Fix deprecated config bindings and config_f closures in bundled data

Regenerate all 5 .rda data objects to silence deprecated $table/$parameter
active binding warnings during R CMD INSTALL lazyload, and update config_f
closures to use direct $factors access instead of $table$factors.

Author: wolski

data-raw/fix_deprecated_config.R

@@ -0,0 +1,86 @@
+# Fix deprecated $table/$parameter active bindings in serialized data objects
+#
+# Root cause: During `R CMD INSTALL`, the lazyload DB creation phase evaluates
+# all active bindings on R6 objects. The `$table` and `$parameter` active
+# bindings on AnalysisConfiguration print deprecation messages when read.
+#
+# Sources of warnings:
+#   1. data_ionstar.rda — IonstarData R6 with $config and $config_N (2 configs)
+#   2. data_IonstarProtein_subsetNorm.rda — list with $config (1 config)
+#   Total: 3 configs × 2 bindings = 6 deprecation messages
+#
+# Fix: Replace the noisy active bindings with silent versions that still return
+# self for backwards compatibility. Uses unlockBinding() to allow replacement
+# on R6's locked environments.
+#
+# Additionally fixes 3 .rda files with config_f closures that used the old
+# config$table$factors[...] syntax.
+
+library(prolfqua)
+
+#' Replace deprecated active bindings on an AnalysisConfiguration with silent versions.
+#' The R6 environment is locked, but unlockBinding() allows replacing individual bindings.
+#' The new binding function uses the R6 enclosing environment so `self` resolves correctly.
+silence_deprecated_bindings <- function(config) {
+  stopifnot(inherits(config, "AnalysisConfiguration"))
+  env <- config  # R6 public env IS the object
+  enclos <- env[[".__enclos_env__"]]
+  for (nm in c("table", "parameter")) {
+    if (exists(nm, envir = env, inherits = FALSE) && bindingIsActive(nm, env)) {
+      unlockBinding(nm, env)
+      silent_fn <- function() self
+      environment(silent_fn) <- enclos
+      makeActiveBinding(nm, silent_fn, env)
+    }
+  }
+  invisible(config)
+}
+
+# --- data_ionstar: IonstarData R6 with config + config_N ---
+load("data/data_ionstar.rda")
+silence_deprecated_bindings(data_ionstar$config)
+silence_deprecated_bindings(data_ionstar$config_N)
+usethis::use_data(data_ionstar, overwrite = TRUE)
+
+# --- data_IonstarProtein_subsetNorm: list with config ---
+load("data/data_IonstarProtein_subsetNorm.rda")
+silence_deprecated_bindings(data_IonstarProtein_subsetNorm$config)
+usethis::use_data(data_IonstarProtein_subsetNorm, overwrite = TRUE)
+
+# --- data_skylinePRMSample_A: fix config_f closure ---
+load("data/data_skylinePRMSample_A.rda")
+data_skylinePRMSample_A$config_f <- function() {
+  config <- create_config_Skyline(isotopeLabel = "Isotope.Label.Type",
+                                   ident_qValue = "Detection.Q.Value")
+  config$factors[["Time"]] = "Sampling.Time.Point"
+  return(config)
+}
+usethis::use_data(data_skylinePRMSample_A, overwrite = TRUE)
+
+# --- data_skylineSRM_HL_A: fix config_f closure ---
+load("data/data_skylineSRM_HL_A.rda")
+data_skylineSRM_HL_A$config_f <- function() {
+  skylineconfig_HL <- create_config_Skyline(isotopeLabel = "Isotope.Label",
+                                             ident_qValue = "annotation_QValue")
+  skylineconfig_HL$factors[["treatment_c"]] <- "Condition2"
+  skylineconfig_HL$factors[["time_c"]] <- "time"
+  skylineconfig_HL$is_response_transformed = FALSE
+  return(skylineconfig_HL)
+}
+usethis::use_data(data_skylineSRM_HL_A, overwrite = TRUE)
+
+# --- data_spectronautDIA250_A: fix config_f closure ---
+load("data/data_spectronautDIA250_A.rda")
+data_spectronautDIA250_A$config_f <- function() {
+  spectronautDIAData250_config <- prolfqua::create_config_Spectronaut_Peptide(
+    isotopeLabel = "Isotope.Label",
+    ident_qValue = "EG.Qvalue")
+  spectronautDIAData250_config$factors[["coding"]] = "coding"
+  spectronautDIAData250_config$factors[["sex"]] = "sex"
+  spectronautDIAData250_config$factors[["age"]] = "age"
+  spectronautDIAData250_config$factors[["Sample_id"]] = "Sample.Name"
+  return(spectronautDIAData250_config)
+}
+usethis::use_data(data_spectronautDIA250_A, overwrite = TRUE)
+
+cat("\nDone. All 5 data objects regenerated.\n")