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

[Peter Dalgaard]

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>
>        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