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. 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
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? 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-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
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 <ripley at stats.ox.ac.uk> >Subject: Re: [Rd] S4 Method Rd Warning >To: Duncan Murdoch <murdoch.duncan at gmail.com> >Cc: D.Strbenac at 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-devel at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-devel >>> >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > >-- >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-------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia