[Bioc-devel] LazyData in DESCRIPTION file
Vincent Carey
@tvjc @end|ng |rom ch@nn|ng@h@rv@rd@edu
Fri May 1 15:05:44 CEST 2020
does
@docType data
help here?
On Fri, May 1, 2020 at 8:52 AM Martin Morgan <mtmorgan.bioc using 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-bounces using r-project.org on behalf of kasperdanielhansen using 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 <tran using 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 <
> > kasperdanielhansen using 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 <tran using 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 <
> >> kasperdanielhansen using 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 <
> stvjc using 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 <
> tran using 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 using 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 using r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >>
> >> --
> >> Best,
> >> Kasper
> >>
> >>
> >>
> >
> > --
> > Best,
> > Kasper
> >
> >
> >
>
> --
> Best,
> Kasper
>
> [[alternative HTML version deleted]]
>
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