Re: [R] Data sets with usage in documentation object but not in code

From: Jonathan Weeks <weeksjp_at_gmail.com>
Date: Fri, 30 Nov 2007 11:19:13 -0700

That worked! Many thanks (to all of you)

Take care

Jon

On Nov 30, 2007 10:50 AM, Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk> wrote:

> Jonathan Weeks wrote:
> > The file is attached.
> >
> > Also, to restate what I said earlier. The package passes the checks
> > without any errors or warnings under R 2.5, but now that it is running
> > under 2.6.1 I get a warning (no errors) about having .Rd files without
> > associated .R files (the datasets are in an .RData file in the data
> > subdirectory). Since the only difference is the version of R, I am not
> > sure what I should be doing differently ( i.e. do I need to specify
> > something else in the NAMESPACE, etc.)
> >
> > Thanks again for your help
> >
> (You shouldn't have included r-help -- they are not going to see the
> attachment)
>
> I think the problem is that you have
>
> Usage:
>
> data(TK07)
>
> but
>
> > data(TK07)
> Warning message:
> In data(TK07) : data set 'TK07' not found
>
> so you should just get rid of the data() bit inside \usage{}
>
> -p
>
>
> > On Nov 30, 2007 10:18 AM, Martin Maechler <maechler_at_stat.math.ethz.ch
> > <mailto:maechler_at_stat.math.ethz.ch>> wrote:
> >
> > >>>>> "JW" == Jonathan Weeks <weeksjp_at_gmail.com
> > <mailto:weeksjp_at_gmail.com>>
> > >>>>> on Fri, 30 Nov 2007 08:46:50 -0700 writes:
> >
> > JW> Thank you both for your help. I still don't know what is
> > happening. I
> > JW> uploaded my package (plink_0.0-3) to
> > ftp://cran.r-project.org/incoming
> >
> > That's a place NOBODY can get it - but the CRAN maintainers,
> > and they are not very pleased to see a package there which does
> > not pass R CMD check.
> >
> > Please use a different place!
> > If you cannot, please
> > copy-paste one of the *.Rd files into an e-mail (reply to this).
> >
> > Martin Maechler, ETH Zurich
> >
> > JW> If you have any other suggestions they would be greatly
> > appreciated
> >
> > JW> Take care
> >
> > JW> Jon
> >
> > JW> On Nov 29, 2007 10:30 AM, Peter Dalgaard
> > <P.Dalgaard_at_biostat.ku.dk <mailto:P.Dalgaard_at_biostat.ku.dk>> wrote:
> >
> > >> Prof Brian Ripley wrote:
> > >> > On Thu, 29 Nov 2007, Jonathan Weeks wrote:
> > >> >
> > >> >
> > >> >> All,
> > >> >>
> > >> >> I recently made some changes to my package and ran R CMD
> > check, but I
> > >> >> am getting a warning regarding my data sets.
> > >> >>
> > >> >> I am running R 2.6.1 I have an image (.RData) file
> > containing five
> > >> >> data sets in the data subdirectory and an .Rd file for
> > each of the
> > >> >> data sets in the man subdirectory. When I run the check I
> > get the
> > >> >> warning
> > >> >> "Data sets with usage in documentation object <dataset
> > name> but not
> > >> >> in code" for each dataset. I did not get this warning
> > with R 2.5
> > >> >>
> > >> >> Does anyone have a suggestion for how to handle this?
> > >> >>
> > >> >
> > >> > Show us a small reproducible example, or (failing that)
> > make the package
> > >> > available for test? It's hard to guess at the cause, and
> > hundreds of
> > >> > packages do similar things.
> > >> >
> > >> >
> > >> You could also look at the output of
> > >>
> > >> tools:::list_data_in_pkg("yourPkg")
> > >>
> > >> and see if it makes you any wiser. (AFAICS, this is the list
> > that the
> > >> usage lines get compared to)
> > >>
> > >> --
> > >> O__ ---- Peter Dalgaard Øster Farimagsgade 5,
> > Entr.B
> > >> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> > >> (*) \(*) -- University of Copenhagen Denmark Ph:
> > (+45)
> > >> 35327918
> > >> ~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk
> > <mailto:p.dalgaard_at_biostat.ku.dk>) FAX: (+45)
> > >> 35327907
> > >>
> >
> > JW> [[alternative HTML version deleted]]
> >
> > JW> ______________________________________________
> > JW> R-help_at_r-project.org <mailto:R-help_at_r-project.org> mailing
> list
> > JW> https://stat.ethz.ch/mailman/listinfo/r-help
> > JW> PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html<http://www.r-project.org/posting-guide.html>
> > <http://www.r-project.org/posting-guide.html>
> > JW> and provide commented, minimal, self-contained,
> > reproducible code.
> >
>
>
> --
> O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45)
> 35327918
> ~~~~~~~~~~ - (p.dalgaard_at_biostat.ku.dk) FAX: (+45)
> 35327907
>

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