[R-pkg-devel] {Disarmed} Re: Data docs
Luis-Miguel Rodríguez Rojas
|mrodr|guezr @end|ng |rom gm@||@com
Sun Oct 27 11:04:53 CET 2019
Thanks a lot Xavier!
This solved my issue.
Best,
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/ ]
On Sun, Oct 27, 2019 at 3:09 AM Xavier Robin <Xavier.Robin using sib.swiss> wrote:
> 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/>
> <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 *MailScanner
> has detected a possible fraud attempt from "gmail.com" claiming to be*
> <mailto:murdoch.duncan using gmail.com> <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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>
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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 01Xavier.Robin using sib.swiss - http://www.sib.swiss
>
>
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