Update package docs to new Roxygen approach

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 3.2.2
-Date: 2023-05-11 15:37:39 UTC
-SHA: 22319bdfde9e607e74ea71381d8025fb5425c474
+Version: 3.2.3
+Date: 2023-09-01 13:06:53 UTC
+SHA: a3fa4e3245d5b431bb7906bdb72b9c6a3b1483e2

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: corehunter
 Title: Multi-Purpose Core Subset Selection
-Version: 3.2.2
-Date: 2023-05-02
+Version: 3.2.3
+Date: 2023-08-31
 Authors@R: c(person("Herman", "De Beukelaer", email = "herman.debeukelaer@gmail.com", role = c("aut", "cre")),
              person("Guy", "Davenport", email = "daveneti@gmail.com", role = "aut"),
              person("Veerle", "Fack", email = "veerle.fack@ugent.be", role = "ths"))

NEWS.md

@@ -1,6 +1,11 @@
 Core Hunter 3
 =============
 
+Version 3.2.3 (31/08/2023)
+--------------------------
+
+ - Fixed broken package documentation due to Roxygen breaking change
+
 Version 3.2.2 (02/05/2023)
 --------------------------
 

R/corehunter.R → R/corehunter-package.R

@@ -10,6 +10,8 @@
 #' The Core Hunter library is implemented in Java 8 as an open source project
 #' (see \url{http://www.corehunter.org}).
 #'
+#' @keywords internal
+#'
 #' @examples
 #' \dontrun{
 #' # sample core based on genetic marker data (default format)
@@ -56,6 +58,8 @@
 #'  \code{\link{sampleCore}}, \code{\link{evaluateCore}},
 #'  \code{\link{objective}}
 #'
-#' @docType package
-#' @name corehunter
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
 NULL

revdep/README.md

@@ -1,24 +1,24 @@
 # Platform
 
-|field    |value                                  |
-|:--------|:--------------------------------------|
-|version  |R version 4.3.0 (2023-04-21 ucrt)      |
-|os       |Windows 11 x64 (build 22621)           |
-|system   |x86_64, mingw32                        |
-|ui       |RStudio                                |
-|language |(EN)                                   |
-|collate  |Dutch_Belgium.utf8                     |
-|ctype    |Dutch_Belgium.utf8                     |
-|tz       |Europe/Brussels                        |
-|date     |2023-05-03                             |
-|rstudio  |2023.03.0+386 Cherry Blossom (desktop) |
-|pandoc   |NA                                     |
+|field    |value                                      |
+|:--------|:------------------------------------------|
+|version  |R version 4.3.0 (2023-04-21 ucrt)          |
+|os       |Windows 11 x64 (build 22621)               |
+|system   |x86_64, mingw32                            |
+|ui       |RStudio                                    |
+|language |(EN)                                       |
+|collate  |Dutch_Belgium.utf8                         |
+|ctype    |nl_NL.UTF-8                                |
+|tz       |Europe/Brussels                            |
+|date     |2023-09-01                                 |
+|rstudio  |2023.06.2+561 Mountain Hydrangea (desktop) |
+|pandoc   |3.1.2 @ C:\PROGRA~1\Pandoc\pandoc.exe      |
 
 # Dependencies
 
 |package     |old   |new   |Δ  |
 |:-----------|:-----|:-----|:--|
-|corehunter  |3.2.1 |3.2.2 |*  |
+|corehunter  |3.2.2 |3.2.3 |*  |
 |naturalsort |0.1.3 |0.1.3 |   |
 |rJava       |1.0-6 |1.0-6 |   |
 

tests/testthat/testExecution.R

@@ -85,28 +85,28 @@ test_that("seed is respected (fast mode)", {
   expect_true(all(sapply(cores, function(core){all.equal(core, cores[[1]])})))
 })
 
-test_that("seed is respected (multi-objective, with normalization)", {
+test_that("seed is respected (multi-objective, with normalization, fast mode)", {
   geno <- genotypeData()
   obj <- list(
     objective("EN", "MR"),
     objective("AN", "CE")
   )
   cores <- lapply(1:5, function(i){
     set.seed(42)
-    naturalsort(sampleCore(geno, obj, size = 2, steps = 10)$sel)
+    naturalsort(sampleCore(geno, obj, size = 2, steps = 5000, mode = "fast")$sel)
   })
   expect_true(all(sapply(cores, function(core){all.equal(core, cores[[1]])})))
 })
 
-test_that("seed is respected (multi-objective, no normalization)", {
+test_that("seed is respected (multi-objective, no normalization, fast mode)", {
   geno <- genotypeData()
   obj <- list(
     objective("EN", "MR"),
     objective("AN", "CE")
   )
   cores <- lapply(1:5, function(i){
     set.seed(42)
-    naturalsort(sampleCore(geno, obj, size = 2, steps = 10, normalize = FALSE)$sel)
+    naturalsort(sampleCore(geno, obj, size = 2, steps = 5000, mode = "fast", normalize = FALSE)$sel)
   })
   expect_true(all(sapply(cores, function(core){all.equal(core, cores[[1]])})))
 })
@@ -119,44 +119,44 @@ test_that("fixed ids are respected", {
 
   # on index
   always <- 1:3
-  core <- sampleCore(geno, size = 3, time = 1, always.selected = always)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", always.selected = always)
   expect_equal(core$sel, c("Alice", "Bob", "Dave"))
   # on id
   always <- c("Alice", "Dave", "Bob")
-  core <- sampleCore(geno, size = 3, time = 1, always.selected = always)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", always.selected = always)
   expect_equal(core$sel, c("Alice", "Bob", "Dave"))
 
   # 2: again by excluding others
 
   # on index
   never <- 4:5
-  core <- sampleCore(geno, size = 3, time = 1, never.selected = never)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", never.selected = never)
   expect_equal(core$sel, c("Alice", "Bob", "Dave"))
   # on id
   never <- c("Bob'", "Carol")
-  core <- sampleCore(geno, size = 3, time = 1, never.selected = never)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", never.selected = never)
   expect_equal(core$sel, c("Alice", "Bob", "Dave"))
 
   # 3: fix some
   always <- c(2,5)
-  core <- sampleCore(geno, size = 3, time = 1, always.selected = always)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", always.selected = always)
   expect_true("Dave" %in% core$sel)
   expect_true("Carol" %in% core$sel)
   ### again with A-NE objective
-  core <- sampleCore(geno, obj = objective("AN"), size = 3, time = 1, always.selected = always)
+  core <- sampleCore(geno, obj = objective("AN"), size = 3, time = 1, mode = "fast", always.selected = always)
   expect_true("Dave" %in% core$sel)
   expect_true("Carol" %in% core$sel)
 
   # 4: exclude some
   never <- c(2,5)
-  core <- sampleCore(geno, size = 3, time = 1, never.selected = never)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", never.selected = never)
   expect_false("Dave" %in% core$sel)
   expect_false("Carol" %in% core$sel)
 
   # 5: fix and exclude one
   always <- 1
   never <- 2
-  core <- sampleCore(geno, size = 3, time = 1, always.selected = always, never.selected = never)
+  core <- sampleCore(geno, size = 3, time = 1, mode = "fast", always.selected = always, never.selected = never)
   expect_true("Alice" %in% core$sel)
   expect_false("Dave" %in% core$sel)
 
@@ -166,13 +166,7 @@ test_that("fixed ids are respected", {
     objective("AN", "MR")
   )
   always <- c(2,5)
-  core <- sampleCore(geno, obj = obj, size = 3, time = 1, always.selected = always)
-  expect_true("Dave" %in% core$sel)
-  expect_true("Carol" %in% core$sel)
-
-  # 7: fast mode
-  always <- c(2,5)
-  core <- sampleCore(geno, size = 3, time = 1, always.selected = always, mode = "f")
+  core <- sampleCore(geno, obj = obj, size = 3, time = 1, mode = "fast", always.selected = always)
   expect_true("Dave" %in% core$sel)
   expect_true("Carol" %in% core$sel)