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refactor: extract duplicated warning/message pattern to .report_messages() #30

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Merged
yassineS merged 1 commit into from
Apr 17, 2026
Merged

refactor: extract duplicated warning/message pattern to .report_messages() #30

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27 changes: 27 additions & 0 deletions R/internal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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7 changes: 1 addition & 6 deletions R/permute.R
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Expand Up @@ -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
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7 changes: 1 addition & 6 deletions R/prune.R
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Expand Up @@ -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
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7 changes: 1 addition & 6 deletions R/rescale.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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