[Bioc-devel] LazyData in DESCRIPTION file

Vinh Tran tr@n @end|ng |rom b|o@un|-|r@nk|urt@de
Fri May 1 15:50:48 CEST 2020 

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 <stvjc using channing.harvard.edu> wrote:
> 
> does 
> 
> @docType data
> 
> help here? 
> 
> On Fri, May 1, 2020 at 8:52 AM Martin Morgan <mtmorgan.bioc using gmail.com <mailto: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 <mailto:bioc-devel-bounces using r-project.org> on behalf of kasperdanielhansen using gmail.com <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto:stvjc using 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 <tran using bio.uni-frankfurt.de <mailto: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 <mailto:Bioc-devel using 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 using r-project.org <mailto:Bioc-devel using 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 using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
> _______________________________________________
> Bioc-devel using r-project.org <mailto:Bioc-devel using 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}}

More information about the Bioc-devel mailing list