fix r cmd check (except vignettes)

insightsengineering · Nov 30, 2023 · 021678d · 021678d
1 parent 6afeae7
commit 021678d
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Showing 18 changed files with 67 additions and 259 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -19,7 +19,6 @@ export(TealReportCard)
 export(as.teal_slices)
 export(as_tdata)
 export(example_module)
-export(get_code.tdata)
 export(get_code_tdata)
 export(get_metadata)
 export(init)
@@ -47,6 +46,6 @@ import(shiny)
 import(teal.data)
 import(teal.slice)
 import(teal.transform)
-importFrom(lifecycle,deprecate_soft)
+importFrom(lifecycle,badge)
 importFrom(magrittr,"%>%")
 importFrom(stats,setNames)
diff --git a/R/init.R b/R/init.R
@@ -10,16 +10,10 @@
 #' End-users: This is the most important function for you to start a
 #' teal app that is composed out of teal modules.
 #'
-#' @param data (`TealData` or `TealDataset` or `TealDatasetConnector` or `list` or `data.frame`
-#' or `MultiAssayExperiment`, `teal_data`, `teal_data_module`)\cr
-#' `R6` object as returned by [teal.data::cdisc_data()], [teal.data::teal_data()],
-#' [teal.data::cdisc_dataset()], [teal.data::dataset()], [teal.data::dataset_connector()] or
-#' [teal.data::cdisc_dataset_connector()] or [teal_data_module()] or a single `data.frame` or
-#' a `MultiAssayExperiment`
-#' or a list of the previous objects or function returning a named list.
-#' NOTE: teal does not guarantee reproducibility of the code when names of the list elements
-#' do not match the original object names. To ensure reproducibility please use [teal.data::teal_data()]
-#' or [teal.data::cdisc_data()] with `check = TRUE` enabled.
+#' @param data (`teal_data`, `teal_data_module`, `named list`)\cr
+#' `teal_data` object as returned by [teal.data::teal_data()] or
+#' `teal_data_modules` or simply a list of a named list of objects
+#' (`data.frame` or `MultiAssayExperiment`).
 #' @param modules (`list`, `teal_modules` or `teal_module`)\cr
 #'   nested list of `teal_modules` or `teal_module` objects or a single
 #'   `teal_modules` or `teal_module` object. These are the specific output modules which
@@ -108,11 +102,22 @@ init <- function(data,
                  footer = tags$p(),
                  id = character(0)) {
   logger::log_trace("init initializing teal app with: data ({ class(data)[1] }).")
-  if (!inherits(data, c("TealData", "teal_data", "teal_data_module"))) {
-    data <- teal.data::to_relational_data(data = data)
+  if (is.list(data)) {
+    checkmate::assert_list(data, names = "named")
+    data <- do.call(teal.data::teal_data, data)
+  }
+  if (inherits(data, "TealData")) {
+    lifecycle::deprecate_stop(
+      when = "0.99.0",
+      what = "init(data)",
+      paste(
+        "TealData is no longer supported. Use teal_data() instead.",
+        "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/988."
+      )
+    )
   }
 
-  checkmate::assert_multi_class(data, c("TealData", "teal_data", "teal_data_module"))
+  checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
   checkmate::assert_multi_class(modules, c("teal_module", "list", "teal_modules"))
   checkmate::assert_string(title, null.ok = TRUE)
   checkmate::assert(
@@ -215,10 +220,6 @@ init <- function(data,
         landing_module <- landing[[1L]]
         do.call(landing_module$server, c(list(id = "landing_module_shiny_id"), landing_module$server_args))
       }
-      if (inherits(data, "TealDataAbstract")) {
-        # copy TealData so that load won't be shared between the session
-        data <- data$copy(deep = TRUE)
-      }
       filter <- deep_copy_filter(filter)
       srv_teal_with_splash(id = id, data = data, modules = modules, filter = filter)
     }

diff --git a/R/module_teal_with_splash.R b/R/module_teal_with_splash.R
@@ -22,7 +22,7 @@ ui_teal_with_splash <- function(id,
                                 title,
                                 header = tags$p("Add Title Here"),
                                 footer = tags$p("Add Footer Here")) {
-  checkmate::assert_multi_class(data, c("TealData", "teal_data", "teal_data_module"))
+  checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
   ns <- NS(id)
 
   # Startup splash screen for delayed loading
@@ -33,11 +33,6 @@ ui_teal_with_splash <- function(id,
     data$ui(ns("teal_data_module"))
   } else if (inherits(data, "teal_data")) {
     div()
-  } else if (inherits(data, "TealDataAbstract") && teal.data::is_pulled(data)) {
-    div()
-  } else {
-    message("App was initialized with delayed data loading.")
-    data$get_ui(ns("startapp_module"))
   }
   ui_teal(
     id = ns("teal"),
@@ -63,7 +58,7 @@ ui_teal_with_splash <- function(id,
 #' If data is not loaded yet, `reactive` returns `NULL`.
 #' @export
 srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
-  checkmate::check_multi_class(data, c("TealData", "teal_data", "teal_data_module"))
+  checkmate::check_multi_class(data, c("teal_data", "teal_data_module"))
 
   moduleServer(id, function(input, output, session) {
     logger::log_trace("srv_teal_with_splash initializing module with data.")
@@ -82,41 +77,13 @@ srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
       data
     } else if (inherits(data, "teal_data")) {
       reactiveVal(data)
-    } else if (inherits(data, "TealDataAbstract") && teal.data::is_pulled(data)) {
-      new_data <- do.call(
-        teal.data::teal_data,
-        c(
-          lapply(data$get_datasets(), function(x) x$get_raw_data()),
-          list(code = data$get_code()),
-          list(join_keys = teal.data::join_keys(data))
-        )
-      )
-      reactiveVal(new_data) # will trigger by setting it
-    } else {
-      raw_data_old <- data$get_server()(id = "startapp_module")
-      raw_data <- reactive({
-        data <- raw_data_old()
-        if (!is.null(data)) {
-          # raw_data is a reactive which returns data only when submit button clicked
-          # otherwise it returns NULL
-          do.call(
-            teal.data::teal_data,
-            c(
-              lapply(data$get_datasets(), function(x) x$get_raw_data()),
-              list(code = data$get_code()),
-              list(join_keys = teal.data::join_keys(data))
-            )
-          )
-        }
-      })
-      raw_data
     }
 
     teal_data_rv_validate <- reactive({
       # custom module can return error
       data <- tryCatch(teal_data_rv(), error = function(e) e)
 
-      # there is an empty reactive event on init!
+      # there is an empty reactive cycle on init!
       if (inherits(data, "shiny.silent.error") && identical(data$message, "")) {
         return(NULL)
       }
@@ -184,7 +151,6 @@ srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
     })
 
 
-
     res <- srv_teal(id = "teal", modules = modules, teal_data_rv = teal_data_rv_validate, filter = filter)
     logger::log_trace("srv_teal_with_splash initialized module with data.")
     return(res)

diff --git a/R/tdata.R b/R/tdata.R
@@ -1,5 +1,6 @@
 #' Create a `tdata` Object
 #'
+#' @description `r lifecycle::badge("deprecated")`
 #' Create a new object called `tdata` which contains `data`, a `reactive` list of data.frames
 #' (or `MultiAssayExperiment`), with attributes:
 #' \itemize{
@@ -37,13 +38,21 @@
 #' isolate(data[["iris"]]())
 #'
 #' # Get code
-#' isolate(get_code(data))
+#' isolate(get_code_tdata(data))
 #'
 #' # Get metadata
 #' get_metadata(data, "iris")
 #'
 #' @export
 new_tdata <- function(data, code = "", join_keys = NULL, metadata = NULL) {
+  lifecycle::deprecate_soft(
+    when = "0.99.0",
+    what = "tdata()",
+    details = paste(
+      "tdata is deprecated and will be removed in the next release. Use `teal_data` instead.\n",
+      "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987."
+    )
+  )
   checkmate::assert_list(
     data,
     any.missing = FALSE, names = "unique",
@@ -54,7 +63,6 @@ new_tdata <- function(data, code = "", join_keys = NULL, metadata = NULL) {
 
   checkmate::assert_list(metadata, names = "unique", null.ok = TRUE)
   checkmate::assert_subset(names(metadata), names(data))
-  for (m in metadata) teal.data::validate_metadata(m)
 
   if (is.reactive(code)) {
     isolate(checkmate::assert_class(code(), "character", .var.name = "code"))
@@ -104,15 +112,6 @@ tdata2env <- function(data) { # nolint
   list2env(lapply(data, function(x) if (is.reactive(x)) x() else x))
 }
 
-#' @rdname tdata
-#' @param x a `tdata` object
-#' @param ... additional arguments for the generic
-#' @export
-get_code.tdata <- function(x, ...) { # nolint
-  # note teal.data which teal depends on defines the get_code method
-  attr(x, "code")()
-}
-
 
 #' Wrapper for `get_code.tdata`
 #' This wrapper is to be used by downstream packages to extract the code of a `tdata` object
@@ -123,7 +122,7 @@ get_code.tdata <- function(x, ...) { # nolint
 #' @export
 get_code_tdata <- function(data) {
   checkmate::assert_class(data, "tdata")
-  get_code(data)
+  attr(data, "code")()
 }
 
 #' Extract `join_keys` from `tdata`

diff --git a/R/teal.R b/R/teal.R
@@ -19,5 +19,5 @@ magrittr::`%>%`
 NULL
 
 # Fix R CMD check notes
-#' @importFrom lifecycle deprecate_soft
-lifecycle::deprecate_soft
+#' @importFrom lifecycle badge
+lifecycle::badge
diff --git a/R/teal_data_module.R b/R/teal_data_module.R
@@ -1,5 +1,6 @@
 #' Data module for `teal` applications
 #'
+#' @description  `r lifecycle::badge("experimental")`
 #' Creates `teal_data_module` object - a `shiny` module to supply or modify data in a `teal` application.
 #'
 #' This function creates a `shiny` module that allows for running data pre-processing code after the app starts.

diff --git a/R/teal_slices.R b/R/teal_slices.R
@@ -51,11 +51,11 @@
 #' )
 #'
 #' app <- teal::init(
+#'   data = list(iris = iris, mtcars = mtcars),
 #'   modules = list(
 #'     module("module1"),
 #'     module("module2")
 #'   ),
-#'   data = list(iris, mtcars),
 #'   filter = filter
 #' )
 #'

diff --git a/man/init.Rd b/man/init.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/man/srv_teal_with_splash.Rd b/man/srv_teal_with_splash.Rd
diff --git a/man/tdata.Rd b/man/tdata.Rd
diff --git a/man/teal_data_module.Rd b/man/teal_data_module.Rd
diff --git a/man/teal_slices.Rd b/man/teal_slices.Rd
diff --git a/man/ui_teal_with_splash.Rd b/man/ui_teal_with_splash.Rd