[Bioc-devel] LazyData in DESCRIPTION file

Vinh Tran tr@n @end|ng |rom b|o@un|-|r@nk|urt@de
Fri May 1 16:46:45 CEST 2020 

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 <tran using 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 <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}}
>>>>> 
>>>>> _______________________________________________
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>>>>> 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]]
>> 
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