Merge pull request #214 from mhpob/dev-internal-func-warnings

Pass R CMD check with no errors
ocean-tracking-network · Feb 16, 2024 · a5f0b1b · a5f0b1b
2 parents 13c5709 + 5c8a9e4
commit a5f0b1b
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Showing 33 changed files with 722 additions and 632 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,4 @@
 ^README\.Rmd$
 ^README-.*\.png$
 ^\.github$
+^R/util-intern_pkg_man\.r$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -47,3 +47,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          error-on: '"error"'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,31 +10,32 @@ Imports:
 		data.table,
 		dplyr,
 		fasterize,
-		fasttime,
 		gdalUtilities,
 		geodist,
 		gdistance,
 		geosphere,
 		jsonlite,
-		knitr,
 		lubridate,
 		magrittr,
-		methods,
 		plotrix,
 		purrr,
 		raster,
 		readxl,
-		rmarkdown,
 		sf,
 		sp,
 		tibble,
 		tidyr,
+		units,
 		zip
 Suggests: 
 		gganimate,
 		gifski,
+		knitr,
+		methods,
 		png,
-    testthat (>= 3.0.0),
+		rmarkdown,
+		terra,
+		testthat (>= 3.0.0),
 		tint
 URL: https://github.com/ocean-tracking-network/glatos
 BugReports: https://github.com/ocean-tracking-network/glatos/issues

diff --git a/R/class-glatos_animals.r b/R/class-glatos_animals.r
@@ -71,24 +71,28 @@
 #' ga_tbl <- as_glatos_animals(x_tbl)
 #'
 #'
+#' # All below will error as invalid
+#'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
 #' x2 <- rename(x,
 #'   fish_name = animal_id,
 #'   release_timestamp = utc_release_date_time
 #' )
 #'
-#' ga2 <- as_glatos_animals(x2)
-#'
+#' try(
+#'   ga2 <- as_glatos_animals(x2)
+#' )
 #'
-#' # data.grame input; wrong column class
+#' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   animal_id = as.integer(animal_id),
 #'   utc_release_date_time = as.character(utc_release_date_time)
 #' )
 #'
-#' ga3 <- as_glatos_animals(x3)
-#'
+#' try(
+#'   ga3 <- as_glatos_animals(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/class-glatos_detections.r b/R/class-glatos_detections.r
@@ -73,24 +73,28 @@
 #' gd_tbl <- as_glatos_detections(x_tbl)
 #'
 #'
+#' # All below will error as invalid
+#'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
 #' x2 <- rename(x,
 #'   fish_id = animal_id,
 #'   det_date_time = detection_timestamp_utc
 #' )
 #'
-#' gd2 <- as_glatos_detections(x2)
-#'
+#' try(
+#'   gd2 <- as_glatos_detections(x2)
+#' )
 #'
 #' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   animal_id = as.integer(animal_id),
 #'   detection_timestamp_utc = as.character(detection_timestamp_utc)
 #' )
 #'
-#' gr3 <- as_glatos_detections(x3)
-#'
+#' try(
+#'   gr3 <- as_glatos_detections(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/class-glatos_receivers.r b/R/class-glatos_receivers.r
@@ -86,6 +86,7 @@
 #'
 #' gr_tbl <- as_glatos_receivers(x_tbl)
 #'
+#' # All below will error as invalid
 #'
 #' # data.frame input; missing column name
 #' library(dplyr) # for rename
@@ -94,17 +95,19 @@
 #'   deploy_timestamp = deploy_date_time
 #' )
 #'
-#' gr2 <- as_glatos_receivers(x2)
-#'
+#' try(
+#'   gr2 <- as_glatos_receivers(x2)
+#' )
 #'
 #' # data.frame input; wrong column class
 #' x3 <- mutate(x,
 #'   ins_serial_no = as.integer(ins_serial_no),
 #'   deploy_date_time = as.character(deploy_date_time)
 #' )
 #'
-#' gr3 <- as_glatos_receivers(x3)
-#'
+#' try(
+#'   gr3 <- as_glatos_receivers(x3)
+#' )
 #'
 #' # Validation and checking
 #'

diff --git a/R/load-read_glatos_detections.r b/R/load-read_glatos_detections.r
@@ -53,9 +53,9 @@ read_glatos_detections <- function(det_file, version = NULL) {
   # Identify detection file version
   id_det_version <- function(det_file) {
     det_col_names <- names(data.table::fread(det_file, nrows = 0))
-    if (all(glatos:::glatos_detection_schema$v1.4$name %in% det_col_names)) {
+    if (all(glatos_detection_schema$v1.4$name %in% det_col_names)) {
       return("1.4")
-    } else if (all(glatos:::glatos_detection_schema$v1.3$name %in% det_col_names)) {
+    } else if (all(glatos_detection_schema$v1.3$name %in% det_col_names)) {
       return("1.3")
     } else {
       stop("Detection file version could not be identified.")
@@ -65,15 +65,15 @@ read_glatos_detections <- function(det_file, version = NULL) {
   if (is.null(version)) {
     version <- id_det_version(det_file)
   } else if (!(paste0("v", version) %in%
-    names(glatos:::glatos_detection_schema))) {
+    names(glatos_detection_schema))) {
     stop(paste0("Detection file version ", version, " is not supported."))
   }
 
   #-Detections v1.3 or v1.4-----------------------------------------------------
   if (version %in% c("1.3", "1.4")) {
     vversion <- paste0("v", version)
 
-    col_classes <- glatos:::glatos_detection_schema[[vversion]]$type
+    col_classes <- glatos_detection_schema[[vversion]]$type
     timestamp_cols <- which(col_classes == "POSIXct")
     date_cols <- which(col_classes == "Date")
     col_classes[c(timestamp_cols, date_cols)] <- "character"
@@ -89,9 +89,9 @@ read_glatos_detections <- function(det_file, version = NULL) {
     options(lubridate.fasttime = TRUE)
     for (j in timestamp_cols) {
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
+        j = glatos_detection_schema[[vversion]]$name[j],
         value = lubridate::parse_date_time(
-          dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]],
+          dtc[[glatos_detection_schema[[vversion]]$name[j]]],
           orders = "ymd HMS",
           tz = "UTC"
         )
@@ -100,15 +100,15 @@ read_glatos_detections <- function(det_file, version = NULL) {
     # coerce dates to date
     for (j in date_cols) {
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
-        value = ifelse(dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]] == "",
+        j = glatos_detection_schema[[vversion]]$name[j],
+        value = ifelse(dtc[[glatos_detection_schema[[vversion]]$name[j]]] == "",
           NA,
-          dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]]
+          dtc[[glatos_detection_schema[[vversion]]$name[j]]]
         )
       )
       data.table::set(dtc,
-        j = glatos:::glatos_detection_schema[[vversion]]$name[j],
-        value = as.Date(dtc[[glatos:::glatos_detection_schema[[vversion]]$name[j]]])
+        j = glatos_detection_schema[[vversion]]$name[j],
+        value = as.Date(dtc[[glatos_detection_schema[[vversion]]$name[j]]])
       )
     }
   }

diff --git a/R/load-read_glatos_receivers.r b/R/load-read_glatos_receivers.r
@@ -49,9 +49,9 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   # Identify file version
   id_file_version <- function(rec_file) {
     col_names <- names(data.table::fread(rec_file, nrows = 0))
-    if (all(glatos:::glatos_receivers_schema$v1.1$name %in% col_names)) {
+    if (all(glatos_receivers_schema$v1.1$name %in% col_names)) {
       return("1.1")
-    } else if (all(glatos:::glatos_receivers_schema$v1.0$name %in% col_names)) {
+    } else if (all(glatos_receivers_schema$v1.0$name %in% col_names)) {
       return("1.0")
     } else {
       stop("Receiver location file version could not be identified.")
@@ -61,7 +61,7 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   if (is.null(version)) {
     version <- id_file_version(rec_file)
   } else if (!(paste0("v", version) %in%
-    names(glatos:::glatos_receivers_schema))) {
+    names(glatos_receivers_schema))) {
     stop(paste0(
       "Receiver locations file version ", version,
       " is not supported."
@@ -72,7 +72,7 @@ read_glatos_receivers <- function(rec_file, version = NULL) {
   if (version %in% c("1.0", "1.1")) {
     ver_txt <- paste0("v", version)
 
-    col_classes <- glatos:::glatos_receivers_schema[[ver_txt]]$type
+    col_classes <- glatos_receivers_schema[[ver_txt]]$type
     timestamp_cols <- which(col_classes == "POSIXct")
     date_cols <- which(col_classes == "Date")
     col_classes[c(timestamp_cols, date_cols)] <- "character"

diff --git a/R/load-read_glatos_workbook.r b/R/load-read_glatos_workbook.r
@@ -109,7 +109,7 @@ read_glatos_workbook <- function(
 
   # Identify workbook version (based on sheet names)
   id_workbook_version <- function(wb_file, sheets) {
-    if (all(names(glatos:::glatos_workbook_schema$v1.3) %in% sheets)) {
+    if (all(names(glatos_workbook_schema$v1.3) %in% sheets)) {
       return("1.3")
     } else {
       stop(paste0(
@@ -124,7 +124,7 @@ read_glatos_workbook <- function(
   if (is.null(wb_version)) {
     wb_version <- id_workbook_version(wb_file, sheets)
   } else if (!(paste0("v", wb_version) %in%
-    names(glatos:::glatos_workbook_schema))) {
+    names(glatos_workbook_schema))) {
     stop(paste0("Workbook version ", wb_version, " is not supported."))
   }
 
@@ -134,7 +134,7 @@ read_glatos_workbook <- function(
 
   #-Workbook v1.3--------------------------------------------------------------
   if (wb_version == "1.3") {
-    wb[names(glatos:::glatos_workbook_schema$v1.3)] <- NA
+    wb[names(glatos_workbook_schema$v1.3)] <- NA
 
     # Get project data
     tmp <- tryCatch(
@@ -170,18 +170,18 @@ read_glatos_workbook <- function(
     # Read all sheets except project
     if (read_all) {
       sheets_to_read <- sheets
-      extra_sheets <- setdiff(sheets, names(glatos:::glatos_workbook_schema[[
+      extra_sheets <- setdiff(sheets, names(glatos_workbook_schema[[
         paste0("v", wb_version)
       ]]))
     } else {
-      sheets_to_read <- names(glatos:::glatos_workbook_schema[[
+      sheets_to_read <- names(glatos_workbook_schema[[
         paste0("v", wb_version)
       ]])
     }
     sheets_to_read <- setdiff(sheets_to_read, "project") # exclude project
 
     for (i in 1:length(sheets_to_read)) {
-      schema_i <- glatos:::glatos_workbook_schema[[
+      schema_i <- glatos_workbook_schema[[
         paste0("v", wb_version)
       ]][[sheets_to_read[i]]]
 
@@ -532,7 +532,7 @@ read_glatos_workbook <- function(
   # assign classes
   wb2$animals <- as_glatos_animals(wb2$animals)
   wb2$receivers <- as_glatos_receivers(wb2$receivers)
-  wb2 <- glatos:::glatos_workbook(wb2)
+  wb2 <- glatos_workbook(wb2)
 
   return(wb2)
 }
diff --git a/R/load-read_otn_deployments.R b/R/load-read_otn_deployments.R
@@ -31,11 +31,13 @@
 #' @author A. Nunes, \email{[email protected]}
 #'
 #' @examples
+#' \dontrun{
 #' # get path to example deployments file
 #' deployment_file <- system.file("extdata", "hfx_deployments.csv",
 #'   package = "glatos"
 #' )
 #' dep <- read_otn_deployments(deployment_file)
+#' }
 #'
 #' @importFrom lubridate parse_date_time
 #' @importFrom tidyr extract