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
> <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}}
>>
>> _______________________________________________
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>>
>>
>> --
>> Best,
>> Kasper
>
>
>
> --
> Best,
> Kasper
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