Dear all, So the final solution for this issue is:
- using @name to define the name of the data set, instead of writing it under the rd comment block (solved the warning of R CMD Check: "Variables with usage in documentation but not in code") - using @docType data (thanks Vincent) to avoid the warning of BiocCheck(): "Add non-empty \\value to the following man pages:..." Many thanks again for your kind help! 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 1. May 2020, at 15:50, Vinh Tran <t...@bio.uni-frankfurt.de> wrote: > > 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 t...{{dropped:10}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
