Fix toJSON warnings and pin SpiecEasi to 1.0.7

DESCRIPTION

@@ -34,7 +34,7 @@ Description: plot.data is an R package for creating client-ready data for variou
 License: Apache License (= 2.0)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.3
 Suggests: 
     covr,
     testthat (>= 2.1.0)

NAMESPACE

@@ -119,14 +119,12 @@ exportMethods(pruneLinksByPredicate)
 exportMethods(relativeRisk)
 exportMethods(sensitivity)
 exportMethods(specificity)
-exportMethods(toJSON)
 import(data.table)
 import(veupathUtils)
 importFrom(S4Vectors,SimpleList)
 importFrom(grDevices,nclass.FD)
 importFrom(grDevices,nclass.Sturges)
 importFrom(jsonlite,prettify)
-importFrom(jsonlite,toJSON)
 importFrom(jsonlite,unbox)
 importFrom(lubridate,as_date)
 importFrom(lubridate,ceiling_date)

R/methods-CorrelationLinks.R

@@ -78,7 +78,6 @@ function(
 
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
-#' @export
 setMethod(toJSONGeneric, signature("CorrelationLinkList"), function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named) 
     tmp <- veupathUtils::S4SimpleListToJSON(object, FALSE)

R/methods-CorrelationNetwork.R

@@ -63,11 +63,10 @@ function(
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
 #' Convert CorrelationNetwork object to JSON
-#' 
+#'
 #' Converts a CorrelationNetwork object to JSON
 #' @param object A CorrelationNetwork object
 #' @param named boolean that declares if names should be included
-#' @export
 setMethod(toJSONGeneric, "CorrelationNetwork", function(object, named = c(TRUE, FALSE)) {
 
   named <- veupathUtils::matchArg(named)    

R/methods-KPartiteNetwork.R

@@ -13,11 +13,10 @@ setMethod("getAllNodeIds", "Partitions", function(object) unlist(lapply(as.list(
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
 #' Convert Partitions object to JSON
-#' 
+#'
 #' Converts a Partitions object to JSON
 #' @param object A Partitions object
 #' @param named boolean that declares if names should be included
-#' @export
 setMethod(toJSONGeneric, "Partitions", function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named)
     tmp <- veupathUtils::S4SimpleListToJSON(object, TRUE)
@@ -28,11 +27,10 @@ setMethod(toJSONGeneric, "Partitions", function(object, named = c(TRUE, FALSE))
 })
 
 #' Convert KPartiteNetwork object to JSON
-#' 
+#'
 #' Converts a KPartiteNetwork object to JSON
 #' @param object A KPartiteNetwork object
 #' @param named boolean that declares if names should be included
-#' @export 
 setMethod(toJSONGeneric, "KPartiteNetwork", function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named)
     tmp <- character()

R/methods-Links.R

@@ -40,11 +40,10 @@ setMethod("getColors", "LinkList", function(object) unlist(lapply(object, functi
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
 #' Convert Link object to JSON
-#' 
+#'
 #' Converts a Link object to JSON
 #' @param object A Link object
 #' @param named boolean that declares if names should be included
-#' @export
 setMethod(toJSONGeneric, "Link", function(object, named = c(FALSE, TRUE)) {
     named <- veupathUtils::matchArg(named)
     tmp <- character()
@@ -63,7 +62,6 @@ setMethod(toJSONGeneric, "Link", function(object, named = c(FALSE, TRUE)) {
     return(tmp)
 })
 
-#' @export
 setMethod(toJSONGeneric, signature("LinkList"), function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named) 
     tmp <- veupathUtils::S4SimpleListToJSON(object, FALSE)

R/methods-Network.R

@@ -172,11 +172,10 @@ pruneLinksBelowWeight <- function(net, threshold, verbose = c(TRUE, FALSE)) {
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
 #' Convert Network object to JSON
-#' 
+#'
 #' Converts a Network object to JSON
 #' @param object A Network object
 #' @param named boolean that declares if names should be included
-#' @export
 setMethod(toJSONGeneric, "BaseNetwork", function(object, named = c(TRUE, FALSE)) {
 
   named <- veupathUtils::matchArg(named)    
@@ -202,7 +201,6 @@ setMethod(toJSONGeneric, "BaseNetwork", function(object, named = c(TRUE, FALSE))
 #' @param pattern optional tmp file prefix
 #' @param verbose boolean that declares if logging is desired
 #' @return character name of a tmp file w ext *.json
-#' @importFrom jsonlite toJSON
 #' @export
 #' @rdname writeNetworkJSON
 setGeneric("writeNetworkJSON", function(x, pattern = NULL, verbose = c(TRUE, FALSE)) standardGeneric("writeNetworkJSON"), signature = c("x"))

R/methods-Nodes.R

@@ -58,11 +58,10 @@ setMethod("getNodeIds", "NodeIdList", function(object) unlist(lapply(as.list(obj
 toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 
 #' Convert Node object to JSON
-#' 
+#'
 #' Converts a Node object to JSON
 #' @param object A Node object
 #' @param named boolean that declares if names should be included
-#' @export
 setMethod(toJSONGeneric, "Node", function(object, named = c(FALSE, TRUE)) {
     named <- veupathUtils::matchArg(named)
     tmp <- character()
@@ -82,7 +81,6 @@ setMethod(toJSONGeneric, "Node", function(object, named = c(FALSE, TRUE)) {
     return(tmp)
 })
 
-#' @export
 setMethod(toJSONGeneric, signature("NodeList"), function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named) 
     tmp <- veupathUtils::S4SimpleListToJSON(object, FALSE)
@@ -92,7 +90,6 @@ setMethod(toJSONGeneric, signature("NodeList"), function(object, named = c(TRUE,
     return(tmp)
 })
 
-#' @export
 setMethod(toJSONGeneric, signature("NodeId"), function(object, named = c(FALSE, TRUE)) {
     named <- veupathUtils::matchArg(named)
     tmp <- character()
@@ -104,7 +101,6 @@ setMethod(toJSONGeneric, signature("NodeId"), function(object, named = c(FALSE,
     return(tmp)
 })
 
-#' @export
 setMethod(toJSONGeneric, signature("NodeIdList"), function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named) 
     tmp <- veupathUtils::S4SimpleListToJSON(object, FALSE)

R/utils-json.R

@@ -257,7 +257,6 @@ getJSON <- function(.pd, evilMode) {
 #' @param .pd a data.table to convert to json and write to a tmp file
 #' @param pattern optional tmp file prefix
 #' @return character name of a tmp file w ext *.json
-#' @importFrom jsonlite toJSON
 #' @importFrom jsonlite prettify
 #' @export
 writeJSON <- function(.pd, evilMode, pattern = NULL, verbose = c(TRUE, FALSE)) {