Minor tweaks for lintr dev version

ropensci · Jun 22, 2024 · 269c947 · 269c947
1 parent 5c7fbad
commit 269c947
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Showing 10 changed files with 34 additions and 34 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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)