From a9612c4eacb567ee2384d8d68ea13f088b98607b Mon Sep 17 00:00:00 2001
From: yassineS <1767457+yassineS@users.noreply.github.com>
Date: Thu, 16 Apr 2026 22:44:37 +0930
Subject: [PATCH] refactor: extract duplicated warning/message pattern to
 .report_messages()

Extracts the 7-line warning/message reporting pattern that was
duplicated in permute.R, prune.R, and rescale.R into a new
.report_messages() helper function in internal.R.

Uses the renamed variables from PR #26 (warning.messages, info.messages,
param.warnings, param.messages) and uses TRUE/FALSE instead of T/F.

Addresses issue #6 from code audit (#23)
---
 R/internal.R | 27 +++++++++++++++++++++++++++
 R/permute.R  |  7 +------
 R/prune.R    |  7 +------
 R/rescale.R  |  7 +------
 4 files changed, 30 insertions(+), 18 deletions(-)

diff --git a/R/internal.R b/R/internal.R
index 7b24108..5b830c2 100644
--- a/R/internal.R
+++ b/R/internal.R
@@ -12,6 +12,33 @@
 }
 
 
+#' @title Report accumulated messages and warnings
+#' @description Centralized reporting of info/warning messages collected
+#' during argument validation. Reads from the calling environment.
+#' @noRd
+.report_messages <- function() {
+   .verbose_msg("\n")
+
+   # Report warnings
+   if (!is.null(warning.messages)) {
+      warning(warning.messages, immediate. = TRUE, call. = FALSE)
+   }
+   if (!is.null(param.warnings)) {
+      warning(param.warnings, immediate. = TRUE, call. = FALSE)
+   }
+
+   # Report info messages
+   if (!is.null(info.messages)) {
+      .verbose_msg(paste0("\n", info.messages, "\n"))
+   }
+   if (!is.null(param.messages)) {
+      .verbose_msg(paste0("\n", param.messages, "\n"))
+   }
+
+   .verbose_msg("\n")
+}
+
+
 #' @title Internal file path checker
 #' @description An internal function to check for correct file paths for
 #'  the required input files. User can either provide path to folder with all
diff --git a/R/permute.R b/R/permute.R
index 3e4d2b4..e2f149c 100644
--- a/R/permute.R
+++ b/R/permute.R
@@ -281,12 +281,7 @@ permute_polylinkr_data <- function(plr_input, permute = TRUE, n_permutations = 5
                   align = "center", col = "cyan", border_col = "cyan"))
 
    # report collated warnings and messages
-   .verbose_msg("\n")
-   if (!is.null(warning.messages)) warning(warning.messages, immediate. = T, call. = F)
-   if (!is.null(info.messages)) .verbose_msg(paste0("\n", info.messages, "\n"))
-   if (!is.null(param.warnings)) warning(param.warnings, immediate. = T, call. = F)
-   if (!is.null(param.messages)) .verbose_msg(paste0("\n", param.messages, "\n"))
-   .verbose_msg("\n")
+   .report_messages()
 
    ##=========================================================================##
    ## PART 2: Calculate standardised gene scores
diff --git a/R/prune.R b/R/prune.R
index b1dbeeb..fcbba18 100644
--- a/R/prune.R
+++ b/R/prune.R
@@ -176,12 +176,7 @@ prune_polylinkr_data <- function(plr_input, n_fdr = 300L, estimate_pi0 = TRUE,
                   align = "center", col = "cyan", border_col = "cyan"))
 
    # report collated warnings and messages
-   .verbose_msg("\n")
-   if (!is.null(warning.messages)) warning(warning.messages, immediate. = T, call. = F)
-   if (!is.null(info.messages)) .verbose_msg(paste0("\n", info.messages, "\n"))
-   if (!is.null(param.warnings)) warning(param.warnings, immediate. = T, call. = F)
-   if (!is.null(param.messages)) .verbose_msg(paste0("\n", param.messages, "\n"))
-   .verbose_msg("\n")
+   .report_messages()
 
    ##=========================================================================##
    ##PART 2: generate FDR sets and empirical prepare objects for pruning step
diff --git a/R/rescale.R b/R/rescale.R
index 4a53dc8..5286ba4 100644
--- a/R/rescale.R
+++ b/R/rescale.R
@@ -250,12 +250,7 @@ rescale_polylinkr_data <- function(plr_input, rescale = TRUE, fast = TRUE, ac =
                   align = "center", col = "cyan", border_col = "cyan"))
 
    # report collated warnings and messages
-   .verbose_msg("\n")
-   if (!is.null(warning.messages)) warning(warning.messages, immediate. = T, call. = F)
-   if (!is.null(info.messages)) .verbose_msg(paste0("\n", info.messages, "\n"))
-   if (!is.null(param.warnings)) warning(param.warnings, immediate. = T, call. = F)
-   if (!is.null(param.messages)) .verbose_msg(paste0("\n", param.messages, "\n"))
-   .verbose_msg("\n")
+   .report_messages()
 
    ##==========================================================================##
    ## PART 2: Calculate genomic autocovariance