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.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]] >> > >> > ______________________________________________ >> > R-package-devel@r-project.org >> <mailto:R-package-devel@r-project.org> mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-package-devel >> > >> > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- 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@sib.swiss - http://www.sib.swiss [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
