diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 4208d60..f463ff4 100644 --- a/CRAN-SUBMISSION +++ b/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 diff --git a/DESCRIPTION b/DESCRIPTION index 43c823d..215142c 100644 --- a/DESCRIPTION +++ b/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")) diff --git a/NEWS.md b/NEWS.md index 7fa992d..bbe3299 100644 --- a/NEWS.md +++ b/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) -------------------------- diff --git a/R/corehunter.R b/R/corehunter-package.R similarity index 96% rename from R/corehunter.R rename to R/corehunter-package.R index 138bdd0..b02bfd8 100644 --- a/R/corehunter.R +++ b/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 diff --git a/man/corehunter.Rd b/man/corehunter-package.Rd similarity index 87% rename from man/corehunter.Rd rename to man/corehunter-package.Rd index 69337ab..ec21562 100644 --- a/man/corehunter.Rd +++ b/man/corehunter-package.Rd @@ -1,8 +1,9 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/corehunter.R +% Please edit documentation in R/corehunter-package.R \docType{package} -\name{corehunter} +\name{corehunter-package} \alias{corehunter} +\alias{corehunter-package} \title{Core Hunter 3} \description{ Core Hunter is a tool to sample diverse, representative subsets from large germplasm @@ -63,3 +64,18 @@ core <- sampleCore(geno.pheno) \code{\link{sampleCore}}, \code{\link{evaluateCore}}, \code{\link{objective}} } +\author{ +\strong{Maintainer}: Herman De Beukelaer \email{herman.debeukelaer@gmail.com} + +Authors: +\itemize{ + \item Guy Davenport \email{daveneti@gmail.com} +} + +Other contributors: +\itemize{ + \item Veerle Fack \email{veerle.fack@ugent.be} [thesis advisor] +} + +} +\keyword{internal} diff --git a/revdep/README.md b/revdep/README.md index 445a0e4..9b6166f 100644 --- a/revdep/README.md +++ b/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 | | diff --git a/tests/testthat/testExecution.R b/tests/testthat/testExecution.R index ffb392d..3b49284 100644 --- a/tests/testthat/testExecution.R +++ b/tests/testthat/testExecution.R @@ -85,7 +85,7 @@ 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"), @@ -93,12 +93,12 @@ test_that("seed is respected (multi-objective, with normalization)", { ) 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"), @@ -106,7 +106,7 @@ test_that("seed is respected (multi-objective, no normalization)", { ) 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)