From 2bd00a1c5b42d4f09065e1a3ab1a4ba3be25ec75 Mon Sep 17 00:00:00 2001
From: Philipp Baumann <baumann-philipp@protonmail.ch>
Date: Wed, 14 Jan 2026 22:38:53 +0100
Subject: [PATCH] chore: lint with yarl

---
 R/asd_sco_binary_format.R      |  2 +-
 R/nicolet_spa_format.R         |  4 ++--
 R/parse_raw_file_for_reading.R | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/asd_sco_binary_format.R b/R/asd_sco_binary_format.R
index 5cf9385..db0bdee 100644
--- a/R/asd_sco_binary_format.R
+++ b/R/asd_sco_binary_format.R
@@ -40,7 +40,7 @@ ASDScoBinary <- R6::R6Class("ASDScoBinary",
 
          spec.df <-
             data.frame(wavenumber=as.integer(rownames(spec.data)),
-                       intensity=spec.data[1:length(spec.data)])
+                       intensity=spec.data[seq_along(spec.data)])
 
          meta.list <- list()
          meta.list[["name"]] <- colnames(spec.data)
diff --git a/R/nicolet_spa_format.R b/R/nicolet_spa_format.R
index fddc1be..6786883 100644
--- a/R/nicolet_spa_format.R
+++ b/R/nicolet_spa_format.R
@@ -66,9 +66,9 @@ key.value.pairs <- function(path) {
 
   for (str in strings.from.spa(path)) {
     delimiter <- NULL
-    if (grepl(str, pattern="=")) {
+    if (grepl(str, pattern="=", fixed = TRUE)) {
       delimiter <- "="
-    } else if (grepl(str, pattern=":")) {
+    } else if (grepl(str, pattern=":", fixed = TRUE)) {
       delimiter <- ":"
     }
 
diff --git a/R/parse_raw_file_for_reading.R b/R/parse_raw_file_for_reading.R
index f32c5cb..9a77e9c 100644
--- a/R/parse_raw_file_for_reading.R
+++ b/R/parse_raw_file_for_reading.R
@@ -26,7 +26,7 @@ if(!dir.exists(out.directory)){dir.create(out.directory)}
 
   SpecSets <- unique(indf$SampleSpectrumSetId)
 
-  for(i in 1:length(SpecSets)){
+  for(i in seq_along(SpecSets)){
     print(paste0('Processing Spectral Set ', i, ' of ', length(SpecSets)))
     specid <- SpecSets[i]
     idxs <- which(indf$SampleSpectrumSetId==specid)
@@ -39,11 +39,11 @@ if(!dir.exists(out.directory)){dir.create(out.directory)}
     idxS <-  which(specdf$Type=='SAMPLE')
     sampDF <- specdf[idxS,]
 
-    for (j in 1:nrow(sampDF)) {
-      srec = sampDF[j,]
+    for (j in seq_len(nrow(sampDF))) {
+      srec <- sampDF[j,]
       #brec = specdf[1,]
 
-      fname = paste0(srec$'Sample ID', '_', srec$SampleSpectrumSetId, '_', srec$SpectrumId)
+      fname <- paste0(srec$'Sample ID', '_', srec$SampleSpectrumSetId, '_', srec$SpectrumId)
       odf <- rbind(bkgDF, srec)
       write.csv(odf, paste0(out.directory, '/', fname, '.hlr'), row.names = F)
 
@@ -93,7 +93,7 @@ parse.scans <- function(path, out.directory) {
 
   indf <- read.csv(path, header = T, check.names=F)
 
-  for(i in 1:nrow(indf)){
+  for(i in seq_len(nrow(indf))){
     rec <- indf[i,]
     print(paste0('Processing Spectra ', i, ' of ', nrow(indf)))
     specid <- paste0( rec$core.label, '_',  rec$core_position)