Check whether a package is ready for submission to rOpenSci’s peer review system. The primary function collates the output of
R CMD check results, along with a number of statistics via the
pkgstats package, and package structure checks expected for rOpenSci submissions. The output of this function immediately indicates whether or not a package is “Ready to Submit”.
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 the
pkgstats README. 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
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
That object has default
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 uses 'roxygen2' ## ✖ Package does not have a 'contributing.md' file ## ✖ Package does not have a 'CITATION' file ## ✖ Package does not have a 'codemeta.json' file ## ✔ All functions have examples ## ✔ Package 'DESCRIPTION' has a URL field ## ✖ Package 'DESCRIPTION' does not have a BugReports field ## ✔ Package name is available ## ✖ Package has no continuous integration checks ## ✖ Package coverage is 0% (should be at least 75%) ## ✔ R CMD check found no errors ## ✔ R CMD check found no warnings ## ✔ All applicable standards [v0.0.1] have been documented in this package ## ## 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
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.)
The full list of checks which packages are expected to pass currently includes:
CITATIONfile in the
<-, but not a mixture of both).
DESCRIPTIONfile must have a “URL” field.
DESCRIPTIONfile must have a “BugReports” field.
R CMD check(implemented via the
rcmdcheckpackage) must generate no warnings or errors.
Several of these are by default only shown when they fail; absence from a resultant checklist may be interpreted to indicate successful checks.
Full details of check results can be seen by
pkgcheck() function (or just by typing the name of this object in the console.) This object is itself a list including the following items:
The first four of these contain information on the package. The remainder include:
summarycontaining summary statistics on package structure (such as lines of code, and numbers of files and functions).
gitcontaining information and statistics on the
gitrepository associated with a package (if any), including date of first commit, total number of commits and of committers.
srrsummarising information on statistical packages generated by the
srrpackage, including a link to a locally-generated HTML report on standards compliance.
file_listas a list of binary flags denoting presence of absence of all files required for an R package to be submitted to rOpenSci
fns_have_exswith a list of any functions which do not have documented examples
left_assignswith a logical value indicating whether or not global assignment operators (
<<-) are used; and a tally of the two types of left-assignment operators (
=). One one of these should be non-zero, reflecting consistent usage of the same type.
pkgstatscontaining several statistics of package structure, along with associated percentiles assessed against the entire distribution of all current CRAN packages.
network_filewith the path to a local HTML file containing a .visjs representation of the network of relationships between objects (such as functions) within a package, within and between each computer language used in the package.
gpcontaining the output of the
goodpracticepacakge, itself including results from:
rcmdcheckpacakge for running
R CMD check
covrpackage for assessing code coverage
cyclocomppackage for quantifying the cyclomatic complexity of package functions
descpackage for analysing the structure of
Note that results from
lintr package are not reported in the check summary, and that
lintr results are reported only in the detailed results, and have no influence on whether a package passes the summary checks.
pkgcheck results to screen is nice, but sometimes it’s even better to have a nicely formatted full-screen representation of check results. 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).
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
md is the output of
pgkcheck 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, in a
pkgcheck subdirectory of the location determined by
You may manually erase the contents of this subdirectory at any time at no risk beyond additional time required to re-generate contents. This default location may also be over-ridden by setting an environmental variable named
pkgcheck_cache_dir. 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.
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.
checklist package for “checking packages and R code”.