From dankoc at gmail.com  Thu May 15 02:11:05 2008
From: dankoc at gmail.com (Charles Danko)
Date: Wed, 14 May 2008 20:11:05 -0400
Subject: [Rd] Warning about undocumented data sets
Message-ID: <8adccabf0805141711t1c072bebt422557f86e306bf0@mail.gmail.com>

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}
\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}



[Rd] Warning about undocumented data sets
Charles Danko