update to 0.18.1 to delete rhdf5 package reference EVERY WHERE

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: antaresViz
 Type: Package
 Title: Antares Visualizations
-Version: 0.18.0
+Version: 0.18.2
 Authors@R: c(
  person("Tatiana", "Vargas", email = "tatiana.vargas@rte-france.com", role = c("aut", "cre")),
  person("Jalal-Edine", "Zawam", role = "aut"),
@@ -45,14 +45,13 @@ Imports:
  leaflet.minicharts (>= 0.5.3),
  assertthat,
  rAmCharts,
- utils
+ utils,
+ lifecycle
 RoxygenNote: 7.2.2
 Suggests: 
  testthat,
  covr,
- rhdf5 (>= 2.20.2),
  ggplot2,
- hexbin,
  knitr,
  visNetwork,
  rmarkdown

NAMESPACE

@@ -56,6 +56,9 @@ importFrom(grDevices,rainbow)
 importFrom(grDevices,rgb)
 importFrom(graphics,par)
 importFrom(graphics,plot.default)
+importFrom(lifecycle,deprecate_warn)
+importFrom(lifecycle,deprecated)
+importFrom(lifecycle,is_present)
 importFrom(methods,is)
 importFrom(plotly,add_bars)
 importFrom(plotly,add_heatmap)

NEWS.md

@@ -1,5 +1,11 @@
 Copyright 2016 RTE Reseau de transport d'electricite
 
+# antaresViz 0.18.2 
+* fix cran issue on test not skip well
+
+# antaresViz 0.18.1
+* delete package dependecies `rhdf5`
+
 # antaresViz 0.18.0
 * fix deprecated dependencies (issue #200)
  * packages `rgeos`, `raster` removed and replaced by `sf`

R/graph_utils.R

@@ -289,71 +289,6 @@
 }
 
 
-
-
-#' List of h5 params
-#' 
-#' @param X_I, list
-#' @param xyCompare, character
-#' 
-#' @noRd
-.h5ParamList <- function(X_I, xyCompare, h5requestFilter = NULL){
- listParam <- lapply(1:length(X_I), function(i){
- x <- X_I[[i]]
- if (.isSimOpts(x)){
- tmp <- .h5Inf(x)
- h5_filter <- h5requestFilter[[i]]
- h5_tables <- c("areas", "districts", "clusters", "links")
- if (!is.null(h5_filter)){
- if (!(is.null(h5_filter$areas) & is.null(h5_filter$districts) & 
- is.null(h5_filter$links) & is.null(h5_filter$clusters))){
- h5_tables <- c("areas", "districts", "clusters", "links")
- h5_tables <- h5_tables[which(c(!is.null(h5_filter$areas), !is.null(h5_filter$districts),
- !is.null(h5_filter$clusters), !is.null(h5_filter$links)))]
- }
- }
- tmp$tabl <- intersect(tmp$tabl, h5_tables)
- rhdf5::H5close()
- tmp
- }else{
- mcY <- unique(unlist(lapply(x, function(y){unique(y$mcYears)})))
- timeStepS <- attributes(x)$timeStep
- tabl <- names(x)
- list(
- timeStepS = timeStepS,
- mcYearS = mcY,
- tabl = tabl
- )
- }
- })
- res <- lapply(.transposeL(listParam), function(x){
- .compareOperation(x, xyCompare)
- })
-
- res$h5requestFilter <- h5requestFilter
- res
-}
-
-#' Load information from h5 file
-#' 
-#' @param x, opts
-#' 
-#' @noRd
-.h5Inf <- function(x){
- fid <- rhdf5::H5Fopen(x$h5path)
- timeStepS <- .getTimeStep(fid)
- timeStepS <- as.character(timeStepS)
- mcYearS <- x$mcYears
- tabl <- .getTableInH5(fid, timeStepS[1])
- rhdf5::H5Fclose(fid)
- xPart = list(
- timeStepS = timeStepS,
- mcYearS = mcYearS,
- tabl = tabl
- )
-}
-
-
 .transposeL <- function(data){
  do.call(c, apply(do.call(rbind, data), 2, list)) 
 }

R/h5_utils.R

@@ -1,109 +1,109 @@
-.convertH5Filtering <- function(h5requestFiltering, x)
-{
- if (length(h5requestFiltering) > 0)
- {
- if (!is.list(h5requestFiltering[[1]])){
- if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
- {
- h5requestFiltering <- rep(list(h5requestFiltering), length(x))
- }else{
- h5requestFiltering <- list(h5requestFiltering)
- }
- }else{
- if (inherits(x, "list")){
- if (length(h5requestFiltering) != length(x)){
- h5requestFiltering <- h5requestFiltering[1:length(x) %% length(h5requestFiltering) + 1]
- }
- }
- }
- }else{
- if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
- {
- h5requestFiltering <- replicate(length(x), list())
- }else{
- h5requestFiltering <- replicate(1, list())
- }
- }
- h5requestFiltering
-}
+# .convertH5Filtering <- function(h5requestFiltering, x)
+# {
+#  if (length(h5requestFiltering) > 0)
+#  {
+#  if (!is.list(h5requestFiltering[[1]])){
+#  if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
+#  {
+#  h5requestFiltering <- rep(list(h5requestFiltering), length(x))
+#  }else{
+#  h5requestFiltering <- list(h5requestFiltering)
+#  }
+#  }else{
+#  if (inherits(x, "list")){
+#  if (length(h5requestFiltering) != length(x)){
+#  h5requestFiltering <- h5requestFiltering[1:length(x) %% length(h5requestFiltering) + 1]
+#  }
+#  }
+#  }
+#  }else{
+#  if (!any(c("simOptions", "antaresDataTable") %in% class(x)))
+#  {
+#  h5requestFiltering <- replicate(length(x), list())
+#  }else{
+#  h5requestFiltering <- replicate(1, list())
+#  }
+#  }
+#  h5requestFiltering
+# }
 
 
 
-.getTableInH5 <- function(fid, timeStep){
- dataExist <- NULL
- if (rhdf5::H5Lexists(fid, paste0(timeStep, "/areas")))
- {
- dataExist <- c(dataExist, "areas")
- }
- if (rhdf5::H5Lexists(fid, paste0(timeStep, "/links")))
- {
- dataExist <- c(dataExist, "links")
- }
- if (rhdf5::H5Lexists(fid, paste0(timeStep, "/clusters")))
- {
- dataExist <- c(dataExist, "clusters")
- }
- if (rhdf5::H5Lexists(fid, paste0(timeStep, "/districts")))
- {
- dataExist <- c(dataExist, "districts")
- }
- dataExist
-}
+# .getTableInH5 <- function(fid, timeStep){
+#  dataExist <- NULL
+#  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/areas")))
+#  {
+#  dataExist <- c(dataExist, "areas")
+#  }
+#  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/links")))
+#  {
+#  dataExist <- c(dataExist, "links")
+#  }
+#  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/clusters")))
+#  {
+#  dataExist <- c(dataExist, "clusters")
+#  }
+#  if (rhdf5::H5Lexists(fid, paste0(timeStep, "/districts")))
+#  {
+#  dataExist <- c(dataExist, "districts")
+#  }
+#  dataExist
+# }
 
-.getVariablesH5 <- function(fid, timeStep, tables){
- sapply(tables, function(X){
- struct <- .getstructure(fid, paste0(timeStep, "/", X, "/mcInd/", "/structure"))$variable
- if ("timeId" %in% struct){
- struct <- struct[struct != "timeId"]
- }
- struct
- }, simplify = FALSE)
-}
+# .getVariablesH5 <- function(fid, timeStep, tables){
+#  sapply(tables, function(X){
+#  struct <- .getstructure(fid, paste0(timeStep, "/", X, "/mcInd/", "/structure"))$variable
+#  if ("timeId" %in% struct){
+#  struct <- struct[struct != "timeId"]
+#  }
+#  struct
+#  }, simplify = FALSE)
+# }
 
-.getClustersNames <- function(fid, timeStep){
- unique(unlist(lapply(strsplit(.getstructure(fid, paste0(timeStep, "/clusters/mcInd/structure"))$cluster, "/"), function(X)X[1])))
-}
+# .getClustersNames <- function(fid, timeStep){
+#  unique(unlist(lapply(strsplit(.getstructure(fid, paste0(timeStep, "/clusters/mcInd/structure"))$cluster, "/"), function(X)X[1])))
+# }
 
-.getElements <- function(opts, tables, fid, timeStep){
- elements <- list()
- if ("areas" %in% tables) elements$areas <- opts$areaList
- if ("links" %in% tables) elements$links <- opts$linkList
- if ("districts" %in% tables) elements$districts <- opts$districtList
- if ("clusters" %in% tables){
- elements$clusters <- .getClustersNames(fid, timeStep)
- }
- elements
-}
+# .getElements <- function(opts, tables, fid, timeStep){
+# elements <- list()
+# if ("areas" %in% tables) elements$areas <- opts$areaList
+# if ("links" %in% tables) elements$links <- opts$linkList
+# if ("districts" %in% tables) elements$districts <- opts$districtList
+# if ("clusters" %in% tables){
+# elements$clusters <- .getClustersNames(fid, timeStep)
+# }
+# elements
+# }
+# 
+# .getDateRange <- function(opts, timeStep){
+# tim <- .timeIdToDate(sort(
+# unique(
+# antaresRead::.h5ReadAntares(opts$h5path, timeStep = timeStep, select = "timeId", 
+# areas = opts$areaList[1], mcYears = opts$mcYears[1], perf = FALSE)$timeId)
+# ), timeStep = timeStep, opts = opts)
+# dt <- as.Date(range(tim))
+# dt
+# }
+# 
+# 
+# .getGraphFunction <- function(type){
+# switch(type,
+# "ts" = .plotTS,
+# "barplot" = .barplot,
+# "monotone" = .plotMonotone,
+# "density" = .density,
+# "cdf" = .cdf,
+# "heatmap" = .heatmap,
+# stop("Invalid type")
+# )
+# }
 
-.getDateRange <- function(opts, timeStep){
- tim <- .timeIdToDate(sort(
- unique(
- antaresRead::.h5ReadAntares(opts$h5path, timeStep = timeStep, select = "timeId", 
- areas = opts$areaList[1], mcYears = opts$mcYears[1], perf = FALSE)$timeId)
- ), timeStep = timeStep, opts = opts)
- dt <- as.Date(range(tim))
- dt
-}
-
-
-.getGraphFunction <- function(type){
- switch(type,
- "ts" = .plotTS,
- "barplot" = .barplot,
- "monotone" = .plotMonotone,
- "density" = .density,
- "cdf" = .cdf,
- "heatmap" = .heatmap,
- stop("Invalid type")
- )
-}
-
-.getTimeStep <- function(fid){
- timeSteps <- sapply(c("hourly", "daily", "weekly", "monthly", "annual"), function(X){
- rhdf5::H5Lexists(fid, X)
- })
- names(timeSteps[which(timeSteps == TRUE)])
-}
+# .getTimeStep <- function(fid){
+# timeSteps <- sapply(c("hourly", "daily", "weekly", "monthly", "annual"), function(X){
+# rhdf5::H5Lexists(fid, X)
+# })
+# names(timeSteps[which(timeSteps == TRUE)])
+# }
 
 .compareOperation <- function(a, opType){
  if (length(a) == 1) return(unlist(unique(a)))

R/h5_utils_plot.R

@@ -1,20 +1,20 @@
 
 
 
-.getstructure <- function(fid, strgp){
- gid <- rhdf5::H5Gopen(fid, strgp)
- data <- rhdf5::h5dump(gid)
- rhdf5::H5Gclose(gid)
- if(length(which(data$reCalcVar!="")) > 0)
- {
- data$reCalcVar <- data$reCalcVar[which(data$reCalcVar!="")]
- data$variable <- c(data$variable, data$reCalcVar)
- data$reCalcVar <- NULL
- }
- data
-}
-
-.tryCloseH5 <- function(){
- try(rhdf5::H5close(), silent = TRUE)
-}
+# .getstructure <- function(fid, strgp){
+#  gid <- rhdf5::H5Gopen(fid, strgp)
+#  data <- rhdf5::h5dump(gid)
+#  rhdf5::H5Gclose(gid)
+#  if(length(which(data$reCalcVar!="")) > 0)
+#  {
+#  data$reCalcVar <- data$reCalcVar[which(data$reCalcVar!="")]
+#  data$variable <- c(data$variable, data$reCalcVar)
+#  data$reCalcVar <- NULL
+#  }
+#  data
+# }
+# 
+# .tryCloseH5 <- function(){
+#  try(rhdf5::H5close(), silent = TRUE)
+# }