\HeaderA{QC}{QC Checks for R Code and/or Documentation}{QC}
\aliasA{checkDocFiles}{QC}{checkDocFiles}
\aliasA{checkDocStyle}{QC}{checkDocStyle}
\aliasA{checkReplaceFuns}{QC}{checkReplaceFuns}
\aliasA{checkS3methods}{QC}{checkS3methods}
\aliasA{print.checkDocFiles}{QC}{print.checkDocFiles}
\aliasA{print.checkDocStyle}{QC}{print.checkDocStyle}
\aliasA{print.checkReplaceFuns}{QC}{print.checkReplaceFuns}
\aliasA{print.checkS3methods}{QC}{print.checkS3methods}
\keyword{utilities}{QC}
\keyword{documentation}{QC}
\begin{Description}\relax
Functions for performing various quality checks.
\end{Description}
\begin{Usage}
\begin{verbatim}
checkDocFiles(package, dir, lib.loc = NULL)
checkDocStyle(package, dir, lib.loc = NULL)
checkReplaceFuns(package, dir, lib.loc = NULL)
checkS3methods(package, dir, lib.loc = NULL)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{package}] a character string naming an installed package.
\item[\code{dir}] a character string specifying the path to a package's root
source directory.  This should contain the subdirectories \code{R}
(for R code) and \file{man} with \R{} documentation sources (in Rd
format).  Only used if \code{package} is not given.
\item[\code{lib.loc}] a character vector of directory names of \R{} libraries,
or \code{NULL}.  The default value of \code{NULL} corresponds to all
libraries currently known.  The specified library trees are used to
to search for \code{package}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\code{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 \dQuote{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.

\code{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 \code{\bsl{}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 \code{\bsl{}method} now being expanded in a way
that class information is preserved, \dQuote{joint} documentation is
no longer necessarily a problem.  (The corresponding information is
still contained in the object returned by \code{checkDocStyle}.)

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

\code{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
\emph{may} be called \code{formula} even if this is not the name used
by the generic.  The rules when \code{...} is involved are subtle:
see the source code.  Functions recognized as S3 generics are those
with a call to \code{UseMethod} in their body, internal S3 generics
(see \code{\LinkA{InternalMethods}{InternalMethods}}), and S3 group generics (see
\code{\LinkA{Math}{Math}}).  Possible dispatch under a different name
is not taken into account.  The generics are sought first in the given
package, then in the \pkg{base} package and (currently) the packages 
\pkg{graphics}, \pkg{stats}, and \pkg{utils} added in R 1.9.0 by
splitting the former \pkg{base}, and, if an installed package is
tested, also in the loaded namespaces/packages listed in the package's
\file{DESCRIPTION} Depends field.

If using an installed package, the checks needing access to all R
objects of the package will load the package (unless it is the
\pkg{base} package), after possibly detaching an already loaded
version of the package.
\end{Details}
\begin{Value}
The functions return objects of class the same as the respective
function names containing the information about problems detected.
There is a \code{print} method for nicely displaying the information
contained in such objects.
\end{Value}
\begin{Section}{Warning}
These functions are still experimental.  Names, interfaces and values
might change in future versions.
\end{Section}

