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Merged
tonywu1999 merged 3 commits into from
Jul 16, 2026
Merged

Remove log4r dependency (replace with base R logging) #141

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63f46a5
Remove log4r dependency (replace with base R logging)
swaraj-neu Jul 16, 2026
2f89788
Remove bracketed roxygen title
swaraj-neu Jul 16, 2026
17be83f
reset version number
tonywu1999 Jul 16, 2026
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1 change: 0 additions & 1 deletion DESCRIPTION
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Expand Up @@ -19,7 +19,6 @@ Depends:
R (>= 4.0)
Imports:
data.table,
log4r,
methods,
checkmate,
utils,
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2 changes: 0 additions & 2 deletions NAMESPACE
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Expand Up @@ -42,8 +42,6 @@ importFrom(data.table,melt)
importFrom(data.table,rbindlist)
importFrom(data.table,setnames)
importFrom(data.table,uniqueN)
importFrom(log4r,console_appender)
importFrom(log4r,file_appender)
importFrom(methods,new)
importFrom(stats,na.omit)
importFrom(utils,sessionInfo)
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55 changes: 43 additions & 12 deletions R/utils_logging.R
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@@ -1,4 +1,4 @@
#' log4r appender used not to write messages
#' Appender used not to write messages
#'
#' A convenience function written to save time on checking if messages should
#' be printed or logs should be written to a file.
Expand All @@ -12,9 +12,41 @@
}


#' Format one log line: level, timestamp, message
#'
#' Message parts are joined with paste0, never sprintf, so a literal percent
#' sign is written verbatim.
#' @keywords internal
.formatLogMessage = function(level, ...) {
timestamp = format(Sys.time(), "%Y-%m-%d %H:%M:%S")
level_field = formatC(level, width = 5L, flag = "-")
paste0(level_field, " [", timestamp, "] ", paste0(..., collapse = ""), "\n")
}


#' File appender: returns a function(level, ...) that writes one line to a file
#' @keywords internal
.fileAppender = function(log_file_path, append = TRUE) {
force(log_file_path)
force(append)
function(level, ...) {
cat(.formatLogMessage(level, ...), file = log_file_path, sep = "",
append = append)
}
}
Comment on lines +27 to +36

@coderabbitai coderabbitai Bot Jul 16, 2026

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🗄️ Data Integrity & Integration | 🟠 Major | ⚡ Quick win

🧩 Analysis chain

🏁 Script executed:

#!/bin/bash
# Verify the behavior of R's cat function when append=FALSE
Rscript -e '
path <- "test_log.txt"
cat("First log line\n", file=path, append=FALSE)
cat("Second log line\n", file=path, append=FALSE)
cat("File contents:\n")
cat(readLines(path), sep="\n")
'

Repository: Vitek-Lab/MSstatsConvert

Length of output: 207

🏁 Script executed:

#!/bin/bash
set -euo pipefail

# Inspect the target file with line numbers and surrounding context.
git ls-files 'R/utils_logging.R'
wc -l R/utils_logging.R
cat -n R/utils_logging.R | sed -n '1,120p'

# Search for .fileAppender usages and related logging helpers.
rg -n "\.fileAppender|append = FALSE|fileAppender|formatLogMessage|log_file_path" R

Repository: Vitek-Lab/MSstatsConvert

Length of output: 11381

Log file is truncated on every write when append = FALSE. In R/utils_logging.R:29-35, the closure passes append = append to cat() for every message, so an existing file gets reopened in truncate mode on each log call and only the last entry survives. Truncate once when the appender is created, then always write with append = TRUE.

🤖 Prompt for AI Agents 
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@R/utils_logging.R` around lines 27 - 36, Update .fileAppender so append =
FALSE truncates the log file once during appender creation, then make each
closure write use append = TRUE. Preserve append = TRUE behavior and ensure
multiple log calls retain all entries.



#' Console appender: returns a function(level, ...) that writes one line to console
#' @keywords internal
.consoleAppender = function() {
function(level, ...) {
cat(.formatLogMessage(level, ...))
}
}


#' Set default logging object when package is loaded
#' @param ... ignored
#' @importFrom log4r file_appender console_appender
#' @return none, sets options called MSstatsLog and MSstatsMsg
#' @keywords internal
.onLoad = function(...) {
Expand All @@ -24,11 +56,11 @@
path = paste0("./MSstats_log_", gsub("[ :\\-]", "_", time_now), ".log")

if (is.null(logs)) {
ms_logs = file_appender(path)
ms_logs = .fileAppender(path)
options(MSstatsLog = ms_logs)
}
if (is.null(msgs)) {
ms_messages = console_appender()
ms_messages = .consoleAppender()
options(MSstatsMsg = ms_messages)
}
}
Expand Down Expand Up @@ -79,24 +111,23 @@ MSstatsLogsSettings = function(use_log_file = TRUE, append = FALSE,

if (use_log_file) {
if (!is.null(log_file_path)) {
file_appender = log4r::file_appender(log_file_path,
append = append)
file_logger = .fileAppender(log_file_path, append = append)
} else {
time_now = Sys.time()
log_file_path = paste0(base, gsub("[ :\\-]", "_", time_now),
".log")
file_appender = log4r::file_appender(log_file_path)
file_logger = .fileAppender(log_file_path)
}
} else {
file_appender = .nullAppender
file_logger = .nullAppender
}

if (verbose) {
console_appender = console_appender()
console_logger = .consoleAppender()
} else {
console_appender = .nullAppender
console_logger = .nullAppender
}
loggers = list(file_appender, console_appender)
loggers = list(file_logger, console_logger)
names(loggers) = paste0(pkg_name, c("Log", "Msg"))
do.call(options, loggers)
invisible(TRUE)
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12 changes: 12 additions & 0 deletions man/dot-consoleAppender.Rd
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12 changes: 12 additions & 0 deletions man/dot-fileAppender.Rd
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13 changes: 13 additions & 0 deletions man/dot-formatLogMessage.Rd
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2 changes: 1 addition & 1 deletion man/dot-nullAppender.Rd
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2 changes: 1 addition & 1 deletion vignettes/msstats_data_format.Rmd
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Expand Up @@ -75,7 +75,7 @@ to store fraction labels.

# Logging

`MSstatsConvert` allows for flexible logging based on the `log4r` package.
`MSstatsConvert` allows for flexible logging.
Information about preprocessing steps can be written to a file, to a console,
to both or to neither.
The `MSstatsLogsSettings` function helps manage log settings.
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