rOpenSci Package Checks • pkgcheck

Check whether a package is ready for submission to rOpenSci’s peer review system. The primary function collates the output of goodpractice, including R CMD check results, a number of statistics via the pkgstats package, and checks for package structure expected for rOpenSci submissions. The output of this function immediately indicates whether or not a package is “Ready to Submit”.

Installation

The easiest way to install this package is via the associated r-universe. As shown there, simply enable the universe with

options (repos = c (
    ropenscireviewtools = "https://ropensci-review-tools.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
))

And then install the usual way with,

install.packages ("pkgcheck")

Alternatively, the package can be installed by first installing either the remotes or pak packages and running one of the following lines:

remotes::install_github ("ropensci-review-tools/pkgcheck")
pak::pkg_install ("ropensci-review-tools/pkgcheck")

The package can then loaded for use with

library (pkgcheck)

Setup

The pkgstats package also requires the system libraries ctags and GNU global to be installed. Procedures to install these libraries on various operating systems are described in a pkgstats vignette. This package also uses the GitHub GraphQL API which requires a local GitHub token to be stored with an unambiguous name including GITHUB, such as GITHUB_TOKEN (recommended), or GITHUB_PAT (for Personal Authorization Token). This can be obtained from GitHub (via your user settings), and stored using

Sys.setenv ("GITHUB_TOKEN" = "<my_token>")

This can also be set permanently by putting this line in your ~/.Renviron file (or creating this if it does not yet exist). Once pkgstats has been successfully installed, the pkgcheck package can then be loaded via a library call:

library (pkgcheck)

Usage

The package primarily has one function, pkgcheck, which accepts the single argument, path, specifying the local location of a git repository to be analysed. The following code generates a reproducible report by first downloading a local clone of a repository called srr-demo, which contains the skeleton of an srr (Software Review Roclets) package, generated with the srr_stats_pkg_skeleton() function:

mydir <- file.path (tempdir (), "srr-demo")
gert::git_clone ("https://github.com/mpadge/srr-demo", path = mydir)
devtools::document (mydir, quiet = TRUE) # Generate documentation entries in "/man" directory
x <- pkgcheck (mydir)

That object has default print and summary methods. The latter can be used to simply check whether a package is ready for submission:

summary (x)
## 
## ── demo 0.0.0.9000 ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## 
## ✔ Package name is available
## ✖ does not have a 'codemeta.json' file.
## ✖ does not have a 'contributing' file.
## ✖ The following function has no documented return value: [test_fn]
## ✔ uses 'roxygen2'.
## ✔ 'DESCRIPTION' has a URL field.
## ✖ 'DESCRIPTION' does not have a BugReports field.
## ✖ Package has no HTML vignettes
## ✖ These functions do not have examples: [test_fn].
## ✖ Package has no continuous integration checks.
## ✖ Package coverage failed
## ✖ Statistical standards should be documented in most package files, yet are mostly only documented in one file.
## ✔ R CMD check found no errors.
## ✔ R CMD check found no warnings.
## 
## ℹ Current status:
## ✖ This package is not ready to be submitted.
##

A package may only be submitted when the summary contains all ticks and no cross symbols. (These symbols are colour-coded with green ticks and red crosses when generated in a terminal; GitHub markdown only renders them in black-and-white.) The object returned from the pkgcheck function is a complex nested list with around a dozen primary components. Full information can be obtained by simply calling the default print method by typing the object name (x).

The `pkgcheck` GitHub action

The pkgcheck package also has an associated GitHub action in the pkgcheck-action repository. You can use this action to run pkgcheck every time you push commits to GitHub, just like the rcmdcheck() checks which can be installed and run via the usethis::use_github_action_check_standard() function. pkgcheck includes an analogous function, use_github_action_pkgcheck(), which will download the workflow file defining the action into your local .github/workflows folder. See the pkgcheck-action repository for more details.

You can also add a pkgcheck badge, just like that rcmdcheck badge, that will always reflect the current state of your repository’s pkgcheck results. To add a badge, copy the following line to your README file, filling in details of the GitHub organization and repository name (<org> and <repo>, respectively):

[![pkgcheck](https://github.com/<org>/<repo>/workflows/pkgcheck/badge.svg)](https://github.com/<org>/<repo>/actions?query=workflow%3Apkgcheck)

What is checked?

All current checks are listed in a separate vignette.

Summary of Check Results

Calling summary() on the object returned by the pkgcheck() function will generate a checklist like that shown above. This checklist will also be automatically generated when a package is first submitted to rOpenSci, and is used by the editors to assess whether to process a submission. Authors must ensure prior to submission that there are no red crosses in the resultant list. (In the unlikely circumstances that a package is unable to pass particular checks, explanations should be given upon submission about why those checks fail, and why review may proceed in spite of such failures.)

Detailed Check Results

Full details of check results can be seen by print-ing the object returned by the pkgcheck() function (or just by typing the name of this object in the console.)

The package includes an additional function, checks_to_markdown(), with a parameter, render, which can be set to TRUE to automatically render a HTML-formatted representation of the check results, and open it in a browser. The formatting differs only slightly from the terminal output, mostly through the components of goodpractice being divided into distinct headings, with explicit statements in cases where components pass all checks (the default screen output inherits directly from that package, and only reports components which do not pass all checks).

This checks_to_markdown() function returns the report in markdown format, suitable for pasting directly into a GitHub issue, or other markdown-compatible place. (The clipr package can be used to copy this directly to your local clipboard with write_clip(md), where md is the output of checks_to_markdown().)

Caching and running `pkgcheck` in the background

Running the pkgcheck function can be time-consuming, primarily because the goodpractice component runs both a full R CMD check, and calculates code coverage of all tests. To avoid re-generating these results each time, the package saves previous reports to a local cache directory defined in Sys.getenv("PKGCHECK_CACHE_DIR").

You may manually erase the contents of this pkgcheck subdirectory at any time at no risk beyond additional time required to re-generate contents. By default checks presume packages use git for version control, with checks updated only when code is updated via git commit. Checks for packages that do not use git are updated when any files are modified.

The first time pkgcheck() is applied to a package, the checks will be stored in the cache directory. Calling that function a second time will then load the cached results, and so enable checks to be returned much faster. For code which is frequently updated, such as for packages working on the final stages prior to submission, it may still be necessary to repeatedly call pkgcheck() after each modification, a step which may still be inconveniently time-consuming. To facilitate frequent re-checking, the package also has a pkgcheck_bg() function which is effectively identical to the main pkgcheck() function, except it runs in the background, enabling you to continue coding while checks are running.

The pkgcheck_bg() function returns a handle to the callr::r_bg() process in which the checks are running. Typing the name of the returned object will immediately indicate whether the checks are still running, or whether they have finished. That handle is itself an R6 object with a number of methods, notably including get_result() which can be used to access the checks once the process has finished. Alternatively, as soon as the background process, the normal (foreground) pkgcheck() function may be called to quickly re-load the cached results.

Prior Work

The checklist package for “checking packages and R code”.

Code of Conduct

Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Contributors

All contributions to this project are gratefully acknowledged using the allcontributors package following the allcontributors specification. Contributions of any kind are welcome!