[R-pkg-devel] {Disarmed} Re: Data docs

[Xavier Robin]

Hi,

It seems you have LazyLoad in your DESCRIPTION:

LazyLoad: yes

I ran into the same warning a few months ago and realized that LazyLoad
has been ignored since R 2.14.0. As a consequence your dataset is not
actually loaded lazily, which triggers the warning.

Apparently the new way to lazy load a dataset is to use LazyData in the
DESCRIPTION:

LazyData: yes

I don't know in which R version LazyData was introduced, but I expect
around the same time.

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file

I ended up making the following change, and the warning disappeared:

https://github.com/xrobin/pROC/commit/77bbb151412643628f2549868700325c8e47cad4

I hope it helps.
Xavier


On 27.10.19 02:14, Duncan Murdoch wrote:
> I think this is a bug.  It starts to appear in R-devel revision 76780,
>
> ------------------------------------------------------------------------
> r76780 | hornik | 2019-07-04 14:55:52 -0400 (Thu, 04 Jul 2019) | 1 line
>
> Tweaks for c76774.
> ------------------------------------------------------------------------
>
> where the default for a new test is set to TRUE.  The new test was
> introduced in 76774,
>
> ------------------------------------------------------------------------
> 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).
> ------------------------------------------------------------------------
>
> 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]]
>>      >
>>      > ______________________________________________
>>      > R-package-devel using r-project.org
>>     <mailto:R-package-devel using r-project.org> mailing list
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>>      >
>>
>
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-- 
Xavier Robin, PhD
University of Basel | Swiss Institute of Bioinformatics
Biozentrum - Klingelbergstrasse 50/70 - 4056 Basel
t: +41 61 207 18 77 | m: +41 78 865 09 01
Xavier.Robin using sib.swiss - http://www.sib.swiss


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