[R-pkg-devel] Data docs

[Duncan Murdoch]

I think this is a bug.  It starts to appear in R-devel revision 76780,

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r76780 | hornik | 2019-07-04 14:55:52 -0400 (Thu, 04 Jul 2019) | 1 line

Tweaks for c76774.
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where the default for a new test is set to TRUE.  The new test was 
introduced in 76774,

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r76774 | hornik | 2019-07-03 05:02:40 -0400 (Wed, 03 Jul 2019) | 2 lines

Have codoc() report variables in usages not in the code.
(Optionally for now).
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Duncan Murdoch


On 26/10/2019 4:54 p.m., Luis-Miguel Rodríguez Rojas wrote:
> Hello Duncan,
> 
> Thanks for your quick response!
> 
> I tried re-building and re-submitting and I'm still getting the same error:
> https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Windows/00check.log
> https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_224156/Debian/00check.log
> 
> I've made the tarball temporarily available directly in the repository 
> in case that helps at all:
> https://github.com/lmrodriguezr/enveomics/blob/master/enveomics.R_1.5.0.tar.gz
> 
> Thanks a lot!
> Miguel.
> 
> --
> Luis M. Rodriguez-R, Ph.D.
> [ https://rodriguez-r.com <https://rodriguez-r.com/> ]
> ---------------------------------
> Research Engineer
> Georgia Institute of Technology
> 311 Ferst Drive, ES&T, Room 3324
> Atlanta, GA 30332, USA
> [ http://enve-omics.gatech.edu/ ]
> 
> 
> 
> On Sat, Oct 26, 2019 at 1:39 PM Duncan Murdoch <murdoch.duncan using gmail.com 
> <mailto:murdoch.duncan using gmail.com>> wrote:
> 
>     On 26/10/2019 11:39 a.m., Luis-Miguel Rodríguez Rojas wrote:
>      > Dear all,
>      >
>      > I maintain a package that has data fields, and didn't have any
>     problems
>      > with this before. However, in my latest update, I'm getting the
>     following
>      > error message from the CRAN tests:
>      >
>      > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
>      > Check: for code/documentation mismatches, Result: WARNING
>      >    Variables with usage in documentation object 'growth.curves'
>     but not in
>      > code:
>      >      'growth.curves'
>      >
>      >    Variables with usage in documentation object 'phyla.counts'
>     but not in
>      > code:
>      >      'phyla.counts'
> 
>     I'm not seeing those messages when testing your package in the same R
>     version as win-builder used, so it could be a transient issue, or a
>     problem with the tarball that you submitted.  In either case, I'd
>     suggest just trying again:  rebuild and submit.
> 
>     Duncan Murdoch
> 
>      >
>      > The variables are indeed NOT in the code, because they're only to
>     be used
>      > in the examples. In this version I moved my documentation from
>     the old (now
>      > defunct) inlinedocs to ROxygen2. In the previous form, I had to
>     define a
>      > structure in the code including both the function and the example, so
>      > technically the code was using the variables. In the new form, I
>     simply
>      > define the examples with the @examples tag (that ends up in the
>     .rd file
>      > within an \examples{} block).
>      >
>      > Does anyone have any idea on how I should define data in the code
>     to avoid
>      > this issue? I could simply add the example lines after the return (so
>      > they're never reached), but that sounds like a horrible hack.
>      >
>      > Just in case it's useful:
>      > GitHub repository (inside the enveomics.R folder):
>      > https://github.com/lmrodriguezr/enveomics/
>      > Full test output:
>      >
>     https://win-builder.r-project.org/incoming_pretest/enveomics.R_1.5.0_20191026_032029/Windows/00check.log
>      >
>      > Thanks!
>      > Miguel.
>      >
>      >
>      > --
>      > Luis M. Rodriguez-R, Ph.D.
>      > [ https://rodriguez-r.com ]
>      > ---------------------------------
>      > Research Engineer
>      > Georgia Institute of Technology
>      > 311 Ferst Drive, ES&T, Room 3324
>      > Atlanta, GA 30332, USA
>      > [ http://enve-omics.gatech.edu/ ]
>      >
>      >       [[alternative HTML version deleted]]
>      >
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