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 on behalf of 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> 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> 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> > 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> 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> >> wrote: >> >>> I see this is guideline 7 at >>> 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> >>> 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 mailing list >>> > 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 mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> -- >> Best, >> Kasper >> >> >> > > -- > Best, > Kasper > > > -- Best, Kasper [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel