[Bioc-devel] LazyData in DESCRIPTION file

[Kasper Daniel Hansen]

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
>> >
>>
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>
>
> --
> Best,
> Kasper
>
>
>

-- 
Best,
Kasper

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