From ripley at stats.ox.ac.uk  Mon Dec  8 13:18:21 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Mon, 8 Dec 2008 12:18:21 +0000 (GMT)
Subject: [Rd] Warning: missing text for item ... in \describe?
In-Reply-To: <493CFD9F.1070406@itwm.fraunhofer.de>
References: <493384DA.9060504@pdf.com> <20081201154004.79ef748b@berwin-nus1>
	<alpine.LFD.2.00.0812051527430.15310@gannet.stats.ox.ac.uk>
	<20081206003504.208fbbce@berwin5>
	<alpine.LFD.2.00.0812051727410.22493@gannet.stats.ox.ac.uk>
	<20081206131350.2eba98d6@absentia>
	<alpine.LFD.2.00.0812060710380.15789@gannet.stats.ox.ac.uk>
	<493CFD9F.1070406@itwm.fraunhofer.de>
Message-ID: <alpine.LFD.2.00.0812081205080.15434@auk.stats.ox.ac.uk>

On Mon, 8 Dec 2008, Dr. Peter Ruckdeschel wrote:

> Hi Brian and Berwin,
>
> thanks for finding the reason for all this trouble.
>> 1) Having run tests on CRAN and BioC overnight, the results are
>> quite depressing.  There are 112 packages on CRAN and a score
>> on BioC with incorrectly rendered help pages because of spaces
>> after \item{foo}.
>> In two cases (fields and MANOR) the text skipped is invalid, so it
>> is not simply a case of ignoring the whitespace.

> As you already have found out the "depressing" number of 112, could you
> please alert the maintainers of these packages --- I would not be surprised
> if I were among them ...

Well, needing to do so on that scale is one of the depressing things. 
However, I am waiting for the CRAN daily checking to catch up, as this 
will appear as warnings in the logs there once they are using a current 
R-devel (the last results are for Dec 4's R-devel).  The current list is 
for CRAN

AIS AMORE BARD BCE BLCOP BSDA BaM Biodem BootCL ElemStatLearn FactoMineR 
FitAR GLDEX GSA Geneland HH Hmisc MBESS MCPAN MSBVAR MiscPsycho 
NestedCohort PASWR PHYLOGR PTAk R2HTML RArcInfo RBGL RFOC RGraphics RII 
RSEIS RobAStBase Rsge SNPassoc SciViews TinnR VDCutil WaveCGH accuracy ada 
ade4 agricolae ars assist bayesm bim bipartite bitops calib candisc 
cghFLasso coda colorRamps compositions crq cwhmisc distrTEst dprep emu 
equivalence fImport fOptions fields fossil gamlss gclus geiger geometry 
gllm gnm impute its kin kknn klaR knnTree lgtdl limSolve locpol logilasso 
logspline modeest muStat netmodels nplplot orthopolynom paleoTS pamr pbatR 
pcalg phangorn playwith polspline psych rankreg rbugs relaimpo rgl rjacobi 
rootSolve samr siar space spectralGP survrec tpr tseriesChaos varSelRF 
varmixt

and for BioC-devel

ABarray GSEAlm GeneticsBase Harshlight KCsmart LPEadj MANOR MCRestimate 
MassSpecWavelet MeasurementError Mfuzz OLIN PLPE RBGL RankProd SAGx SLGI 
VanillaICE affyQCReport affylmGUI cghMCR copa ecolitk explorase flowCore 
flowViz gcrma genArise impute limmaGUI lumi made4 pamr rama rflowcyt 
rtracklayer simpleaffy snapCGH splicegear sscore


>> 2) On the original subject line, I found a different reason.  E.g. I
>> get the
>> message on distrMod, which has (sqrt-methods.Rd, also
>> solve-methods.Rd)
>>
>> \section{Methods}{\describe{
>> \item{sqrt}{\code{signature(x = "PosSemDefSymmMatrix")}: produces a
>> symmetric, p.s.d. matrix \eqn{y} such that  \eqn{x = y^2}}
>> }}
>
> You indicate that the problem could easily be solved by inserting
> punctuation.
>
> I would have no problems with this as a binding restriction, and
> probably the same
> goes for other maintainers.
> So could you perhaps add a corresponding recommendation
> to the "Writing R extensions" manual?

Yes, I am working on some recommendations for R-exts.  Hopefully more of 
these problems can be detected and given as warnings now we are aware of 
them.

> I have just uploaded a quick patch for the sqrt() and solve() ".Rd"
> files of distrMod
> inserting a "." at the closing brace of \eqn{} in both cases.
>
> Should be on CRAN  soon...
>
> Best,
> Peter
>
> -- 
> Dr. Peter Ruckdeschel, Abteilung Finanzmathematik, F3.17
> Fraunhofer ITWM, Fraunhofer Platz 1, 67663 Kaiserslautern
> Telefon:  +49 631/31600-4699
> Fax    :  +49 631/31600-5699
> E-Mail :  peter.ruckdeschel at itwm.fraunhofer.de
>
>
>

-- 
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] Warning: missing text for item ... in \describe?
Prof Brian Ripley