Move Benchmark.R to prolfquabenchmark and remove unused dependencies

Benchmark R6 class and helpers (ionstar_bench_preprocess, make_benchmark,
ms_bench_add_scores, ms_bench_auc) were used exclusively by prolfquabenchmark.
Moving them there reduces prolfqua's API surface. Also removes ggpubr and
ggridges from Imports (no longer needed) and fixes phantom data_Yeast2Factor
documentation.

Author: wolski

DESCRIPTION

@@ -35,8 +35,6 @@ Imports:
     ggplot2,
     ggbeeswarm,
     ggrepel,
-    ggridges,
-    ggpubr,
     limma,
     lme4,
     lmerTest,

NAMESPACE

@@ -1,9 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,pheatmap)
-export(.summarise_missing_contrasts)
 export(AnalysisConfiguration)
-export(Benchmark)
 export(Contrasts)
 export(ContrastsDEqMSFacade)
 export(ContrastsFirth)
@@ -83,7 +81,6 @@ export(impute_with_zcomp)
 export(intensity_summary_by_hkeys)
 export(interaction_contrasts)
 export(interaction_missing_stats)
-export(ionstar_bench_preprocess)
 export(isSingular_lm)
 export(jackknife)
 export(jackknife_matrix)
@@ -97,7 +94,6 @@ export(linfct_from_model)
 export(linfct_matrix_contrasts)
 export(list_to_AnalysisConfiguration)
 export(main_effect_contrasts)
-export(make_benchmark)
 export(make_interaction_column)
 export(make_reduced_hierarchy_config)
 export(matrix_to_tibble)
@@ -115,8 +111,6 @@ export(moderated_p_deqms)
 export(moderated_p_deqms_long)
 export(moderated_p_limma)
 export(moderated_p_limma_long)
-export(ms_bench_add_scores)
-export(ms_bench_auc)
 export(multigroup_volcano)
 export(my_contest)
 export(my_contrast)

R/A_dataset_docu.R

@@ -169,9 +169,3 @@ NULL
 #' @docType data
 #' @keywords internal
 "data_spectronautDIA250_A"
-
-#' example of 2 Factor data
-#' @family data
-#' @docType data
-#' @keywords internal
-"data_Yeast2Factor"