From 269c947dbcd037fbffc2686605045fc767380d44 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Sat, 22 Jun 2024 14:08:54 +0200
Subject: [PATCH] Minor tweaks for lintr dev version

---
 R/convert_tocsv.R               |  4 ++--
 R/get_metadata.R                |  4 ++--
 R/get_spec.R                    |  4 ++--
 R/parse_avantes_binary.R        | 12 ++++++------
 R/parse_avantes_converted.R     | 10 +++++-----
 R/parse_generic.R               | 14 +++++++-------
 R/parse_jdx.R                   |  2 +-
 R/parse_oceanoptics_converted.R | 10 +++++-----
 R/parse_procspec.R              |  2 +-
 R/parse_spc.R                   |  6 +++---
 10 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/R/convert_tocsv.R b/R/convert_tocsv.R
index 1cc1aa0..5c4cf43 100644
--- a/R/convert_tocsv.R
+++ b/R/convert_tocsv.R
@@ -63,7 +63,7 @@ lr_convert_tocsv <- function(where = NULL, ext = "txt", decimal = ".",
           overwrite = overwrite, metadata = metadata
         ),
         error = function(e) {
-          warning(conditionMessage(e))
+          warning(conditionMessage(e), call. = FALSE)
           return(NULL)
         })
     })
@@ -81,7 +81,7 @@ lr_convert_tocsv <- function(where = NULL, ext = "txt", decimal = ".",
 
     warning(
       "Could not import one or more files:\n",
-      paste0(files[whichfailed], collapse = "\n"),
+      paste(files[whichfailed], collapse = "\n"),
       call. = FALSE
     )
   }
diff --git a/R/get_metadata.R b/R/get_metadata.R
index ac7f032..5d4bf87 100644
--- a/R/get_metadata.R
+++ b/R/get_metadata.R
@@ -88,7 +88,7 @@ lr_get_metadata <- function(where = getwd(), ext = "ProcSpec", sep = NULL,
       tryCatch(
         gmd(x),
         error = function(e) {
-          warning(conditionMessage(e))
+          warning(conditionMessage(e), call. = FALSE)
           return(NULL)
         })
     })
@@ -104,7 +104,7 @@ lr_get_metadata <- function(where = getwd(), ext = "ProcSpec", sep = NULL,
 
     warning(
       "Could not import one or more files:\n",
-      paste0(files[whichfailed], collapse = "\n"),
+      paste(files[whichfailed], collapse = "\n"),
       call. = FALSE
     )
 
diff --git a/R/get_spec.R b/R/get_spec.R
index 5a94f94..e70d025 100644
--- a/R/get_spec.R
+++ b/R/get_spec.R
@@ -113,7 +113,7 @@ lr_get_spec <- function(where = getwd(), ext = "txt", lim = c(300, 700),
       tryCatch(
         gsp(x),
         error = function(e) {
-          warning(conditionMessage(e))
+          warning(conditionMessage(e), call. = FALSE)
           return(NULL)
         }
       )
@@ -129,7 +129,7 @@ lr_get_spec <- function(where = getwd(), ext = "txt", lim = c(300, 700),
   } else if (length(whichfailed) > 0) {
 
     warning("Could not import one or more files:\n",
-      paste0(files[whichfailed], collapse = "\n"),
+      paste(files[whichfailed], collapse = "\n"),
       call. = FALSE
     )
 
diff --git a/R/parse_avantes_binary.R b/R/parse_avantes_binary.R
index 101a2c4..b168ec0 100644
--- a/R/parse_avantes_binary.R
+++ b/R/parse_avantes_binary.R
@@ -103,9 +103,9 @@ lr_parse_trm <- function(filename) {
                      c("scope", "white", "dark"))
   } else {# scope mode
     data <- data.frame(
-      "scope" = readBin(f, "numeric", ipixlast - ipixfirst + 1, 4, endian = "little"),
-      "white" = NA_real_,
-      "dark"  = NA_real_
+      scope = readBin(f, "numeric", ipixlast - ipixfirst + 1, 4, endian = "little"),
+      white = NA_real_,
+      dark  = NA_real_
     )
   }
 
@@ -142,7 +142,7 @@ lr_parse_trm <- function(filename) {
                 dark_average, white_average, scope_average,
                 dark_boxcar, white_boxcar, scope_boxcar)
 
-  return(list("data" = data, "metadata" = metadata))
+  return(list(data = data, metadata = metadata))
 }
 
 #' @rdname lr_parse_trm
@@ -302,9 +302,9 @@ lr_parse_rfl8 <- function(filename, specnum = 1L) {
 
     mergegroup <- intToUtf8(readBin(f, "raw", n = 10, endian = "little"))
 
-    data <- as.data.frame(cbind("wl" = xcoord,
+    data <- as.data.frame(cbind(wl = xcoord,
                                 dark,
-                                "white" = reference,
+                                white = reference,
                                 scope))
     data$processed <- lr_compute_processed(data)
 
diff --git a/R/parse_avantes_converted.R b/R/parse_avantes_converted.R
index c875874..beb5a1a 100644
--- a/R/parse_avantes_converted.R
+++ b/R/parse_avantes_converted.R
@@ -77,11 +77,11 @@ lr_parse_ttt <- function(filename) {
 
   storage.mode(data) <- "numeric"
 
-  cornames <- c("wl" = "Wave",
-                "dark" = "Dark",
-                "white" = "Ref",
-                "scope" = "Sample",
-                "processed" = "Transmittance")
+  cornames <- c(wl = "Wave",
+                dark = "Dark",
+                white = "Ref",
+                scope = "Sample",
+                processed = "Transmittance")
 
   data_final <- setNames(
     as.data.frame(matrix(NA_real_, nrow = nrow(data), ncol = 5)),
diff --git a/R/parse_generic.R b/R/parse_generic.R
index 14a19d5..0bde57e 100644
--- a/R/parse_generic.R
+++ b/R/parse_generic.R
@@ -51,7 +51,7 @@
 
 lr_parse_generic <- function(filename, decimal = ".", sep = NULL) {
 
-  seps <- paste0(c("[[:blank:]]", sep), collapse = "|\\")
+  seps <- paste(c("[[:blank:]]", sep), collapse = "|\\")
 
   # Code from pavo::getspec
 
@@ -102,13 +102,13 @@ lr_parse_generic <- function(filename, decimal = ".", sep = NULL) {
 
   metadata <- rep(NA_character_, 13)
 
-  data <- data.frame("wl" = rawsplit[, 1],
-                     "dark" = NA_real_,
-                     "white" = NA_real_,
-                     "scope" = NA_real_,
-                     "processed" = rawsplit[, dim(rawsplit)[2]])
+  data <- data.frame(wl = rawsplit[, 1],
+                     dark = NA_real_,
+                     white = NA_real_,
+                     scope = NA_real_,
+                     processed = rawsplit[, dim(rawsplit)[2]])
 
   data <- data[order(data$wl), ]
 
-  return(list("data" = data, "metadata" = metadata))
+  return(list(data = data, metadata = metadata))
 }
diff --git a/R/parse_jdx.R b/R/parse_jdx.R
index c9a42c5..1c0b20f 100644
--- a/R/parse_jdx.R
+++ b/R/parse_jdx.R
@@ -99,6 +99,6 @@ lr_parse_jdx <- function(filename) {
 
   data$processed <- lr_compute_processed(data)
 
-  return(list("data" = data, "metadata" = metadata))
+  return(list(data = data, metadata = metadata))
 
 }
diff --git a/R/parse_oceanoptics_converted.R b/R/parse_oceanoptics_converted.R
index 17d4fd0..74f2000 100644
--- a/R/parse_oceanoptics_converted.R
+++ b/R/parse_oceanoptics_converted.R
@@ -150,11 +150,11 @@ lr_parse_jaz <- function(filename) {
   }
   storage.mode(data) <- "numeric"
 
-  cornames <- c("wl" = "W",
-                "dark" = "D",
-                "white" = "R",
-                "scope" = "S",
-                "processed" = "P")
+  cornames <- c(wl = "W",
+                dark = "D",
+                white = "R",
+                scope = "S",
+                processed = "P")
 
   data_final <- setNames(
     as.data.frame(matrix(NA_real_, nrow = nrow(data), ncol = 5)),
diff --git a/R/parse_procspec.R b/R/parse_procspec.R
index a21e110..f46744c 100644
--- a/R/parse_procspec.R
+++ b/R/parse_procspec.R
@@ -95,5 +95,5 @@ lr_parse_procspec <- function(filename) {
                 dark_average, white_average, scope_average,
                 dark_boxcar, white_boxcar, scope_boxcar)
 
-  return(list("data" = as.data.frame(specdf), "metadata" = metadata))
+  return(list(data = as.data.frame(specdf), metadata = metadata))
 }
diff --git a/R/parse_spc.R b/R/parse_spc.R
index 839de7e..dcb8dfe 100644
--- a/R/parse_spc.R
+++ b/R/parse_spc.R
@@ -46,9 +46,9 @@ lr_parse_spc <- function(filename) {
   processed <- readBin(f, "numeric", n = dat_len, size = 4, endian = "little")
 
   data <- cbind(wl,
-                "dark" = NA_real_,
-                "white" = NA_real_,
-                "scope" = NA_real_,
+                dark = NA_real_,
+                white = NA_real_,
+                scope = NA_real_,
                 processed)
 
   metadata <- rep(NA_character_, 13)