[Bioc-devel] library checking: question on require/depends

[Sean Davis]

On Tue, Jul 29, 2008 at 3:40 PM, mattia pelizzola
<mattia.pelizzola at gmail.com> wrote:
> Hi,
>
> On Tue, Jul 29, 2008 at 2:43 PM, Laurent Gautier <lgautier at gmail.com> wrote:
>> Adding it in "Suggests" will keep R CMD check happy, as Sean told it.
>>
>
> Thanks, I just did not know that still I needed to have all the
> "Suggests" library installed. Now the warning is gone.

Just to clarify, the "Suggests" libraries do NOT need to be installed.
 That is the difference between Suggests and Depends; all libraries in
Depends must be installed for the new package to be installed.

>> One question, still:
>> Are you using the those packages in examples ? In that case, using a
>> smaller dataset might be a good idea.
>> If there is not any suitable smaller dataset currently avalaible, it
>> could be nice to create a demo-oriented one, with one chromosome for
>> example. This could also be used by other packages needing full
>> genome.
>>
>
> Yes, I'm using one of the suggested packages in the examples and I'm
> releasing a small dataset with the library, just for demonstration
> purposes.

>> 2008/7/29 Sean Davis <sdavis2 at mail.nih.gov>:
>>> On Tue, Jul 29, 2008 at 1:51 PM, mattia pelizzola
>>> <mattia.pelizzola at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I'm working on a new package. The 'build' is ok, but when running
>>>> 'check' I get a warning that I'm not sure on how to eliminate it.
>>>> The warning is :
>>>>
>>>> * checking for unstated dependencies in R code ... WARNING
>>>> 'library' or 'require' calls not declared from:
>>>>  BSgenome.Hsapiens.UCSC.hg17 BSgenome.Hsapiens.UCSC.hg18
>>>>
>>>> The reason of course is that I'm using the require function and I'm
>>>> not adding these libraries in 'Depends' or 'Suggests'. The point is
>>>> that I would not like to oblige users to install both hg17 and hg18
>>>> libraries, since they are huge (800Mb). This is going to be even more
>>>> important if I would support many other annotation libraries. The idea
>>>> was then to use require to load only the one requested from the user
>>>> (either hg17 or hg18).
>>>>
>>>> I'm going to submit this library to Bioconductor. Can I ignore this
>>>> warning, should I add all the annotation libraries in 'Depends', or is
>>>> there another way to fix this warning?
>>>
>>> This is what "Suggests" is for.
>>>
>>> Sean
>>>
>>> _______________________________________________
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>>>
>>
>
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