From 51c9e98bc8fd0fd83dc02468cf476671f2f5efd4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:45:39 +0000
Subject: [PATCH 01/10] Initial plan


From 4fcc767e941d0c40096a56172b7d958f6d0796d9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:48:59 +0000
Subject: [PATCH 02/10] refactor: replace stringr/stringi usage with base R

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 DESCRIPTION                     |  2 --
 NAMESPACE                       | 10 ------
 NEWS.md                         |  1 +
 R/interact.R                    |  3 +-
 R/read_log_file.R               | 64 +++++++++++++++------------------
 R/writer.R                      | 26 ++++----------
 tests/testthat/test-writer.R    |  1 -
 vignettes/generate-lockfile.Rmd |  3 +-
 8 files changed, 37 insertions(+), 73 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5fb05bb4..b629de88 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -45,9 +45,7 @@ Imports:
     rlang,
     stats,
     tidyr,
-    stringr,
     sessioninfo (>= 1.2),
-    stringi,
     tibble,
     digest,
     lifecycle,
diff --git a/NAMESPACE b/NAMESPACE
index f41f44b9..8616cf0a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,16 +33,6 @@ importFrom(purrr,set_names)
 importFrom(rlang,.data)
 importFrom(sessioninfo,session_info)
 importFrom(stats,aggregate)
-importFrom(stringi,stri_wrap)
-importFrom(stringr,str_c)
-importFrom(stringr,str_count)
-importFrom(stringr,str_detect)
-importFrom(stringr,str_extract)
-importFrom(stringr,str_remove)
-importFrom(stringr,str_remove_all)
-importFrom(stringr,str_replace_all)
-importFrom(stringr,str_starts)
-importFrom(stringr,str_trim)
 importFrom(tibble,tibble)
 importFrom(tidyr,all_of)
 importFrom(tidyr,complete)
diff --git a/NEWS.md b/NEWS.md
index 06acc05d..76088750 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -5,6 +5,7 @@
 ## Updates
 
 - Removed .dcf file for old Addin (#280)
+- Reworked string handling to use base R and removed `{stringr}`/`{stringi}` dependencies.
 
 ## Documentation
 
diff --git a/R/interact.R b/R/interact.R
index 00f3b527..cfe05b7e 100644
--- a/R/interact.R
+++ b/R/interact.R
@@ -140,7 +140,6 @@ run_file <- function(file) {
 #' Safely run an R script and record results, outputs, messages, errors, warnings
 #'
 #' @importFrom purrr safely discard
-#' @importFrom stringr str_starts
 #'
 #' @param file File to run
 #'
@@ -150,7 +149,7 @@ run_file <- function(file) {
 #'
 run_safely_loudly <- function(file) {
   ret <- loudly(run_safely(file))
-  set_log_element("messages", discard(ret$messages, ~ str_starts(.x, "Error")))
+  set_log_element("messages", discard(ret$messages, ~ startsWith(.x, "Error")))
   set_log_element("output", ret$output)
   set_log_element("result", ret$result$result)
   set_log_element("warnings", ret$warnings)
diff --git a/R/read_log_file.R b/R/read_log_file.R
index c3cdad90..6b45d155 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -2,11 +2,6 @@
 #'
 #' @param log_txt String vector. Object with log text lines
 #'
-#' @importFrom stringr str_detect
-#' @importFrom stringr str_count
-#' @importFrom stringr str_remove
-#' @importFrom stringr str_replace_all
-#'
 #' @return tibble that ensures formatted subsections
 #'
 #' @examples
@@ -19,21 +14,21 @@
 reformat_subsections <- function(log_txt) {
   adj_log_txt <- c()
   for (i in log_txt) {
-    adj_tf <- stringr::str_detect(
-      i,
-      "Errors:|Warnings:|Messages:|Output:|Result:"
+    adj_tf <- grepl(
+      "Errors:|Warnings:|Messages:|Output:|Result:",
+      i
     )
     if (adj_tf) {
-      nrem <- stringr::str_count(i)
-      i <- stringr::str_remove(i, ":")
+      nrem <- nchar(i)
+      i <- sub(":", "", i)
       i <-
         paste("-", i, paste(rep("-", 54 - nrem), collapse = ""),
           collapse = ""
         )
     }
     # replace utf8 line and double line to ascii due to cli symbol variation
-    i <- stringr::str_replace_all(i, "\u2550", "=")
-    i <- stringr::str_replace_all(i, "\u2500", "=")
+    i <- gsub("\u2550", "=", i, fixed = TRUE)
+    i <- gsub("\u2500", "=", i, fixed = TRUE)
     adj_log_txt <- c(adj_log_txt, i)
   }
   return(adj_log_txt)
@@ -43,8 +38,6 @@ reformat_subsections <- function(log_txt) {
 #'
 #' @param adj_log_txt String vector. Object with formatted log text lines
 #'
-#' @importFrom stringr str_remove_all
-#'
 #' @return list that includes nested log sections
 #'
 #' @noRd
@@ -67,8 +60,7 @@ nest_sections <- function(adj_log_txt) {
       }
     }
   }
-  sect_headers <-
-    stringr::str_remove_all(sect_headers, "-?\\s{3,}-?")
+  sect_headers <- gsub("-?\\s{3,}-?", "", sect_headers)
   names(sect_info) <- sect_headers
 
   return(sect_info)
@@ -79,26 +71,27 @@ nest_sections <- function(adj_log_txt) {
 #' @param adj_log_txt String vector. Object with formatted log text lines
 #' @param sect_info String vector. Object with nested sections
 #'
-#' @importFrom stringr str_extract
-#' @importFrom stringr str_trim
-#' @importFrom stringr str_remove_all
-#'
 #' @return list that includes nested log subsections
 #'
 #' @noRd
 #'
 nest_subsections <- function(adj_log_txt, sect_info) {
+  extract_match <- function(x, pattern) {
+    reg_match <- regexpr(pattern, x, perl = TRUE)
+    result <- regmatches(x, reg_match)
+    result[reg_match == -1] <- NA_character_
+    result
+  }
+
   subsect_headers <- stats::na.omit(
-    stringr::str_extract(adj_log_txt, "[\\-|\\=]\\s\\w+\\s(\\w+\\s)?[\\-|\\=]{3,70}")
+    extract_match(adj_log_txt, "[\\-|\\=]\\s\\w+\\s(\\w+\\s)?[\\-|\\=]{3,70}")
   )
   subset_sections <- function(section) {
     subsect_status <- FALSE
     subsect_info <- list()
     for (i in section) {
       if (i %in% subsect_headers) {
-        latest_subsect <- stringr::str_trim(
-          stringr::str_remove_all(i, "[\\-|\\=]")
-        )
+        latest_subsect <- trimws(gsub("[\\-|\\=]", "", i))
         subsect_status <- TRUE
       } else if (subsect_status) {
         subsect_info[[latest_subsect]] <-
@@ -135,7 +128,6 @@ nest_log <- function(adj_log_txt) {
 #'
 #' @importFrom tibble tibble
 #' @importFrom tidyr separate
-#' @importFrom stringr str_replace_all
 #' @importFrom dplyr rename_with
 #' @importFrom dplyr mutate
 #'
@@ -170,7 +162,7 @@ parse_log <- function(nested_log) {
     parsed_log$`User and File Information` <-
       nested_log$`User and File Information` %>%
       unlist() %>%
-      stringr::str_trim() %>%
+      trimws() %>%
       tibble::tibble() %>%
       tidyr::separate(".",
         sep = "\\: ",
@@ -182,7 +174,7 @@ parse_log <- function(nested_log) {
     parsed_log$`Session Information`$`Session info` <-
       nested_log$`Session Information`$`Session info` %>%
       unlist() %>%
-      stringr::str_trim() %>%
+      trimws() %>%
       tibble::tibble() %>%
       tidyr::separate(".",
         sep = "\\s",
@@ -190,13 +182,13 @@ parse_log <- function(nested_log) {
         extra = "merge",
         fill = "right"
       ) %>%
-      dplyr::mutate(dplyr::across(tidyselect::where(is.character), stringr::str_trim))
+      dplyr::mutate(dplyr::across(tidyselect::where(is.character), trimws))
     parsed_log$`Session Information`$`Packages` <-
       nested_log$`Session Information`$`Packages` %>%
       # remove indicator whether the package is attached to the search path
-      stringr::str_replace_all("\\*", " ") %>%
+      gsub("\\*", " ", x = .) %>%
       # account for loaded packages due to load_all()
-      stringr::str_replace_all(" P ", "   ") %>%
+      gsub(" P ", "   ", x = .) %>%
       readr::read_table(skip = 1, col_names = FALSE)
 
     # handle case where log is has 7 columns due to sessioninfo v1.2.2 or earlier
@@ -213,8 +205,8 @@ parse_log <- function(nested_log) {
           "r_version"
         )) %>%
         dplyr::mutate(
-          lang = stringr::str_remove(lang, "\\("),
-          r_version = stringr::str_remove(r_version, "\\)")
+          lang = sub("\\(", "", lang),
+          r_version = sub("\\)", "", r_version)
         )
     } else {
       parsed_log$`Session Information`$`Packages` <-
@@ -230,7 +222,7 @@ parse_log <- function(nested_log) {
 
     parsed_log$`Session Information`$`External software` <-
       nested_log$`Session Information`$`External software` %>%
-      stringr::str_trim() %>%
+      trimws() %>%
       tibble::tibble() %>%
       tidyr::separate(".",
         sep = "\\s",
@@ -238,14 +230,14 @@ parse_log <- function(nested_log) {
         extra = "merge",
         fill = "right"
       ) %>%
-      dplyr::mutate(dplyr::across(tidyselect::where(is.character), stringr::str_trim))
+      dplyr::mutate(dplyr::across(tidyselect::where(is.character), trimws))
   }
 
   if ("Repo URLs" %in% names(nested_log)) {
     parsed_log$`Repo URLs` <-
       nested_log$`Repo URLs` %>%
       unlist() %>%
-      stringr::str_trim() %>%
+      trimws() %>%
       tibble::tibble() %>%
       tidyr::separate(".",
         sep = "\\:\\s+",
@@ -269,7 +261,7 @@ parse_log <- function(nested_log) {
         sep = "\\} ",
         into = c("library", "function_names")
       ) %>%
-      dplyr::mutate(library = stringr::str_remove(library, "\\{"))
+      dplyr::mutate(library = sub("\\{", "", library))
   }
 
   if ("Program Run Time Information" %in% names(nested_log)) {
diff --git a/R/writer.R b/R/writer.R
index 6f94b114..5f34bb7e 100644
--- a/R/writer.R
+++ b/R/writer.R
@@ -43,8 +43,6 @@ write_metadata <- function() {
 #' Format log.rx's session info attribute for writing
 #'
 #' @importFrom purrr map_chr
-#' @importFrom stringi stri_wrap
-#' @importFrom stringr str_c
 #'
 #' @return A vector of log.rx's session info attribute
 #'
@@ -59,11 +57,8 @@ write_session_info <- function() {
       .x
     )) %>%
     # wrap any other elements over 80 characters
-    map_chr(~ stri_wrap(.x,
-      width = 80, exdent = 2, simplify = FALSE, use_length = TRUE,
-      normalize = FALSE, whitespace_only = TRUE
-    ) %>%
-      map_chr(~ str_c(.x, collapse = "\n\t", character(1))))
+    map_chr(~ strwrap(.x, width = 80, exdent = 2) %>%
+      paste(collapse = "\n\t"))
 
   return(session_info)
 }
@@ -247,7 +242,7 @@ write_errors <- function() {
 
   paste0(
     "Errors:\n\t",
-    str_replace_all(errors$message, "\n", "\n\t")
+    gsub("\n", "\n\t", errors$message, fixed = TRUE)
   )
 }
 
@@ -269,7 +264,6 @@ write_warnings <- function() {
 #' Format messages attribute for writing
 #'
 #' @importFrom purrr map
-#' @importFrom stringr str_remove_all
 #'
 #' @return A formatted vector of messages
 #'
@@ -277,7 +271,7 @@ write_warnings <- function() {
 #'
 write_messages <- function() {
   messages <- get_log_element("messages") %>%
-    map(~ str_remove_all(.x, "\n"))
+    map(~ gsub("\n", "", .x, fixed = TRUE))
 
   paste0(
     "Messages:\n\t",
@@ -287,8 +281,6 @@ write_messages <- function() {
 
 #' Format output attribute for writing
 #'
-#' @importFrom stringr str_replace_all
-#'
 #' @return A formatted vector of output
 #'
 #' @noRd
@@ -298,7 +290,7 @@ write_output <- function() {
 
   paste0(
     "Output:\n\t",
-    str_replace_all(output, "\n", "\n\t")
+    gsub("\n", "\n\t", output, fixed = TRUE)
   )
 }
 
@@ -361,12 +353,6 @@ write_extra_info <- function() {
       call. = FALSE
     )
   }
-  if (!requireNamespace("stringr", quietly = TRUE)) {
-    stop(
-      "Package \"stringr\" must be installed to use this function.",
-      call. = FALSE
-    )
-  }
   extra_info <- get_log_element("extra_info")
   results <- yaml::as.yaml(
     extra_info,
@@ -375,6 +361,6 @@ write_extra_info <- function() {
       logical = yaml::verbatim_logical
     )
   )
-  results <- stringr::str_split(results, pattern = "\n")[[1]]
+  results <- strsplit(results, split = "\n", fixed = TRUE)[[1]]
   return(results)
 }
diff --git a/tests/testthat/test-writer.R b/tests/testthat/test-writer.R
index b8805b7b..f3a5a786 100644
--- a/tests/testthat/test-writer.R
+++ b/tests/testthat/test-writer.R
@@ -292,7 +292,6 @@ test_that("write_repo_urls will return a formatted log output element", {
 
 test_that("write_extra_info will return a formatted log output element", {
   skip_if_not_installed("yaml")
-  skip_if_not_installed("stringr")
   options("log.rx" = NULL)
   ref_extra_info1 <- list("some info", "more info")
   fp <- test_path("ref", "safely_loudly_test_file_result.R")
diff --git a/vignettes/generate-lockfile.Rmd b/vignettes/generate-lockfile.Rmd
index f8a1c99c..49da2f70 100644
--- a/vignettes/generate-lockfile.Rmd
+++ b/vignettes/generate-lockfile.Rmd
@@ -19,7 +19,6 @@ knitr::opts_chunk$set(
 
 ```{r setup, message = FALSE}
 library(logrx)
-library(stringr)
 library(dplyr)
 library(tidyr)
 library(renv)
@@ -55,7 +54,7 @@ Create a renv lockfile based on the used packages mentioned in the log file.
 
 ```{r gen_lockfile, error = TRUE}
 pkgs <- parsedFile$`Used Package and Functions` %>%
-  transmute(package_name = str_extract(library, "(?<=package\\:).+"))
+  transmute(package_name = sub("^.*package\\:", "", library))
 
 used_pkgs <- parsedFile$`Session Information`$Packages %>%
   filter(package %in% pkgs$package_name)

From 6515d987fb6a824ea2f6bf966f1b11f1f8d89ba3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:49:36 +0000
Subject: [PATCH 03/10] chore: address review feedback on base regex migration

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R               | 1 +
 vignettes/generate-lockfile.Rmd | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index 6b45d155..c0d501b4 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -76,6 +76,7 @@ nest_sections <- function(adj_log_txt) {
 #' @noRd
 #'
 nest_subsections <- function(adj_log_txt, sect_info) {
+  # Extract the first regex match from each string, returning NA for no match.
   extract_match <- function(x, pattern) {
     reg_match <- regexpr(pattern, x, perl = TRUE)
     result <- regmatches(x, reg_match)
diff --git a/vignettes/generate-lockfile.Rmd b/vignettes/generate-lockfile.Rmd
index 49da2f70..3d795a91 100644
--- a/vignettes/generate-lockfile.Rmd
+++ b/vignettes/generate-lockfile.Rmd
@@ -54,7 +54,7 @@ Create a renv lockfile based on the used packages mentioned in the log file.
 
 ```{r gen_lockfile, error = TRUE}
 pkgs <- parsedFile$`Used Package and Functions` %>%
-  transmute(package_name = sub("^.*package\\:", "", library))
+  transmute(package_name = sub("^package\\:", "", library))
 
 used_pkgs <- parsedFile$`Session Information`$Packages %>%
   filter(package %in% pkgs$package_name)

From 121f47b36346cd6b86c1e1525942c97891547b0e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:50:07 +0000
Subject: [PATCH 04/10] style: improve variable and helper comment clarity

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index c0d501b4..d8f9576e 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -19,10 +19,10 @@ reformat_subsections <- function(log_txt) {
       i
     )
     if (adj_tf) {
-      nrem <- nchar(i)
+      char_count <- nchar(i)
       i <- sub(":", "", i)
       i <-
-        paste("-", i, paste(rep("-", 54 - nrem), collapse = ""),
+        paste("-", i, paste(rep("-", 54 - char_count), collapse = ""),
           collapse = ""
         )
     }
@@ -76,7 +76,7 @@ nest_sections <- function(adj_log_txt) {
 #' @noRd
 #'
 nest_subsections <- function(adj_log_txt, sect_info) {
-  # Extract the first regex match from each string, returning NA for no match.
+  # Extract the first regex match from each string and return NA when no match exists.
   extract_match <- function(x, pattern) {
     reg_match <- regexpr(pattern, x, perl = TRUE)
     result <- regmatches(x, reg_match)

From 2e141d0165e3c2e6ee04b72f0a4ee808b9b758d3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:50:56 +0000
Subject: [PATCH 05/10] test: cover subsection extraction behavior and fix
 header padding

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R           |  2 +-
 tests/testthat/test-parse.R | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index d8f9576e..07a7d7cb 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -19,8 +19,8 @@ reformat_subsections <- function(log_txt) {
       i
     )
     if (adj_tf) {
-      char_count <- nchar(i)
       i <- sub(":", "", i)
+      char_count <- nchar(i)
       i <-
         paste("-", i, paste(rep("-", 54 - char_count), collapse = ""),
           collapse = ""
diff --git a/tests/testthat/test-parse.R b/tests/testthat/test-parse.R
index 12ffa984..2ae4726f 100644
--- a/tests/testthat/test-parse.R
+++ b/tests/testthat/test-parse.R
@@ -55,3 +55,24 @@ test_that("read_log_file will parse a logrx log file and create the necessary ob
   rm(scriptPath, logDir, parsedFile)
   log_remove()
 })
+
+test_that("nest_subsections handles both matched and unmatched subsection headers", {
+  matched_headers <- c("- Session info -------")
+  section_with_header <- list(
+    `Session Information` = c("- Session info -------", " setting value", " foo bar")
+  )
+
+  matched_result <- logrx:::nest_subsections(matched_headers, section_with_header)
+  expect_named(matched_result[[1]], "Session info")
+  expect_identical(
+    matched_result[[1]][["Session info"]],
+    c(" setting value", " foo bar")
+  )
+
+  no_headers <- c("plain text")
+  section_without_header <- list(`Session Information` = c("line one", "line two"))
+  unmatched_result <- logrx:::nest_subsections(no_headers, section_without_header)
+  expect_length(unmatched_result[[1]], 2)
+  expect_identical(unmatched_result[[1]][[1]], "line one")
+  expect_identical(unmatched_result[[1]][[2]], "line two")
+})

From 2b0f9f70221c9855c4b52e24f2628a41dd61c21b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:51:30 +0000
Subject: [PATCH 06/10] fix: harden regex extraction and preserve original
 padding behavior

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index 07a7d7cb..50bd9090 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -19,8 +19,8 @@ reformat_subsections <- function(log_txt) {
       i
     )
     if (adj_tf) {
-      i <- sub(":", "", i)
       char_count <- nchar(i)
+      i <- sub(":", "", i)
       i <-
         paste("-", i, paste(rep("-", 54 - char_count), collapse = ""),
           collapse = ""
@@ -79,8 +79,11 @@ nest_subsections <- function(adj_log_txt, sect_info) {
   # Extract the first regex match from each string and return NA when no match exists.
   extract_match <- function(x, pattern) {
     reg_match <- regexpr(pattern, x, perl = TRUE)
-    result <- regmatches(x, reg_match)
-    result[reg_match == -1] <- NA_character_
+    result <- rep(NA_character_, length(x))
+    has_match <- reg_match != -1
+    if (any(has_match)) {
+      result[has_match] <- regmatches(x[has_match], reg_match[has_match])
+    }
     result
   }
 

From 4f765c086d07412817a431edde90d581fc74a707 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:52:06 +0000
Subject: [PATCH 07/10] chore: align wrap behavior and improve helper naming

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R | 6 +++---
 R/writer.R        | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index 50bd9090..f3c4a394 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -78,11 +78,11 @@ nest_sections <- function(adj_log_txt) {
 nest_subsections <- function(adj_log_txt, sect_info) {
   # Extract the first regex match from each string and return NA when no match exists.
   extract_match <- function(x, pattern) {
-    reg_match <- regexpr(pattern, x, perl = TRUE)
+    match_positions <- regexpr(pattern, x, perl = TRUE)
     result <- rep(NA_character_, length(x))
-    has_match <- reg_match != -1
+    has_match <- match_positions != -1
     if (any(has_match)) {
-      result[has_match] <- regmatches(x[has_match], reg_match[has_match])
+      result[has_match] <- regmatches(x[has_match], match_positions[has_match])
     }
     result
   }
diff --git a/R/writer.R b/R/writer.R
index 5f34bb7e..d905889c 100644
--- a/R/writer.R
+++ b/R/writer.R
@@ -57,7 +57,7 @@ write_session_info <- function() {
       .x
     )) %>%
     # wrap any other elements over 80 characters
-    map_chr(~ strwrap(.x, width = 80, exdent = 2) %>%
+    map_chr(~ strwrap(.x, width = 80, exdent = 2, whitespace = FALSE) %>%
       paste(collapse = "\n\t"))
 
   return(session_info)

From 466528c27bfd5afc41377dbc86f6a49bf35c18c0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:52:56 +0000
Subject: [PATCH 08/10] fix: resolve remaining review nits in base string
 replacements

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R               | 4 ++--
 R/writer.R                      | 2 +-
 vignettes/generate-lockfile.Rmd | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index f3c4a394..a65cb927 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -190,9 +190,9 @@ parse_log <- function(nested_log) {
     parsed_log$`Session Information`$`Packages` <-
       nested_log$`Session Information`$`Packages` %>%
       # remove indicator whether the package is attached to the search path
-      gsub("\\*", " ", x = .) %>%
+      gsub("*", " ", x = ., fixed = TRUE) %>%
       # account for loaded packages due to load_all()
-      gsub(" P ", "   ", x = .) %>%
+      gsub(" P ", "   ", x = ., fixed = TRUE) %>%
       readr::read_table(skip = 1, col_names = FALSE)
 
     # handle case where log is has 7 columns due to sessioninfo v1.2.2 or earlier
diff --git a/R/writer.R b/R/writer.R
index d905889c..5f34bb7e 100644
--- a/R/writer.R
+++ b/R/writer.R
@@ -57,7 +57,7 @@ write_session_info <- function() {
       .x
     )) %>%
     # wrap any other elements over 80 characters
-    map_chr(~ strwrap(.x, width = 80, exdent = 2, whitespace = FALSE) %>%
+    map_chr(~ strwrap(.x, width = 80, exdent = 2) %>%
       paste(collapse = "\n\t"))
 
   return(session_info)
diff --git a/vignettes/generate-lockfile.Rmd b/vignettes/generate-lockfile.Rmd
index 3d795a91..816d0109 100644
--- a/vignettes/generate-lockfile.Rmd
+++ b/vignettes/generate-lockfile.Rmd
@@ -54,7 +54,7 @@ Create a renv lockfile based on the used packages mentioned in the log file.
 
 ```{r gen_lockfile, error = TRUE}
 pkgs <- parsedFile$`Used Package and Functions` %>%
-  transmute(package_name = sub("^package\\:", "", library))
+  transmute(package_name = sub("package:", "", library, fixed = TRUE))
 
 used_pkgs <- parsedFile$`Session Information`$Packages %>%
   filter(package %in% pkgs$package_name)

From 6f9e32b41048c78df53f0d7c2c3fe4ab4f1955b9 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:53:41 +0000
Subject: [PATCH 09/10] chore: clarify extract helper and normalize gsub call
 style

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index a65cb927..8d605049 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -76,7 +76,8 @@ nest_sections <- function(adj_log_txt) {
 #' @noRd
 #'
 nest_subsections <- function(adj_log_txt, sect_info) {
-  # Extract the first regex match from each string and return NA when no match exists.
+  # Extract the first regex match from each string in `x` using `pattern`.
+  # Returns a character vector the same length as `x`, with `NA` for no match.
   extract_match <- function(x, pattern) {
     match_positions <- regexpr(pattern, x, perl = TRUE)
     result <- rep(NA_character_, length(x))
@@ -190,9 +191,9 @@ parse_log <- function(nested_log) {
     parsed_log$`Session Information`$`Packages` <-
       nested_log$`Session Information`$`Packages` %>%
       # remove indicator whether the package is attached to the search path
-      gsub("*", " ", x = ., fixed = TRUE) %>%
+      gsub("\\*", " ", ., fixed = TRUE) %>%
       # account for loaded packages due to load_all()
-      gsub(" P ", "   ", x = ., fixed = TRUE) %>%
+      gsub(" P ", "   ", ., fixed = TRUE) %>%
       readr::read_table(skip = 1, col_names = FALSE)
 
     # handle case where log is has 7 columns due to sessioninfo v1.2.2 or earlier

From d22a87ca325de82b8b7abe147d547b4ed1fa909f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sun, 19 Apr 2026 19:54:10 +0000
Subject: [PATCH 10/10] docs: expand inline helper parameter description

Agent-Logs-Url: https://github.com/pharmaverse/logrx/sessions/1f987006-2fc0-4e5a-83dd-83305347351d

Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
---
 R/read_log_file.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/read_log_file.R b/R/read_log_file.R
index 8d605049..9793214a 100644
--- a/R/read_log_file.R
+++ b/R/read_log_file.R
@@ -77,6 +77,8 @@ nest_sections <- function(adj_log_txt) {
 #'
 nest_subsections <- function(adj_log_txt, sect_info) {
   # Extract the first regex match from each string in `x` using `pattern`.
+  # x: character vector of strings to inspect.
+  # pattern: regular expression pattern to extract.
   # Returns a character vector the same length as `x`, with `NA` for no match.
   extract_match <- function(x, pattern) {
     match_positions <- regexpr(pattern, x, perl = TRUE)