Extending or modifying checks

This vignette describes how to modify or extend the existing suite of checks implemented by pkgcheck. Each of the internal checks is defined in a separate file in the R directory of this package with the prefix of check_ (or checks_ for files which define multiple, related checks). Checks only require two main functions, the first defining the check itself, and the second defining summary and print methods based on the result of the first function. The check functions must have a prefix pkgchk_, and the second functions defining output methods specifying must have a prefix output_pkgchk_. These two kind of function are now described in the following two sections.

Both of these functions must also accept a single input parameter of a pkgcheck object, by convention named checks. This object is a list of four main items:

pkg which summarises data extracted from pkgstats::pkgstats(), and includes essential information on the package being checked.
info which contains information used in checks, including info$git detailing git repository information, info$pkgstats containing a summary of a few statistics generated from pkgstats::pkgstats(), along with statistical comparisons against distributions from all current CRAN packages, an info$network_file specifying a local directory to a vis.js visualisation of the function call network of the package, and an info$badges item containing information from GitHub workflows and associated badges, where available.
checks which contains a list of all objects returned from all pkgchk_...() functions, which are used as input to output_pkgchk_...() functions.
meta containing a named character vector of versions of the core packages used in pkgcheck.

pkgcheck objects generally also include a fifth item, goodpractice, containing the results of goodpractice checks. The checks item passed to each pkgchk_...() function contains all information on the package, info, meta, and (optionally) goodpractice items. Checks may use any of this information, or even add additional information as demonstrated below. The checks$checks list represents the output of check functions, and may not be used in any way within pkgchk_...() functions.

Click here to see structure of full pkgcheck object

This is the output of applying pkgcheck to a package generated with the srr function srr_stats_pkg_skeleton(), with goodpractice = FALSE to suppress that part of the results.

#> List of 4
#>  $ pkg   :List of 8
#>   ..$ name        : chr "dummypkg"
#>   ..$ path        : chr "/tmp/RtmpkguwJc/dummypkg"
#>   ..$ version     : chr "0.0.0.9000"
#>   ..$ url         : chr(0) 
#>   ..$ BugReports  : chr(0) 
#>   ..$ license     : chr "GPL-3"
#>   ..$ summary     :List of 12
#>   .. ..$ num_authors         : int 1
#>   .. ..$ num_vignettes       : int 0
#>   .. ..$ num_data            : int 0
#>   .. ..$ imported_pkgs       : int 1
#>   .. ..$ num_exported_fns    : int 1
#>   .. ..$ num_non_exported_fns: int 2
#>   .. ..$ num_src_fns         : int 2
#>   .. ..$ loc_exported_fns    : int 3
#>   .. ..$ loc_non_exported_fns: int 3
#>   .. ..$ loc_src_fns         : int 5
#>   .. ..$ num_params_per_fn   : int 0
#>   .. ..$ languages           : chr [1:2] "C++: 72%" "R: 28%"
#>   ..$ dependencies:'data.frame': 4 obs. of  2 variables:
#>   .. ..$ type   : chr [1:4] "depends" "imports" "suggests" "linking_to"
#>   .. ..$ package: chr [1:4] "NA" "Rcpp" "testthat" "Rcpp"
#>  $ info  :List of 5
#>   ..$ git         : list()
#>   ..$ srr         :List of 5
#>   .. ..$ message     : chr [1:108] "This package still has TODO standards and can not be submitted" "Package can not be submitted because the following standards [v0.1.0] are missing from your code:" "" "G1.0" ...
#>   .. ..$ categories  : chr "Regression and Supervised Learning"
#>   .. ..$ missing_stds: chr "G1.0, G1.4a, G1.6, G2.0a, G2.1a, G2.2, G2.3a, G2.3b, G2.4, G2.4a, G2.4b, G2.4c, G2.4d, G2.4e, G2.5, G2.6, G2.7,"| __truncated__
#>   .. ..$ report_file : chr "/home/smexus/.cache/pkgcheck/static/dummypkg_srr2021-10-15-16:46:34.html"
#>   .. ..$ okay        : logi FALSE
#>   ..$ pkgstats    :'data.frame': 25 obs. of  4 variables:
#>   .. ..$ measure   : chr [1:25] "files_R" "files_src" "files_vignettes" "files_tests" ...
#>   .. ..$ value     : num [1:25] 4 2 0 2 10 26 6 0 3 1 ...
#>   .. ..$ percentile: num [1:25] 23.284 77.356 0 64.15 0.445 ...
#>   .. ..$ noteworthy: chr [1:25] "" "" "TRUE" "" ...
#>   .. ..- attr(*, "language")= chr [1:2] "C++: 72%" "R: 28%"
#>   .. ..- attr(*, "files")= chr [1:2] "C++: 2" "R: 4"
#>   ..$ network_file: chr "/home/smexus/.cache/pkgcheck/static/dummypkg_pkgstats.html"
#>   ..$ badges      : list()
#>  $ checks:List of 12
#>   ..$ fns_have_exs     : Named logi FALSE
#>   .. ..- attr(*, "names")= chr "test_fn.Rd"
#>   ..$ has_bugs         : logi FALSE
#>   ..$ has_citation     : logi FALSE
#>   ..$ has_codemeta     : logi FALSE
#>   ..$ has_contrib_md   : logi FALSE
#>   ..$ has_scrap        : chr(0) 
#>   ..$ has_url          : logi FALSE
#>   ..$ has_vignette     : logi FALSE
#>   ..$ left_assign      :List of 2
#>   .. ..$ global: logi FALSE
#>   .. ..$ usage : Named num [1:2] 2 0
#>   .. .. ..- attr(*, "names")= chr [1:2] "<-" "="
#>   ..$ on_cran          : logi FALSE
#>   ..$ pkgname_available: logi TRUE
#>   ..$ uses_roxygen2    : logi TRUE
#>  $ meta  : Named chr [1:3] "0.0.2.25" "0.0.2.96" "0.0.1.120"
#>   ..- attr(*, "names")= chr [1:3] "pkgstats" "pkgcheck" "srr"
#>  - attr(*, "class")= chr [1:2] "pkgcheck" "list"
#> NULL

1. The check function

An example is the check for whether a package has a citation, defined in R/check_has_citation.R:

#' Check whether a package has a `inst/CITATION` file.
#'
#' "CITATION" files are required for all rOpenSci packages, as documented [in
#' our "*Packaging
#' Guide*](https://devguide.ropensci.org/pkg_building.html#citation-file). This
#' does not check the contents of that file in any way.
#'
#' @param checks A 'pkgcheck' object with full \pkg{pkgstats} summary and
#' \pkg{goodpractice} results.
#' @noRd
pkgchk_has_citation <- function (checks) {

    "CITATION" %in% list.files (fs::path (checks$pkg$path, "inst"))
}

This check is particularly simple, because a "CITATION" file must have exactly that name, and must be in the inst sub-directory. This function returns a simple logical of TRUE if the expected "CITATION" file is present, otherwise it returns FALSE. This function, and all functions beginning with the prefix pkgchk_, will be automatically called by the main pkgcheck() function, and the value stored in checks$checks$has_citation. The name of the item within the checks$checks list is the name of the function with the pkgchk_ prefix removed.

A more complicated example is the function to check whether a package contains files which should not be there – internally called “scrap” files. The check function itself, defined in R/check-scrap.R, checks for the presence of files matching an internally-defined list including files used to locally cache folder thumbnails such as ".DS_Store" or "Thumbs.db". The function returns a character vector of the names of any “scrap” files which can be used by the print method to provide details of files which should be removed. This illustrates the first general principle of these check functions; that,

Any information needed when summarising or printing the check result should be returned from the main check function.

A second important principle is that,

Check functions should never return NULL, rather should always return an empty vector (such as integer(0)).

The following section considers how these return values from check functions are converted to summary and print output.

2. The output function

All output_pkgchk_...() functions must also accept the single input parameter of checks, in which the checks$checks sub-list will already have been populated by calling all pkgchk_...() functions described in the previous section. The pkgchk_has_citation() function will create an entry of checks$checks$has_citation which contains the binary flag indicating whether or not a "CITATION" file is present. Similarly, the the pkgchk_has_scrap() function will create checks$checks$has_scrap which will contain names of any scrap files present, and a length-zero vector otherwise.

The output_pkgchk_has_citation() function then looks like this:

output_pkgchk_has_citation <- function (checks) {

    out <- list (
        check_pass = checks$checks$has_citation,
        summary = "",
        print = ""
    )

    # disabled:
    # https://github.com/ropensci-review-tools/pkgcheck/issues/115
    # out$summary <- paste0 (
    #    ifelse (out$check_pass, "has", "does not have"),
    #    " a 'CITATION' file."
    # )

    return (out)
}

The first lines are common to all output_pkgchk_...() functions, and define the generic return object. This object must be a list with the following three items:

check_pass as binary flag indicating whether or not a check was passed;
summary containing text used to generate the summary output; and
print containing information used to generate the print output, itself a list of the following items:
- A msg_pre to display at the start of the print result;
- An object to be printed, such as a vector of values, or a data.frame.
- A msg_post to display at the end of the print result following the object.

summary and print methods may be suppressed by assigning values of "". The above example of pkgcheck_has_citation has print = "", and so no information from this check will appear as output of the print method. The summary field is commented-out in the current version, but left to illustrate here that it has a value that is specified for both TRUE and FALSE values of check_pass, via an ifelse statement. The value is determined by the result of the main pkgchk_has_citation() call, and is converted into a green tick if TRUE, or a red cross if FALSE.

Checks for which print information is desired require a non-empty print item, as in the output_pkgchk_has_scrap() function:

output_pkgchk_has_scrap <- function (checks) {

    out <- list (
        check_pass = length (checks$checks$has_scrap) == 0L,
        summary = "",
        print = ""
    )

    if (!out$check_pass) {
        out$summary <- "Package contains unexpected files."
        out$print <- list (
            msg_pre = paste0 (
                "Package contains the ",
                "following unexpected files:"
            ),
            obj = checks$checks$has_scrap,
            msg_post = character (0)
        )
    }

    return (out)
}

In this case, both summary and print methods are only triggered if (!out$check_pass) – so only if the check fails. The print method generates the heading specified in out$print$msg_pre, with any vector-valued objects stored in the corresponding obj list item displayed as formatted lists. A package with “scrap” files, "a" and "b", would thus have out$print$obj <- c ("a", "b"), and when printed would look like this:

#> ✖ Package contains the following unexpected files:
#> • a
#> • b

This formatting is also translated into corresponding markdown and HTML formatting in the checks_to_markdown() function.

The design of these pkgchk_ and output_pkgchk_ functions aims to make the package readily extensible, and we welcome discussions about developing new checks. The primary criterion for new package-internal checks is that they must be of very general applicability, in that they should check for a condition that almost every package should or should not meet.

The package also has a mechanism to easily incorporate more specific, locally-defined checks, as explored in the following section.

3. Creating new checks

3.1 New Local Checks (for package users)

The main pkgcheck() function has an additional parameter, extra_env which specifies,

Additional environments from which to collate checks. Other package names may be appended using c, as in c(.GlobalEnv, “mypkg”).

This allows specific checks to be defined locally, and run by passing the name of the environment in which those checks are defined in this parameter. This section illustrates the process using the bundled “tarball” (that is, .tar.gz file) of one version of the pkgstats package included with that package.

f <- system.file ("extdata", "pkgstats_9.9.tar.gz", package = "pkgstats")
path <- pkgstats::extract_tarball (f)
checks <- pkgcheck (path)
summary (checks)

#> 
#> ── pkgstats 9.9 ────────────────────────────────────────────────────────────────
#> 
#> ✔ Package name is available
#> ✖ does not have a 'codemeta.json' file.
#> ✖ does not have a 'contributing' file.
#> ✔ uses 'roxygen2'.
#> ✔ 'DESCRIPTION' has a URL field.
#> ✔ 'DESCRIPTION' has a BugReports field.
#> ✖ Package has no HTML vignettes
#> ✖ These functions do not have examples: [pkgstats_from_archive].
#> ✔ Package has continuous integration checks.
#> ✖ Package coverage failed
#> ✖ R CMD check found 1 error.
#> ✔ R CMD check found no warnings.
#> 
#> ℹ Current status:
#> ✖ This package is not ready to be submitted.

Let’s now presume I have a reputation in the R community for all of my packages starting with “aa”, to ensure they are always listed first. This section demonstrates how to implement a check that only passes if the first two letters of the package name are “aa”. The first step described above is to define the check itself via a function prefixed with pkgchk_. The easiest approach would be for the pkgcheck_ function to directly check the name, and return a logical flag indicating whether or not the same starts with “aa”. The resultant summary and print methods can, however, only use the information provided by the initial pkgchk_ function. That means if we want to print the actual name in the result of either of those functions, to show that it indeed does not form the desired patter, we need to return that information. The check function is then simply:

pkgchk_starts_with_aa <- function (checks) {
    checks$pkg$name
}

We then need to define the output functions:

output_pkgchk_starts_with_aa <- function (checks) {

    out <- list (
                 check_pass = grepl ("^aa",
                                     checks$checks$starts_with_aa,
                                     ignore.case = TRUE),
                 summary = "",
                 print = ""
    )

    out$summary <- paste0 ("Package name [",
                           checks$checks$starts_with_aa,
                           "] does ",
                           ifelse (out$check_pass,
                                   "",
                                   "NOT"),
                           " start with 'aa'")

    return (out)
}

If we simply define those function in the global workspace of our current R session, calling pkgcheck() again will automatically detect those checks and include them in our output:

#> 
#> ── pkgstats 9.9 ────────────────────────────────────────────────────────────────
#> 
#> ✔ Package name is available
#> ✖ does not have a 'codemeta.json' file.
#> ✖ does not have a 'contributing' file.
#> ✔ uses 'roxygen2'.
#> ✔ 'DESCRIPTION' has a URL field.
#> ✔ 'DESCRIPTION' has a BugReports field.
#> ✖ Package has no HTML vignettes
#> ✖ These functions do not have examples: [pkgstats_from_archive].
#> ✔ Package has continuous integration checks.
#> ✖ Package coverage failed
#> ✖ Package name [pkgstats] does NOT start with 'aa'
#> ✖ R CMD check found 1 error.
#> ✔ R CMD check found no warnings.
#> 
#> ℹ Current status:
#> ✖ This package is not ready to be submitted.

Customised personal checks can be incorporated by defining them in a local package, loading that into the workspace, and passing the name of the package to the extra_env parameter.

3.2 New `pkgcheck` Checks (for `pkgcheck` developers)

New checks can be added to this package by creating new files in the /R directory prefixed with pkgchk_, and including the two functions described above (a check and an output function). The check name will then need to be included in the order_checks() function in the R/summarise-checks.R file, which determines the order of checks in the summary output. Checks which are not defined in this ordering, including any defined via extra_env parameters, appear after all of the standard checks, and prior to the R CMD check results which always appear last. This order may only be modified by editing the list in that function. The order of check results in the print method is also hard-coded, defined in the main print.pkgcheck method. As explicitly stated in that function, any new checks should also be included in the print method just after the first reference to "misc_checks", via an additional line:

print_check_screen (x, "<name-of-new-check>", pkg_env)

The print_check_screen() function will then automatically activate the print method of any new checks. This line should be added even if a new check has no print method (as in the starts_with_aa example above), to provide an explicit record of all internally-defined miscellaneous checks.

Finally, any new checks also need to be included in tests. The test suites run on generic, mostly empty packages constructed with the srr::srr_stats_pkg_skeleton() function, as in the main test-pkgcheck.R test functions. Additional tests are also performed on the pkgstats tarball illustrated above. The default results of any new checks will be automatically tested by the existing test suite, but it is important to test all potential results. The test-extra-checks.R file is the main location for testing additional tests, with lines in that file demonstrating how the main results can be readily modified to reflect alternative outputs of check functions (such as pkgchk_has_scrap and pkgchk_obsolete_pkg_deps). The output functions defined as part of checks, including any new checks, do not need to be explicitly tested, as the entire output is tested via testthat snapshots. Snapshot results need to be updated to reflect any additional tests. Finally, the test-list-checks.R file tests the total number of internally-defined checks as expect_length (ncks, ..). The number tested there also needs to be incremented by one for each new check.

Mark Padgham

2024-11-20

1. The check function

2. The output function

3. Creating new checks

3.1 New Local Checks (for package users)

3.2 New `pkgcheck` Checks (for `pkgcheck` developers)

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Extending or modifying checks

Mark Padgham

2024-11-20

1. The check function

2. The output function

3. Creating new checks

3.1 New Local Checks (for package users)

3.2 New pkgcheck Checks (for pkgcheck developers)

3.2 New `pkgcheck` Checks (for `pkgcheck` developers)