Ensures required packages are in Imports section (#774)

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Fixes #518 

Note on removals:

- Remove `broom` as the `broom:glances` method can be replaced with
`generics::glances`
  - According to my tests (methods are being deprecated as well)

#### Changes description

- Removed conditional use of packages
- Removes `{broom}` dependency
- Uses `rlang ` conditionally
- Uses Suggested packages conditional on tests

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Lluís Revilla <[email protected]>
Co-authored-by: m7pr <[email protected]>

Author: 4 people

.github/workflows/scheduled.yaml

@@ -38,6 +38,8 @@ jobs:
       strategy: ${{ matrix.test-strategy }}
       additional-env-vars: |
         PKG_SYSREQS_DRY_RUN=true
+      extra-deps: |
+        MultiAssayExperiment (>= 1.32.0);SummarizedExperiment (>= 1.36.0);teal.slice (>= 0.5.1.9021)
   branch-cleanup:
     if: >
       github.event_name == 'schedule' || (

DESCRIPTION

@@ -27,72 +27,72 @@ Depends:
     ggplot2 (>= 3.4.0),
     R (>= 3.6),
     shiny (>= 1.6.0),
-    teal (>= 0.15.2.9091),
+    teal (>= 0.15.2.9103),
     teal.transform (>= 0.5.0.9015)
 Imports:
     checkmate (>= 2.1.0),
+    colourpicker (>= 1.3.0),
     dplyr (>= 1.0.5),
     DT (>= 0.13),
     forcats (>= 1.0.0),
+    generics (>= 0.1.3),
+    ggExtra (>= 0.10.1),
+    ggpmisc (>= 0.4.3),
+    ggpp (>= 0.5.8-1),
+    ggrepel (>= 0.9.6),
+    goftest (>= 1.2-3),
     grid,
+    gridExtra (>= 2.3),
+    htmlwidgets (>= 1.6.4),
+    jsonlite (>= 1.8.9),
+    lattice (>= 0.18-4),
+    MASS (>= 7.3-61),
+    rtables (>= 0.6.8),
     rlistings (>= 0.2.8),
-    scales,
-    shinyjs,
+    scales (>= 1.3.0),
+    shinyjs (>= 2.1.0),
     shinyTree (>= 0.2.8),
-    shinyvalidate,
+    shinyvalidate (>= 0.1.3),
     shinyWidgets (>= 0.5.1),
+    sparkline (>= 2.0),
     stats,
     stringr (>= 1.4.1),
     teal.code (>= 0.5.0.9012),
     teal.data (>= 0.6.0.9015),
     teal.logger (>= 0.3.0.9003),
-    teal.reporter (>= 0.3.0),
+    teal.reporter (>= 0.3.1.9023),
     teal.widgets (>= 0.4.0),
     tern (>= 0.9.5),
     tibble (>= 2.0.0),
     tidyr (>= 0.8.3),
     tools,
     utils
 Suggests:
-    broom (>= 0.7.10),
-    colourpicker,
-    ggExtra,
-    ggpmisc (>= 0.4.3),
-    ggpp,
-    ggrepel,
-    goftest,
-    gridExtra,
-    htmlwidgets,
-    jsonlite,
     knitr (>= 1.42),
-    lattice (>= 0.18-4),
-    lifecycle (>= 0.2.0),
     logger (>= 0.2.0),
-    MASS,
     nestcolor (>= 0.1.0),
     pkgload,
     rlang (>= 1.0.0),
     rmarkdown (>= 2.23),
     roxy.shinylive,
-    rtables (>= 0.6.8),
     rvest,
     shinytest2,
-    sparkline,
+    lifecycle (>= 0.2.0),
     testthat (>= 3.1.9),
     withr (>= 2.0.0)
 VignetteBuilder:
     knitr,
     rmarkdown
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
-    rstudio/shiny, insightsengineering/teal,
+    rstudio/shiny, insightsengineering/teal, insightsengineering/teal.slice,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
     rstudio/DT, tidyverse/forcats, r-lib/lifecycle, r-lib/scales,
     daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
     dreamRs/shinyWidgets, tidyverse/stringr,
     insightsengineering/teal.code, insightsengineering/teal.data,
     insightsengineering/teal.logger, insightsengineering/teal.reporter,
     insightsengineering/teal.widgets, insightsengineering/tern,
-    tidyverse/tibble, tidyverse/tidyr, tidymodels/broom,
+    tidyverse/tibble, tidyverse/tidyr,
     daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
     slowkow/ggrepel, baddstats/goftest, ramnathv/htmlwidgets,
     jeroen/jsonlite, yihui/knitr, daroczig/logger, deepayan/lattice,

R/tm_g_distribution.R

@@ -60,7 +60,7 @@
 #' interactive <- function() TRUE
 #' {{ next_example }}
 # nolint start: line_length_linter.
-#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggpp", quietly = TRUE) && require("goftest", quietly = TRUE) && require("MASS", quietly = TRUE) && require("broom", quietly = TRUE)
+#' @examples
 # nolint end: line_length_linter.
 #' # general data example
 #' data <- teal_data()
@@ -88,7 +88,7 @@
 #' interactive <- function() TRUE
 #' {{ next_example }}
 # nolint start: line_length_linter.
-#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggpp", quietly = TRUE) && require("goftest", quietly = TRUE) && require("MASS", quietly = TRUE) && require("broom", quietly = TRUE)
+#' @examples
 # nolint end: line_length_linter.
 #' # CDISC data example
 #' data <- teal_data()
@@ -153,16 +153,6 @@ tm_g_distribution <- function(label = "Distribution Module",
                               decorators = NULL) {
   message("Initializing tm_g_distribution")
 
-  # Requires Suggested packages
-  extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")
-  missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
-  if (length(missing_packages) > 0L) {
-    stop(sprintf(
-      "Cannot load package(s): %s.\nInstall or restart your session.",
-      toString(missing_packages)
-    ))
-  }
-
   # Normalize the parameters
   if (inherits(dist_var, "data_extract_spec")) dist_var <- list(dist_var)
   if (inherits(strata_var, "data_extract_spec")) strata_var <- list(strata_var)
@@ -1227,7 +1217,7 @@ srv_distribution <- function(id,
               expr = {
                 test_table_data <- ANL %>%
                   dplyr::select(dist_var) %>%
-                  with(., broom::glance(do.call(test, args))) %>%
+                  with(., generics::glance(do.call(test, args))) %>%
                   dplyr::mutate_if(is.numeric, round, 3)
               },
               env = env
@@ -1241,7 +1231,7 @@ srv_distribution <- function(id,
                 test_table_data <- ANL %>%
                   dplyr::select(dist_var, s_var, g_var) %>%
                   dplyr::group_by_at(dplyr::vars(dplyr::any_of(groups))) %>%
-                  dplyr::do(tests = broom::glance(do.call(test, args))) %>%
+                  dplyr::do(tests = generics::glance(do.call(test, args))) %>%
                   tidyr::unnest(tests) %>%
                   dplyr::mutate_if(is.numeric, round, 3)
               },

R/tm_g_scatterplot.R

@@ -44,7 +44,7 @@
 #' interactive <- function() TRUE
 #' {{ next_example }}
 # nolint start: line_length_linter.
-#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggExtra", quietly = TRUE) && require("colourpicker", quietly = TRUE)
+#' @examples
 # nolint end: line_length_linter.
 #' # general data example
 #' data <- teal_data()
@@ -133,7 +133,7 @@
 #' interactive <- function() TRUE
 #' {{ next_example }}
 # nolint start: line_length_linter.
-#' @examplesIf require("ggpmisc", quietly = TRUE) && require("ggExtra", quietly = TRUE) && require("colourpicker", quietly = TRUE)
+#' @examples
 # nolint end: line_length_linter.
 #' # CDISC data example
 #' data <- teal_data()
@@ -242,16 +242,6 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              decorators = NULL) {
   message("Initializing tm_g_scatterplot")
 
-  # Requires Suggested packages
-  extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")
-  missing_packages <- Filter(function(x) !requireNamespace(x, quietly = TRUE), extra_packages)
-  if (length(missing_packages) > 0L) {
-    stop(sprintf(
-      "Cannot load package(s): %s.\nInstall or restart your session.",
-      toString(missing_packages)
-    ))
-  }
-
   # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)

R/tm_g_scatterplotmatrix.R

@@ -30,7 +30,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("lattice", quietly = TRUE)
+#' @examples
 #' # general data example
 #' data <- teal_data()
 #' data <- within(data, {
@@ -117,7 +117,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("lattice", quietly = TRUE)
+#' @examples
 #' # CDISC data example
 #' data <- teal_data()
 #' data <- within(data, {
@@ -180,11 +180,6 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    decorators = NULL) {
   message("Initializing tm_g_scatterplotmatrix")
 
-  # Requires Suggested packages
-  if (!requireNamespace("lattice", quietly = TRUE)) {
-    stop("Cannot load lattice - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(variables, "data_extract_spec")) variables <- list(variables)
 

R/tm_missing_data.R

@@ -50,7 +50,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("gridExtra", quietly = TRUE) && require("rlang", quietly = TRUE)
+#' @examples
 #' # general example data
 #' data <- teal_data()
 #' data <- within(data, {
@@ -84,7 +84,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("gridExtra", quietly = TRUE) && require("rlang", quietly = TRUE)
+#' @examples
 #' # CDISC example data
 #' data <- teal_data()
 #' data <- within(data, {
@@ -120,14 +120,6 @@ tm_missing_data <- function(label = "Missing data",
                             decorators = NULL) {
   message("Initializing tm_missing_data")
 
-  # Requires Suggested packages
-  if (!requireNamespace("gridExtra", quietly = TRUE)) {
-    stop("Cannot load gridExtra - please install the package or restart your session.")
-  }
-  if (!requireNamespace("rlang", quietly = TRUE)) {
-    stop("Cannot load rlang - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(ggplot2_args, "ggplot2_args")) ggplot2_args <- list(default = ggplot2_args)
 
@@ -1173,6 +1165,13 @@ srv_missing_data <- function(id,
         ggtheme = input$ggtheme
       )
 
+      # Unlikely that `rlang` is not available, new hashing may be expensive
+      hashing_function <- if (requireNamespace("rlang", quietly = TRUE)) {
+        quote(rlang::hash)
+      } else {
+        function(x) paste(as.integer(x), collapse = "")
+      }
+
       teal.code::eval_code(
         common_code_q(),
         substitute(
@@ -1187,41 +1186,44 @@ srv_missing_data <- function(id,
           )
         ) %>%
         teal.code::eval_code(
-          quote({
-            summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
-              dplyr::group_by_at(parent_keys) %>%
-              dplyr::mutate(id = dplyr::cur_group_id()) %>%
-              dplyr::ungroup() %>%
-              dplyr::group_by_at(c(parent_keys, "id")) %>%
-              dplyr::summarise_all(anyNA) %>%
-              dplyr::ungroup()
-
-            # order subjects by decreasing number of missing and then by
-            # missingness pattern (defined using sha1)
-            order_subjects <- summary_plot_patients %>%
-              dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::transmute(
-                id = dplyr::row_number(),
-                number_NA = apply(., 1, sum),
-                sha = apply(., 1, rlang::hash)
-              ) %>%
-              dplyr::arrange(dplyr::desc(number_NA), sha) %>%
-              getElement(name = "id")
-
-            # order columns by decreasing percent of missing values
-            ordered_columns <- summary_plot_patients %>%
-              dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::summarise(
-                column = create_cols_labels(colnames(.)),
-                na_count = apply(., MARGIN = 2, FUN = sum),
-                na_percent = na_count / nrow(.) * 100
-              ) %>%
-              dplyr::arrange(na_percent, dplyr::desc(column))
-
-            summary_plot_patients <- summary_plot_patients %>%
-              tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
-              dplyr::mutate(col = create_cols_labels(col))
-          })
+          substitute(
+            expr = {
+              summary_plot_patients <- ANL[, c(parent_keys, analysis_vars)] %>%
+                dplyr::group_by_at(parent_keys) %>%
+                dplyr::mutate(id = dplyr::cur_group_id()) %>%
+                dplyr::ungroup() %>%
+                dplyr::group_by_at(c(parent_keys, "id")) %>%
+                dplyr::summarise_all(anyNA) %>%
+                dplyr::ungroup()
+
+              # order subjects by decreasing number of missing and then by
+              # missingness pattern (defined using sha1)
+              order_subjects <- summary_plot_patients %>%
+                dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::transmute(
+                  id = dplyr::row_number(),
+                  number_NA = apply(., 1, sum),
+                  sha = apply(., 1, hashing_function)
+                ) %>%
+                dplyr::arrange(dplyr::desc(number_NA), sha) %>%
+                getElement(name = "id")
+
+              # order columns by decreasing percent of missing values
+              ordered_columns <- summary_plot_patients %>%
+                dplyr::select(-"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::summarise(
+                  column = create_cols_labels(colnames(.)),
+                  na_count = apply(., MARGIN = 2, FUN = sum),
+                  na_percent = na_count / nrow(.) * 100
+                ) %>%
+                dplyr::arrange(na_percent, dplyr::desc(column))
+
+              summary_plot_patients <- summary_plot_patients %>%
+                tidyr::gather("col", "isna", -"id", -dplyr::all_of(parent_keys)) %>%
+                dplyr::mutate(col = create_cols_labels(col))
+            },
+            env = list(hashing_function = hashing_function)
+          )
         ) %>%
         teal.code::eval_code(
           substitute(

R/tm_t_crosstable.R

@@ -37,7 +37,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("rtables", quietly = TRUE)
+#' @examples
 #' # general data example
 #' data <- teal_data()
 #' data <- within(data, {
@@ -86,7 +86,7 @@
 #' library(teal.modules.general)
 #' interactive <- function() TRUE
 #' {{ next_example }}
-#' @examplesIf require("rtables", quietly = TRUE)
+#' @examples
 #' # CDISC data example
 #' data <- teal_data()
 #' data <- within(data, {
@@ -146,11 +146,6 @@ tm_t_crosstable <- function(label = "Cross Table",
                             decorators = NULL) {
   message("Initializing tm_t_crosstable")
 
-  # Requires Suggested packages
-  if (!requireNamespace("rtables", quietly = TRUE)) {
-    stop("Cannot load rtables - please install the package or restart your session.")
-  }
-
   # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)
   if (inherits(y, "data_extract_spec")) y <- list(y)