From ripley at stats.ox.ac.uk  Wed Feb  1 21:00:22 2006
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 1 Feb 2006 20:00:22 +0000 (GMT)
Subject: [Rd] Rd files with unknown sections
In-Reply-To: <43E10C40.8030105@fhcrc.org>
References: <43E10C40.8030105@fhcrc.org>
Message-ID: <Pine.LNX.4.61.0602011953260.29877@gannet.stats>

On Wed, 1 Feb 2006, Herve Pages wrote:

> Hi,
>
>
> With recent versions of R-devel, "R CMD check" complains about
> some "Rd files with unknown sections".
>
> hpages at gladstone:~> R CMD check multtest_1.9.4.tar.gz
> ...
> ...
> * checking Rd files ... WARNING
> Rd files with unknown sections:
>  /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/boot.resample.Rd:
>    notes
>  /home/hpages/multtest.Rcheck/00_pkg_src/multtest/man/MTP.Rd: notes
>
> See chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
> ...
> ...
>
> WARNING: There was 1 warning, see
>  /home/hpages/multtest.Rcheck/00check.log
> for details
>
> I've tried with other Bioconductor packages and "R CMD check" complains
> that "alias", "warning", "detail", etc... are "unknown sections".
>
> I get these warnings with R-devel built from a snapshot tarball
> from 2006-01-23 (r37152) and 2006-01-31 (r37220).
> I don't get it with R-devel tarball from 2006-01-04 (r36984).

It is new test (thanks to Kurt Hornik).  Those are all incorrect, and 
will result in incorrect output (or at least, not the intended output). 
It is

\note
\alias  (the warning I see is \alais)
\details

and there is no \warning (etc), you need \section(Warning}{...}

Previously (as Rd is not a defined format with e.g. a DTD), almost all 
errors were silently ignored.

All the reports I have looked at are genuine user errors.  (The same 
applies to the recent subdirectory checks.)

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595



[Rd] Rd files with unknown sections
Prof Brian Ripley