Preparing Your Package for for Submission

All code for this document is located here.

# Startup Process

Most of the work we will cover here will get you up and running for submission to our GitHub-based platform. We will use the usethis package to help us with the process of package development. If you do not have the package installed, please run:

install.packages("usethis")

After usethis is installed, you should go through the following process:

# Version Control using Git

We will use the git version control system for our repositories. Other version control systems exist, such as Subversion and Mercurial, but we require git for our packages as this is the most popular modern version control system.

## Setting up Git

### RStudio

If you use RStudio to set up your packages, please check “Create a git repository” when setting up your package. Once a repository is set up, you can use the Tools → Version Control menu in RStudio for committing and pushing if you do not want to use the command line.

### Using usethis

In R, you can use usethis to set up the git repository. If you are in the root directory of the package (the place with DESCRIPTION, NAMESPACE, etc. files), you can run:

usethis::use_git()

If you would like to pass in the path of the directory instead, use:

usethis::use_git(pkg = "/path/to/repository")

Now you should have a folder on your machine (it may be hidden) that stores your commits and changes.

# Hosting Git Repositories on GitHub

Our platform is based on GitHub, which is an online server of the to host git repositories. There are other online repositories for git, such as BitBucket and GitLab. Although hosting on these repositories should be valid, we currently require all developers to currently host on GitHub. GitHub is the most popular platform in our experience and all hooks/backend development we use is based on that. Note, git is a system/software, usually installed on your machine, and GitHub is the online server hosting it. In order to host your repository on GitHub, you must sign up for an account at https://github.com/.

## Setting up GitHub

### Using the GitHub Website

In order to set up your repository for GitHub, you can either use the website. When you are logged into Github, click the plus sign in the top right hand corner , and then click “New Repository” In the top right hand corner. We highly recommend naming the GitHub repository the same name as the package.

### Using usethis

Using usethis, you can use the use_github. In order to use this command, you must have a personal access token (PAT) from https://github.com/settings/tokens. Make sure at least the public_repo option is checked. If you have a token set in the GITHUB_PAT environment variable, usethis will use that.

If you do not have the GITHUB_PAT environment variable set, you must specify auth_token = "YOUR_TOKEN_HERE" in the following commands.

If you are in the root directory of the package (the place with DESCRIPTION, NAMESPACE, etc. files), you can run:

usethis::use_github()

If you would like to pass in the path of the directory instead, use:

usethis::use_git(pkg = "/path/to/repository")

Check the GitHub website to ensure you have set up your GitHub repository. You should be able to see the “Push” button enabled when you go to Tools → Version Control → Commit in RStudio.

# Setting Up a README file

Once you have your package set up, you should make a README.md file. You can either use a REAMDE.md file straight out, without R code or a README.Rmd file that you knit/render to a README.md file.

usethis::use_readme_rmd()
usethis::use_readme_md()

The README.md file is written in Markdown and you can use the GitHub Markdown flavor. A REAMDE file is important because it generates the content at the bottom of a GitHub repository, such as how to install or use the package. You can also put your badges for number of downloads, version on CRAN (if applicable), continuous integration status, and code coverage.

# Using Continuous Integration

## Travis

The Travis CI is a continuous integration service that we will use to build and check R packages on Linux and Mac OS X operating systems. In order to use Travis, you must have an account. We recommend to use sign in to Travis CI with your GitHub account. You need to authorize Travis CI to have access to your GitHub repositories. If you have private repositories, those are hosted on https://travis-ci.com, whereas public ones are hosted on https://travis-ci.org. After authorizing, you should be able to “Sync Accounts” to see your repositories and turn on integration.

### Configuring Travis

To create the configuration necessary for Travis CI to build and check the package, the easiest way is to use the use_travis command:

usethis::use_travis()

This will add a .travis.yml (a YAML file) file to your folder and added this to your .Rbuildignore file. We recommend adding the following options to your .travis.yml file:

warnings_are_errors: true

so that warnings are treated as errors, which we require in our platform.

If you would like to test on Mac OSX and Linux (the default is Linux only), add the following lines.

os:
- linux
- osx

If you would like to use our platform’s customized Travis configuration file, you can use the YAML file, but make sure you rename it to .travis.yml in your folder.

### Enabling Travis

Using use_travis will open a URL (https://travis-ci.org/GITHUB_USERNAME/REPO) so you can enable Travis to run on this package. If you use our custom Travis URL, you will have to go that URL yourself.

In your README.md, add the following lines for a travis shield:

 [![Travis-CI Build Status] (https://travis-ci.org/GITHUB_USERNAME/REPO.svg?branch=master)] (https://travis-ci.org/GITHUB_USERNAME/REPO)

where you change GITHUB_USERNAME/REPO to your information. Once you add/commit the changes to README.md, you should have a badge after your package builds to let you know if it passes or fails.

## Appveyor

Appveyor is a continuous integration service that builds projects on Windows machines. Although some packages may not be able to compile on Windows machines, we strive to compile all packages on all 3 main operating systems.

To enable Appveyor for this repository, the easiest way is to use the use_appveyor command:

usethis::use_appveyor()

This will add a appveyor.yml YAML file to your folder and added this to your .Rbuildignore file. We recommend adding the following options to your .travis.yml file:

environment:
global:
WARNINGS_ARE_ERRORS: 1

so that warnings are treated as errors, which we require in our platform.

If you would like to use our platform’s customized Appveyor configuration file, you can use the YAML file, but make sure you rename it to appveyor.yml in your folder.

### Enabling Appveyor

You must go to https://ci.appveyor.com/projects/new, go to the repository and then click “Add”. Once you commit and push to the GitHub repository, then Appveyor should build and check your package.

In your README.md, add the following lines for a travis shield:

[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/GITHUB_USERNAME/REPO?branch=master&svg=true)](https://ci.appveyor.com/project/GITHUB_USERNAME/REPO)

where you change GITHUB_USERNAME/REPO to your information. Once you add/commit the changes to README.md, you should have a badge after your package builds to let you know if it passes or fails.

Before you push to GitHub, you can check your package so that all things are in order. We recommend using devtools::check(args = "--as-cran"). This will check your package and documentation for consistency and inform you of any warnings or errors. We use the --as-cran as it performs checks additional checks similar to CRAN.

If checking in RStudio, you can add this argument in Build → Configure Build Tools, and add --as-cran under the “Check options”.

You also can do this at the command line using R CMD check --as-cran, but you should build a source tarball of your package first.

# Creating Unit Tests using testthat

Unit tests make it easier to identify problems when you make changes to your package. For example, a new function may work but may not handle a previous case or bug that you had fixed. Creating a unit test for this bug can ensure that if the output changes to something unexpectedly, you are notified.

We recommend checking out Hadley Wickham’s tutorial on testing for unit tests. We recommend using the testthat package. In order to use the testthat package, the easiest way is to use

usethis::use_testthat()

which should make a tests folder. Add as many tests as necessary to try to get your code coverage as close to 100% as possible.

# Creating a Vignette

To make your package more user-friendly (and therefore more likely to be used), we strongly suggest you provide a vignette with your package. To create a vignette, run the following command:

usethis::use_vignette("my-vignette")

where you’d change my-vignette to the filename of the vignette (which means no spaces!). This will create an R Markdown vignette with the following metadata:

---
title: "Vignette Title"
author: "Vignette Author"
date: "2021-02-18"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Vignette Title}
%\VignetteEngine{knitr::rmarkdown}
\usepackage[utf8]{inputenc}
---

Change the title: "Vignette Title" area to have the title you’d like inside the document. You can change the %\VignetteIndexEntry{Vignette Title} to the same title; this will be the title of the vignette in the documentation of the pacakge. When you run browseVignettes("YOUR_PACKAGE"), the entry there will be pulled from VignetteIndexEntry.

You can make multiple vignettes for the different types of analyses or use cases for your package.

## Building Vignettes

In order to build your vignettes, you can use the following command:

devtools::build_vignettes()

# Using Code Coverage

Code Coverage measures the percentage of code is run when testing occurs. The covr package by Jim Hester provides a great interface for code coverage in R packages. You can check the code coverage of your package using:

covr::package_coverage()

which will provide you with a report. We suggest adding the argument type = "all" so that the code coverage is calculated after going through the unit tests, vignettes, and examples. The default is to only use the coverage of the unit tests. Thus, you would run:

covr::package_coverage(type = "all")

## Code Coverage and Continuous Integration

The covr package also provides an interface for 2 online code coverage tools: Coveralls and Codecov. We use Coveralls as we have had better success setting up the API for our backend, but both are very good.

To check the code coverage of the package after each build, the easist way is to use use_coverage:

usethis::use_coverage(type = "coveralls")
usethis::use_coverage(type = "codecov")

where you would use the one whichever service you prefer (they should be the same). This will add the covr package to the “Suggests” field of the DESCRIPTION (if not in another dependency). The message states to add:

after_success:
- Rscript -e 'covr::coveralls()'

or

after_success:
- Rscript -e 'covr::codecov()'

to the .travis.yml file (respective to the service you use).

We suggest adding the argument type = "all" so that the code coverage is calculated after going through the unit tests, vignettes, and examples. The default is to only use the coverage of the unit tests. Thus, you would add:

after_success:
- Rscript -e 'covr::coveralls(type = "all")'

or

after_success:
- Rscript -e 'covr::codecov(type = "all")'

to the .travis.yml file, respectively.

Now that you’ve performed all the checks and ensured that the package is thoroughly tested, you can submit your package. Please provide your name, email, and link to the GitHub repository on the Neuroconductor or OSLER submission pages. The maintainer of the package will receive and email to verify this is a valid submission and the package will begin the changes to your package and integration.

# Deploying Binary Packages on GitHub

In order to push objects back to GitHub, you must add a deploy statements to your CI configuration files. In general, this workflow is designed if you tag a commit and push that tag to GitHub.

## Creating the Binary Package

In your configuration files, you need to add the following to tell R to build a binary package when running R CMD check:

r_check_args: "--as-cran --install-args=--build"

before_deploy:
- if [[ ${#TRAVIS_TAG} -gt 0 ]]; then R CMD INSTALL --build .; fi;  to the configuration file so that a binary is built, but only when the commit is tagged. NB: these outputs may have different filenames than the workflow using --install-args=--build. ## Travis CI Travis supported documentation is here. For Travis, you should download the travis command line interface (cli) on your machine. I suggest Mac users use the HomeBrew workflow. You should have your GitHub Personal Authentication Token (PAT) set to the GITHUB_PAT environment variable (export GITHUB_PAT=... in ~/.bash_profile or ~/.profile). Once this is installed, in the Terminal, you must change directories to the package directory and run: travis setup releases You will have to provide your login credentials for GitHub. This will add a deploy field to your confiration file. You should change some things around so that Travis knows that you are deploying. My recommended deploy is: deploy: provider: releases skip_cleanup: true api_key: secure: ... file_glob: true file: PACKAGE_NAME*.t*gz on: tags: true repo: GITHUB_USERNAME/PACKAGE_NAME where PACKAGE_NAME is the package name, and GITHUB_USERNAME is your GitHub username. Breaking this down: 1. provider: releases - this will push to the releases page of GitHub 2. skip_cleanup: true - don’t delete things made in the build process 3. api_key: secure - your Encrypted GitHub PAT 4. file_glob: true - allow some regular expression matching 5. file: PACKAGE_NAME*.t*gz - this will match anything with your package name and extensions such as tar.gz (for binary Linux builds or the source build of the package) and .tgz (binary builds of MacOS). 6. tags: true - only build a release if the commit is tagged 7. repo: - this key is only valid for this repo. ### Building on Multiple OS NB: if you are building for both Linux and MacOSX, for example if you have: os: - linux - osx in your Traivs configuration, you should add: before_deploy: # so no overwrite of linux build - if [[ "${TRAVIS_OS_NAME}" = "osx" ]]; then rm -f *.tar.gz; fi

to you Travis so that the source build (with extension .tar.gz) doesn’t overwrite the Linux binary on GitHub (they will have the same name if you use --install-args=--build.

## Appveyor

Appveyor supported documentation is here.

For Appveyor, you must add the following to your appveyor.yml:

deploy:
provider: GitHub
description: 'Windows Binary'
auth_token:
secure: ENCRYPTED_GITHUB_PAT_FROM_APPVEYOR_WEBSITE
draft: false
prerelease: false
on:
appveyor_repo_tag: true

which is a similar flavor to the Travis configuration. In order to deploy, you need to Encrypt your GITHUB_PAT at https://ci.appveyor.com/tools/encrypt and replace ENCRYPTED_GITHUB_PAT_FROM_APPVEYOR_WEBSITE with the result. This will push a binary .zip file to GitHub.

NB: If you change the PATH around in Appveyor, you may set the default system from MinGW to MSYS, which may not cause a binary to be built. As long as you have

environment:
global:
R_CHECK_INSTALL_ARGS: "--install-args=--build --no-multiarch"

in your appveyor.yml, that should run regardless (though may not be the universal workflow for the standard Windows user with Rtools).

# Short Version

The condensed version of this worklow is to run (in R):

usethis::use_git()
usethis::use_github() # must have GITHUB_PAT set up
usethis::use_vignette("my-vignette")
usethis::use_testthat()
usethis::use_appveyor()
usethis::use_travis()
usethis::use_coverage(type = "coveralls")

And edit the following files:

## .travis.yml

Add (or change in terms of code coverage) the following lines:

warnings_are_errors: true
after_success:
- Rscript -e 'covr::coveralls(type = "all")'

to .travis.yml.

## appveyor.yml

environment:
global:
WARNINGS_ARE_ERRORS: 1

to appveyor.yml.

## README.md

Add the following lines, changing GITHUB_USERNAME/REPO to the correct version

 [![Travis-CI Build Status] (https://travis-ci.org/GITHUB_USERNAME/REPO.svg?branch=master)] (https://travis-ci.org/GITHUB_USERNAME/REPO)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/GITHUB_USERNAME/REPO?branch=master&svg=true)](https://ci.appveyor.com/project/GITHUB_USERNAME/REPO)

to the README.md.

## CI and Authentication Tokens

If you need access to a secure key, such as a GitHub Personal Acccess Token (PAT), you do not to set them in your YAML files. Specifically with GitHub, if you push a secure key to a repository, GitHub will automatically deactivate that token (this may only apply to public repositories). In order to set an environment variable, such as GITHUB_PAT for GitHub authentication, you have to change the settings on the repository on the respective CI website.

### Travis CI

In Travis CI you have to go to: https://travis-ci.org/USERNAME/REPO/settings, then the section labeled “Environment Variables”. Put GITHUB_PAT as the name and paste your unencrypted GitHub PAT in the Value field. When you build on Travis CI, you should see:

Setting environment variables from repository settings
\$ export GITHUB_PAT=[secure]

in the build logs. Now you can use the environment variable GITHUB_PAT in your code.

### Appveyor

In Appveyor you have to go to: https://ci.appveyor.com/project/USERNAME/REPO/settings, then the section labeled “Environment” and click “Add Variable”. Put GITHUB_PAT as the name and paste your unencrypted GitHub PAT in the Value field. I believe you should click the lock to encrypt it.

# Session Info

devtools::session_info()