Functions for performing various quality control (QC) checks on R code and documentation, notably on R packages.
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)
a character string naming an installed package.
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.
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.
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.
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.