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

[mattia pelizzola]

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.

> 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.

Thanks,

mattia

>
> 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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>