Fixed Warnings and some Notes happening during check()

DESCRIPTION

@@ -8,7 +8,7 @@ Description: PICAFlow (Pipeline for Integrative and Comprehensive Analysis of Fl
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports:
   parallel,
   doSNOW,

NAMESPACE

@@ -9,6 +9,7 @@ export(UMAP_downsampledDataset)
 export(analyzePeaks)
 export(applyClusterModel)
 export(bindData)
+export(checkNewVersion)
 export(clustersPercentagesHeatmap)
 export(clustersPhenotypesHeatmap)
 export(collapseCloseClusters)

R/0_Preprocessing.R

@@ -6,9 +6,9 @@
 
 checkNewVersion = function()
 {
-  latestRelease = gh("GET /repos/{owner}/{repo}/releases", owner = "PaulRegnier", repo = "PICAFlow")
-  latestRelease = as.character(releases[[1]][["tag_name"]])
-  installedRelease = as.character(packageVersion("PICAFlow"))
+  latestRelease = gh::gh("GET /repos/{owner}/{repo}/releases", owner = "PaulRegnier", repo = "PICAFlow")
+  latestRelease = as.character(latestRelease[[1]][["tag_name"]])
+  installedRelease = as.character(utils::packageVersion("PICAFlow"))
 
   if(installedRelease != latestRelease)
   {
@@ -107,7 +107,7 @@ convertToRDS = function(conversionTable = NULL)
       if (is.null(conversionTable) == FALSE)
       {
 
-        foreach(t = 1:ncol(conversionTable)) %do%
+        foreach::foreach(t = 1:ncol(conversionTable)) %do%
           {
             currentColumnData = conversionTable[, t]
 
@@ -434,6 +434,8 @@ subsetData = function(parametersToKeep = NULL, customNames = NULL)
 #'
 #' @param maxEventsNumber The maximum number of events to use for data displaying. Defaults to `10000`.
 #'
+#' @param options A list containing any desired parameter to pass to the Shiny application
+#'
 #' @importFrom foreach %do%
 #'
 #' @export

R/1_Transformation.R

@@ -77,6 +77,8 @@ mergeSamples = function(suffix = NULL, useStructureFromReferenceSample = 0)
 #'
 #' @param fs_shiny A flowSet generated using `mergeData()` function. Defaults to `NULL`.
 #'
+#' @param options A list containing any desired parameter to pass to the Shiny application
+#'
 #' @importFrom foreach %do%
 #'
 #' @export