Prevent parallellism during examples and tests to pass CRAN-prechecks

IOHprofiler · Sep 20, 2023 · 7073928 · 7073928
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commit 7073928
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Showing 18 changed files with 30 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: IOHanalyzer
 Type: Package
 Title: Data Analysis Part of 'IOHprofiler'
-Version: 0.1.8.1
+Version: 0.1.8.2
 Maintainer: Diederick Vermetten <d.l.vermetten@liacs.leidenuniv.nl>
 Authors@R: c(
     person("Hao", "Wang", email = "h.wang@liacs.leidenuniv.nl", role = "aut", comment = c(ORCID = "0000-0002-4933-5181")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -189,10 +189,12 @@ importFrom(data.table,copy)
 importFrom(data.table,data.table)
 importFrom(data.table,frank)
 importFrom(data.table,fread)
+importFrom(data.table,getDTthreads)
 importFrom(data.table,is.data.table)
 importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
+importFrom(data.table,setDTthreads)
 importFrom(data.table,setnames)
 importFrom(data.table,setorder)
 importFrom(data.table,setorderv)

diff --git a/R/DataSetList.R b/R/DataSetList.R
@@ -1237,6 +1237,7 @@ generate_data.ECDF <- function(dsList, targets, scale_log = F, which = 'by_RT',
 #'
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' generate_data.AUC(dsl, get_ECDF_targets(dsl))
 #' generate_data.AUC(NULL, NULL, dt_ecdf = generate_data.ECDF(dsl, get_ECDF_targets(dsl)))
 generate_data.AUC <- function(dsList, targets, scale_log = F, which = 'by_RT', dt_ecdf = NULL,
@@ -1480,6 +1481,7 @@ generate_data.Aggr <- function(dsList, aggr_on = 'funcId', targets = NULL, which
 #'
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' generate_data.ECDF_raw(subset(dsl, funcId == 1), c(10, 15, 16))
 generate_data.ECDF_raw <- function(dsList, targets, scale_log = F) {
   V1 <- NULL #Set local binding to remove warnings
@@ -1783,6 +1785,7 @@ generate_data.EAF <- function(dsList, n_sets = 11, subsampling = 100, scale_xlog
 #' @param normalize Whether to normalize the resulting integrals to [0,1] (Based on `min_val` and `max_va`)
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' generate_data.ECDF_From_EAF(generate_data.EAF(subset(dsl, funcId == 1)), 1, 16, maximization = TRUE)
 generate_data.ECDF_From_EAF <- function(eaf_table, min_val, max_val, maximization = F,
                                         scale_log = F, normalize = T) {

diff --git a/R/IOHanalyzer.R b/R/IOHanalyzer.R
@@ -8,7 +8,7 @@
 #' @importFrom RColorBrewer brewer.pal
 #' @importFrom colorRamps primary.colors
 #' @importFrom data.table as.data.table rbindlist data.table fread := melt is.data.table
-#' @importFrom data.table setorderv frank setnames rbindlist copy transpose setDT setorder
+#' @importFrom data.table setorderv frank setnames rbindlist copy transpose setDT setorder getDTthreads setDTthreads
 #' @importFrom plotly add_annotations add_trace orca plot_ly rename_ subplot layout
 #' @importFrom plotly animation_opts save_image add_polygons hide_colorbar add_contour colorbar
 #' @importFrom ggplot2 aes geom_jitter geom_line geom_ribbon geom_violin ggplot element_text

diff --git a/R/plotDataSetList.R b/R/plotDataSetList.R
@@ -143,6 +143,7 @@ Plot.RT.Histogram <- function(dsList, ftarget, plot_mode = 'overlay', use.equal.
 #' the running times of the DataSetList at the target function values
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.RT.ECDF_Per_Target(subset(dsl, funcId == 1), 14)
 Plot.RT.ECDF_Per_Target <- function(dsList, ftargets, scale.xlog = F)
   UseMethod("Plot.RT.ECDF_Per_Target", dsList)
@@ -160,6 +161,7 @@ Plot.RT.ECDF_Per_Target <- function(dsList, ftargets, scale.xlog = F)
 #' the running times of the DataSetList
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.RT.ECDF_Single_Func(subset(dsl, funcId == 1))
 Plot.RT.ECDF_Single_Func <- function(dsList, fstart = NULL, fstop = NULL,
                               fstep = NULL, show.per_target = F,
@@ -175,6 +177,7 @@ Plot.RT.ECDF_Single_Func <- function(dsList, fstart = NULL, fstop = NULL,
 #' @return A radarplot of the area under the aggregated ECDF-curve of the DataSetList
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.RT.ECDF_AUC(subset(dsl, funcId == 1))
 Plot.RT.ECDF_AUC <- function(dsList, fstart = NULL,
                         fstop = NULL, fstep = NULL,
@@ -222,6 +225,7 @@ Plot.FV.Histogram <- function(dsList, runtime, plot_mode='overlay', use.equal.bi
 #' the fucntion values of the DataSetList at the target runtimes
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.FV.ECDF_Per_Target(subset(dsl, funcId == 1), 10)
 Plot.FV.ECDF_Per_Target <- function(dsList, runtimes, scale.xlog = F, scale.reverse = F)
   UseMethod("Plot.FV.ECDF_Per_Target", dsList)
@@ -240,6 +244,7 @@ Plot.FV.ECDF_Per_Target <- function(dsList, runtimes, scale.xlog = F, scale.reve
 #' the function values of the DataSetList
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.FV.ECDF_Single_Func(subset(dsl, funcId == 1))
 Plot.FV.ECDF_Single_Func <- function(dsList, rt_min = NULL, rt_max = NULL,
                               rt_step = NULL, scale.xlog = F,
@@ -255,6 +260,7 @@ Plot.FV.ECDF_Single_Func <- function(dsList, rt_min = NULL, rt_max = NULL,
 #' @return A radarplot of the area under the aggregated ECDF-curve of the DataSetList
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.FV.ECDF_AUC(subset(dsl, funcId == 1))
 Plot.FV.ECDF_AUC <- function(dsList, rt_min = NULL, rt_max = NULL,
                         rt_step = NULL) UseMethod("Plot.FV.ECDF_AUC", dsList)
@@ -316,6 +322,7 @@ Plot.FV.Parameters <- function(dsList, rt_min = NULL, rt_max = NULL,
 #' the running times of the DataSetList
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' Plot.RT.ECDF_Multi_Func(dsl)
 Plot.RT.ECDF_Multi_Func <- function(dsList, targets = NULL, scale.xlog = F)
   UseMethod("Plot.RT.ECDF_Multi_Func", dsList)

diff --git a/R/stats.R b/R/stats.R
@@ -1001,6 +1001,7 @@ get_marg_contrib_ecdf <- function(id, perm, j, dt) {
 #'
 #' @export
 #' @examples
+#' \dontshow{data.table::setDTthreads(1)}
 #' dsl_sub <- subset(dsl, funcId == 1)
 #' get_shapley_values(dsl_sub, get_ECDF_targets(dsl_sub), group_size = 2)
 get_shapley_values <- function(dsList, targets, scale.log = T, group_size = 5, max_perm_size = 10, normalize = T){

diff --git a/man/Plot.FV.ECDF_AUC.Rd b/man/Plot.FV.ECDF_AUC.Rd
diff --git a/man/Plot.FV.ECDF_Per_Target.Rd b/man/Plot.FV.ECDF_Per_Target.Rd
diff --git a/man/Plot.FV.ECDF_Single_Func.Rd b/man/Plot.FV.ECDF_Single_Func.Rd
diff --git a/man/Plot.RT.ECDF_AUC.Rd b/man/Plot.RT.ECDF_AUC.Rd
diff --git a/man/Plot.RT.ECDF_Multi_Func.Rd b/man/Plot.RT.ECDF_Multi_Func.Rd
diff --git a/man/Plot.RT.ECDF_Per_Target.Rd b/man/Plot.RT.ECDF_Per_Target.Rd
diff --git a/man/Plot.RT.ECDF_Single_Func.Rd b/man/Plot.RT.ECDF_Single_Func.Rd
diff --git a/man/generate_data.AUC.Rd b/man/generate_data.AUC.Rd
diff --git a/man/generate_data.ECDF_From_EAF.Rd b/man/generate_data.ECDF_From_EAF.Rd
diff --git a/man/generate_data.ECDF_raw.Rd b/man/generate_data.ECDF_raw.Rd
diff --git a/man/get_shapley_values.Rd b/man/get_shapley_values.Rd
diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,4 +1,8 @@
 library(testthat)
 library(IOHanalyzer)
+library(data.table)
 
+threads <- getDTthreads()
+setDTthreads(1)
 test_check("IOHanalyzer")
+setDTthreads(threads)