Dear all, Following Martin's guide, I added @name to the rd comment and replace the dataset name by NULL, the warning went away.
Previously, it was: #' An example of a final processed & filtered phylogenetic profile. #’ … #’ … "finalProcessedProfile" Now, it becomes #' An example of a final processed & filtered phylogenetic profile. #' @name finalProcessedProfile #’ … #’ … NULL The command ?finalProcessedProfile still works fine :-) Many thanks for your help! Best, Vinh -------------------------------- Dr. Vinh Tran Dept. for Applied Bioinformatics Inst. for Cell Biology and Neuroscience Goethe University Frankfurt Biologicum, Room 3.209 Phone +49 (0)69/798-42118 > On 1. May 2020, at 15:05, Vincent Carey <st...@channing.harvard.edu> wrote: > > does > > @docType data > > help here? > > On Fri, May 1, 2020 at 8:52 AM Martin Morgan <mtmorgan.b...@gmail.com > <mailto:mtmorgan.b...@gmail.com>> wrote: > One can write arbitrary documentation pages in roxygen2; the page doesn’t > have to rely on automatic generation from data objects. For instance filling > in the following template would get you (close to) what you want > > #' @rdname > #' @name > #' @description > #' @usage > #' @details > #' @return > #' @examples > NULL > > But as Kasper says it could well be that there's a better roxygen2 solution > (and that it doesn't make sense to choose data storage format based on > perceived document tool limitation). > > Martin > > On 5/1/20, 8:17 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" > <bioc-devel-boun...@r-project.org <mailto:bioc-devel-boun...@r-project.org> > on behalf of kasperdanielhan...@gmail.com > <mailto:kasperdanielhan...@gmail.com>> wrote: > > Your diagnose sounds reasonable to me. I don't use roxygen2 myself, so I > can't really help here (and this is one of several reasons: it adds > another > layer of potential problems to the documentation process). Perhaps someone > who uses roxygen2 can comment? Or perhaps they (roxygen2 developers) have > a > GitHub or email list? > > Best, > Kasper > > On Fri, May 1, 2020 at 5:51 AM Vinh Tran <t...@bio.uni-frankfurt.de > <mailto:t...@bio.uni-frankfurt.de>> wrote: > > > Dear Kasper, > > > > I think the issue was not with the loading data in the examples of the > > functions, but with the Rd documents of the datasets themselves, where > it > > says “usage{data_name}” instead of “usage{data(data_name)}”. These Rd > > documents are however automatically created using roxygen2. I still > cannot > > find any other solutions yet except using "LazyData: true”. > > > > Best regards, > > Vinh > > > > -------------------------------- > > Dr. Vinh Tran > > > > Dept. for Applied Bioinformatics > > Inst. for Cell Biology and Neuroscience > > Goethe University Frankfurt > > > > Biologicum, Room 3.209 > > Phone +49 (0)69/798-42118 > > > > On 30. Apr 2020, at 16:02, Kasper Daniel Hansen < > > kasperdanielhan...@gmail.com <mailto:kasperdanielhan...@gmail.com>> > wrote: > > > > This seems really weird, and I don't think you should be using lazyData > to > > get a message to disappear. Is there a GitHub page where we can browse > the > > code and do you have the full output of R CMD check somewhere? > > > > On Thu, Apr 30, 2020 at 9:05 AM Vinh Tran <t...@bio.uni-frankfurt.de > <mailto:t...@bio.uni-frankfurt.de>> > > wrote: > > > >> Dear Kasper, > >> > >> Many thanks for your reply. Yes, I am using data() to load the data. > >> However, the problem is, when I checked my package using CMD Check, it > >> threw me the warning that I am using that data only in the example but > not > >> in code. I see the disadvantages of LazyData, but I just want to know > in > >> this case, how can I solve that issue by not using LazyData. If you > have > >> any solutions, I am very appreciated! > >> > >> Btw, I added “LazyData: true” to the DESCRIPTION and the warning went > >> away. So, I am not sure if it must always be uppercase. > >> > >> Best regards, > >> Vinh > >> > >> -------------------------------- > >> Dr. Vinh Tran > >> > >> Dept. for Applied Bioinformatics > >> Inst. for Cell Biology and Neuroscience > >> Goethe University Frankfurt > >> > >> Biologicum, Room 3.209 > >> Phone +49 (0)69/798-42118 > >> > >> On 30. Apr 2020, at 14:55, Kasper Daniel Hansen < > >> kasperdanielhan...@gmail.com <mailto:kasperdanielhan...@gmail.com>> > wrote: > >> > >> If you don't have lazy data on, you should be able to load the data by > >> using data(). Let us say you example data is called expData. > >> > >> With lazy data > >> print(expData) > >> > >> Without lazy data you need explicit loading > >> data(expData) > >> print(expData) > >> > >> For the purpose of examples, there is also a user-level advantage of > >> using an explicit data() statement: the user can see that the data > comes > >> from somewhere, instead of appearing out of nowhere. For examples, I > >> actually only see advantages of not using lazyData, because of these > >> explicit statements. > >> > >> My historical impression: I would say that when lazyData was > introduced, > >> it seems to me that the intention was widespread use. It seems to me > that > >> the tides have turned against lazy data and the official > recommendation is > >> to not use it unless you have good reasons. One disadvantage with > >> widespread use of lazyData is that the names of these objects have to > be > >> accessible somewhere. > >> > >> Note: one thing I have realized very belatedly is that the lazyData > field > >> is a boolean, the right statements are one of > >> lazyData: TRUE > >> lazyData: FALSE > >> For example, I think it has to be all uppercase. > >> > >> Best, > >> Kasper > >> > >> On Wed, Apr 29, 2020 at 6:05 PM Vincent Carey > <st...@channing.harvard.edu <mailto:st...@channing.harvard.edu>> > >> wrote: > >> > >>> I see this is guideline 7 at > >>> https://bioconductor.org/developers/package-guidelines/ > <https://bioconductor.org/developers/package-guidelines/> > >>> > >>> I have used LazyData: TRUE so that [pkgname]::[entity] can be used > >>> instead > >>> of data(). The > >>> claim that it is "rarely a good thing" and slows down package loading > can > >>> be weighed against > >>> convenience. I am not sure you should use LazyData to avoid a > >>> documentation warning > >>> however. Can you give more details on what package is generating the > >>> warning? > >>> > >>> On Wed, Apr 29, 2020 at 5:34 PM Vinh Tran <t...@bio.uni-frankfurt.de > <mailto:t...@bio.uni-frankfurt.de>> > >>> wrote: > >>> > >>> > Dear Bioc members, > >>> > > >>> > I have just encountered a warning during the CHECK that some data > >>> objects > >>> > are used in the documents but not in code (e.g. “Variables with > usage > >>> in > >>> > documentation object ‘ppTree’ but not in code"). They are the demo > >>> data, > >>> > that I am using only in the examples for demonstrate the usage of > some > >>> > functions. Adding LazyData: True to the DESCRIPTION can solve that > >>> issue, > >>> > but according to the package guidelines it is not recommended. Could > >>> you > >>> > please show me what should I do in this case? The demo data is only > >>> about > >>> > 15 KB at max. > >>> > > >>> > Many thanks for your advices! > >>> > > >>> > Best regards, > >>> > Vinh > >>> > > >>> > -------------------------------- > >>> > Dr. Vinh Tran > >>> > > >>> > Dept. for Applied Bioinformatics > >>> > Inst. for Cell Biology and Neuroscience > >>> > Goethe University Frankfurt > >>> > > >>> > Biologicum, Room 3.209 > >>> > Phone +49 (0)69/798-42118 > >>> > > >>> > > >>> > [[alternative HTML version deleted]] > >>> > > >>> > _______________________________________________ > >>> > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > >>> > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > >>> > > >>> > >>> -- > >>> The information in this e-mail is intended only for the > ...{{dropped:18}} > >>> > >>> _______________________________________________ > >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing > list > >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > >>> > >> > >> > >> -- > >> Best, > >> Kasper > >> > >> > >> > > > > -- > > Best, > > Kasper > > > > > > > > -- > Best, > Kasper > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > _______________________________________________ > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org> mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > <https://stat.ethz.ch/mailman/listinfo/bioc-devel> > > The information in this e-mail is intended only for th...{{dropped:16}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel