From plummer@iarc.fr  Thu Nov 29 15:58:05 2001
From: plummer@iarc.fr (Martyn Plummer)
Date: Thu, 29 Nov 2001 16:58:05 +0100 (CET)
Subject: [Rd] R CMD check
Message-ID: <XFMail.20011129165805.plummer@iarc.fr>

[Sent to R-help by mistake. Sorry]

I have been checking my package coda with the current R-devel
using "R CMD check".  As usual, this has uncovered a large number
of errors and inconsistencies in my documentation, for which I
am very grateful.

The only problem I have is with code/documentation mismatches when I
have written a method for a generic function, e.g.

* checking for code/documentation mismatches ... WARNING
Objects with usage in documentation object `plot.mcmc' but missing from code:
[1] "plot"

Objects with usage in documentation object `summary.mcmc' but missing from
code:[1] "summary"

Objects with usage in documentation object `time.mcmc' but missing from code:
[1] "end"   "start" "time" 

Objects with usage in documentation object `window.mcmc' but missing from code:
[1] "window"

This occurs because, for example, I have documented the usage of 
summary.mcmc as

\usage{
summary(data, quantiles = c(0.025, 0.25, 0.5, 0.75, 0.975), ...)
}

I'm being encouraged to document it as

\usage{
summary.mcmc(data, quantiles = c(0.025, 0.25, 0.5, 0.75, 0.975), ...)
}

but I don't think this is right. Surely the correct usage of a method
is to call the generic function?

Martyn
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[Rd] R CMD check
Martyn Plummer