First commit r template package

.Rbuildignore

+^\.gitlab\-ci\.yml$
+^\.git$
+^\.gitignore$
+^README\.md$

.gitlab-ci.yml

+stages: 
+  - create
+  - tests
+  - build
+
+R-base-create:
+  stage: create
+  tags:
+    - "r-base-biosp"
+  script:
+    # generate Documentation
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    # create the package
+    - "R CMD build . --resave-data"
+  artifacts:
+    paths:
+      # keep the package for later jobs
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+      # can use $CI_PROJECT_NAME if package name the same
+
+R-devel-create:
+  stage: create
+  tags:
+    - "r-devel-biosp"  
+  script:
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    - "R CMD build . --resave-data"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+  allow_failure: true
+
+R-Mac-create:
+  stage: create
+  tags:
+    - "Mac"  
+    - "R"
+  script:
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    - "R CMD build . --resave-data"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+
+R-Windows-create:
+  stage: create
+  tags:
+    - "win10"
+    - "R"
+    - "binaries"
+  script:
+    - "Rscript -e \"roxygen2::roxygenize('.', roclets=c('rd', 'collate', 'namespace'))\""
+    - "R CMD build . --resave-data"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+
+R-base-tests:
+  stage: tests
+  tags:
+    - "r-base-biosp"
+  script:
+    - "R CMD check --as-cran $(ls -rt *_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+  dependencies:
+    - R-base-create
+
+R-devel-tests:
+  stage: tests
+  tags:
+    - "r-devel-biosp"  
+  script:
+    - "R CMD check --as-cran $(ls -rt *_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+  allow_failure: true
+  dependencies:
+    - R-devel-create
+
+R-Mac-tests:
+  stage: tests
+  tags:
+    - "Mac"  
+    - "R"
+  script:
+    - "R CMD check --as-cran $(ls -rt *_* |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+  dependencies:
+    - R-Mac-create
+
+R-Windows-tests:
+  stage: tests
+  tags:
+    - "win10"
+    - "R"
+    - "binaries"
+  script:
+    - "R CMD check --as-cran $(ls -rt *_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tar.gz |tail -1)"
+  dependencies:
+    - R-Windows-create
+
+release-R:
+  stage: build
+  tags:
+    - "r-base-biosp"
+  script:
+    - "echo \"Nothing to do\""
+  artifacts:
+    paths:
+      - "$(ls -rt *_* |tail -1)"
+  only:
+    - tags
+  dependencies:
+    - R-base-tests
+
+release-Windows:
+  stage: build
+  tags:
+    - "win10"
+    - "R"
+    - "binaries"
+  script:
+    - "R CMD INSTALL --build --force-biarch $(ls -rt *_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.zip |tail -1)"
+  only:
+    - tags
+  dependencies:
+    - R-Windows-tests
+
+release-MacOS:
+  stage: build
+  tags:
+    - "Mac"  
+    - "R"
+  script:
+    - "R CMD INSTALL --build $(ls -rt *_*.tar.gz |tail -1)"
+  artifacts:
+    paths:
+      - "$(ls -rt *_*.tgz | tail -1)"
+  only:
+    - tags
+  dependencies:
+    - R-Mac-tests
+

DESCRIPTION

+Package: PackageRTemplate
+Type: Package
+Encoding: UTF-8
+Title: R Template Package
+Version: 0.1.0
+Date: 2019-11-05
+Authors@R: person("Jean-Francois", "Rey", role = c("aut","cre"), email = "jean-francois.rey@inra.fr")
+Author: Jean-Francois Rey [cre, aut]
+Maintainer: Jean-Francois Rey <jean-francois.rey@inra.fr>
+Description: A R package template to manage the package and the CI/CD pipeline.
+URL: https://gitlab.paca.inra.fr/r-ecosystem/cookbooks/r-packages-ci-cd
+BugReports: https://gitlab.paca.inra.fr/r-ecosystem/cookbooks/r-packages-ci-cd/issues
+License: GPL (>= 3) | file LICENSE
+LazyData: true
+BuildVignettes: true
+Biarch: true
+Depends:
+    methods,
+    utils,
+    grDevices (>= 3.0.0),
+    graphics (>= 3.0.0),
+    R (>= 3.3.0)
+Imports:
+    stats (>= 3.0.2)
+Collate:
+    'packagertemplate.R'
+    'awesomemethod.R'
+LinkingTo: testthat
+RoxygenNote: 6.1.1
+Suggests:
+    testthat

R/awesomemethod.R

+# R Package Template fr CI/CD piepline.
+# Copyright (C) 2016 Jean-François Rey <jean-françois.rey@inra.fr>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+#' An awesome method that return if the parameter is TRUE
+#' @title Test parameter is TRUE
+#' @name awesomemethod
+#' @param bool a boolean (default TRUE)
+#' @return TRUE if bool is TRUE otherwise FALSE
+#' @include packagertemplate.R
+#' @export
+awesomemethod <- function(bool = TRUE) {
+  return(bool == TRUE)
+}

R/packagertemplate.R

+# R Package Template fr CI/CD piepline.
+# Copyright (C) 2016 Jean-François Rey <jean-françois.rey@inra.fr>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+#' @encoding UTF-8
+#' @title R Package Template
+#' @description A R package template to manage the package and the CI/CD piepline.
+#' @aliases packagertemplate-package
+#'
+#' @author Jean-Francois Rey \email{jean-francois.rey@@inra.fr}
+#'
+#' Maintainer: Jean-Francois Rey \email{jean-francois.rey@@inra.fr}
+#' @docType package
+#' @name packagertemplate-package
+#' @details \tabular{ll}{
+#'          Package: \tab PackageRTemplate\cr
+#'          Type: \tab Package\cr
+#'          Version: \tab 0.1.0\cr
+#'          Date: \tab 2019-11-05\cr
+#'          License: \tab GPL (>=3)\cr
+#'          }
+#'
+#' The PackageRTemplate package implements a R package template and how to manage CI/CD pipeline.
+#' @keywords R package CI CD GitLab
+#' @examples
+#' \dontrun{
+#' library("PackageRTemplate")
+#' }
+#' @import methods
+#' @import graphics
+#' @import stats
+"_PACKAGE"
+

README.md

+# R Packages Continuous Integration and Deployment (CI/CD) pipeline
+
+This project hosts the repository of a Cookbook to manage a R package.
+
+This template generate the documentation, build the package, run unit tests, check --as--cran, create package binaries for Windows and Mac OS...  
+
+[useR2019 poster __R package development using GitLab CI/CD pipeline__ , JF Rey, L Houde, 2019](inst/userR2019-poster_JF_REY.pdf)
+
+** Table of Contents** 
+
+- [Prerequisites](#prerequisites)
+- [Files](#files)
+- [Principle](#principle)
+- [Set GitLab](#set-gitlab)
+  - [The Project](#the-project-repository)
+  - [The Runners](#the-runners)
+- [The .gitlab-ci.yml file](#the-gitlab-ciyml-file)
+- [Author](#author)
+- [License](#license)
+
+## Prerequisites
+
+* Have to know:
+  * GitLab project management
+  * R Packages
+
+* Should to know:
+  * GitLab Runners principle
+  * GitLab CI/CD principle
+  * R Package CRAN policy
+
+## Branches
+
+There are severals version of this project, depending if the package need compilations, vignettes... :
+
+* simple R package : [master](tree/master)
+* R package and c++ code source : [Rcpp](tree/rcpp)
+
+## Files
+
+* __[.gitlab-ci.yml](.gitlab-ci.yml)__ : file configuring the CI/CD pipeline
+* R Package stuff : 
+  * __[DESCRIPTION](DESCRIPTION)__ : the DESCRIPTION file update by roxygen2
+  * __[NAMESPACE](NAMESPACE)__ : the NAMESPACE file generated by roxygen2
+  * __[.Rbuildignore](.Rbuildignore)__ : regex for files to not include in package
+  * __[R/](R)__ : R source code directory
+  * __[man/](man)__ : documentation directory generated by roxygen2
+  * __[test/](tests)__ : testthat direcotry, instruction for tests
+  * __[inst/](inst)__ : directory of files to add in package at install
+  * __[LICENSE](LICENSE)__ : the license file
+
+## Principle
+
+![GitLab CI/CD R Package pipeline](inst/GitLab_CI_CD_pipeline_RPackage.png)
+
+* At push (and commit), in GitLab repository, the pipeline is trigger.
+* GitLab use __[.gitlab-ci.yml](.gitlab-ci.yml)__ file to set the pipeline and run it on runners.
+  * First it generates the package
+  * Then it run tests
+  * And finally build binaries packages
+
+## set up GitLab
+
+### The project repository
+
+You can fork this project and use it as a template.
+
+* Files in the project: [Files](#files)  
+
+You need to enable __Pipelines__ in the project setting (_Setting -> General -> Visibility_)
+and enable __Shared Runners__ (_Setting -> CI/CD -> Runners_).  
+
+### The runners
+
+Four Runners are availables for R Packaging in the shared runners :  
+* r-base-biosp : it's the current version of R for Linux OS (nightly build as docker image). [See here](https://gitlab.paca.inra.fr/r-ecosystem/r-docker-images) for more information.  
+* r-devel-biosp : it's the in development version of R (the next version) for Linux OS (nightly build as docker image). [See here](https://gitlab.paca.inra.fr/r-ecosystem/r-docker-images) for more information.  
+* R win10 binaries : a Windows 10 Virtual Machine with the current R and Rtools version.  
+* R Mac : a Mac OS High Sierra with the current R and Rtools version.  
+
+If you need you can add your own runner or ask GitLab administrator to set up a new one.  
+
+
+## The .gitlab-ci.yml file
+
+__[.gitlab-ci.yml](.gitlab-ci.yml)__ is the configuration file for the CI/CD pipeline.  
+It set up three stages (create, tests and build) and severals jobs by stages.  
+
+* create : update Description, NAMESPACE, and man (roxygen2). Create the package.  
+* tests : Test the package (--as-cran)
+* build : Build the package source tar.gz and binary version for MacOS (.tgz) and Windows (.zip)
+
+You need to set up this file for your project.
+
+Each jobs produces artifacts mainly in _build_ stage it produces R packages delivery for Linux, Windows and Mac OS.  
+
+## Author
+
+[Jean-François Rey](https://jeff.biosp.org) \<jean-francois.rey at inra dot fr\>
+
+## License
+
+See [LICENSE](LICENSE)

tests/testthat.R

+library(testthat)
+library(PackageRTemplate)
+
+test_check("PackageRTemplate")

tests/testthat/test-method.R

+context("test-method")
+
+test_that("awesomemethod return values", {
+  expect_equal(awesomemethod(), TRUE)
+  expect_equal(awesomemethod(FALSE), FALSE)
+  expect_equal(awesomemethod(TRUE), TRUE)
+
+
+})