208 CRAN requirements for the first submission [skip vbump]

.Rbuildignore

@@ -1,3 +1,5 @@
+LICENSE
+dev/internal_examples.R
 ^.*\.Rproj$
 ^Jenkinsfile$
 ^Makefile$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: teal.reporter
-Title: Reporting Tools for Shiny Modules
-Version: 0.2.0.9003
+Title: Reporting Tools for 'shiny' Modules
+Version: 0.2.1
 Date: 2023-09-05
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = "cre"),
@@ -9,9 +9,10 @@ Authors@R: c(
     person(c("Mahmoud", "mahmoud.hallal@roche.com"), "Hallal", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: Reporting tools for your shiny modules to generate
-    reproducible analysis.
-License: Apache License 2.0 | file LICENSE
+Description:
+    Prebuilt 'shiny' modules containing tools for the generation of 'rmarkdown' reports, supporting reproducible
+    research and analysis.
+License: Apache License 2.0
 URL: https://github.com/insightsengineering/teal.reporter,
     https://insightsengineering.github.io/teal.reporter/
 BugReports: https://github.com/insightsengineering/teal.reporter/issues

NEWS.md

@@ -1,8 +1,10 @@
-# teal.reporter 0.2.0.9003
+# teal.reporter 0.2.1
 
 ### Miscellaneous
 
 * Specify minimal version of dependent packages.
+* Fixed CRAN requirements for the first CRAN submission.
+* Removed manual pages for non-exported objects.
 
 # teal.reporter 0.2.0
 

R/Archiver.R

@@ -6,9 +6,6 @@ Archiver <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns an `Archiver` object.
     #'
     #' @return an `Archiver` object
-    #' @examples
-    #' archiver <- teal.reporter:::Archiver$new()
-    #'
     initialize = function() {
       invisible(self)
     },
@@ -39,9 +36,6 @@ FileArchiver <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns a `FileArchiver` object.
     #'
     #' @return a `FileArchiver` object
-    #' @examples
-    #' archiver <- teal.reporter:::FileArchiver$new()
-    #'
     initialize = function() {
       tmp_dir <- tempdir()
       output_dir <- file.path(tmp_dir, sprintf("archive_%s", gsub("[.]", "", format(Sys.time(), "%Y%m%d%H%M%OS4"))))
@@ -56,9 +50,6 @@ FileArchiver <- R6::R6Class( # nolint: object_name_linter.
     #' @description get `output_dir` field
     #'
     #' @return `character` a `output_dir` field path.
-    #' @examples
-    #' archiver <- teal.reporter:::FileArchiver$new()
-    #' archiver$get_output_dir()
     get_output_dir = function() {
       private$output_dir
     }
@@ -77,22 +68,8 @@ JSONArchiver <- R6::R6Class( # nolint: object_name_linter.
     #' @description write a `Reporter` instance in to this `JSONArchiver` object.
     #'
     #' @param reporter `Reporter` instance.
-    #' @return invisibly self
-    #' @examples
-    #' card1 <- teal.reporter:::ReportCard$new()
     #'
-    #' card1$append_text("Header 2 text", "header2")
-    #' card1$append_text("A paragraph of default text", "header2")
-    #' card1$append_plot(
-    #'  ggplot2::ggplot(iris, ggplot2::aes(x = Petal.Length)) + ggplot2::geom_histogram()
-    #' )
-    #'
-    #' reporter <- teal.reporter:::Reporter$new()
-    #' reporter$append_cards(list(card1))
-    #'
-    #' archiver <- teal.reporter:::JSONArchiver$new()
-    #' archiver$write(reporter)
-    #' archiver$get_output_dir()
+    #' @return invisibly self
     write = function(reporter) {
       checkmate::assert_class(reporter, "Reporter")
       unlink(list.files(private$output_dir, recursive = TRUE, full.names = TRUE))
@@ -102,26 +79,8 @@ JSONArchiver <- R6::R6Class( # nolint: object_name_linter.
     #' @description read a `Reporter` instance from a directory with `JSONArchiver`.
     #'
     #' @param path `character(1)` a path to the directory with all proper files.
-    #' @return `Reporter` instance.
-    #' @examples
-    #' card1 <- teal.reporter:::ReportCard$new()
-    #'
-    #' card1$append_text("Header 2 text", "header2")
-    #' card1$append_text("A paragraph of default text", "header2")
-    #' card1$append_plot(
-    #'  ggplot2::ggplot(iris, ggplot2::aes(x = Petal.Length)) + ggplot2::geom_histogram()
-    #' )
-    #'
-    #' reporter <- teal.reporter:::Reporter$new()
-    #' reporter$append_cards(list(card1))
     #'
-    #' archiver <- teal.reporter:::JSONArchiver$new()
-    #' archiver$write(reporter)
-    #' archiver$get_output_dir()
-    #'
-    #' archiver$read()$get_cards()[[1]]$get_content()
-    #' blocks <- teal.reporter:::Reporter$new()$from_reporter(archiver$read())$get_blocks()
-    #' doc <- teal.reporter:::Renderer$new()$render(blocks)
+    #' @return `Reporter` instance.
     read = function(path = NULL) {
       checkmate::assert(
         checkmate::check_null(path),

R/ContentBlock.R

@@ -8,21 +8,15 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @details Returns a `ContentBlock` object with no content and the default style.
     #'
     #' @return `ContentBlock`
-    #' @examples
-    #' block <- teal.reporter:::ContentBlock$new()
-    #'
     initialize = function() {
       private$content <- character(0)
       invisible(self)
     },
     #' @description Sets content of this `ContentBlock`.
     #'
     #' @param content (`character(0)` or `character(1)`) a string literal or a file path assigned to this `ContentBlock`
-    #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::ContentBlock$new()
-    #' block$set_content("Base64 encoded picture")
     #'
+    #' @return invisibly self
     set_content = function(content) {
       checkmate::assert_character(content, min.len = 0, max.len = 1)
       private$content <- content
@@ -31,36 +25,33 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns the absolute path to content of this `ContentBlock`
     #'
     #' @return `character` content of this `ContentBlock`
-    #' @examples
-    #' block <- teal.reporter:::ContentBlock$new()
-    #' block$get_content()
-    #'
     get_content = function() {
       private$content
     },
     #' @description Create the `ContentBlock` from a list.
+    #'
     #' @param x `named list` with two fields `c("text", "style")`.
     #' Use the `get_available_styles` method to get all possible styles.
+    #'
     #' @return invisibly self
     from_list = function(x) {
       invisible(self)
     },
     #' @description Convert the `ContentBlock` to a list.
+    #'
     #' @return `named list` with a text and style.
     to_list = function() {
       list()
     }
   ),
   private = list(
     content = character(0),
-
     # @description The copy constructor.
     #
     # @param name `character(1)` the name of the field
     # @param value the value assigned to the field
     #
     # @return the value of the copied field
-    #
     deep_clone = function(name, value) {
       if (name == "content" && checkmate::test_file_exists(value)) {
         extension <- ""

R/FileBlock.R

@@ -1,27 +1,22 @@
 #' @title `FileBlock`
 #' @keywords internal
-#'
 FileBlock <- R6::R6Class( # nolint: object_name_linter.
   classname = "FileBlock",
   inherit = ContentBlock,
   public = list(
     #' @description finalize of this `FileBlock`.
     #'
     #' @details Removes the temporary file created in the constructor.
-    #'
     finalize = function() {
       try(unlink(super$get_content()))
     },
     #' @description Create the `FileBlock` from a list.
     #' The list should contain one named field, `"basename"`.
+    #'
     #' @param x `named list` with one field `"basename"`, a name of the file.
     #' @param output_dir `character` with a path to the directory where a file will be copied.
+    #'
     #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::FileBlock$new()
-    #' file_path <- tempfile(fileext = ".png")
-    #' saveRDS(iris, file_path)
-    #' block$from_list(list(basename = basename(file_path)), dirname(file_path))
     from_list = function(x, output_dir) {
       checkmate::assert_list(x)
       checkmate::assert_names(names(x), must.include = "basename")
@@ -34,11 +29,10 @@ FileBlock <- R6::R6Class( # nolint: object_name_linter.
       invisible(self)
     },
     #' @description Convert the `FileBlock` to a list.
+    #'
     #' @param output_dir `character` with a path to the directory where a file will be copied.
+    #'
     #' @return `named list` with a `basename` of the file.
-    #' @examples
-    #' block <- teal.reporter:::FileBlock$new()
-    #' block$to_list(tempdir())
     to_list = function(output_dir) {
       base_name <- basename(super$get_content())
       file.copy(super$get_content(), file.path(output_dir, base_name))

R/NewpageBlock.R

@@ -1,6 +1,5 @@
 #' @title `NewpageBlock`
 #' @keywords internal
-#'
 NewpageBlock <- R6::R6Class( # nolint: object_name_linter.
   classname = "NewpageBlock",
   inherit = ContentBlock,
@@ -10,9 +9,6 @@ NewpageBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @details Returns a `NewpageBlock` object with no content and the default style.
     #'
     #' @return `NewpageBlock`
-    #' @examples
-    #' block <- teal.reporter:::NewpageBlock$new()
-    #'
     initialize = function() {
       super$set_content("\n\\newpage\n")
       invisible(self)

R/PictureBlock.R

@@ -1,15 +1,15 @@
 #' @title `PictureBlock`
 #' @keywords internal
-#'
+#' @noRd
 PictureBlock <- R6::R6Class( # nolint: object_name_linter.
   classname = "PictureBlock",
   inherit = FileBlock,
   public = list(
     #' @description Returns a new `PictureBlock` object.
     #'
     #' @param plot (`ggplot`, `grid`) a picture in this `PictureBlock`
-    #' @return a `PictureBlock` object
     #'
+    #' @return a `PictureBlock` object
     initialize = function(plot) {
       if (!missing(plot)) {
         self$set_content(plot)
@@ -21,16 +21,8 @@ PictureBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @details throws if argument is not a `ggplot`, `grob` or `trellis` plot.
     #'
     #' @param content (`ggplot`, `grob`, `trellis`) a picture in this `PictureBlock`
-    #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$set_content(ggplot2::ggplot(iris))
     #'
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$set_content(lattice::bwplot(1))
-    #'
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$set_content(ggplot2::ggplotGrob(ggplot2::ggplot(iris)))
+    #' @return invisibly self
     set_content = function(content) {
       checkmate::assert_multi_class(content, private$supported_plots)
       path <- tempfile(fileext = ".png")
@@ -57,11 +49,8 @@ PictureBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @details throws if argument is not `character(1)`.
     #'
     #' @param title (`character(1)`) a string assigned to this `PictureBlock`
-    #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$set_title("Title")
     #'
+    #' @return invisibly self
     set_title = function(title) {
       checkmate::assert_string(title)
       private$title <- title
@@ -70,21 +59,14 @@ PictureBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns the title of this `PictureBlock`
     #'
     #' @return the content of this `PictureBlock`
-    #' @examples
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$get_title()
-    #'
     get_title = function() {
       private$title
     },
     #' @description Sets the dimensions of this `PictureBlock`
     #'
     #' @param dim `numeric` figure dimensions (width and height) in pixels, length 2.
-    #' @return `self`
-    #' @examples
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$set_dim(c(800, 600))
     #'
+    #' @return `self`
     set_dim = function(dim) {
       checkmate::assert_numeric(dim, len = 2)
       private$dim <- dim
@@ -93,10 +75,6 @@ PictureBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns the dimensions of this `PictureBlock`
     #'
     #' @return `numeric` the array of 2 numeric values representing width and height in pixels.
-    #' @examples
-    #' block <- teal.reporter:::PictureBlock$new()
-    #' block$get_dim()
-    #'
     get_dim = function() {
       private$dim
     }

R/RcodeBlock.R

@@ -12,9 +12,6 @@ RcodeBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @param ... any `rmarkdown` R chunk parameter and it value.
     #'
     #' @return `RcodeBlock`
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #'
     initialize = function(content = character(0), ...) {
       super$set_content(content)
       self$set_params(list(...))
@@ -25,11 +22,8 @@ RcodeBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @details The parameters has bearing on the rendering of this block.
     #'
     #' @param params (`list`) any `rmarkdown` R chunk parameter and its value.
-    #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #' block$set_params(list(echo = TRUE))
     #'
+    #' @return invisibly self
     set_params = function(params) {
       checkmate::assert_list(params, names = "named")
       checkmate::assert_subset(names(params), self$get_available_params())
@@ -39,30 +33,21 @@ RcodeBlock <- R6::R6Class( # nolint: object_name_linter.
     #' @description Returns the parameters of this `RcodeBlock`.
     #'
     #' @return `character` the parameters of this `RcodeBlock`
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #' block$get_params()
-    #'
     get_params = function() {
       private$params
     },
     #' @description Returns an array of parameters available to this `RcodeBlock`.
     #'
     #' @return a `character` array of parameters
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #' block$get_available_params()
-    #'
     get_available_params = function() {
       names(knitr::opts_chunk$get())
     },
     #' @description Create the `RcodeBlock` from a list.
+    #'
     #' @param x `named list` with two fields `c("text", "params")`.
     #' Use the `get_available_params` method to get all possible parameters.
+    #'
     #' @return invisibly self
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #' block$from_list(list(text = "sth", params = list()))
     from_list = function(x) {
       checkmate::assert_list(x)
       checkmate::assert_names(names(x), must.include = c("text", "params"))
@@ -71,10 +56,8 @@ RcodeBlock <- R6::R6Class( # nolint: object_name_linter.
       invisible(self)
     },
     #' @description Convert the `RcodeBlock` to a list.
+    #'
     #' @return `named list` with a text and `params`.
-    #' @examples
-    #' block <- teal.reporter:::RcodeBlock$new()
-    #' block$to_list()
     to_list = function() {
       list(text = self$get_content(), params = self$get_params())
     }