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

From: Peter Dalgaard <P.Dalgaard_at_biostat.ku.dk>
Date: Fri, 30 Nov 2007 18:50:27 +0100

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@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>
> 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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Received on Fri 30 Nov 2007 - 17:54:18 GMT

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