Merge pull request #1782 from infotroph/remove-deprecated

remove deprecated functions in PEcAn.utils. Closes #1719

CHANGELOG.md

@@ -8,6 +8,18 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 
 ## [Unreleased]
 
+### Fixes
+
+### Added
+
+### Removed
+- Removed deprecated copies of PEcAn.utils::SafeList, PEcAn.utils::listToXml (both moved to PEcAn.settings in v 1.5.2), and PEcAn.utils::fqdn (moved to PEcAn.remote in 1.5.2). This fixes the masses of deprecation warnings in otherwise normal run logs (#1719).
+
+### Changed
+
+
+## [1.5.2] - 2017-??-??
+
 ### Fixes
 - Updated models/ed/data/pftmapping.csv to include two new BETYdb PFTs
 - Simple fix to models/ed/R/write.configs.ed.R to properly align pss and css file prefix

base/utils/NAMESPACE

@@ -1,10 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("$",SafeList)
-S3method(listToXml,default)
-export(SafeList)
 export(arrhenius.scaling)
-export(as.SafeList)
 export(as.sequence)
 export(bugs.rdist)
 export(clear.scratch)
@@ -20,7 +16,6 @@ export(do_conversions)
 export(download.file)
 export(download.url)
 export(ensemble.filename)
-export(fqdn)
 export(full.path)
 export(get.ensemble.inputs)
 export(get.ensemble.samples)
@@ -32,10 +27,8 @@ export(get.results)
 export(get.run.id)
 export(get.sa.sample.list)
 export(get.sa.samples)
-export(is.SafeList)
 export(left.pad.zeros)
 export(listToArgString)
-export(listToXml)
 export(load.modelpkg)
 export(logger.debug)
 export(logger.error)

base/utils/R/utils.R

@@ -170,64 +170,6 @@ get.run.id <- function(run.type, index, trait = NULL, pft.name = NULL) {
   return(result)
 } # get.run.id
 
-
-##' @export
-listToXml <- function(x, ...) {
-  .Deprecated("PEcAn.settings::listToXml")
-  UseMethod("listToXml")
-} # listToXml
-
-
-#--------------------------------------------------------------------------------------------------#
-##' Convert List to XML
-##'
-##' DEPRECATED. Use \code{\link[PEcAn.settings:listToXml.default]{PEcAn.settings::listToXml.default}} instead.
-##' Can convert list or other object to an xml object using xmlNode
-##' @title List to XML
-##' @param item 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) {
-  .Deprecated("PEcAn.settings::listToXml.default")
-
-  # just a textnode, or empty node with attributes
-  if (typeof(item) != "list") {
-    if (length(item) > 1) {
-      xml <- XML::xmlNode(tag)
-      for (name in names(item)) {
-        XML::xmlAttrs(xml)[[name]] <- item[[name]]
-      }
-      return(xml)
-    } else {
-      return(XML::xmlNode(tag, item))
-    }
-  }
-
-  # create the node
-  if (identical(names(item), c("text", ".attrs"))) {
-    # special case a node with text and attributes
-    xml <- XML::xmlNode(tag, item[["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]))
-      }
-    }
-  }
-
-  # add attributes to node
-  attrs <- item[[".attrs"]]
-  for (name in names(attrs)) {
-    XML::xmlAttrs(xml)[[name]] <- attrs[[name]]
-  }
-  return(xml)
-} # listToXml.default
-
-
 #--------------------------------------------------------------------------------------------------#
 ##' Zero bounded density using log density transform
 ##'