[Bioc-devel] help with imports for new package and other questions

[Hervé Pagès]

Hi Lorena,

In your particular case it seems to me that you're using dplyr
internally for convenient data frame transformations (nothing that
couldn't be done with plain R BTW), and that you're only using a few
dplyr symbols for this. The codetoolsBioC package could be useful to
help you identify these things and import them selectively. It seems
to me that these things are: %>%, group_by, filter, and summarise,
but I could be missing some. OTOH your package defines the IsomirDataSeq
class which extends the SummarizedExperiment class, and thus relies
largely on the GenomicRanges/SummarizedExperiment infrastructure.
So I would highly recommend that you *fully* import BiocGenerics,
S4Vectors, IRanges, and SummarizedExperiment. That will make the
maintenance of your NAMESPACE file much easier in the long run than
importing selectively from these packages.

I also remember seeing selective imports from the methods package
in NAMESPACE files generated with codetoolsBioC. Unless there is a
good reason for doing so, these should be avoided and the methods
package fully imported.

Cheers,
H.

On 08/14/2015 06:57 AM, Lo wrote:
> Hi,
>
> I am trying to get right my new package
> (http://github.com/lpantano/isomiRs). But I am having some problems with
> the packages I import.
>
> The main problem is that I get warnings while loading my packages
> because some dplyr replaces functions in others packages like S4Vectors
> and others.
>
> This is my NAMESPACE
>
> import(BiocGenerics)
> import(S4Vectors)
> import(IRanges)
> import(GenomicRanges)
> import(SummarizedExperiment)
> import(dplyr)
> importFrom(plyr, join_all)
> import(DESeq2)
> import(methods)
> import(RColorBrewer)
> import(gplots)
> import(ggplot2)
> import(GGally)
> import(DiscriMiner)
>
> and these are the warnings:
>
> ** preparing package for lazy loading
> Warning: replacing previous import by ‘dplyr::slice’ when loading ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::collapse’ when loading
> ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::intersect’ when loading
> ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::setdiff’ when loading
> ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::union’ when loading ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::rename’ when loading
> ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::combine’ when loading
> ‘isomiRs’
> Warning: replacing previous import by ‘dplyr::desc’ when loading ‘isomiRs’
> Warning: replacing previous import by ‘gplots::space’ when loading
> ‘isomiRs’
> ** help
>
>
> I need to solve this to avoid warnings. I tried something like use
> `importFrom` to only import some functions but don't know if importFrom
> is something I shouldn't use or I should.
>
> I would also appreciate very much if some one can point me to the right
> way to solve the following:
>
> * I failed to create good documentation for some functions, data of my
> package. Can anyone point me to a good example of a dataset
> documentation, so I could create a good one for my dataset example.
>
> * I have some problems with my coding style, like sometimes I have `=`
> insted of `<-` and I forgot to add spaces like this ` <- `. Any one
> knows of a plugin for any editor to help me find that. Because I am
> always missing some of them by eye.
>
> Thanks a lot in advance for any help in any point.
>
> Lorena
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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