From murdoch at stats.uwo.ca  Thu May 15 04:01:06 2008
From: murdoch at stats.uwo.ca (Duncan Murdoch)
Date: Wed, 14 May 2008 22:01:06 -0400
Subject: [Rd] Warning about undocumented data sets
In-Reply-To: <8adccabf0805141711t1c072bebt422557f86e306bf0@mail.gmail.com>
References: <8adccabf0805141711t1c072bebt422557f86e306bf0@mail.gmail.com>
Message-ID: <482B9962.5010302@stats.uwo.ca>

Charles Danko wrote:
> Hi, List,
>
> Sorry in advance if this turns out to be a stupid question -- I've
> been trying to work it out for awhile, and I don't have any new ideas
> -- I'm very new to R documentation/ LATEX.
>
> I am running "R CMD check " on a package that I am trying to write;
> the only warning is:
> * checking for missing documentation entries ... WARNING
> Undocumented data sets:
>   Einter KG
> All user-level objects in a package should have documentation entries.
> See the chapter 'Writing R documentation files' in manual 'Writing R
> Extensions'.
>
> I have checked "Writing R Extensions" manual, found here:
> http://stuff.mit.edu/afs/sipb/project/r-project/arch/i386_rhel3/lib/R/doc/manual/R-exts.html
>
> As instructed in the Documenting data sets, Einter and KG both have
> corresponding .Rd files in the PACKAGE/man/ directory.
>
> The contents of the applicable .Rd files are pasted below.
>
> Does anyone have any suggestions!
>
> Thanks very much in advance!
> Charles
>
> PACKAGE/man/KG.Rd:
> \name{KG}
> \docType{data}
> \alias{gene positions}
>   

You need

\alias{KG}

if you want ?KG to find the page.  That's what check is telling you.

Duncan Murdoch
> \title{Position of known genes in the first 2 Mb of human chromosome 1-3. }
> \description{
>   A data frame with 146 observations on the following 5 variables.
>   \describe{
>     \item{\code{name}}{a factor with levels \code{AB003592}
> \code{AB007916} \code{AB010962} \code{AB033099} \code{AB051503}
> \code{AB052096} \code{AF002246} \code{AF006011} \code{AF057061}
> \code{AF057062} \code{AF067519} \code{AF070597} \code{AF070603}
> \code{AF116687} \code{AF153686} \code{AF161351} \code{AF178986}
> \code{AF241229} \code{AF250320} \code{AF274944} \code{AF305818}
> \code{AF343078} \code{AF346307} \code{AF461903} \code{AF469129}
> \code{AF490905} \code{AJ003029} \code{AJ278736} \code{AK000549}
> \code{AK000591} \code{AK000615} \code{AK000886} \code{AK001208}
> \code{AK021939} \code{AK023110} \code{AK023114} \code{AK023356}
> \code{AK024448} \code{AK024481} \code{AK027269} \code{AK027277}
> \code{AK055593} \code{AK056065} \code{AK074112} \code{AK075017}
> \code{AK091144} \code{AK093189} \code{AK093239} \code{AK093438}
> \code{AK093927} \code{AK093954} \code{AK094155} \code{AK094502}
> \code{AK094642} \code{AK097327} \code{AK123641} \code{AK124054}
> \code{AK124125} \code{AK125828} \code{AK125883} \code{AK126501}
> \code{AK126870} \code{AK127149} \code{AK127994} \code{AK128042}
> \code{AK128271} \code{AK128357} \code{AK128434} \code{AK128780}
> \code{AK128833} \code{AL049665} \code{AL050373} \code{AL136813}
> \code{AL137269} \code{AL137714} \code{AL834179} \code{AL834441}
> \code{AY037150} \code{AY050570} \code{AY116620} \code{AY217347}
> \code{AY358391} \code{AY358490} \code{AY358517} \code{AY358544}
> \code{AY358877} \code{BC000675} \code{BC003543} \code{BC004186}
> \code{BC004366} \code{BC004874} \code{BC007422} \code{BC008041}
> \code{BC008070} \code{BC008374} \code{BC008375} \code{BC008788}
> \code{BC009938} \code{BC013904} \code{BC014101} \code{BC014270}
> \code{BC014316} \code{BC014464} \code{BC015393} \code{BC015400}
> \code{BC015549} \code{BC016010} \code{BC016333} \code{BC017225}
> \code{BC017762} \code{BC018701} \code{BC018779} \code{BC020699}
> \code{BC021851} \code{BC022808} \code{BC025719} \code{BC029929}
> \code{BC030778} \code{BC031359} \code{BC032379} \code{BC034304}
> \code{BC046345} \code{BC047001} \code{BC048328} \code{BC050454}
> \code{BC051194} \code{BC059409} \code{BC062579} \code{BC063107}
> \code{BC063682} \code{BC066360} \code{BT007082} \code{BT007136}
> \code{BT007305} \code{BX537637} \code{J02969} \code{M37712}
> \code{M83653} \code{NM_003327} \code{X04526} \code{X75962}
> \code{Y16846}}
>     \item{\code{chrom}}{a factor with levels \code{chr1} \code{chr2}
> \code{chr3}}
>     \item{\code{strand}}{a factor with levels \code{-} \code{+}}
>     \item{\code{txStart}}{a numeric vector}
>     \item{\code{txEnd}}{a numeric vector}
>   }
> }
> \usage{data(KG)}
> \format{data frame}
> \source{The UCSC genome browser (http://genome.ucsc.edu).}
> \keyword{datasets}
>
> PACKAGE/man/Einter.Rd:
> \name{Einter}
> \docType{data}
> \alias{intensities}
> \title{Sample intensities for human promoter tiling array. }
> \description{
> Einter is a data frame consisting of 3 position information columns
> (Unique ID, Start position of probe, Chromosome) and normalized
> intensity data from 4 samples.  Data is given for the first 3Mb of
> human chromosomes 1-3.
>
> >From the Affymetrix human promoter tiling array v02-3.
> }
> \usage{data(Einter)}
> \format{data frame}
> \source{Unpublished data, courtosy of Yanli Zhang and Frank Middleton.}
> \keyword{datasets}
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] Warning about undocumented data sets
Duncan Murdoch