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}
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 >