fix-notes/warnings/errors in base packages

base/remote/R/remote.execute.R.R

@@ -6,10 +6,11 @@
 #'
 #' @title Execute command remotely
 #' @param script the script to be invoked, as a list of commands.
-#' @param args a character vector of arguments to command.
 #' @param host settings host list
 #' @param user the username to use for remote login
 #' @param verbose should the output be printed to the console
+#' @param R Path to the R executable or binary file.
+#' @param scratchdir Path to the scratch directory for temporary files during remote execution.
 #' @return the captured output of the command (both stdout and stderr)
 #' @author Rob Kooper
 #' @export

base/remote/R/remote.execute.cmd.R

@@ -5,7 +5,7 @@
 #' machine it will execute the command locally without ssh.
 #'
 #' @title Execute command remotely
-#' @param command the system command to be invoked, as a character string.
+#' @param cmd the system command to be invoked, as a character string.
 #' @param host host structure to execute command on
 #' @param args a character vector of arguments to command.
 #' @param stderr should stderr be returned as well.

base/remote/R/test_remote.R

@@ -1,6 +1,8 @@
 #' Test remote execution
 #'
 #' @inheritParams remote.execute.cmd
+#' 
+#' @param ... additional arguments.
 #'
 #' @return `TRUE` is remote execution is successful.
 #' If unsuccessful, depends on the value of `stderr`.

base/settings/R/MultiSettings.R

@@ -138,6 +138,11 @@ names.MultiSettings <- function(x) {
   stop("Can't name MultiSettings this way. Use settingNames() instead.")
 }
 
+#' function that can retrieve or update the names of multi-settings.
+#' 
+#' @param multiSettings object for which to retrieve or set the names.
+#' @param settingNames  names to be set for the multi-settings object.
+#' 
 #' @export
 settingNames <- function(multiSettings, settingNames) {
   if (missing(settingNames)) {
@@ -159,6 +164,10 @@ print.MultiSettings <- function(x, printAll = FALSE, ...) {
   }
 }
 
+#' generic function for printing contents of objects.
+#'
+#' @param x object to be printed.
+#'
 #' @export
 printAll <- function(x) {
   UseMethod("printAll", x)
@@ -196,7 +205,10 @@ listToXml.MultiSettings <- function(item, tag, collapse = TRUE) {
   NextMethod()
 } # listToXml.MultiSettings
 
-
+#' generic function for expanding multi-settings.
+#'
+#' @param x object to be expanded.
+#'
 #' @export
 expandMultiSettings <- function(x) {
   UseMethod("expandMultiSettings")

base/settings/R/addSecrets.R

@@ -15,6 +15,7 @@
 #'
 #' @title Add Users secrets
 #' @param settings settings file
+#' @param force Logical: add secrets even if they have been added previously?
 #' @return will return the updated settings values
 #' @author Rob Kooper
 #' @export addSecrets

base/settings/R/check.all.settings.R

@@ -279,6 +279,7 @@ check.bety.version <- function(dbcon) {
 #' - pfts with at least one pft defined
 #' @title Check Settings
 #' @param settings settings file
+#' @param force Logical: Rerun check even if these settings have been checked previously?
 #' @return will return the updated settings values with defaults set.
 #' @author Rob Kooper, David LeBauer
 #' @export check.settings
@@ -614,6 +615,7 @@ check.settings <- function(settings, force = FALSE) {
 
 #' @title Check Run Settings
 #' @param settings settings file
+#' @param dbcon database connection.
 #' @export check.run.settings
 check.run.settings <- function(settings, dbcon = NULL) {
   scipen <- getOption("scipen")
@@ -805,6 +807,7 @@ check.run.settings <- function(settings, dbcon = NULL) {
 
 #' @title Check Model Settings
 #' @param settings settings file
+#' @param dbcon database connection.
 #' @export check.model.settings
 check.model.settings <- function(settings, dbcon = NULL) {
   # check modelid with values
@@ -1077,6 +1080,7 @@ check.database.settings <- function(settings) {
 #' @param settings settings file
 #' @export check.ensemble.settings
 check.ensemble.settings <- function(settings) {
+
   # check ensemble
   if (!is.null(settings$ensemble)) {
     if (is.null(settings$ensemble$variable)) {
@@ -1097,6 +1101,10 @@ check.ensemble.settings <- function(settings) {
 
     if (is.null(settings$ensemble$start.year)) {
       if (!is.null(settings$run$start.date)) {
+        startdate <- lubridate::parse_date_time(
+          settings$run$start.date,
+          "ymd_HMS",
+          truncated = 3)
         settings$ensemble$start.year <- lubridate::year(
           settings$run$start.date)
         PEcAn.logger::logger.info(
@@ -1116,6 +1124,10 @@ check.ensemble.settings <- function(settings) {
 
     if (is.null(settings$ensemble$end.year)) {
       if (!is.null(settings$run$end.date)) {
+        enddate <- lubridate::parse_date_time(
+          settings$run$end.date,
+          "ymd_HMS",
+          truncated = 3)
         settings$ensemble$end.year <- lubridate::year(settings$run$end.date)
         PEcAn.logger::logger.info(
           "No end date passed to ensemble - using the run date (",

base/settings/R/clean.settings.R

@@ -15,6 +15,7 @@
 #' @param inputfile the PEcAn settings file to be used.
 #' @param outputfile the name of file to which the settings will be
 #'        written inside the outputdir.
+#' @param write Indicates whether to write the modified settings to a file.
 #' @return list of all settings as saved to the XML file(s)
 #' @export clean.settings
 #' @author Rob Kooper

base/settings/R/fix.deprecated.settings.R

@@ -10,6 +10,7 @@
 #'
 #' @title Fix Deprecated Settings
 #' @param settings settings list
+#' @param force Logical: re-run fixing of deprecated settings even if it has been done previously?
 #' @return updated settings list
 #' @author Ryan Kelly
 #' @export fix.deprecated.settings

base/settings/R/listToXml.R

@@ -1,3 +1,7 @@
+#' A generic function to convert list to XML
+#'
+#' @param x list to be converted
+#' @param ... arguments passed to methods
 #' @export
 listToXml <- function(x, ...) {
   UseMethod("listToXml")
@@ -8,43 +12,49 @@ listToXml <- function(x, ...) {
 #'
 #' Can convert list or other object to an xml object using xmlNode
 #' @title List to XML
-#' @param item object to be converted.
+#' @param x object to be converted.
 #'   Despite the function name, need not actually be a list
-#' @param tag xml tag
 #' @return xmlNode
 #' @export
 #' @author David LeBauer, Carl Davidson, Rob Kooper
-listToXml.default <- function(item, tag) {
-
+listToXml.default <- function(x, ...) {
+  args <- list(...)
+  if (length(args) == 0) {
+    PEcAn.logger::logger.error("no tag provided")
+  } else if ("tag" %in% names(args)) {
+    tag <- args$tag
+  } else {
+    tag <- args[[1]]
+  }
   # just a textnode, or empty node with attributes
-  if (typeof(item) != "list") {
-    if (length(item) > 1) {
+  if (typeof(x) != "list") {
+    if (length(x) > 1) {
       xml <- XML::xmlNode(tag)
-      for (name in names(item)) {
-        XML::xmlAttrs(xml)[[name]] <- item[[name]]
+      for (name in names(x)) {
+        XML::xmlAttrs(xml)[[name]] <- x[[name]]
       }
       return(xml)
     } else {
-      return(XML::xmlNode(tag, item))
+      return(XML::xmlNode(tag, x))
     }
   }
-
+  
   # create the node
-  if (identical(names(item), c("text", ".attrs"))) {
+  if (identical(names(x), c("text", ".attrs"))) {
     # special case a node with text and attributes
-    xml <- XML::xmlNode(tag, item[["text"]])
+    xml <- XML::xmlNode(tag, x[["text"]])
   } else {
     # node with child nodes
     xml <- XML::xmlNode(tag)
-    for (i in seq_along(item)) {
-      if (is.null(names(item)) || names(item)[i] != ".attrs") {
-        xml <- XML::append.xmlNode(xml, listToXml(item[[i]], names(item)[i]))
+    for (i in seq_along(x)) {
+      if (is.null(names(x)) || names(x)[i] != ".attrs") {
+        xml <- XML::append.xmlNode(xml, listToXml(x[[i]], names(x)[i]))
       }
     }
   }
-
+  
   # add attributes to node
-  attrs <- item[[".attrs"]]
+  attrs <- x[[".attrs"]]
   for (name in names(attrs)) {
     XML::xmlAttrs(xml)[[name]] <- attrs[[name]]
   }

base/settings/R/update.settings.R

@@ -12,6 +12,7 @@
 #' @title Update Settings
 #' @name update.settings
 #' @param settings settings file
+#' @param force Logical: update even if settings have previously been updated?.
 #' @return will return the updated settings values
 #' @export update.settings
 #' @author Rob Kooper