feat: replace logger with lightweight console logging + ZIP export

DESCRIPTION

@@ -26,22 +26,33 @@ 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,
     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
@@ -52,8 +63,6 @@ Suggests:
     flextable,
     ggh4x,
     haven,
-    htmltools,
-    htmlwidgets,
     jsonlite,
     knitr,
     lintr (>= 3.2.0),
@@ -64,25 +73,16 @@ Suggests:
     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

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
+    )
   }
 }

inst/shiny/app.R

@@ -3,7 +3,6 @@ require(aNCA)
 require(bslib)
 require(dplyr)
 require(htmlwidgets)
-require(logger)
 require(formatters)
 require(magrittr)
 require(plotly)
@@ -16,7 +15,7 @@ require(shinyjs)
 require(shinyjqui)
 require(shinyWidgets)
 require(stats)
-require(stringi)
+
 require(tidyr)
 require(tools)
 require(utils)

inst/shiny/functions/logging.R

@@ -0,0 +1,84 @@
+# Lightweight logging system for the aNCA Shiny app.
+#
+# Replaces the `logger` package with console-only output and in-memory
+# log capture for ZIP export. Supports glue-style interpolation and
+# paste-style multi-argument calls.
+#
+# Log levels: TRACE < DEBUG < INFO < SUCCESS < WARN < ERROR
+# Default threshold: INFO (configurable via aNCA_LOG_LEVEL env var).
+#
+# The log captures application-level events only — not raw R console
+# output. Warnings and errors from third-party packages appear only
+# when explicitly caught by tryCatch blocks with log_warn/log_error.
+#
+# The in-memory buffer is exported as session_log.txt in the ZIP
+# download. For a full reference of logged events, see:
+# https://pharmaverse.github.io/aNCA/articles/session_log.html
+
+.log_env <- new.env(parent = emptyenv())
+.log_env$threshold <- "INFO"
+.log_env$buffer <- character(0)
+
+.LOG_LEVELS <- c(TRACE = 1L, DEBUG = 2L, INFO = 3L, SUCCESS = 4L, WARN = 5L, ERROR = 6L)
+
+#' Initialise the logging system.
+#'
+#' Reads the threshold from the `aNCA_LOG_LEVEL` environment variable
+#' (default `"INFO"`) and clears the in-memory log buffer.
+setup_logger <- function() {
+  level <- toupper(Sys.getenv("aNCA_LOG_LEVEL", "INFO"))
+  if (!level %in% names(.LOG_LEVELS)) level <- "INFO"
+  .log_env$threshold <- level
+  .log_env$buffer <- character(0)
+}
+
+#' Core logging function.
+#' @param level Character: one of the log level names.
+#' @param ... Message parts. If the first argument contains `{`, it is
+#'   evaluated as a glue string in the caller's environment. Otherwise
+#'   all arguments are pasted together.
+#' @noRd
+.log_msg <- function(level, ...) {
+  if (.LOG_LEVELS[[level]] < .LOG_LEVELS[[.log_env$threshold]]) return(invisible(NULL))
+
+  args <- list(...)
+  if (length(args) == 0L) {
+    msg <- ""
+  } else if (length(args) == 1L && grepl("\\{", args[[1]])) {
+    msg <- tryCatch(
+      glue::glue(args[[1]], .envir = parent.frame(2)),
+      error = function(e) paste0(args, collapse = "")
+    )
+  } else {
+    msg <- paste0(args, collapse = "")
+  }
+
+  timestamp <- format(Sys.time(), "%Y-%m-%d %H:%M:%S")
+  line <- paste0("[", timestamp, "] ", level, ": ", msg)
+
+  .log_env$buffer <- c(.log_env$buffer, line)
+  message(line)
+  invisible(NULL)
+}
+
+# Public log functions matching the logger API
+log_trace   <- function(...) .log_msg("TRACE", ...)
+log_debug   <- function(...) .log_msg("DEBUG", ...)
+log_info    <- function(...) .log_msg("INFO", ...)
+log_success <- function(...) .log_msg("SUCCESS", ...)
+log_warn    <- function(...) .log_msg("WARN", ...)
+log_error   <- function(...) .log_msg("ERROR", ...)
+
+#' Logs a list or data frame at DEBUG level.
+#'
+#' @param title Title for the log entry.
+#' @param l     List or data.frame to log.
+log_debug_list <- function(title, l) {
+  log_debug(aNCA:::.concatenate_list(title, l))
+}
+
+#' Return the in-memory log buffer as a character vector.
+#' @noRd
+get_log_buffer <- function() {
+  .log_env$buffer
+}

inst/shiny/functions/utils.R

@@ -1,45 +1,3 @@
-#' Sets up the logger package for the application.
-#'
-#' @details
-#' The application logs everything to a log file located in `/log` directory. If such folder
-#' does not exist, it will be created. Logfile for each session will be separate. The application
-#' will keep 5 log files at any given time - if this number is exceeded, the oldest log file
-#' will be deleted.
-#'
-#' In addition, information of the level specified by the user will be logged to console.
-#' As a default, this level is INFO - this is so that the user has good information on what is
-#' happening inside the app, but is not overwhelmed with tracing and debugging information. This
-#' level can be changed using `aNCA_LOG_LEVEL` environmental variable, set for example in
-#' `.Renviron` file.
-setup_logger <- function() {
-  log_layout(layout_glue_colors)
-  log_formatter(formatter_glue)
-  log_threshold(TRACE)
-  log_threshold(Sys.getenv("aNCA_LOG_LEVEL", "INFO"), index = 2)
-
-  log_dir <- "./log"
-  if (!dir.exists(log_dir)) dir.create(log_dir)
-  existing_logs <- list.files(log_dir, full.names = TRUE)
-  if (length(existing_logs) >= 5) file.remove(sort(existing_logs)[1]) # keep only five log files
-  logfile_name <- paste0(log_dir, "/aNCA_app_", format(Sys.time(), "%y%m%d-%H%M%S-"), ".log")
-
-  log_appender(appender_file(logfile_name))
-  log_appender(appender_console, index = 2)
-}
-
-#' Logs a list and data frame objects.
-#'
-#' @details
-#' Utilitary function for logging a list object (like mapping list or used settings) in
-#' a nice format. Parses a list into nice string and logs at DEBUG level. Can also process
-#' data frames, which will be converted into a list of rows.
-#'
-#' @param title Title for the logs.
-#' @param l     List object to be parsed into log. Can also be a data.frame.
-log_debug_list <- function(title, l) {
-  log_debug(aNCA:::.concatenate_list(title, l))
-}
-
 #' Needed to properly reset reactable.extras widgets
 #'
 #' @details

inst/shiny/functions/zip-utils.R

@@ -428,6 +428,12 @@ prepare_export_files <- function(target_dir,
                  detail = "Saving session info...")
     .export_session_info(target_dir)
   }
+
+  if ("session_log" %in% input$res_tree) {
+    progress$set(message = "Creating exports...",
+                 detail = "Saving session log...")
+    .export_session_log(target_dir)
+  }
   progress$inc(0.8)
 
   .clean_export_dir(target_dir, input, custom_names)
@@ -640,6 +646,45 @@ prepare_export_files <- function(target_dir,
   writeLines(lines, file.path(target_dir, "session_info.txt"))
 }
 
+#' Export the in-memory session log to a text file.
+#' @param target_dir Target directory for the export.
+#' @keywords internal
+.export_session_log <- function(target_dir) {
+  log_buffer <- get_log_buffer()
+
+  threshold <- .log_env$threshold
+  header <- c(
+    "# aNCA Session Log",
+    "#",
+    "# This file contains application events captured during your session.",
+    "# It records data upload, mapping, NCA settings, parameter selection,",
+    "# slope adjustments, exclusions, calculation results, and exports.",
+    "#",
+    "# Warnings and errors from these operations are included when caught",
+    "# by the application. Unexpected R errors or warnings from third-party",
+    "# packages that are not explicitly handled will NOT appear here.",
+    "#",
+    paste0("# Log level: ", threshold,
+           " (configurable via aNCA_LOG_LEVEL env var)"),
+    paste0("# Levels shown at current threshold: ",
+           paste(names(.LOG_LEVELS)[.LOG_LEVELS >= .LOG_LEVELS[[threshold]]],
+                 collapse = ", ")),
+    "#",
+    "# For a full reference of logged events, see:",
+    "# https://pharmaverse.github.io/aNCA/articles/session_log.html",
+    "#",
+    paste0("# Generated: ", format(Sys.time(), "%Y-%m-%d %H:%M:%S %Z")),
+    "# -------------------------------------------------------------------",
+    ""
+  )
+
+  if (length(log_buffer) == 0L) {
+    log_buffer <- "(No log entries captured during this session.)"
+  }
+
+  writeLines(c(header, log_buffer), file.path(target_dir, "session_log.txt"))
+}
+
 #' Clean Export Directory
 #' @param target_dir Target directory to clean
 #' @param input Shiny input object
@@ -677,6 +722,10 @@ prepare_export_files <- function(target_dir,
     files_req <- c(files_req, grep("session_info\\.txt$", all_files,
                                    value = TRUE))
   }
+  if ("session_log" %in% fnames) {
+    files_req <- c(files_req, grep("session_log\\.txt$", all_files,
+                                   value = TRUE))
+  }
   file.remove(all_files[!all_files %in% files_req])
 
   # Recursive directory cleanup — remove dirs that contain no files at any depth

inst/shiny/modules/tab_nca/zip.R

@@ -678,7 +678,7 @@ zip_server <- function(id, res_nca, adnca_data, settings, grouping_vars) {
     }
     items$extras            <- TREE_LIST$extras
   } else {
-    items$extras <- TREE_LIST$extras[c("settings_file", "session_info")]
+    items$extras <- TREE_LIST$extras[c("settings_file", "session_info", "session_log")]
   }
 
   items
@@ -713,7 +713,8 @@ TREE_LIST <- list(
     results_slides = "",
     r_script = "",
     settings_file = "",
-    session_info = ""
+    session_info = "",
+    session_log = ""
   )
 )
 

inst/shiny/modules/tab_tlg.R

@@ -250,7 +250,11 @@ 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 +292,11 @@ 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)