Merge pull request #37 from corehunter/release/3.2.2

Release/3.2.2

.Rbuildignore

@@ -4,3 +4,5 @@
 ^data-raw$
 cran-comments.md
 ^revdep$
+^\.github$
+^CRAN-SUBMISSION$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-standard.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [master, release/*]
+  pull_request:
+    branches: [master, release/*]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [develop, master, release/*]
+  pull_request:
+    branches: [develop, master, release/*]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 3.2.2
+Date: 2023-05-11 15:37:39 UTC
+SHA: 22319bdfde9e607e74ea71381d8025fb5425c474

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: corehunter
 Title: Multi-Purpose Core Subset Selection
-Version: 3.2.1
-Date: 2018-04-16
+Version: 3.2.2
+Date: 2023-05-02
 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"))
@@ -16,9 +16,8 @@ Description: Core Hunter is a tool to sample diverse, representative subsets fro
     <http://www.corehunter.org>).
 Depends: R (>= 3.2.3), rJava (>= 0.9-8)
 Imports: naturalsort (>= 0.1.2), methods
-SystemRequirements: Java JRE 8 or higher
+SystemRequirements: Java (>= 8)
 License: MIT + file LICENSE
-LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 7.2.3
 Suggests: testthat, mockr, StatMatch
 Encoding: UTF-8

NEWS.md

@@ -1,6 +1,11 @@
 Core Hunter 3
 =============
 
+Version 3.2.2 (02/05/2023)
+--------------------------
+
+ - Standardized minimal Java version (>= 8) in system requirements.
+
 Version 3.2.1 (16/04/2018)
 --------------------------
 

R/data.R

@@ -64,6 +64,7 @@ exampleData <- function(){
 #' @return Core Hunter data of class \code{chdata}.
 #'
 #' @examples
+#' \dontrun{
 #' geno.file <- system.file("extdata", "genotypes.csv", package = "corehunter")
 #' pheno.file <- system.file("extdata", "phenotypes.csv", package = "corehunter")
 #' dist.file <- system.file("extdata", "distances.csv", package = "corehunter")
@@ -73,6 +74,7 @@ exampleData <- function(){
 #'   phenotypes(file = pheno.file),
 #'   distances(file = dist.file)
 #' )
+#' }
 #'
 #' @seealso \code{\link{genotypes}}, \code{\link{phenotypes}}, \code{\link{distances}}
 #'
@@ -162,7 +164,7 @@ print.chdata <- function(x, ...){
 #' Create Core Hunter distance data from matrix or file.
 #'
 #' Specify either a symmetric distance matrix or the file from which to read the matrix.
-#' See \url{www.corehunter.org} for documentation and examples of the distance matrix
+#' See \url{https://www.corehunter.org} for documentation and examples of the distance matrix
 #' file format used by Core Hunter.
 #'
 #' @param data Symmetric distance matrix. Unique row and column headers are required,
@@ -316,7 +318,7 @@ print.chdist <- function(x, include.size = TRUE, ...){
 #' Create Core Hunter genotype data from data frame, matrix or file.
 #'
 #' Specify either a data frame or matrix, or a file from which to read the genotypes.
-#' See \url{www.corehunter.org} for documentation and examples of the genotype data
+#' See \url{https://www.corehunter.org} for documentation and examples of the genotype data
 #' file format used by Core Hunter.
 #'
 #' @param data Data frame or matrix containing the genotypes (individuals x markers)
@@ -347,7 +349,7 @@ print.chdist <- function(x, include.size = TRUE, ...){
 #'    In case a data frame is provided, an optional first column \code{NAME}
 #'    may be included to specify item names. The remaining columns should follow
 #'    the format as described above.
-#'    See \url{www.corehunter.org} for more details about the supported genotype formats.
+#'    See \url{https://www.corehunter.org} for more details about the supported genotype formats.
 #'    Note that both the \code{frequency} and \code{biparental} format syntactically also
 #'    comply with the \code{default} format but with different semantics, meaning that it
 #'    is very important to specify the correct format. Some checks have been built in that
@@ -386,6 +388,7 @@ print.chdist <- function(x, include.size = TRUE, ...){
 #' }
 #'
 #' @examples
+#' \dontrun{
 #' # create from data frame or matrix
 #'
 #' # default format
@@ -437,6 +440,7 @@ print.chdist <- function(x, include.size = TRUE, ...){
 #' # frequencies
 #' geno.file <- system.file("extdata", "genotypes-frequency.csv", package = "corehunter")
 #' geno <- genotypes(file = geno.file, format = "frequency")
+#' }
 #'
 #' @import rJava
 #' @export
@@ -742,7 +746,7 @@ print.chgeno <- function(x, include.size = TRUE, ...){
 #' Create Core Hunter phenotype data from data frame or file.
 #'
 #' Specify either a data frame containing the phenotypic trait observations
-#' or a file from which to read the data. See \url{www.corehunter.org} for
+#' or a file from which to read the data. See \url{https://www.corehunter.org} for
 #' documentation and examples of the phenotype data format used by Core Hunter.
 #'
 #' @param data Data frame containing one row per individual and one column per trait.

README.md

@@ -3,13 +3,12 @@
 ### Latest release
 
 [![CRAN version](http://www.r-pkg.org/badges/version/corehunter)](https://CRAN.R-project.org/package=corehunter)
-[![Coverage Status](http://img.shields.io/coveralls/corehunter/corehunter3-r/master.svg)](https://coveralls.io/r/corehunter/corehunter3-r)
-[![Build Status](https://img.shields.io/travis/corehunter/corehunter3-r/master.svg)](https://travis-ci.org/corehunter/corehunter3-r)
+![Build Status](https://github.com/corehunter/corehunter3-r/actions/workflows/check-standard.yaml/badge.svg)
+
 
 ### Development snapshot
 
-[![Coverage Status](http://img.shields.io/coveralls/corehunter/corehunter3-r/develop.svg)](https://coveralls.io/r/corehunter/corehunter3-r)
-[![Build Status](https://img.shields.io/travis/corehunter/corehunter3-r/develop.svg)](https://travis-ci.org/corehunter/corehunter3-r)
+![Build Status](https://github.com/corehunter/corehunter3-r/actions/workflows/check-standard.yaml/badge.svg?branch=develop)
 
 Core Hunter is a tool to sample diverse, representative subsets from large germplasm collections, with minimum redundancy. Such so-called core collections have applications in plant breeding and genetic resource management in general. Core Hunter can construct cores based on genetic marker data, phenotypic traits or precomputed distance matrices, optimizing one of many provided evaluation measures depending on the precise purpose of the core (e.g. high diversity, representativeness, or allelic richness). In addition, multiple measures can be simultaneously optimized as part of a weighted index to bring the different perspectives closer together. The Core Hunter library is implemented in Java 8 as an open source project (see 
 <http://www.corehunter.org>).

cran-comments.md

@@ -1,24 +1,18 @@
-This is a resubmission that addresses the NOTEs raised by CRAN's automatic checks.
-The following changes have been made:
- * updated Date field
-
 ## Test environments
 
-* local OS X install, R 3.4.3
-* ubuntu 14.04 (on travis-ci), R 3.4.2 & R devel
-* win-builder (devel and release)
+* local Windows 11 install: R 4.3.0
+* GitHub actions:
+  * Windows Server 2022: R 4.3.0
+  * Mac OS: R 4.3.0
+  * Ubuntu 22.04: R 4.3.0, R 4.2.3 & R devel
 
 ## R CMD check results
 
-There were no ERRORs or WARNINGs.
-
-There was one NOTE on Travis CI:
-
-* checking R code for possible problems ... NOTE
-  Picked up _JAVA_OPTIONS: -Xmx2048m -Xms512m
+0 errors | 0 warnings | 0 notes
 
-  This note is due to the Travis build server's Java options.
+## Reverse dependencies
 
-## Downstream dependencies
+We checked 1 reverse dependency, comparing R CMD check results across CRAN and dev versions of this package.
 
-There are currently no downstream dependencies for this package.
+ * We saw 0 new problems
+ * We failed to check 0 packages