Auto tests

.Rbuildignore

@@ -0,0 +1,4 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+.github
+BIGf90_0.3.0.pdf

.github/workflows/R-CMD-check.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: [main, auto_tests]
+  pull_request:
+    branches: [main, auto_tests]
+
+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

.gitignore

@@ -0,0 +1,3 @@
+.DS_store
+.Rproj.user
+BIGf90.Rproj

DESCRIPTION

@@ -1,18 +1,20 @@
 Package: BIGf90
 Title: R face front for running K-fold crossvalidation, estimating ebvs and variance component estimation with Blupf90 modules
 Version: 0.3.0
-Authors: Josue Chinchilla-Vargas, Alexander M. Sandercock and Breeding Insight Team
-Maintainer:Josue Chinchilla-Vargas <jc3635@cornell.edu>
+Authors@R: c(person("Josue", "Chinchilla-Vargas", role = c("aut", "cre"), email = "jc3635@cornell.edu"), 
+             person("Alexander", "Sandercock", role = "aut"),
+             person("Breeding Insight Team", role = "ctb"))
+Maintainer: Josue Chinchilla-Vargas <jc3635@cornell.edu>
 Description: This package provides R functions to run several BLUPf90 modules. Along with an R function to run K-fold crossvalidation for univariate analyses through blupf90+. 
     The output table from the K-fold crossvalidation function calculates accuracy as cor(y,ebv^) and cor(y*,ebv^) along with bias of ebvs calculated as reg(y,ebv.)
     You will need to create the .par file to feed into Renumf90 manually. Once this is done, there are functions to run Renumf90, Blupf90+, Predictf90, Gibbsf90+ and Postgibbsf90.
     If you need to learn how to use the blupf90 suite of programs refer to nce.ads.uga.edu/wiki/doku.php?id=start. Please remember to cite Blupf90 appropriately along with this package  when used for publications.
     To run the functions in this package you will need to have a directory with all the blupf90 executables so that you can indicate the path for R to find the execs.
     As of version 0.3.0, all functions have been tested in PC and Unix environments, we have noticed that PC environments tend to have issues about permissions, so it is advised to run RStudio as administrator when planning to use this package.
-License: Apache 2.0
+License: Apache License (== 2.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     base (>= 4.3.1),
     dplyr (>= 1.1.4),

R/clean_ebvs.R

@@ -10,11 +10,11 @@
 #' @return a tab-separated file that includes the original id and ebv for all individuals for which an EBV was produced.
 #' @import dplyr
 #' @examples
-#' ## Example
-#'
-#'clean_ebvs(3,
-#'"my_clean_ebvs")
 #'
+#' \donttest{
+#'   #clean_ebvs(3, "my_clean_ebvs")
+#' }
+#' 
 #' @export
 clean_ebvs <- function(random_effect_col, solutions_output_name) {
 

R/run_renum.R

@@ -8,11 +8,13 @@
 #' @param path_2_execs path to a folder that holds the renumf90 executable. This field should be in quotes "".
 #' @param raw_par_file name of the .par file that will be processed.  This field should be in quotes "".
 #' @examples
-#' ## Example
-#'
-#' # run_renum(path_2_execs = "/Users/johndoe/Desktop/bf90_execs/",
-#'  raw_par_file = "weight_2022_no_cov_cv.par")
-#'
+#' 
+#' \donttest{
+#'  #run_renum(path_2_execs = "path/bf90_execs/", 
+#'  #raw_par_file = "weight_2022_no_cov_cv.par")
+#' }
+#' 
+#' 
 #' @export
 run_renum <- function(path_2_execs, raw_par_file) {