R: QC Checks for R Code and/or Documentation

QC {tools} | R Documentation

## QC Checks for R Code and/or Documentation

### Description

Functions for performing various quality control (QC) checks on R code and documentation, notably on R packages.

### Usage

    checkDocFiles(package, dir, lib.loc = NULL)
    checkDocStyle(package, dir, lib.loc = NULL)
    checkReplaceFuns(package, dir, lib.loc = NULL)
    checkS3methods(package, dir, lib.loc = NULL)

    langElts
    nonS3methods(package)

### Arguments

`package` | a character string naming an installed package.
`dir` | a character string specifying the path to a package's root source directory. This should contain the subdirectories ‘R’ (for R code) and ‘man’ with R documentation sources (in Rd format). Only used if `package` is not given.
`lib.loc` | a character vector of directory names of R libraries, or `NULL`. The default value of `NULL` corresponds to all libraries currently known. The specified library trees are used to search for `package`.

### Details

`checkDocFiles` checks, for all Rd files in a package, whether all arguments shown in the usage sections of the Rd file are documented in its arguments section. It also reports duplicated entries in the arguments section, and ‘over-documented’ arguments which are given in the arguments section but not in the usage. Note that the match is for the usage section and not a possibly existing synopsis section, as the usage is what gets displayed.

`checkDocStyle` investigates how (S3) methods are shown in the usages of the Rd files in a package. It reports the methods shown by their full name rather than using the Rd `\method` markup for indicating S3 methods. Earlier versions of R also reported about methods shown along with their generic, which typically caused problems for the documentation of the primary argument in the generic and its methods. With `\method` now being expanded in a way that class information is preserved, joint documentation is no longer necessarily a problem. (The corresponding information is still contained in the object returned by `checkDocStyle`.)

`checkReplaceFuns` checks whether replacement functions or S3/S4 replacement methods in the package R code have their final argument named `value`.

`checkS3methods` checks whether all S3 methods defined in the package R code have all arguments of the corresponding generic, with positional arguments of the generics in the same positions for the method. As an exception, the first argument of a formula method may be called `formula` even if this is not the name used by the generic. The rules when `...` is involved are subtle: see the source code. Functions recognized as S3 generics are those with a call to `UseMethod` in their body, internal S3 generics (see InternalMethods), and S3 group generics (see `Math`). Possible dispatch under a different name is not taken into account. The generics are sought first in the given package, then in the base package and (currently) the packages graphics, stats, and utils added in R 1.9.0 by splitting the former base, and, if an installed package is tested, also in the loaded namespaces/packages listed in the package's ‘DESCRIPTION’ Depends field.

`nonS3methods(package)` returns a `character` vector with the names of the functions in `package` which ‘look’ like S3 methods, but are not. Using `package = NULL` returns all known examples.

`langElts` is a character vector of names of “language elements” of R. These are implemented as “very primitive” functions (no argument list; `print()`ing as `.Primitive("<name>")`).

If using an installed package, the checks needing access to all R objects of the package will load the package (unless it is the base package), after possibly detaching an already loaded version of the package.

### Value

The functions return objects of class the same as the respective function names containing the information about problems detected. There are `print` methods for nicely displaying the information contained in such objects.

[Package tools version 4.0.5 Index]