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.dun...@gmail.com
<mailto:murdoch.dun...@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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