Thanks for this. I was thinking the spaces rule only applied within the \alias{} statements. I'm not sure why I thought this.
---- Original message ---- >Date: Mon, 30 Aug 2010 18:43:35 +0100 (BST) >From: Prof Brian Ripley <rip...@stats.ox.ac.uk> >Subject: Re: [Rd] S4 Method Rd Warning >To: Duncan Murdoch <murdoch.dun...@gmail.com> >Cc: d.strbe...@garvan.org.au > >On Mon, 30 Aug 2010, Duncan Murdoch wrote: > >> On 30/08/2010 1:00 AM, Dario Strbenac wrote: >>> Hello, >>> >>> I am using R 2.11.0. I have a curious problem where I get a warning in R >>> CMD check which is seemingly not relevant to my Rd file. >>> >> >> 2.11.0 isn't the current release, and there have been fixes to this stuff >> since 2.11.1 was released. Could you try 2.11.1-patched or the devel >> version >> of 2.12.0 and see if you still get the warnings? > >But there are incorrect spaces at e.g. {GRanges, BSgenome}. Classes >in signatures are comma-separated, not comma+space separated. > >If we've changed it, we are now accepting errorneous files AFAICS. > >> >> Duncan Murdoch >>> The warning says : >>> >>> * checking Rd \usage sections ... WARNING >>> Bad \usage lines found in documentation object 'enrichmentCalc': >>> <unescaped bksl>S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, >>> organism, seqLen=NULL, ...) >>> <unescaped bksl>S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, >>> organism, seqLen=NULL, do.warn=FALSE) >>> <unescaped bksl>S4method{enrichmentCalc}{GRanges, BSgenome}(rs, >>> organism, seqLen=NULL) >>> >>> Functions with \usage entries need to have the appropriate \alias entries, >>> and all their arguments documented. >>> The \usage entries must correspond to syntactically valid R code. >>> See the chapter 'Writing R documentation files' in manual 'Writing R >>> Extensions'. >>> >>> But, I have documented all the arguments, and I have all the aliases. What >>> else could it be warning me about ? >>> >>> The Rd file contents are : >>> >>> \name{enrichmentCalc} >>> \alias{enrichmentCalc} >>> \alias{enrichmentCalc,GenomeDataList,BSgenome-method} >>> \alias{enrichmentCalc,GenomeData,BSgenome-method} >>> \alias{enrichmentCalc,GRanges,BSgenome-method} >>> >>> \title{Calculate sequencing enrichment} >>> \description{A description} >>> \usage{ >>> \S4method{enrichmentCalc}{GenomeDataList, BSgenome}(rs, organism, >>> seqLen=NULL, ...) >>> \S4method{enrichmentCalc}{GenomeData, BSgenome}(rs, organism, >>> seqLen=NULL, do.warn=FALSE) >>> \S4method{enrichmentCalc}{GRanges, BSgenome}(rs, organism, seqLen=NULL) >>> } >>> \arguments{ >>> \item{rs}{jjj} >>> \item{organism}{ghi} >>> \item{seqLen}{def} >>> \item{do.warn}{abc} >>> \item{...}{xyz} >>> } >>> \details{ >>> Details. >>> } >>> \value{ >>> Text here. >>> } >>> \author{A Person} >>> \examples{ >>> #See the manual >>> } >>> >>> Thanks, >>> Dario. >>> >>> -------------------------------------- >>> Dario Strbenac >>> Research Assistant >>> Cancer Epigenetics >>> Garvan Institute of Medical Research >>> Darlinghurst NSW 2010 >>> Australia >>> >>> ______________________________________________ >>> r-de...@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> ______________________________________________ >> r-de...@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > >-- >Brian D. Ripley, rip...@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 -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.