fix: move required Shiny app packages from Suggests to Imports

.github/PULL_REQUEST_TEMPLATE.md

@@ -24,6 +24,7 @@ How to test features not covered by unit tests.
 - [ ] R script works with the new implementation (if applicable)
 - [ ] Settings upload works with the new implementation (if applicable)
 - [ ] If any `.scss` change was done, run `data-raw/compile_css.R`
+- [ ] If a package dependency was added/changed, run `data-raw/test_suggests_hidden.R`
 
 ## Notes to reviewer
 

DESCRIPTION

@@ -26,22 +26,34 @@ Description: An interactive 'shiny' application for performing non-compartmental
   Noncompartmental Analysis: The PKNCA R Package" <doi:10.1007/s10928-015-9432-2>.
 License: Apache License (>= 2)
 Imports: 
+    bslib,
     dplyr,
     formatters,
     ggplot2,
     glue,
+    htmltools,
+    htmlwidgets,
+    logger,
     magrittr,
     PKNCA (>= 0.12.1),
     plotly (>= 4.11.0),
     purrr,
+    reactable,
+    reactable.extras,
     rlang,
+    shiny,
+    shinycssloaders,
+    shinyjs,
+    shinyjqui,
+    shinyWidgets,
     stats,
     tern,
     tidyr,
     units,
     utils,
     writexl,
-    yaml
+    yaml,
+    zip
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
@@ -52,37 +64,25 @@ Suggests:
     flextable,
     ggh4x,
     haven,
-    htmltools,
-    htmlwidgets,
     jsonlite,
     knitr,
     lintr (>= 3.2.0),
-    logger,
     markdown,
     mockery,
     nestcolor,
     officer,
     pak,
     readxl,
-    reactable,
-    reactable.extras,
     rlistings,
     rmarkdown,
     sass,
     scales,
-    shiny,
-    shinycssloaders,
-    shinyjs,
-    shinyjqui,
     shinytest2,
-    shinyWidgets,
-    stringi,
     testthat (>= 3.0.0),
     tools,
     quarto,
     vdiffr,
-    withr,
-    zip
+    withr
 Config/testthat/edition: 3
 Language: en-US
 URL: https://pharmaverse.github.io/aNCA/, https://github.com/pharmaverse/aNCA

NAMESPACE

@@ -175,8 +175,20 @@ importFrom(units,deparse_unit)
 importFrom(units,drop_units)
 importFrom(units,set_units)
 importFrom(units,units_options)
+importFrom(bslib,page_sidebar)
+importFrom(htmltools,tags)
+importFrom(htmlwidgets,onRender)
+importFrom(logger,log_info)
+importFrom(reactable,reactable)
+importFrom(reactable.extras,reactable_extras_dependency)
+importFrom(shiny,runApp)
+importFrom(shinycssloaders,withSpinner)
+importFrom(shinyWidgets,pickerInput)
+importFrom(shinyjs,useShinyjs)
+importFrom(shinyjqui,orderInput)
 importFrom(utils,capture.output)
 importFrom(utils,read.csv)
 importFrom(writexl,write_xlsx)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)
+importFrom(zip,zipr)

R/imports-shiny.R

@@ -0,0 +1,19 @@
+# Declare Imports used only by the Shiny app (inst/shiny/).
+#
+# R CMD check requires that every package in Imports has at least one
+# @importFrom directive. These packages are used in the Shiny app code
+# (inst/shiny/) which R CMD check does not scan for namespace usage.
+
+#' @importFrom bslib page_sidebar
+#' @importFrom htmltools tags
+#' @importFrom htmlwidgets onRender
+#' @importFrom logger log_info
+#' @importFrom reactable reactable
+#' @importFrom reactable.extras reactable_extras_dependency
+#' @importFrom shiny runApp
+#' @importFrom shinycssloaders withSpinner
+#' @importFrom shinyjs useShinyjs
+#' @importFrom shinyjqui orderInput
+#' @importFrom shinyWidgets pickerInput
+#' @importFrom zip zipr
+NULL

R/run_app.R

@@ -86,43 +86,24 @@ run_app <- function(datapath = NULL, settings = NULL,
 }
 
 #' Check if all dependencies required to run shiny application are installed.
-#' If not, install them.
-#' This list of packages should also be provided as `Suggests` in the DESCRIPTION file.
+#'
+#' Reads the Imports field from DESCRIPTION and verifies each package is
+#' available. This keeps the check in sync with DESCRIPTION automatically.
 #' @noRd
 check_app_dependencies <- function() {
-  deps <- c(
-    "bslib",
-    "dplyr",
-    "htmlwidgets",
-    "logger",
-    "formatters",
-    "magrittr",
-    "plotly",
-    "purrr",
-    "reactable",
-    "reactable.extras",
-    "shiny",
-    "shinycssloaders",
-    "shinyjs",
-    "shinyjqui",
-    "shinyWidgets",
-    "stats",
-    "stringi",
-    "tidyr",
-    "tools",
-    "utils",
-    "rlang",
-    "yaml"
-  )
+  desc <- read.dcf(system.file("DESCRIPTION", package = "aNCA"), fields = "Imports")
+  deps <- trimws(unlist(strsplit(desc[1, "Imports"], ",")))
+  deps <- gsub("\\s*\\(.*\\)", "", deps) # strip version constraints
+  deps <- deps[nzchar(deps)]
 
-  missing_packages <- purrr::keep(deps, function(dep) !requireNamespace(dep, quietly = TRUE))
+  missing_packages <- deps[!vapply(deps, requireNamespace, logical(1), quietly = TRUE)]
 
-  if (length(missing_packages) != 0) {
-    stop(paste0(
-      "Some packages required for Shiny application are missing. ",
-      "You can install them by running `install.packages(c(",
-      paste0("'", missing_packages, "'", collapse = ", "),
-      "))`"
-    ))
+  if (length(missing_packages) > 0) {
+    stop(
+      "Some packages required for the Shiny application are missing. ",
+      "You can install them by running:\n",
+      "  install.packages(c(", paste0("'", missing_packages, "'", collapse = ", "), "))",
+      call. = FALSE
+    )
   }
 }

data-raw/test_suggests_hidden.R

@@ -0,0 +1,52 @@
+# Manual test: verify run_app() works without Suggests packages
+#
+# This script hides all Suggests packages (except testthat/covr needed by
+# devtools) and launches the app. Use it to verify that:
+#
+#   1. The app starts without errors.
+#   2. Core workflow works (upload → map → NCA → export).
+#   3. Optional features (SAS import, PowerPoint export, listings) show
+#      graceful messages instead of crashing.
+#
+# Usage:
+#   1. Open a fresh R session (Ctrl+Shift+F10 in RStudio).
+#   2. source("data-raw/test_suggests_hidden.R")
+#   3. Test the app manually.
+#   4. Stop the app (Ctrl+C / Esc), then run restore_packages() to unhide.
+#
+# WARNING: Do NOT run this in CI. It renames package directories on disk.
+
+# --- Hide Suggests packages ---
+desc <- read.dcf("DESCRIPTION", fields = "Suggests")
+hide <- trimws(unlist(strsplit(desc[1, "Suggests"], ",")))
+hide <- gsub("\\s*\\(.*\\)", "", hide)
+hide <- hide[nzchar(hide)]
+
+# Keep packages that devtools::load_all() needs
+hide <- setdiff(hide, c("testthat", "covr"))
+
+lib <- .libPaths()[1]
+hidden <- character(0)
+
+for (pkg in hide) {
+  from <- file.path(lib, pkg)
+  if (dir.exists(from)) {
+    file.rename(from, paste0(from, "_HIDDEN"))
+    hidden <- c(hidden, pkg)
+  }
+}
+cat("Hidden:", paste(hidden, collapse = ", "), "\n")
+
+# --- Load and run ---
+devtools::load_all()
+aNCA::run_app()
+
+# --- Restore function (call after stopping the app) ---
+restore_packages <- function() {
+  for (pkg in hidden) {
+    to <- file.path(lib, pkg)
+    from <- paste0(to, "_HIDDEN")
+    if (dir.exists(from)) file.rename(from, to)
+  }
+  cat("Restored:", paste(hidden, collapse = ", "), "\n")
+}

inst/shiny/app.R

@@ -16,7 +16,7 @@ require(shinyjs)
 require(shinyjqui)
 require(shinyWidgets)
 require(stats)
-require(stringi)
+
 require(tidyr)
 require(tools)
 require(utils)

inst/shiny/modules/tab_about.R

@@ -202,9 +202,9 @@ tab_about_server <- function(id) {
     })
 
     # Session info — computed once per session (doesn't change at runtime)
-    session_info_text <- paste(
-      utils::capture.output(utils::sessionInfo()),
-      collapse = "\n"
+    session_info_text <- tryCatch(
+      paste(utils::capture.output(utils::sessionInfo()), collapse = "\n"),
+      error = function(e) paste("Session info unavailable:", e$message)
     )
 
     output$session_info <- renderText({

inst/shiny/modules/tab_tlg.R

@@ -250,7 +250,10 @@ tab_tlg_server <- function(id, data) {
       panels <- lapply(tlg_order_graphs, function(g_id) {
         graph_ui <- {
           g_def <- .TLG_DEFINITIONS[[g_id]]
-          module_id <- paste0(g_id, stringi::stri_rand_strings(1, 5))
+          module_id <- paste0(
+            g_id,
+            paste0(sample(c(letters, 0:9), 5, replace = TRUE), collapse = "")
+          )
 
           if (exists(g_def$fun)) {
             tlg_module_server(module_id, data, "graph", get(g_def$fun), g_def$options)
@@ -288,7 +291,10 @@ tab_tlg_server <- function(id, data) {
         panels <- lapply(tlg_order_listings, function(g_id) {
           list_ui <- {
             g_def <- .TLG_DEFINITIONS[[g_id]]
-            module_id <- paste0(g_id, stringi::stri_rand_strings(1, 5))
+            module_id <- paste0(
+              g_id,
+              paste0(sample(c(letters, 0:9), 5, replace = TRUE), collapse = "")
+            )
 
             if (exists(g_def$fun)) {
               tlg_module_server(module_id, data, "listing", get(g_def$fun), g_def$options)