gear", "car_name"),
-#'   cell_size = "wt",
-#'   shape = "rounded_rect",
+#'   data = df,
+#'   levels = c("B"),
+#'   cell_size = "size",
+#'   shape = "circle",
+#'   positioning = "regular",
 #'   seed = 123
 #' )
 #'
-#' # draw treemap
-#' drawTreemap(tm, label_size = 2)
+#' # plot treemap with each cell colored by name (default)
+#' drawTreemap(tm, label_size = 1, color_type = "categorical")
 #'
-#' # draw different variants of the same treemap on one page using
-#' # the 'layout' and 'position' arguments (indicating rows and columns)
-#' drawTreemap(tm, title = "treemap 1", label_size = 2,
-#'   color_type = "categorical", color_level = 1,
-#'   layout = c(1,3), position = c(1, 1))
+#' # plot treemap with each cell colored by name, but larger cells
+#' # lighter and smaller cells darker
+#' drawTreemap(tm, label_size = 1, color_type = "both")
 #'
-#' drawTreemap(tm, title = "treemap 2", label_size = 2,
-#'   color_type = "categorical", color_level = 2, border_size = 3,
-#'   add = TRUE, layout = c(1,3), position = c(1, 2))
-#'
-#' drawTreemap(tm, title = "treemap 3", label_size = 2,
-#'   color_type = "cell_size", color_level = 2,
-#'   color_palette = heat.colors(10),
-#'   border_color = grey(0.4), label_color = grey(0.4),
-#'   add = TRUE, layout = c(1,3), position = c(1, 3),
-#'   title_color = "black")
+#' # plot treemap with different color palette and style
+#' drawTreemap(tm, label_size = 1, label_color = grey(0.3),
+#'             border_color = grey(0.3), color_palette = heat.colors(6)
+#' )
 #'
 #' @importFrom Rcpp evalCpp
 #' @importFrom grid grid.newpage

README.Rmd

@@ -1,7 +1,7 @@
 ---
 output:  github_document
 title: "WeightedTreemaps"
-author: "Michael Jahn, David Leslie, Ahmadou Dicko"
+author: "Michael Jahn, David Leslie, Ahmadou Dicko, Paul Murrell"
 date: "`r Sys.Date()`"
 vignette: >
   %\VignetteIndexEntry{WeightedTreemaps}
@@ -21,7 +21,8 @@ knitr::opts_chunk$set(
 <img src="images/logo.png" align="right" />
 
 <!-- badges start -->
-[![R build status](https://github.com/m-jahn/WeightedTreemaps/workflows/R-CMD-check/badge.svg)](https://github.com/m-jahn/WeightedTreemaps/actions)
+[![CRAN status](https://www.r-pkg.org/badges/version/WeightedTreemaps)](https://CRAN.R-project.org/package=WeightedTreemaps)
+[![R-CMD-check](https://github.com/m-jahn/WeightedTreemaps/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/m-jahn/WeightedTreemaps/actions/workflows/R-CMD-check.yaml)
 ![GitHub issues](https://img.shields.io/github/issues/m-jahn/WeightedTreemaps)
 ![GitHub last commit](https://img.shields.io/github/last-commit/m-jahn/WeightedTreemaps)
 ![Platform](https://img.shields.io/badge/platform-all-green)
@@ -57,6 +58,12 @@ drawTreemap(tm, label_size = 2.5, label_color = "white", title = "An example")
 
 ## News
 
+*14 December 2023*
+
+The package was finally released on CRAN!
+Prerequisite was testing and troubleshooting of C++ related compilation problems,
+and re-release of the CGAL dependency package `RcppCGAL` with latest version.
+
 *25 March 2021*
 
 A **Shiny app** for generating treemaps from custom data is now available on **[Shinyapps.io](https://m-jahn.shinyapps.io/ShinyTreemaps/)!**
@@ -76,11 +83,17 @@ The **Sunburst treemap** is a computationally less demanding treemap that does n
 
 The C++ code computing the actual Voronoi tesselation requires the [CGAL](https://www.cgal.org/download.html) library headers. Thanks to [Ahmadou Dicko](https://github.com/dickoa), installing the complete CGAL library locally is no longer necessary. Instead, the package depends on the CGAL headers that are available as R packages on CRAN. The package was using CGAL 4 (package `cgal4h`), but now moved to the latest CGAL 5.5+ version available as package `RcppCGAL`. The dependencies are usually installed automatically and manual installation of CGAL (headers) should not be necessary.
 
-**NOTE**: The `RcppCGAL` package is currently (September 2023) not available on CRAN! Please install it [manually from Github](https://github.com/ericdunipace/RcppCGAL).
+Note: If the `RcppCGAL` package is temporarily not available on CRAN (as happened 2023), please install it [manually from Github](https://github.com/ericdunipace/RcppCGAL).
 
 ## Installation
 
-To install the package directly from github, use the following function from the `devtools` package in your R session:
+To install the package from CRAN, use:
+
+```{r, eval = FALSE}
+install.packages("WeightedTreemaps")
+```
+
+To install the package directly from github, use the following function from the `devtools` package:
 
 ```{r, eval = FALSE}
 devtools::install_github("m-jahn/WeightedTreemaps")

README.md

@@ -1,16 +1,17 @@
 WeightedTreemaps
 ================
-Michael Jahn, David Leslie, Ahmadou Dicko
-2023-12-12
+Michael Jahn, David Leslie, Ahmadou Dicko, Paul Murrell
+2024-01-07
 
 <!-- include logo-->
 
 <img src="images/logo.png" align="right" />
 
 <!-- badges start -->
 
-[![R build
-status](https://github.com/m-jahn/WeightedTreemaps/workflows/R-CMD-check/badge.svg)](https://github.com/m-jahn/WeightedTreemaps/actions)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/WeightedTreemaps)](https://CRAN.R-project.org/package=WeightedTreemaps)
+[![R-CMD-check](https://github.com/m-jahn/WeightedTreemaps/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/m-jahn/WeightedTreemaps/actions/workflows/R-CMD-check.yaml)
 ![GitHub
 issues](https://img.shields.io/github/issues/m-jahn/WeightedTreemaps)
 ![GitHub last
@@ -28,6 +29,12 @@ hierarchical data.
 
 ## News
 
+*14 December 2023*
+
+The package was finally released on CRAN! Prerequisite was testing and
+troubleshooting of C++ related compilation problems, and re-release of
+the CGAL dependency package `RcppCGAL` with latest version.
+
 *25 March 2021*
 
 A **Shiny app** for generating treemaps from custom data is now
@@ -83,14 +90,20 @@ was using CGAL 4 (package `cgal4h`), but now moved to the latest CGAL
 usually installed automatically and manual installation of CGAL
 (headers) should not be necessary.
 
-**NOTE**: The `RcppCGAL` package is currently (September 2023) not
-available on CRAN! Please install it [manually from
+Note: If the `RcppCGAL` package is temporarily not available on CRAN (as
+happened 2023), please install it [manually from
 Github](https://github.com/ericdunipace/RcppCGAL).
 
 ## Installation
 
+To install the package from CRAN, use:
+
+``` r
+install.packages("WeightedTreemaps")
+```
+
 To install the package directly from github, use the following function
-from the `devtools` package in your R session:
+from the `devtools` package:
 
 ``` r
 devtools::install_github("m-jahn/WeightedTreemaps")
@@ -135,7 +148,7 @@ Draw the treemap.
 drawTreemap(tm, label_size = 2.5, label_color = "white")
 ```
 
-<img src="images/unnamed-chunk-6-1.png" width="50%" style="display: block; margin: auto;" />
+<img src="images/unnamed-chunk-7-1.png" width="50%" style="display: block; margin: auto;" />
 
 The `voronoiTreemap()` and `drawTreemap()` functions are separated in
 order to allow drawing of the same treemap object in different ways.
@@ -170,7 +183,7 @@ drawTreemap(tm, title = "treemap 4", label_size = 2,
   title_color = "black", legend = TRUE)
 ```
 
-<img src="images/unnamed-chunk-7-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="images/unnamed-chunk-8-1.png" width="100%" style="display: block; margin: auto;" />
 
 ### Positioning of cells
 
@@ -223,7 +236,7 @@ drawTreemap(tm3, title = "positioning = 'clustered'", border_size = 3,
   add = TRUE, layout = c(1,3), position = c(1, 3))
 ```
 
-<img src="images/unnamed-chunk-9-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="images/unnamed-chunk-10-1.png" width="100%" style="display: block; margin: auto;" />
 
 ### Custom initial shapes
 
@@ -271,7 +284,7 @@ drawTreemap(tm2, add = TRUE, layout = c(1,3), position = c(1, 2))
 drawTreemap(tm3, add = TRUE, layout = c(1,3), position = c(1, 3))
 ```
 
-<img src="images/unnamed-chunk-12-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="images/unnamed-chunk-13-1.png" width="100%" style="display: block; margin: auto;" />
 
 ### Advanced example for Voronoi treemaps
 
@@ -546,7 +559,7 @@ drawTreemap(tm,
 )
 ```
 
-<img src="images/unnamed-chunk-22-1.png" width="100%" style="display: block; margin: auto;" />
+<img src="images/unnamed-chunk-23-1.png" width="100%" style="display: block; margin: auto;" />
 
 ## References and other treemap packages
 

cran-comments.md

@@ -1,26 +1,4 @@
-## Resubmission
-
-This package was submitted previously, but returned with the following comments:
-
-1. "If there are references describing the methods in your package, please
-add these in the description field of your DESCRIPTION file ..."
-
--> one reference was added to the DESCRIPTION.
-
-2. "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) ... Missing Rd-tags: poly_sortpoints.Rd: \value"
-
--> the documentation in \value fields was extended for several functions.
-The function with a missing \value was removed.
-
-3. "You write information messages to the console that cannot be easily
-suppressed. It is more R like to generate objects that can be used to extract the
-information a user is interested in, and then print() that object.
-Instead of print()/cat() rather use message()/warning() ..."
-
--> all cat() and print() statements were replaced by message(). Messages are
-now only printed when the user specifies verbose = TRUE.
+## Update
 
 ## Test environments
 
@@ -32,33 +10,19 @@ now only printed when the user specifies verbose = TRUE.
 - ubuntu-latest (release)
 - ubuntu-latest (oldrel-1)
 
-
 ### with `rhub::check_for_cran()`
 
 - Fedora Linux, R-devel, clang, gfortran
 - Debian Linux, R-release, GCC
 - Windows Server 2022, R-devel, 64 bit
 - Ubuntu Linux 20.04.1 LTS, R-release, GCC
+- Debian Linux, R-devel, GCC ASAN/UBSAN
 
 ## R CMD check results
 
 There were no ERRORs or WARNINGs.
 
-There were 2 NOTEs:
-
-1. Note:
-
-```
-File ‘WeightedTreemaps/libs/WeightedTreemaps.so’:
-  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
-    Object: ‘voronoiDiagram.o’. Compiled code should not call entry 
-    points which might terminate R nor write to stdout/stderr instead
-    of to the console, nor use Fortran I/O nor system RNGs.
-```
-
-The C++ function `voronoiDiagram.cpp` does not contain any such entry points. This Note occasionally turns up on Mac OS tests, probably caused by the upstream dependency CGAL headers (R package `RcppCGAL`) or boost headers (`BH`).
-
-2. Note:
+There was 1 NOTE:
 
 ```
 checking installed package size ... NOTE
@@ -70,6 +34,9 @@ checking installed package size ... NOTE
 
 Installed package size exceeding 5 MB is caused by the compiled function `voronoiDiagram.o`. The size of this file can not be reduced.
 
+There were "additional issues" brought up with from ASAN/UBSAN sanitizer checks.
+These were fixed in the current version.
+
 ## Downstream dependencies
 
 - There are currently no downstream dependencies for this package